@article{duscher2018transcriptional,
title = {Transcriptional profiling of the mutualistic bacterium Vibrio fischeri and an hfq mutant under modeled microgravity},
author = { Alexandrea A Duscher and Ana Conesa and Mary Bishop and Madeline M Vroom and Sergio D Zubizarreta and Jamie S Foster},
url = {https://doi.org/10.1038/s41526-018-0060-1},
doi = {10.1038/s41526-018-0060-1},
year = {2018},
date = {2018-12-18},
journal = {npj Microgravity},
volume = {4},
number = {1},
pages = {25},
publisher = {Nature Publishing Group},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{10.3389/fgene.2018.00578,
title = {Elucidating the Role of Chromatin State and Transcription Factors on the Regulation of the Yeast Metabolic Cycle: A Multi-Omic Integrative Approach},
author = {Víctor Sánchez-Gaya and Salvador Casaní-Galdón and Manuel Ugidos and Zheng Kuang and Jane Mellor and Ana Conesa and Sonia Tarazona},
url = {https://www.frontiersin.org/article/10.3389/fgene.2018.00578},
doi = {10.3389/fgene.2018.00578},
issn = {1664-8021},
year = {2018},
date = {2018-11-30},
journal = {Frontiers in Genetics},
volume = {9},
pages = {578},
abstract = {The Yeast Metabolic Cycle (YMC) is a model system in which levels of around 60% of the yeast transcripts cycle over time. The spatial and temporal resolution provided by the YMC has revealed that changes in the yeast metabolic landscape and chromatin status can be related to cycling gene expression. However, the interplay between histone modifications and transcription factor activity during the YMC is still poorly understood. Here we apply an innovative statistical approach to integrate chromatin state (ChIP-seq) and gene expression (RNA-seq) data to investigate the transcriptional control during the YMC. By using the multivariate regression models N-PLS (Partial Least Squares) and MORE (Multi-Omics REgulation) methodologies, we assess the contribution of histone marks and transcription factors to the regulation of gene expression in the YMC. We found that H3K18ac and H3K9ac were the most important histone modifications, whereas Sfp1, Hfi1, Pip2, Mig2 and Yhp1 emerged as the most relevant transcription factors. A significant association in the co-regulation of gene expression was found between H3K18ac and the transcription factors Pip2 (involved in fatty acids metabolism), Xbp1 (cyclin implicated in the regulation of carbohydrate and amino acid metabolism), and Hfi1 (involved in the formation of the SAGA complex). These results evidence the crucial role of histone lysine acetylation levels in the regulation of gene expression in the YMC through the coordinated action of transcription factors and lysine acetyl transferases.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{García-Solano2018,
title = {Two histologically colorectal carcinomas subsets from the serrated pathway show different methylome signatures and diagnostic biomarkers},
author = {José García Solano and María C. Turpin and Daniel Torres-Moreno and Francisco Huertas-López and Anne Tuomisto and Markus J. Mäkinen and Ana Conesa and Pablo Conesa-Zamora},
url = {https://doi.org/10.1186/s13148-018-0571-3},
doi = {10.1186/s13148-018-0571-3},
issn = {1868-7083},
year = {2018},
date = {2018-11-09},
journal = {Clinical Epigenetics},
volume = {10},
number = {1},
pages = {141},
abstract = {Altered methylation patterns are driving forces in colorectal carcinogenesis. The serrated adenocarcinoma (SAC) and sporadic colorectal carcinoma showing histological and molecular features of microsatellite instability (hmMSI-H) are two endpoints of the so-called serrated pathological route sharing some characteristics but displaying a totally different immune response and clinical outcome. However, there are no studies comparing the methylome of these two subtypes of colorectal carcinomas. The methylation status of 450,000 CpG sites using the Infinium Human Methylation 450 BeadChip array was investigated in 48 colorectal specimens, including 39 SACs and 9 matched hmMSI-H.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{fabregas2018overexpression,
title = {Overexpression of the vascular brassinosteroid receptor BRL3 confers drought resistance without penalizing plant growth},
author = {Norma Fábregas and Fidel Lozano-Elena and David Blasco-Escámez and Takayuki Tohge and Cristina Martínez-Andújar and Alfonso Albacete and Sonia Osorio and Mariana Bustamante and José Luis Riechmann and Takahito Nomura and Takao Yokota Ana Conesa and Francisco Pérez Alfocea and Alisdair R. Fernie,2 and Ana I. Caño-Delgado},
url = {https://doi.org/10.1038/s41467-018-06861-3},
doi = {10.1038/s41467-018-06861-3},
year = {2018},
date = {2018-11-08},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {4680},
publisher = {Nature Publishing Group},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{doi:10.1002/mrd.23082,
title = {Changes in the uterine metabolome of the cow during the first seven days after estrus},
author = { Paula Tríbulo and Leandro Balzano-Nogueira and Ana Conesa and Luiz G. Siqueira and Peter J. Hansen},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/mrd.23082},
doi = {10.1002/mrd.23082},
year = {2018},
date = {2018-11-01},
journal = {Molecular Reproduction and Development},
volume = {0},
number = {ja},
abstract = {Abstract The uterine microenvironment during the first 7 days after ovulation accommodates and facilitates sperm transit to the oviduct and constitutes the sole source of nutrients required for development of preimplantation embryos. Knowledge of the composition of uterine fluid is largely incomplete. Using untargeted mass spectrometry, we characterized the uterine metabolome during the first 7 days of the estrous cycle. Bovine uteri were collected on day 0 (N=4), 3 (N=4), 5 (N=3) and 7 (N=4) relative to ovulation and flushed with Dulbecco’s phosphate-buffered saline. A total of 1,993 molecular features were detected of which 184 peaks with putative identification represent 147 unique metabolites, including amino acids, benzoic acids, lipid molecules, carbohydrates, purines, pyrimidines, vitamins, and other intermediate and secondary metabolites. Results revealed changes in the uterine metabolome as the cow transitions from ovulation to day 7 of the estrous cycle. The majority of metabolites reached maximum intensity on either day 5 or day 7 relative to ovulation. Moreover, several metabolites found in uterine fluid have signaling capabilities and some have been shown to affect preimplantation embryonic development. In conclusion, the metabolome of the bovine uterus changes during early stages of the estrous cycle and is likely to participate in the regulation of preimplantation embryonic development. Data reported here will serve as basis for future studies aiming to evaluate maternal regulation of preimplantation embryonic development and optimal conditions for culture of embryos. This article is protected by copyright. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ARROYOCRESPO20188,
title = {Tumor microenvironment-targeted poly-L-glutamic acid-based combination conjugate for enhanced triple negative breast cancer treatment},
author = {Juan J. Arroyo-Crespo and Ana Armiñán and David Charbonnier and Leandro Balzano-Nogueira and Francisco Huertas-López and Cristina Martí and Sonia Tarazona and Jerónimo Forteza and Ana Conesa and María J. Vicent},
url = {http://www.sciencedirect.com/science/article/pii/S0142961218306604},
doi = {https://doi.org/10.1016/j.biomaterials.2018.09.023},
issn = {0142-9612},
year = {2018},
date = {2018-09-18},
journal = {Biomaterials},
volume = {186},
pages = {8 - 21},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{COLLIDULA20181500,
title = {Gene expression profile and molecular pathway datasets resulting from benzo(a)pyrene exposure in the liver and testis of adult tilapia},
author = {Reyna Cristina Colli-Dula and Xiefan Fang and David Moraga-Amador and Nacira Albornoz-Abud and Roberto Zamora-Bustillos and Ana Conesa and Omar Zapata-Perez and Diego Moreno and Emanuel Hernandez-Nuñez},
url = {http://www.sciencedirect.com/science/article/pii/S2352340918310667},
doi = {https://doi.org/10.1016/j.dib.2018.08.206},
issn = {2352-3409},
year = {2018},
date = {2018-09-05},
journal = {Data in Brief},
volume = {20},
pages = {1500 - 1509},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Newman2923,
title = {Event Analysis: Using Transcript Events To Improve Estimates of Abundance in RNA-seq Data},
author = { Jeremy R. B. Newman and Patrick Concannon and Manuel Tardaguila and Ana Conesa and Lauren M. McIntyre},
url = {http://www.g3journal.org/content/8/9/2923},
doi = {10.1534/g3.118.200373},
year = {2018},
date = {2018-08-30},
journal = {G3: Genes, Genomes, Genetics},
volume = {8},
number = {9},
pages = {2923--2940},
publisher = {G3: Genes, Genomes, Genetics},
abstract = {Alternative splicing leverages genomic content by allowing the synthesis of multiple transcripts and, by implication, protein isoforms, from a single gene. However, estimating the abundance of transcripts produced in a given tissue from short sequencing reads is difficult and can result in both the construction of transcripts that do not exist, and the failure to identify true transcripts. An alternative approach is to catalog the events that make up isoforms (splice junctions and exons). We present here the Event Analysis (EA) approach, where we project transcripts onto the genome and identify overlapping/unique regions and junctions. In addition, all possible logical junctions are assembled into a catalog. Transcripts are filtered before quantitation based on simple measures: the proportion of the events detected, and the coverage. We find that mapping to a junction catalog is more efficient at detecting novel junctions than mapping in a splice aware manner. We identify 99.8% of true transcripts while iReckon identifies 82% of the true transcripts and creates more transcripts not included in the simulation than were initially used in the simulation. Using PacBio Iso-seq data from a mouse neural progenitor cell model, EA detects 60% of the novel junctions that are combinations of existing exons while only 43% are detected by STAR. EA further detects ~5,000 annotated junctions missed by STAR. Filtering transcripts based on the proportion of the transcript detected and the number of reads on average supporting that transcript captures 95% of the PacBio transcriptome. Filtering the reference transcriptome before quantitation, results in is a more stable estimate of isoform abundance, with improved correlation between replicates. This was particularly evident when EA is applied to an RNA-seq study of type 1 diabetes (T1D), where the coefficient of variation among subjects (n = 81) in the transcript abundance estimates was substantially reduced compared to the estimation using the full reference. EA focuses on individual transcriptional events. These events can be quantitate and analyzed directly or used to identify the probable set of expressed transcripts. Simple rules based on detected events and coverage used in filtering result in a dramatic improvement in isoform estimation without the use of ancillary data (e.g., ChIP, long reads) that may not be available for many studies.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Arzalluz-Luque2018,
title = {Single-cell RNAseq for the study of isoforms---how is that possible?},
author = {Ángeles Arzalluz-Luque and Conesa Ana },
url = {http://doi.org/10.1186/s13059-018-1496-z},
doi = {10.1186/s13059-018-1496-z},
issn = {1474-760X},
year = {2018},
date = {2018-08-10},
journal = {Genome Biology},
volume = {19},
number = {1},
pages = {110},
abstract = {Single-cell RNAseq and alternative splicing studies have recently become two of the most prominent applications of RNAseq. However, the combination of both is still challenging, and few research efforts have been dedicated to the intersection between them. Cell-level insight on isoform expression is required to fully understand the biology of alternative splicing, but it is still an open question to what extent isoform expression analysis at the single-cell level is actually feasible. Here, we establish a set of four conditions that are required for a successful single-cell-level isoform study and evaluate how these conditions are met by these technologies in published research.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Colli-Dula2018,
title = {Transcriptome analysis reveals novel insights into the response of low-dose benzo(a)pyrene exposure in male tilapia},
author = {Reyna Cristina Colli-Dula and Xiefan Fang and David Moraga-Amador and Nacira Albornoz-Abud and Roberto Zamora-Bustillos and Ana Conesa and Omar Zapata-Perez and Diego Moreno and Emanuel Hernandez-Nuñez},
url = {http://www.sciencedirect.com/science/article/pii/S0166445X18303503},
doi = {10.1016/j.aquatox.2018.06.005},
issn = {0166-445X},
year = {2018},
date = {2018-08-01},
journal = {Aquatic Toxicology},
volume = {201},
pages = {162 - 173},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{tarazona2018multiomics,
title = {Multiomics Data Integration in Time Series Experiments},
author = { Sonia Tarazona and Leandro Balzano-Nogueira and Ana Conesa},
url = {https://doi.org/10.1016/bs.coac.2018.06.005},
doi = {10.1016/bs.coac.2018.06.005},
year = {2018},
date = {2018-07-31},
publisher = {Elsevier},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Hernández-de-Diego2018,
title = {PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data},
author = {Hernández-de-Diego, Rafael and Tarazona, Sonia and Martínez-Mira, Carlos and Balzano-Nogueira, Leandro and Furió-Tarí, Pedro and Pappas, Jr ,Georgios J and Conesa, Ana},
url = {http://dx.doi.org/10.1093/nar/gky466},
doi = {http://dx.doi.org/10.1093/nar/gky466},
year = {2018},
date = {2018-07-02},
journal = {Nucleic Acids Research},
pages = {gky466},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{10.3389/fmicb.2018.01359,
title = {Comparative Metagenomics Provides Insight Into the Ecosystem Functioning of the Shark Bay Stromatolites, Western Australia},
author = {Joany Babilonia and Ana Conesa and Giorgio Casaburi and Cecile Pereira and Artemis S. Louyakis and R. Pamela Reid and Jamie S. Foster},
url = {http://www.frontiersin.org/article/10.3389/fmicb.2018.01359},
doi = {10.3389/fmicb.2018.01359},
issn = {1664-302X},
year = {2018},
date = {2018-06-25},
journal = {Frontiers in Microbiology},
volume = {9},
pages = {1359},
abstract = {Stromatolites are organosedimentary build-ups that have formed as a result of the sediment trapping, binding and precipitating activities of microbes. Today, extant systems provide an ideal platform for understanding the structure, composition, and interactions between stromatolite-forming microbial communities and their respective environments. In this study, we compared the metagenomes of three prevalent stromatolite-forming microbial mat types in the Spaven Province of Hamelin Pool, Shark Bay located in Western Australia. These stromatolite-forming mat types included an intertidal pustular mat as well as a smooth and colloform mat types located in the subtidal zone. Additionally, the metagenomes of an adjacent, non-lithifying mat located in the upper intertidal zone were also sequenced for comparative purposes. Taxonomic and functional gene analyses revealed distinctive differences between the lithifying and non-lithifying mat types, which strongly correlated with water depth. Three distinct populations emerged including the upper intertidal non-lithifying mats, the intertidal pustular mats associated with unlaminated carbonate build-ups, and the subtidal colloform and smooth mat types associated with laminated structures. Functional analysis of metagenomes revealed that amongst stromatolite-forming mats there was an enrichment of photosynthesis pathways in the pustular stromatolite-forming mats. In the colloform and smooth stromatolite-forming mats, however, there was an increase in the abundance of genes associated with those heterotrophic metabolisms typically associated with carbonate mineralization, such as sulfate reduction. The comparative metagenomic analyses suggest that stromatolites of Hamelin Pool may form by two distinctive processes that are highly dependent on water depth. These results provide key insight into the potential adaptive strategies and synergistic interactions between microbes and their environments that may lead to stromatolite formation and accretion.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{doi:10.1093/gbe/evy116,
title = {Evidence of the Red-Queen Hypothesis from Accelerated Rates of Evolution of Genes Involved in Biotic Interactions in Pneumocystis},
author = { Luis Delaye and Susana Ruiz-Ruiz and Enrique Calderon and Sonia Tarazona and Ana Conesa and Andrés Moya},
url = {http://dx.doi.org/10.1093/gbe/evy116},
doi = {10.1093/gbe/evy116},
year = {2018},
date = {2018-06-01},
journal = {Genome Biology and Evolution},
volume = {10},
number = {6},
pages = {1596-1606},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Zhu2018,
title = {GRAM-CNN: a deep learning approach with local context for named entity recognition in biomedical text},
author = {Zhu, Qile and Li, Xiaolin and Conesa, Ana and Pereira, Cécile},
url = {http://dx.doi.org/10.1093/bioinformatics/btx815},
doi = {10.1093/bioinformatics/btx815},
year = {2018},
date = {2018-05-01},
journal = {Bioinformatics},
volume = {34},
number = {9},
pages = {1547-1554},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{García-Molinero2018,
title = {The SAGA/TREX-2 subunit Sus1 binds widely to transcribed genes and affects mRNA turnover globally},
author = {García-Molinero, Varinia and Garcíaa-Martínez, José and Reja, Rohit and Furió-Tarí, Pedro and Antúnez, Oreto and Vinayachandran, Vinesh and Conesa, Ana and Pugh, B. Franklin and Pérez-Ortín, José E. and Rodríguez-Navarro, Susana},
url = {http://doi.org/10.1186/s13072-018-0184-2},
doi = {10.1186/s13072-018-0184-2},
year = {2018},
date = {2018-03-29},
journal = {Epigenetics & Chromatin},
volume = {11},
number = {1},
pages = {13},
abstract = {Eukaryotic transcription is regulated through two complexes, the general transcription factor IID (TFIID) and the coactivator Spt--Ada--Gcn5 acetyltransferase (SAGA). Recent findings confirm that both TFIID and SAGA contribute to the synthesis of nearly all transcripts and are recruited genome-wide in yeast. However, how this broad recruitment confers selectivity under specific conditions remains an open question.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Tardaguila2018,
title = {SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification},
author = {Tardaguila, Manuel and de la Fuente, Lorena and Marti, Cristina and Pereira, Cécile and Pardo-Palacios, Francisco Jose and del Risco, Hector and Ferrell, Marc and Mellado, Maravillas and Macchietto, Marissa and Verheggen, Kenneth and Edelmann, Mariola and Ezkurdia, Iakes and Vazquez, Jesus and Tress, Michael and Mortazavi, Ali and Martens, Lennart and Rodriguez-Navarro, Susana and Moreno-Manzano, Victoria and Conesa, Ana},
url = {http://genome.cshlp.org/content/early/2018/02/09/gr.222976.117.abstract},
doi = {10.1101/gr.222976.117},
year = {2018},
date = {2018-02-09},
journal = {Genome Research},
abstract = {High-throughput sequencing of full-length transcripts using long reads has paved the way for the discovery of thousands of novel transcripts, even in well-annotated mammalian species. The advances in sequencing technology have created a need for studies and tools that can characterize these novel variants. Here, we present SQANTI, an automated pipeline for the classification of long-read transcripts that can assess the quality of data and the preprocessing pipeline using 47 unique descriptors. We apply SQANTI to a neuronal mouse transcriptome using Pacific Biosciences (PacBio) long reads and illustrate how the tool is effective in characterizing and describing the composition of the full-length transcriptome. We perform extensive evaluation of ToFU PacBio transcripts by PCR to reveal that an important number of the novel transcripts are technical artifacts of the sequencing approach and that SQANTI quality descriptors can be used to engineer a filtering strategy to remove them. Most novel transcripts in this curated transcriptome are novel combinations of existing splice sites, resulting more frequently in novel ORFs than novel UTRs, and are enriched in both general metabolic and neural-specific functions. We show that these new transcripts have a major impact in the correct quantification of transcript levels by state-of-the-art short-read-based quantification algorithms. By comparing our iso-transcriptome with public proteomics databases, we find that alternative isoforms are elusive to proteogenomics detection. SQANTI allows the user to maximize the analytical outcome of long-read technologies by providing the tools to deliver quality-evaluated and curated full-length transcriptomes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{doi:10.1093/bioinformatics/btx578,
title = {Identification and visualization of differential isoform expression in RNA-seq time series},
author = { María José Nueda and Jordi Martorell-Marugan and Cristina Martí and Sonia Tarazona and Ana Conesa},
url = {http://dx.doi.org/10.1093/bioinformatics/btx578},
doi = {10.1093/bioinformatics/btx578},
year = {2018},
date = {2018-02-01},
journal = {Bioinformatics},
volume = {34},
number = {3},
pages = {524-526},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{martinez2018mosim,
title = {MOSim: Multi-Omics Simulation in R},
author = { Carlos Martínez-Mira and Ana Conesa and Sonia Tarazona},
url = {https://doi.org/10.1101/421834},
doi = {10.1101/421834},
year = {2018},
date = {2018-01-01},
journal = {bioRxiv},
pages = {421834},
publisher = {Cold Spring Harbor Laboratory},
keywords = {},
pubstate = {forthcoming},
tppubtype = {article}
}

@article{ISI:000417056500003,
title = {Growth of Chlamydia pneumoniae Is Enhanced in Cell swith Impaired
Mitochondrial Function},
author = { N. Kaeding and I. Kaufhold and C. Mueller and M. Szaszak and K. Shima and T. Weinmaier and R. Lomas and A. Conesa and P. Schmitt-Kopplin and T. Rattei and J. Rupp},
url = {http://dx.doi.org/10.3389/fcimb.2017.00499},
doi = {10.3389/fcimb.2017.00499},
issn = {2235-2988},
year = {2017},
date = {2017-12-01},
journal = {FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY},
volume = {7},
abstract = {Effective growth and replication of obligate intracellular pathogens
depend on host cell metabolism. How this is connected to host cell
mitochondrial function has not been studied so far. Recent studies
suggest that growth of intracellular bacteria such as Chlamydia
pneumoniae is enhanced in a low oxygen environment, arguing for a
particular mechanistic role of the mitochondrial respiration in
controlling intracellular progeny. Metabolic changes in C. pneumoniae
infected epithelial cells were analyzed under normoxic (O-2 approximate
to 20%) and hypoxic conditions (O-2 < 3%). We observed that infection
of epithelial cells with C. pneumoniae under normoxia impaired
mitochondrial function characterized by an enhanced mitochondrial
membrane potential and ROS generation. Knockdown and mutation of the
host cell ATP synthase resulted in an increased chlamydial replication
already under normoxic conditions. As expected, mitochondrial
hyperpolarization was observed in non-infected control cells cultured
under hypoxic conditions, which was beneficial for C. pneumoniae growth.
Taken together, functional and genetically encoded mitochondrial
dysfunction strongly promotes intracellular growth of C. pneumoniae.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000414165900003,
title = {Disease-specific biases in alternative splicing and tissue-specific
dysregulation revealed by multitissue profiling of lymphocyte gene
expression in type 1 diabetes},
author = { J. R. B. Newman and A. Conesa and M. Mika and F. N. New and S. Onengut-Gumuscu and M. A. Atkinson and S. S. Rich and L. M. McIntyre and P. Concannon},
url = {http://dx.doi.org/10.1101/gr.217984.116},
doi = {10.1101/gr.217984.116},
issn = {1088-9051},
year = {2017},
date = {2017-11-01},
journal = {GENOME RESEARCH},
volume = {27},
number = {11},
pages = {1807-1815},
abstract = {Genome-wide association studies (GWAS) have identified multiple, shared
allelic associations with many autoimmune diseases. However, the
pathogenic contributions of variants residing in risk loci remain
unresolved. The location of the majority of shared disease-associated
variants in noncoding regions suggests they contribute to risk of
autoimmunity through effects on gene expression in the immune system. In
the current study, we test this hypothesis by applying RNA sequencing to
CD4(+), CD8(+), and CD19(+) lymphocyte populations isolated from 81
subjects with type 1 diabetes (T1D). We characterize and compare the
expression patterns across these cell types for three gene sets: all
genes, the set of genes implicated in autoimmune disease risk by GWAS, and the subset of these genes specifically implicated in T1D. We
performed RNA sequencing and aligned the reads to both the human
reference genome and a catalog of all possible splicing events developed
from the genome, thereby providing a comprehensive evaluation of the
roles of gene expression and alternative splicing (AS) in autoimmunity.
Autoimmune candidate genes displayed greater expression specificity in
the three lymphocyte populations relative to other genes, with
significantly increased levels of splicing events, particularly those
predicted to have substantial effects on protein isoform structure and
function (e.g., intron retention, exon skipping). The majority of
single-nucleotide polymorphisms within T1D-associated loci were also
associated with one or more cis-expression quantitative trait loci
(ciseQTLs) and/or splicing eQTLs. Our findings highlight a substantial, and previously underrecognized, role for AS in the pathogenesis of
autoimmune disorders and particularly for T1D.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{doi:10.1093/bib/bbx122,
title = {A benchmarking of workflows for detecting differential splicing and differential expression at isoform level in human RNA-seq studies},
author = { Gabriela A. Merino and Ana Conesa and Elmer A. Fernández},
url = {http://dx.doi.org/10.1093/bib/bbx122},
doi = {10.1093/bib/bbx122},
year = {2017},
date = {2017-10-13},
journal = {Briefings in Bioinformatics},
pages = {bbx122},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000411824103042,
title = {Certolizumab Pegol Effectiveness and Retention Rate in Psoriatic
Arthritis. Real Life Data},
author = { A. Conesa and M. Fernandez and R. Exposito and J. Campos and J. Ramon Lamua and M. del Pilar Navarro and P. Rubio-Munoz and P. Ahijado-Guzman and C. M. Gonzalez},
issn = {2326-5191},
year = {2017},
date = {2017-10-01},
journal = {ARTHRITIS & RHEUMATOLOGY},
volume = {69},
number = {10},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000411981000002,
title = {The eBioKit, a stand-alone educational platform for bioinformatics},
author = { R. Hernandez-de-Diego and E. P. de Villiers and T. Klingstrom and H. Gourle and A. Conesa and E. Bongcam-Rudloff},
url = {http://dx.doi.org/10.1371/journal.pcbi.1005616},
doi = {10.1371/journal.pcbi.1005616},
issn = {1553-734X},
year = {2017},
date = {2017-09-01},
journal = {PLOS COMPUTATIONAL BIOLOGY},
volume = {13},
number = {9},
abstract = {Bioinformatics skills have become essential for many research areas;
however, the availability of qualified researchers is usually lower than
the demand and training to increase the number of able bioinformaticians
is an important task for the bioinformatics community. When conducting
training or hands-on tutorials, the lack of control over the analysis
tools and repositories often results in undesirable situations during
training, as unavailable online tools or version conflicts may delay, complicate, or even prevent the successful completion of a training
event. The eBioKit is a stand-alone educational platform that hosts
numerous tools and databases for bioinformatics research and allows
training to take place in a controlled environment. A key advantage of
the eBioKit over other existing teaching solutions is that all the
required software and databases are locally installed on the system, significantly reducing the dependence on the internet. Furthermore, the
architecture of the eBioKit has demonstrated itself to be an excellent
balance between portability and performance, not only making the eBioKit
an exceptional educational tool but also providing small research groups
with a platform to incorporate bioinformatics analysis in their
research. As a result, the eBioKit has formed an integral part of
training and research performed by a wide variety of universities and
organizations such as the Pan African Bioinformatics Network (H3ABioNet)
as part of the initiative Human Heredity and Health in Africa
(H3Africa), the Southern Africa Network for Biosciences (SAnBio)
initiative, the Biosciences eastern and central Africa (BecA) hub, and
the International Glossina Genome Initiative.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000411874500006,
title = {Guidelines for Developing Successful Short Advanced Courses in Systems
Medicine and Systems Biology},
author = { D. Gomez-Cabrero and F. Marabita and S. Tarazona and I. Cano and J. Roca and A. Conesa and P. Sabatier and J. Tegner},
url = {http://dx.doi.org/10.1016/j.cels.2017.05.013},
doi = {10.1016/j.cels.2017.05.013},
issn = {2405-4712},
year = {2017},
date = {2017-09-01},
journal = {CELL SYSTEMS},
volume = {5},
number = {3},
pages = {168-175},
abstract = {Systems medicine and systems biology have inherent educational
challenges. These have largely been addressed either by providing new
masters programs or by redesigning undergraduate programs. In contrast, short courses can respond to a different need: they can provide
condensed updates for professionals across academia, the clinic, and
industry. These courses have received less attention. Here, we share our
experiences in developing and providing such courses to current and
future leaders in systems biology and systems medicine. We present
guidelines for how to reproduce our courses, and we offer suggestions
for how to select students who will nurture an interdisciplinary
learning environment and thrive there.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000402747300007,
title = {Dynamic Gene Regulatory Networks of Human Myeloid Differentiation},
author = { R. N. Ramirez and N. C. El-Ali and M. A. Mager and D. Wyman and A. Conesa and A. Mortazavi},
url = {http://dx.doi.org/10.1016/j.cels.2017.03.005},
doi = {10.1016/j.cels.2017.03.005},
issn = {2405-4712},
year = {2017},
date = {2017-04-01},
journal = {CELL SYSTEMS},
volume = {4},
number = {4},
pages = {416+},
abstract = {The reconstruction of gene regulatory networks underlying cell
differentiation from high-throughput gene expression and chromatin data
remains a challenge. Here, we derive dynamic gene regulatory networks
for human myeloid differentiation using a 5-day time series of RNA-seq
and ATAC-seq data. We profile HL-60 promyelocytes differentiating into
macrophages, neutrophils, monocytes, and monocyte-derived macrophages.
We find a rapid response in the expression of key transcription factors
and lineage markers that only regulate a subset of their targets at a
given time, which is followed by chromatin accessibility changes that
occur later along with further gene expression changes. We observe
differences between promyelocyte-and monocytederived macrophages at both
the transcriptional and chromatin landscape level, despite using the
same differentiation stimulus, which suggest that the path taken by
cells in the differentiation landscape defines their end cell state.
More generally, our approach of combining neighboring time points and
replicates to achieve greater sequencing depth can efficiently infer
footprint-based regulatory networks from long series data.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000399043900345,
title = {Network Biology of Menstrual Cycle to Understand the Key Drivers of
Endometrial Receptivity.},
author = { P. Sebastian-Leon and A. Conesa and V. Arnau and J. Remohi and A. Pellicer and C. Simon and P. Diaz-Gimeno},
issn = {1933-7191},
year = {2017},
date = {2017-03-01},
journal = {REPRODUCTIVE SCIENCES},
volume = {24},
number = {1},
pages = {162A},
organization = {Soc Reprod Invest},
note = {64th Annual Scientific Meeting of the
Society-for-Reproductive-Investigation (SRI), Orlando, FL, MAR 15-18, 2017},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000392353200004,
title = {Identification of miRNA from Bouteloua gracilis, a drought tolerant
grass, by deep sequencing and their in silico analysis},
author = { P. Lucia Ordonez-Baquera and E. Gonzalez-Rodriguez and G. Armando Aguado-Santacruz and Q. Rascon-Cruz and A. Conesa and V. Moreno-Brito and R. Echavarria and J. Dominguez-Viveros},
url = {http://dx.doi.org/10.1016/j.compbiolchem.2016.11.001},
doi = {10.1016/j.compbiolchem.2016.11.001},
issn = {1476-9271},
year = {2017},
date = {2017-02-01},
journal = {COMPUTATIONAL BIOLOGY AND CHEMISTRY},
volume = {66},
pages = {26-35},
abstract = {Background: MicroRNAs (miRNAs) are small non-coding RNA molecules that
regulate signal transduction, development, metabolism, and stress
responses in plants through post-transcriptional degradation and/or
translational repression of target mRNAs. Several studies have addressed
the role of miRNAs in model plant species, but miRNA expression and
function in economically important forage crops, such as Bouteloua
gracilis (Poaceae), a high-quality and drought-resistant grass
distributed in semiarid regions of the United States and northern Mexico
remain unknown.
Results: We applied high-throughput sequencing technology and
bioinformatics analysis and identified 31 conserved miRNA families and
53 novel putative miRNAs with different abundance of reads in
chlorophyllic cell cultures derived from B. gracilis. Some conserved
miRNA families were highly abundant and possessed predicted targets
involved in metabolism, plant growth and development, and stress
responses. We also predicted additional identified novel miRNAs with
specific targets, including B. gracilis ESTs, which were detected under
drought stress conditions.
Conclusions: Here we report 31 conserved miRNA families and 53 putative
novel miRNAs in B. gracilis. Our results suggested the presence of
regulatory miRNAs involved in modulating physiological and stress
responses in this grass species. (C) 2016 Elsevier Ltd. All rights
reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000390471900128,
title = {Impacts of abundance of Candidatus Liberibacter on the citrus
phyto-microbiome},
author = { R. Blaustein and J. Meyer and A. Conesa and G. Lorca and M. Teplitski},
issn = {0031-949X},
year = {2016},
date = {2016-12-01},
journal = {PHYTOPATHOLOGY},
volume = {106},
number = {12, S},
pages = {25-26},
organization = {Amer Phytopathol Soc},
note = {Annual Meeting of the American-Phytopathological-Society (APS), Tampa, FL, JUL 30-AUG 03, 2016},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000392470500001,
title = {RGmatch: matching genomic regions to proximal genes in omics data
integration},
author = { P. Furio-Tari and A. Conesa and S. Tarazona},
url = {http://dx.doi.org/10.1186/s12859-016-1293-1},
doi = {10.1186/s12859-016-1293-1},
issn = {1471-2105},
year = {2016},
date = {2016-11-01},
journal = {BMC BIOINFORMATICS},
volume = {17},
number = {15},
abstract = {Background: The integrative analysis of multiple genomics data often
requires that genome coordinates-based signals have to be associated
with proximal genes. The relative location of a genomic region with
respect to the gene (gene area) is important for functional data
interpretation; hence algorithms that match regions to genes should be
able to deliver insight into this information.
Results: In this work we review the tools that are publicly available
for making region-to-gene associations. We also present a novel method, RGmatch, a flexible and easy-to-use Python tool that computes
associations either at the gene, transcript, or exon level, applying a
set of rules to annotate each region-gene association with the region
location within the gene. RGmatch can be applied to any organism as long
as genome annotation is available. Furthermore, we qualitatively and
quantitatively compare RGmatch to other tools.
Conclusions: RGmatch simplifies the association of a genomic region with
its closest gene. At the same time, it is a powerful tool because the
rules used to annotate these associations are very easy to modify
according to the researcher's specific interests. Some important
differences between RGmatch and other similar tools already in existence
are RGmatch's flexibility, its wide range of user options, compatibility
with any annotatable organism, and its comprehensive and user-friendly
output.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000387621900001,
title = {Making sense of big data in health research: towards an EU action plan
(vol 8, pg 71, 2016)},
author = { C. Auffray and R. Balling and I. Barroso and L. Bencze and M. Benson and J. Bergeron and E. Bernal-Delgado and N. Blomberg and C. Bock and A. Conesa and S. Del Signore and C. Delogne and P. Devilee and A. Di Meglio and M. Eijkemans and P. Flicek and N. Graf and V. Grimm and H. Guchelaar and Y. Guo and I. G. Gut and A. Hanbury and S. Hanif and R. Hilgers and A. Honrado and D. R. Hose and J. Houwing-Duistermaat and T. Hubbard and S. H. Janacek and H. Karanikas and T. Kievits and M. Kohler and A. Kremer and J. Lanfear and T. Lengauer and E. Maes and T. Meert and W. Muller and D. Nickel and P. Oledzki and B. Pedersen and M. Petkovic and K. Pliakos and M. Rattray and J. Redon i Mas and R. Schneider and T. Sengstag and X. Serra-Picamal and W. Spek and L. A. I. Vaas and O. van Batenburg and M. Vandelaer and P. Varnai and P. Villoslada and J. A. Vizcaino and J. P. M. Wubbe and G. Zanetti},
url = {http://dx.doi.org/10.1186/s13073-016-0376-y},
doi = {10.1186/s13073-016-0376-y},
issn = {1756-994X},
year = {2016},
date = {2016-11-01},
journal = {GENOME MEDICINE},
volume = {8},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000383344400010,
title = {Transcriptome modulation during host shift is driven by secondary
metabolites in desert Drosophila},
author = { D. N. De Panis and J. Padro and P. Furio-Tari and S. Tarazona and P. S. Milla Carmona and I. M. Soto and H. Dopazo and A. Conesa and E. Hasson},
url = {http://dx.doi.org/10.1111/mec.13785},
doi = {10.1111/mec.13785},
issn = {0962-1083},
year = {2016},
date = {2016-09-01},
journal = {MOLECULAR ECOLOGY},
volume = {25},
number = {18},
pages = {4534-4550},
abstract = {High-throughput transcriptome studies are breaking new ground to
investigate the responses that organisms deploy in alternative
environments. Nevertheless, much remains to be understood about the
genetic basis of host plant adaptation. Here, we investigate genome-wide
expression in the fly Drosophila buzzatii raised in different
conditions. This species uses decaying tissues of cactus of the genus
Opuntia as primary rearing substrate and secondarily, the necrotic
tissues of the columnar cactus Trichocereus terscheckii. The latter
constitutes a harmful host, rich in mescaline and other related
phenylethylamine alkaloids. We assessed the transcriptomic responses of
larvae reared in Opuntia sulphurea and T. terscheckii, with and without
the addition of alkaloids extracted from the latter. Whole-genome
expression profiles were massively modulated by the rearing environment, mainly by the presence of T. terscheckii alkaloids. Differentially
expressed genes were mainly related to detoxification, oxidation-reduction and stress response; however, we also found genes
involved in development and neurobiological processes. In conclusion, our study contributes new data onto the role of transcriptional
plasticity in response to alternative rearing environments.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000383427700002,
title = {A survey of best practices for RNA-seq data analysis (vol 17, 13, 2016)},
author = { A. Conesa and P. Madrigal and S. Tarazona and D. Gomez-Cabrero and A. Cervera and A. McPherson and M. W. Szczesniak and D. J. Gaffney and L. L. Elo and X. Zhang and A. Mortazavi},
url = {http://dx.doi.org/10.1186/s13059-016-1047-4},
doi = {10.1186/s13059-016-1047-4},
issn = {1474-760X},
year = {2016},
date = {2016-08-01},
journal = {GENOME BIOLOGY},
volume = {17},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000379786800029,
title = {spongeScan: A web for detecting microRNA binding elements in lncRNA
sequences},
author = { P. Furio-Tari and S. Tarazona and T. Gabaldon and A. J. Enright and A. Conesa},
url = {http://dx.doi.org/10.1093/nar/gkw443},
doi = {10.1093/nar/gkw443},
issn = {0305-1048},
year = {2016},
date = {2016-07-01},
journal = {NUCLEIC ACIDS RESEARCH},
volume = {44},
number = {W1},
pages = {W176-W180},
abstract = {Non-coding RNA transcripts such as microRNAs (miRNAs) and long
non-coding RNAs (lncRNAs) are important genetic regulators. However, the
functions of many of these transcripts are still not clearly understood.
Recently, it has become apparent that there is significant crosstalk
between miRNAs and lncRNAs and that this creates competition for binding
between the miRNA, a lncRNA and other regulatory targets. Indeed, various competitive endogenous RNAs (ceRNAs) have already been
identified where a lncRNA acts by sequestering miRNAs. This implies the
down-regulation in the interaction of the miRNAs with their mRNA
targets, what has been called a sponge effect. Multiple approaches exist
for the prediction of miRNA targets in mRNAs. However, few methods exist
for the prediction of miRNA response elements (MREs) in lncRNAs acting
as ceRNAs (sponges). Here, we present spongeScan
(http://spongescan.rc.ufl.edu), a graphical web tool to compute and
visualize putative MREs in lncRNAs, along with different measures to
assess their likely behavior as ceRNAs.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000381318400009,
title = {Separating common from distinctive variation},
author = { F. M. van der Kloet and P. Sebastian-Leon and A. Conesa and A. K. Smilde and J. A. Westerhuis},
url = {http://dx.doi.org/10.1186/s12859-016-1037-2},
doi = {10.1186/s12859-016-1037-2},
issn = {1471-2105},
year = {2016},
date = {2016-06-01},
journal = {BMC BIOINFORMATICS},
volume = {17},
number = {5},
abstract = {Background: Joint and individual variation explained (JIVE), distinct
and common simultaneous component analysis (DISCO) and O2-PLS, a
two-block (X-Y) latent variable regression method with an integral OSC
filter can all be used for the integrated analysis of multiple data sets
and decompose them in three terms: a low(er)-rank approximation
capturing common variation across data sets, low(er)-rank approximations
for structured variation distinctive for each data set, and residual
noise. In this paper these three methods are compared with respect to
their mathematical properties and their respective ways of defining
common and distinctive variation.
Results: The methods are all applied on simulated data and mRNA and
miRNA data-sets from GlioBlastoma Multiform (GBM) brain tumors to
examine their overlap and differences. When the common variation is
abundant, all methods are able to find the correct solution. With real
data however, complexities in the data are treated differently by the
three methods.
Conclusions: All three methods have their own approach to estimate
common and distinctive variation with their specific strength and
weaknesses. Due to their orthogonality properties and their used
algorithms their view on the data is slightly different. By assuming
orthogonality between common and distinctive, true natural or biological
phenomena that may not be orthogonal at all might be misinterpreted.},
note = {Conference on Statistical Methods for Omics Data Integration and
Analysis, Heraklion, GREECE, NOV 10-12, 2014},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000378592900001,
title = {Making sense of big data in health research: Towards an EU action plan},
author = { C. Auffray and R. Balling and I. Barroso and L. Bencze and M. Benson and J. Bergeron and E. Bernal-Delgado and N. Blomberg and C. Bock and A. Conesa and S. Del Signore and C. Delogne and P. Devilee and A. Di Meglio and M. Eijkemans and P. Flicek and N. Graf and V. Grimm and H. Guchelaar and Y. Guo and I. G. Gut and A. Hanbury and S. Hanif and R. Hilgers and A. Honrado and D. R. Hose and J. Houwing-Duistermaat and T. Hubbard and S. H. Janacek and H. Karanikas and T. Kievits and M. Kohler and A. Kremer and J. Lanfear and T. Lengauer and E. Maes and T. Meert and W. Mueller and D. Nickel and P. Oledzki and B. Pedersen and M. Petkovic and K. Pliakos and M. Rattray and J. Redon i Mas and R. Schneider and T. Sengstag and X. Serra-Picamal and W. Spek and L. A. I. Vaas and O. van Batenburg and M. Vandelaer and P. Varnai and P. Villoslada and J. A. Vizcaino and J. P. M. Wubbe and G. Zanetti},
url = {http://dx.doi.org/10.1186/s13073-016-0323-y},
doi = {10.1186/s13073-016-0323-y},
issn = {1756-994X},
year = {2016},
date = {2016-06-01},
journal = {GENOME MEDICINE},
volume = {8},
abstract = {Medicine and healthcare are undergoing profound changes. Whole-genome
sequencing and high-resolution imaging technologies are key drivers of
this rapid and crucial transformation. Technological innovation combined
with automation and miniaturization has triggered an explosion in data
production that will soon reach exabyte proportions. How are we going to
deal with this exponential increase in data production? The potential of
``big data'' for improving health is enormous but, at the same time, we face a wide range of challenges to overcome urgently. Europe is very
proud of its cultural diversity; however, exploitation of the data made
available through advances in genomic medicine, imaging, and a wide
range of mobile health applications or connected devices is hampered by
numerous historical, technical, legal, and political barriers. European
health systems and databases are diverse and fragmented. There is a lack
of harmonization of data formats, processing, analysis, and data
transfer, which leads to incompatibilities and lost opportunities. Legal
frameworks for data sharing are evolving. Clinicians, researchers, and
citizens need improved methods, tools, and training to generate, analyze, and query data effectively. Addressing these barriers will
contribute to creating the European Single Market for health, which will
improve health arid healthcare for all Europearis.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000368360100020,
title = {Qualimap 2: advanced multi-sample quality control for high-throughput
sequencing data},
author = { K. Okonechnikov and A. Conesa and F. Garcia-Alcalde},
url = {http://dx.doi.org/10.1093/bioinformatics/btv566},
doi = {10.1093/bioinformatics/btv566},
issn = {1367-4803},
year = {2016},
date = {2016-01-01},
journal = {BIOINFORMATICS},
volume = {32},
number = {2},
pages = {292-294},
abstract = {Motivation: Detection of random errors and systematic biases is a
crucial step of a robust pipeline for processing high-throughput
sequencing (HTS) data. Bioinformatics software tools capable of
performing this task are available, either for general analysis of HTS
data or targeted to a specific sequencing technology. However, most of
the existing QC instruments only allow processing of one sample at a
time.
Results: Qualimap 2 represents a next step in the QC analysis of HTS
data. Along with comprehensive single-sample analysis of alignment data, it includes new modes that allow simultaneous processing and comparison
of multiple samples. As with the first version, the new features are
available via both graphical and command line interface. Additionally, it includes a large number of improvements proposed by the user
community.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000368903900004,
title = {A survey of best practices for RNA-seq data analysis},
author = { A. Conesa and P. Madrigal and S. Tarazona and D. Gomez-Cabrero and A. Cervera and A. McPherson and M. W. Szczesniak and D. J. Gaffney and L. L. Elo and X. Zhang and A. Mortazavi},
url = {http://dx.doi.org/10.1186/s13059-016-0881-8},
doi = {10.1186/s13059-016-0881-8},
issn = {1474-760X},
year = {2016},
date = {2016-01-01},
journal = {GENOME BIOLOGY},
volume = {17},
abstract = {RNA-sequencing (RNA-seq) has a wide variety of applications, but no
single analysis pipeline can be used in all cases. We review all of the
major steps in RNA-seq data analysis, including experimental design, quality control, read alignment, quantification of gene and transcript
levels, visualization, differential gene expression, alternative
splicing, functional analysis, gene fusion detection and eQTL mapping.
We highlight the challenges associated with each step. We discuss the
analysis of small RNAs and the integration of RNA-seq with other
functional genomics techniques. Finally, we discuss the outlook for
novel technologies that are changing the state of the art in
transcriptomics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000366410900003,
title = {Data quality aware analysis of differential expression in RNA-seq with
NOISeq R/Bioc package},
author = { S. Tarazona and P. Furio-Tari and D. Turra and A. Di Pietro and M. Jose Nueda and A. Ferrer and A. Conesa},
url = {http://dx.doi.org/10.1093/nar/gkv711},
doi = {10.1093/nar/gkv711},
issn = {0305-1048},
year = {2015},
date = {2015-12-01},
journal = {NUCLEIC ACIDS RESEARCH},
volume = {43},
number = {21},
abstract = {As the use of RNA-seq has popularized, there is an increasing
consciousness of the importance of experimental design, bias removal, accurate quantification and control of false positives for proper data
analysis. We introduce the NOISeq R-package for quality control and
analysis of count data. We show how the available diagnostic tools can
be used to monitor quality issues, make pre-processing decisions and
improve analysis. We demonstrate that the nonparametric NOISeqBIO
efficiently controls false discoveries in experiments with biological
replication and outperforms state-of-the-art methods. NOISeq is a
comprehensive resource that meets current needs for robust data-aware
analysis of RNA-seq differential expression.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000361363000001,
title = {Methylome profiling reveals functions and genes which are differentially
methylated in serrated compared to conventional colorectal carcinoma},
author = { P. Conesa-Zamora and J. Garcia-Solano and M. del Carmen Turpin and P. Sebastian-Leon and D. Torres-Moreno and E. Estrada and A. Tuomisto and J. Wilce and M. J. Maekinen and M. Perez-Guillermo and A. Conesa},
url = {http://dx.doi.org/10.1186/s13148-015-0128-7},
doi = {10.1186/s13148-015-0128-7},
issn = {1868-7083},
year = {2015},
date = {2015-09-01},
journal = {CLINICAL EPIGENETICS},
volume = {7},
abstract = {Background: Serrated adenocarcinoma (SAC) is a recently recognized
colorectal cancer (CRC) subtype accounting for 7.5-8.7 % of CRCs. It
has been shown that SAC has a worse prognosis and different histological
and molecular features compared to conventional carcinoma (CC) but, to
date, there is no study analysing its methylome profile.
Results: The methylation status of 450,000 CpG sites using the Infinium
Human Methylation 450 BeadChip array was investigated in 103 colorectal
specimens, including 39 SACs and 34 matched CCs, from Spanish and
Finnish patients. Microarray data showed a higher representation of
morphogenesis-, neurogenesis-, cytoskeleton-and vesicle
transport-related functions and also significant differential
methylation of 15 genes, including the iodothyronine deiodinase DIO3 and
the forkhead family transcription factor FOXD2 genes which were
validated at the CpG, mRNA and protein level using pyrosequencing, methylation-specific PCR, quantitative polymerase chain reaction (qPCR)
and immunohistochemistry. A quantification study of the methylation
status of CpG sequences in FOXD2 demonstrated a novel region controlling
gene expression. Moreover, differences in these markers were also
evident when comparing SAC with CRC showing molecular and histological
features of high-level microsatellite instability.
Conclusions: This methylome study demonstrates distinct epigenetic
regulation patterns in SAC which are consistent to previous expression
profile studies and that DIO3 and FOXD2 might be molecular targets for a
specific histology-oriented treatment of CRC.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000363355400007,
title = {Comparative RNA-seq analysis of the Tritrichomonas foetus PIG30/1
isolate from pigs reveals close association with Tritrichomonas foetus
BP-4 isolate `bovine genotype'},
author = { V. Morin-Adeline and K. Mueller and A. Conesa and J. Slapeta},
url = {http://dx.doi.org/10.1016/j.vetpar.2015.08.012},
doi = {10.1016/j.vetpar.2015.08.012},
issn = {0304-4017},
year = {2015},
date = {2015-09-01},
journal = {VETERINARY PARASITOLOGY},
volume = {212},
number = {3-4},
pages = {111-117},
abstract = {Tritrichomonas foetus was described as a commensal of the stomach, caecum and nasal cavity of pigs before it was recognised as the cause of
reproductive tract disease of cattle. T. foetus also causes chronic
large bowel diarrhoea in domestic cats. Multi-locus genotyping and
comparative transcriptome analysis has previously revealed that T.
foetus isolated from cat and cattle hosts are genetically distinct, referred to as the `feline genotype' and `bovine genotype', respectively. Conversely, multi-locus genotyping has grouped porcine T.
foetus with the `bovine genotype'. To compare the extent of the
similarity between porcine T. foetus and cattle `bovine genotype'
isolates, RNA-sequencing (RNA-seq) was used to produce the first
cell-wide transcriptome library of porcine T. foetus PIG30/1.
Comparative transcriptome analysis of the PIG30/1 with the published
bovine (BP-4) and feline (G10/1) transcriptomes revealed that the
porcine T. foetus shares a 4.7 fold greater number of orthologous genes
with the bovine T. foetus than with the feline T. foetus. Comparing
transcription of the virulence factors, cysteine proteases (CP) between
the three isolates, the porcine T. foetus was found to preferentially
transcribe CP8 like the `bovine genotype' T. foetus, compared to thehigh
transcription of CP7 seen for `feline genotype' T. foetus. At the
cell-wide transcriptome level, the porcine T. foetus isolate (PIG30/1)
groups closer with the `bovine genotype' T. foetus rather than the
`feline genotype' T. foetus. (C) 2015 Elsevier B.V. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000360039300003,
title = {RNAseq analysis of Aspergillus fumigatus in blood reveals a just wait
and see resting stage behavior},
author = { H. Irmer and S. Tarazona and C. Sasse and P. Olbermann and J. Loeffler and S. Krappmann and A. Conesa and G. H. Braus},
url = {http://dx.doi.org/10.1186/s12864-015-1853-1},
doi = {10.1186/s12864-015-1853-1},
issn = {1471-2164},
year = {2015},
date = {2015-08-01},
journal = {BMC GENOMICS},
volume = {16},
abstract = {Background: Invasive aspergillosis is started after germination of
Aspergillus fumigatus conidia that are inhaled by susceptible
individuals. Fungal hyphae can grow in the lung through the epithelial
tissue and disseminate hematogenously to invade into other organs. Low
fungaemia indicates that fungal elements do not reside in the
bloodstream for long.
Results: We analyzed whether blood represents a hostile environment to
which the physiology of A. fumigatus has to adapt. An in vitro model of
A. fumigatus infection was established by incubating mycelium in blood.
Our model allowed to discern the changes of the gene expression profile
of A. fumigatus at various stages of the infection. The majority of
described virulence factors that are connected to pulmonary infections
appeared not to be activated during the blood phase. Three active
processes were identified that presumably help the fungus to survive the
blood environment in an advanced phase of the infection: iron
homeostasis, secondary metabolism, and the formation of detoxifying
enzymes.
Conclusions: We propose that A. fumigatus is hardly able to propagate in
blood. After an early stage of sensing the environment, virtually all
uptake mechanisms and energy-consuming metabolic pathways are shut-down.
The fungus appears to adapt by trans-differentiation into a resting
mycelial stage. This might reflect the harsh conditions in blood where
A. fumigatus cannot take up sufficient nutrients to establish
self-defense mechanisms combined with significant growth.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000355704700013,
title = {Genome-wide changes in histone H3 lysine 27 trimethylation associated
with bud dormancy release in peach},
author = { L. de la Fuente and A. Conesa and A. Lloret and M. Luisa Badenes and G. Rios},
url = {http://dx.doi.org/10.1007/s11295-015-0869-7},
doi = {10.1007/s11295-015-0869-7},
issn = {1614-2942},
year = {2015},
date = {2015-06-01},
journal = {TREE GENETICS & GENOMES},
volume = {11},
number = {3},
abstract = {Bud dormancy is an evolutionary adaptation of perennial plants to the
seasonal fluctuation of temperatures in temperate climates, affected by
intrinsic and environmental signals. Recent investigations point to a
relevant role of epigenetic mechanisms in the regulation of bud
dormancy. We have performed a chromatin immunoprecipitation sequencing
(ChIP-seq) analysis of histone H3 lysine-27 trimethylation (H3K27me3), a
chromatin mark associated with stable gene silencing, in dormant (D) and
dormancy-released (ND) buds of peach (Prunus persica). H3K27me3 regions
were more abundant in gene-rich euchromatic zones of chromosomes and
associated with gene bodies. The dormancy regulators DORMANCY-ASSOCIATED
MADS-box (DAM) 1, DAM4, DAM5 and DAM6 were found significantly enriched
in H3K27me3 in ND samples, in close agreement with their
dormancy-specific expression. The DAM locus was modified at specific
short regions, allowing the uneven regulation of distinct DAM genes.
Additional regulatory factors related to meristem activity and flowering
genes from Arabidopsis thaliana were differentially H3K27 trimethylated, which suggests that meristem reactivation and flower development could
be also epigenetically regulated in reproductive buds of peach. A (GA)n
motif and CACTA-type transposon-related sequences were found
over-represented in H3K27me3 regions.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000350585600002,
title = {Two independent epigenetic biomarkers predict survival in neuroblastoma},
author = { Y. Yanez and E. Grau and V. C. Rodriguez-Cortez and D. Hervas and E. Vidal and R. Noguera and M. Hernandez and V. Segura and A. Canete and A. Conesa and J. Font de Mora and V. Castel},
url = {http://dx.doi.org/10.1186/s13148-015-0054-8},
doi = {10.1186/s13148-015-0054-8},
issn = {1868-7083},
year = {2015},
date = {2015-02-01},
journal = {CLINICAL EPIGENETICS},
volume = {7},
abstract = {Background: Neuroblastoma (NB) is the most common extracranial pediatric
solid tumor with a highly variable clinical course, ranging from
spontaneous regression to life-threatening disease. Survival rates for
high-risk NB patients remain disappointingly low despite multimodal
treatment. Thus, there is an urgent clinical need for additional
biomarkers to improve risk stratification, treatment management, and
survival rates in children with aggressive NB.
Results: Using gene promoter methylation analysis in 48 neuroblastoma
tumors with microarray technology, we found a strong association between survival and gene promoter hypermethylation (P = 0.036).
Hypermethylation of 70 genes significantly differentiated high-risk
survivor patients from those who died during follow-up time. Sixteen
genes with relevant roles in cancer biology were further validated in an
additional cohort of 83 neuroblastoma tumors by bisulfite
pyrosequencing. High promoter methylation rates of these genes were
found in patients with metastatic tumors (either stage metastatic (M) or
metastatic special (MS)), 18 months or older at first diagnosis, MYCN
amplification, relapsed, and dead. Notably, the degree of methylation of
retinoblastoma 1 (RB1) and teratocarcinoma-derived growth factor 1
(TDGF1) predicts event-free and overall survival independently of the
established risk factors. In addition, low RB1 mRNA expression levels
associate with poor prognosis suggesting that promoter methylation could
contribute to the transcriptional silencing of this gene in NB.
Conclusions: We found a new epigenetic signature predictive for NB
patients' outcome: the methylation status of RB1 and TDGF1 associate
with poorer survival. This information is useful to assess prognosis and
improve treatment selection.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000345790500001,
title = {Comparative transcriptomics reveals striking similarities between the
bovine and feline isolates of Tritrichomonas foetus: consequences for in
silico drug-target identification},
author = { V. Morin-Adeline and R. Lomas and D. O'Meally and C. Stack and A. Conesa and J. Slapeta},
url = {http://dx.doi.org/10.1186/1471-2164-15-955},
doi = {10.1186/1471-2164-15-955},
issn = {1471-2164},
year = {2014},
date = {2014-11-01},
journal = {BMC GENOMICS},
volume = {15},
abstract = {Background: Few, if any, protozoan parasites are reported to exhibit
extreme organ tropism like the flagellate Tritrichomonas foetus. In
cattle, T. foetus infects the reproductive system causing abortion, whereas the infection in cats results in chronic large bowel diarrhoea.
In the absence of a T. foetus genome, we utilized a de novo approach to
assemble the transcriptome of the bovine and feline genotype to identify
host-specific adaptations and virulence factors specific to each
genotype. Furthermore, a subset of orthologs was used to characterize
putative druggable targets and expose complications of in silico drug
target mining in species with indefinite host-ranges.
Results: Illumina RNA-seq reads were assembled into two representative
bovine and feline transcriptomes containing 42,363 and 36,559 contigs, respectively. Coding and non-coding regions of the genome libraries
revealed striking similarities, with 24,620 shared homolog pairs reduced
down to 7,547 coding orthologs between the two genotypes. The
transcriptomes were near identical in functional category distribution;
with no indication of selective pressure acting on orthologs despite
differences in parasite origins/host. Orthologs formed a large
proportion of highly expressed transcripts in both genotypes (bovine
genotype: 76%, feline genotype: 56%). Mining the libraries for
protease virulence factors revealed the cysteine proteases (CP) to be
the most common. In total, 483 and 445 bovine and feline T. foetus
transcripts were identified as putative proteases based on MEROPS
database, with 9 hits to putative protease inhibitors. In bovine T.
foetus, CP8 is the preferentially transcribed CP while in the feline
genotype, transcription of CP7 showed higher abundance. In silico
druggability analysis of the two genotypes revealed that when host
sequences are taken into account, drug targets are genotype-specific.
Conclusion: Gene discovery analysis based on RNA-seq data analysis
revealed prominent similarities between the bovine and feline T. foetus, suggesting recent adaptation to their respective host/niche. T. foetus
represents a unique case of a mammalian protozoan expanding its
parasitic grasp across distantly related host lineages. Consequences of
the host-range for in silico drug targeting are exposed here, demonstrating that targets of the parasite in one host are not
necessarily ideal for the same parasite in another host.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000347559200001,
title = {Understanding disease mechanisms with models of signaling pathway
activities},
author = { P. Sebastian-Leon and E. Vidal and P. Minguez and A. Conesa and S. Tarazona and A. Amadoz and C. Armero and F. Salavert and A. Vidal-Puig and D. Montaner and J. Dopazo},
url = {http://dx.doi.org/10.1186/s12918-014-0121-3},
doi = {10.1186/s12918-014-0121-3},
issn = {1752-0509},
year = {2014},
date = {2014-10-01},
journal = {BMC SYSTEMS BIOLOGY},
volume = {8},
abstract = {Background: Understanding the aspects of the cell functionality that
account for disease or drug action mechanisms is one of the main
challenges in the analysis of genomic data and is on the basis of the
future implementation of precision medicine.
Results: Here we propose a simple probabilistic model in which signaling
pathways are separated into elementary sub-pathways or signal
transmission circuits (which ultimately trigger cell functions) and then
transforms gene expression measurements into probabilities of activation
of such signal transmission circuits. Using this model, differential
activation of such circuits between biological conditions can be
estimated. Thus, circuit activation statuses can be interpreted as
biomarkers that discriminate among the compared conditions. This type of
mechanism-based biomarkers accounts for cell functional activities and
can easily be associated to disease or drug action mechanisms. The
accuracy of the proposed model is demonstrated with simulations and real
datasets.
Conclusions: The proposed model provides detailed information that
enables the interpretation disease mechanisms as a consequence of the
complex combinations of altered gene expression values. Moreover, it
offers a framework for suggesting possible ways of therapeutic
intervention in a pathologically perturbed system.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000342600300030,
title = {A comprehensive assessment of RNA-seq accuracy, reproducibility and
information content by the Sequencing Quality Control Consortium},
author = { Z. Su and P. P. Labaj and S. Li and J. Thierry-Mieg and D. Thierry-Mieg and W. Shi and C. Wang and G. P. Schroth and R. A. Setterquist and J. F. Thompson and W. D. Jones and W. Xiao and W. Xu and R. V. Jensen and R. Kelly and J. Xu and A. Conesa and C. Furlanello and H. Gao and H. Hong and N. Jafari and S. Letovsky and Y. Liao and F. Lu and E. J. Oakeley and Z. Peng and C. A. Praul and J. Santoyo-Lopez and A. Scherer and T. Shi and G. K. Smyth and F. Staedtler and P. Sykacek and X. Tan and E. A. Thompson and J. Vandesompele and M. D. Wang and J. Wang and R. D. Wolfinger and J. Zavadil and S. S. Auerbach and W. Bao and H. Binder and T. Blomquist and M. H. Brilliant and P. R. Bushel and W. Cain and J. G. Catalano and C. Chang and T. Chen and G. Chen and R. Chen and M. Chierici and T. Chu and D. Clevert and Y. Deng and A. Derti and V. Devanarayan and Z. Dong and J. Dopazo and T. Du and H. Fang and Y. Fang and M. Fasold and A. Fernandez and M. Fischer and P. Furio-Tari and J. C. Fuscoe and F. Caiment and S. Gaj and J. Gandara and H. Gao and W. Ge and Y. Gondo and B. Gong and M. Gong and Z. Gong and B. Green and C. Guo and L. Guo and L. Guo and J. Hadfield and J. Hellemans and S. Hochreiter and M. Jia and M. Jian and C. D. Johnson and S. Kay and J. Kleinjans and S. Lababidi and S. Levy and Q. Li and L. Li and L. Li and P. Li and Y. Li and H. Li and J. Li and S. Li and S. M. Lin and F. J. Lopez and X. Lu and H. Luo and X. Ma and J. Meehan and D. B. Megherbi and N. Mei and B. Mu and B. Ning and A. Pandey and J. Perez-Florido and R. G. Perkins and R. Peters and J. H. Phan and M. Pirooznia and F. Qian and T. Qing and L. Rainbow and P. Rocca-Serra and L. Sambourg and S. Sansone and S. Schwartz and R. Shah and J. Shen and T. M. Smith and O. Stegle and N. Stralis-Pavese and E. Stupka and Y. Suzuki and L. T. Szkotnicki and M. Tinning and B. Tu and J. van Deft and A. Vela-Boza and E. Venturini and S. J. Walker and L. Wan and W. Wang and J. Wang and J. Wang and E. D. Wieben and J. C. Willey and P. Wu and J. Xuan and Y. Yang and Z. Ye and Y. Yin and Y. Yu and Y. Yuan and J. Zhang and K. K. Zhang and W. Zhang and W. Zhang and Y. Zhang and C. Zhao and Y. Zheng and Y. Zhou and P. Zumbo and W. Tong and D. P. Kreil and C. E. Mason and L. Shi},
url = {http://dx.doi.org/10.1038/nbt.2957},
doi = {10.1038/nbt.2957},
issn = {1087-0156},
year = {2014},
date = {2014-09-01},
journal = {NATURE BIOTECHNOLOGY},
volume = {32},
number = {9},
pages = {903-914},
abstract = {We present primary results from the Sequencing Quality Control (SEQC)
project, coordinated by the US Food and Drug Administration. Examining
Illumina HiSeq, Life Technologies SOLiD and Roche 454 platforms at
multiple laboratory sites using reference RNA samples with built-in
controls, we assess RNA sequencing (RNA-seq) performance for junction
discovery and differential expression profiling and compare it to
microarray and quantitative PCR (qPCR) data using complementary metrics.
At all sequencing depths, we discover unannotated exon-exon junctions, with >80% validated by qPCR. We find that measurements of relative
expression are accurate and reproducible across sites and platforms if
specific-filters are used. In contrast, RNA-seq and microarrays do not
provide accurate absolute measurements, and gene-specific biases are
observed for all examined platforms, including qPCR. Measurement
performance depends on the platform and data analysis pipeline, and
variation is large for transcript-level profiling. The complete SEQC
data sets, comprising >100 billion reads (10Tb), provide unique
resources for evaluating RNA-seq analyses for clinical and regulatory
settings.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000342913000008,
title = {Next maSigPro: updating maSigPro bioconductor package for RNA-seq time
series},
author = { M. J. Nueda and S. Tarazona and A. Conesa},
url = {http://dx.doi.org/10.1093/bioinformatics/btu333},
doi = {10.1093/bioinformatics/btu333},
issn = {1367-4803},
year = {2014},
date = {2014-09-01},
journal = {BIOINFORMATICS},
volume = {30},
number = {18},
pages = {2598-2602},
abstract = {Motivation: The widespread adoption of RNA-seq to quantitatively measure
gene expression has increased the scope of sequencing experimental
designs to include time-course experiments. maSigPro is an R package
specifically suited for the analysis of time-course gene expression
data, which was developed originally for microarrays and hence was
limited in its application to count data.
Results: We have updated maSigPro to support RNA-seq time series
analysis by introducing generalized linear models in the algorithm to
support the modeling of count data while maintaining the traditional
functionalities of the package. We show a good performance of the
maSigPro-GLM method in several simulated time-course scenarios and in a
real experimental dataset.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000343030500001,
title = {Assessing technical performance in differential gene expression
experiments with external spike-in RNA control ratio mixtures},
author = { S. A. Munro and S. P. Lund and P. S. Pine and H. Binder and D. Clevert and A. Conesa and J. Dopazo and M. Fasold and S. Hochreiter and H. Hong and N. Jafari and D. P. Kreil and P. P. Labaj and S. Li and Y. Liao and S. M. Lin and J. Meehan and C. E. Mason and J. Santoyo-Lopez and R. A. Setterquist and L. Shi and W. Shi and G. K. Smyth and N. Stralis-Pavese and Z. Su and W. Tong and C. Wang and J. Wang and J. Xu and Z. Ye and Y. Yang and Y. Yu and M. Salit},
url = {http://dx.doi.org/10.1038/ncomms6125},
doi = {10.1038/ncomms6125},
issn = {2041-1723},
year = {2014},
date = {2014-09-01},
journal = {NATURE COMMUNICATIONS},
volume = {5},
abstract = {There is a critical need for standard approaches to assess, report and
compare the technical performance of genome-scale differential gene
expression experiments. Here we assess technical performance with a
proposed standard `dashboard' of metrics derived from analysis of
external spike-in RNA control ratio mixtures. These control ratio
mixtures with defined abundance ratios enable assessment of diagnostic
performance of differentially expressed transcript lists, limit of
detection of ratio (LODR) estimates and expression ratio variability and
measurement bias. The performance metrics suite is applicable to
analysis of a typical experiment, and here we also apply these metrics
to evaluate technical performance among laboratories. An interlaboratory
study using identical samples shared among 12 laboratories with three
different measurement processes demonstrates generally consistent
diagnostic power across 11 laboratories. Ratio measurement variability
and bias are also comparable among laboratories for the same measurement
process. We observe different biases for measurement processes using
different mRNA-enrichment protocols.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000351589702079,
title = {Differentially expressed functions and genes between serrated
adenocarcinoma and sporadic colorectal carcinoma showing histological
and molecular features of high level of microsatellite instability},
author = { M. Turpin Sevilla and R. Carbonell-Munoz and J. Garcia-Solano and D. Torres-Moreno and F. Garcia-Garcia and A. Conesa and M. Perez-Guillermo and P. Conesa-Zamora},
issn = {0959-8049},
year = {2014},
date = {2014-07-01},
journal = {EUROPEAN JOURNAL OF CANCER},
volume = {50},
number = {5},
pages = {S219},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000338246200001,
title = {Relationship between genome and epigenome - challenges and requirements
for future research},
author = { G. Almouzni and L. Altucci and B. Amati and N. Ashley and D. Baulcombe and N. Beaujean and C. Bock and E. Bongcam-Rudloff and J. Bousquet and S. Braun and B. Bressac-de Paillerets and M. Bussemakers and L. Clarke and A. Conesa and X. Estivill and A. Fazeli and N. Grgurevic and I. Gut and B. T. Heijmans and S. Hermouet and J. Houwing-Duistermaat and I. Iacobucci and J. Ilas and R. Kandimalla and S. Krauss-Etschmann and P. Lasko and S. Lehmann and A. Lindroth and G. Majdic and E. Marcotte and G. Martinelli and N. Martinet and E. Meyer and C. Miceli and K. Mills and M. Moreno-Villanueva and G. Morvan and D. Nickel and B. Niesler and M. Nowacki and J. Nowak and S. Ossowski and M. Pelizzola and R. Pochet and U. Potocnik and M. Radwanska and J. Raes and M. Rattray and M. D. Robinson and B. Roelen and S. Sauer and D. Schinzer and E. Slagboom and T. Spector and H. G. Stunnenberg and E. Tiligada and M. Torres-Padilla and R. Tsonaka and A. Van Soom and M. Vidakovic and M. Widschwendter},
url = {http://dx.doi.org/10.1186/1471-2164-15-487},
doi = {10.1186/1471-2164-15-487},
issn = {1471-2164},
year = {2014},
date = {2014-06-01},
journal = {BMC GENOMICS},
volume = {15},
abstract = {Understanding the links between genetic, epigenetic and non-genetic
factors throughout the lifespan and across generations and their role in
disease susceptibility and disease progression offer entirely new
avenues and solutions to major problems in our society. To overcome the
numerous challenges, we have come up with nine major conclusions to set
the vision for future policies and research agendas at the European
level.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000333499100007,
title = {Sequencing and functional analysis of the genome of a nematode
egg-parasitic fungus, Pochonia chlamydosporia},
author = { E. Larriba and M. D. L. A. Jaime and J. Carbonell-Caballero and A. Conesa and J. Dopazo and C. Nislow and J. Martin-Nieto and L. Vicente Lopez-Llorca},
url = {http://dx.doi.org/10.1016/j.fgb.2014.02.002},
doi = {10.1016/j.fgb.2014.02.002},
issn = {1087-1845},
year = {2014},
date = {2014-04-01},
journal = {FUNGAL GENETICS AND BIOLOGY},
volume = {65},
pages = {69-80},
abstract = {Pochonia chlamydosporia is a worldwide-distributed soil fungus with a
great capacity to infect and destroy the eggs and kill females of
plant-parasitic nematodes. Additionally, it has the ability to colonize
endophytically roots of economically-important crop plants, thereby
promoting their growth and eliciting plant defenses. This multitrophic
behavior makes P. chlamydosporia a potentially useful tool for
sustainable agriculture approaches. We sequenced and assembled similar
to 41 Mb of P. chlamydosporia genomic DNA and predicted 12,122 gene
models, of which many were homologous to genes of fungal pathogens of
invertebrates and fungal plant pathogens. Predicted genes (65%) were
functionally annotated according to Gene Ontology, and 16% of them
found to share homology with genes in the Pathogen Host Interactions
(PHI) database. The genome of this fungus is highly enriched in genes
encoding hydrolytic enzymes, such as proteases, glycoside hydrolases and
carbohydrate esterases. We used RNA-Seq technology in order to identify
the genes expressed during endophytic behavior of P. chlamydosporia when
colonizing barley roots. Functional annotation of these genes showed
that hydrolytic enzymes and transporters are expressed during
endophytism. This structural and functional analysis of the P.
chlamydosporia genome provides a starting point for understanding the
molecular mechanisms involved in the multitrophic lifestyle of this
fungus. The genomic information provided here should also prove useful
for enhancing the capabilities of this fungus as a biocontrol agent of
plant-parasitic nematodes and as a plant growth-promoting organism. (C)
2014 Elsevier Inc. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000333681300001,
title = {Data integration in the era of omics: current and future challenges},
author = { D. Gomez-Cabrero and I. Abugessaisa and D. Maier and A. Teschendorff and M. Merkenschlager and A. Gisel and E. Ballestar and E. Bongcam-Rudloff and A. Conesa and J. Tegner},
url = {http://dx.doi.org/10.1186/1752-0509-8-S2-I1},
doi = {10.1186/1752-0509-8-S2-I1},
issn = {1752-0509},
year = {2014},
date = {2014-03-01},
journal = {BMC SYSTEMS BIOLOGY},
volume = {8},
number = {2},
abstract = {To integrate heterogeneous and large omics data constitutes not only a
conceptual challenge but a practical hurdle in the daily analysis of
omics data. With the rise of novel omics technologies and through
large-scale consortia projects, biological systems are being further
investigated at an unprecedented scale generating heterogeneous and
often large data sets. These data-sets encourage researchers to develop
novel data integration methodologies. In this introduction we review the
definition and characterize current efforts on data integration in the
life sciences. We have used a web-survey to assess current research
projects on data-integration to tap into the views, needs and challenges
as currently perceived by parts of the research community.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000333681300002,
title = {The common ground of genomics and systems biology},
author = { A. Conesa and A. Mortazavi},
url = {http://dx.doi.org/10.1186/1752-0509-8-S2-S1},
doi = {10.1186/1752-0509-8-S2-S1},
issn = {1752-0509},
year = {2014},
date = {2014-03-01},
journal = {BMC SYSTEMS BIOLOGY},
volume = {8},
number = {2},
abstract = {The rise of systems biology is intertwined with that of genomics, yet
their primordial relationship to one another is ill-defined. We discuss
how the growth of genomics provided a critical boost to the popularity
of systems biology. We describe the parts of genomics that share common
areas of interest with systems biology today in the areas of gene
expression, network inference, chromatin state analysis, pathway
analysis, personalized medicine, and upcoming areas of synergy as
genomics continues to expand its scope across all biomedical fields.},
note = {High-Throughput Omics and Data Integration Workshop, Barcelona, SPAIN, FEB 13-15, 2013},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000333681300008,
title = {Pathway network inference from gene expression data},
author = { I. Ponzoni and M. J. Nueda and S. Tarazona and S. Goetz and D. Montaner and J. S. Dussaut and J. Dopazo and A. Conesa},
url = {http://dx.doi.org/10.1186/1752-0509-8-S2-S7},
doi = {10.1186/1752-0509-8-S2-S7},
issn = {1752-0509},
year = {2014},
date = {2014-03-01},
journal = {BMC SYSTEMS BIOLOGY},
volume = {8},
number = {2},
abstract = {Background: The development of high-throughput omics technologies
enabled genome-wide measurements of the activity of cellular elements
and provides the analytical resources for the progress of the Systems
Biology discipline. Analysis and interpretation of gene expression data
has evolved from the gene to the pathway and interaction level, i.e.
from the detection of differentially expressed genes, to the
establishment of gene interaction networks and the identification of
enriched functional categories. Still, the understanding of biological
systems requires a further level of analysis that addresses the
characterization of the interaction between functional modules.
Results: We present a novel computational methodology to study the
functional interconnections among the molecular elements of a biological
system. The PANA approach uses high-throughput genomics measurements and
a functional annotation scheme to extract an activity profile from each
functional block -or pathway-followed by machine-learning methods to
infer the relationships between these functional profiles. The result is
a global, interconnected network of pathways that represents the
functional cross-talk within the molecular system. We have applied this
approach to describe the functional transcriptional connections during
the yeast cell cycle and to identify pathways that change their
connectivity in a disease condition using an Alzheimer example.
Conclusions: PANA is a useful tool to deepen in our understanding of the
functional interdependences that operate within complex biological
systems. We show the approach is algorithmically consistent and the
inferred network is well supported by the available functional data. The
method allows the dissection of the molecular basis of the functional
connections and we describe the different regulatory mechanisms that
explain the network's topology obtained for the yeast cell cycle data.},
note = {High-Throughput Omics and Data Integration Workshop, Barcelona, SPAIN, FEB 13-15, 2013},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000333681300010,
title = {STATegra EMS: an Experiment Management System for complex
next-generation omics experiments},
author = { R. Hernandez de Diego and N. Boix-Chova and D. Gomez-Cabrero and J. Tegner and I. Abugessaisa and A. Conesa},
url = {http://dx.doi.org/10.1186/1752-0509-8-S2-S9},
doi = {10.1186/1752-0509-8-S2-S9},
issn = {1752-0509},
year = {2014},
date = {2014-03-01},
journal = {BMC SYSTEMS BIOLOGY},
volume = {8},
number = {2},
abstract = {High-throughput sequencing assays are now routinely used to study
different aspects of genome organization. As decreasing costs and
widespread availability of sequencing enable more laboratories to use
sequencing assays in their research projects, the number of samples and
replicates in these experiments can quickly grow to several dozens of
samples and thus require standardized annotation, storage and management
of preprocessing steps. As a part of the STATegra project, we have
developed an Experiment Management System (EMS) for high throughput
omics data that supports different types of sequencing-based assays such
as RNA-seq, ChIP-seq, Methyl-seq, etc, as well as proteomics and
metabolomics data. The STATegra EMS provides metadata annotation of
experimental design, samples and processing pipelines, as well as
storage of different types of data files, from raw data to ready-to-use
measurements. The system has been developed to provide research
laboratories with a freely-available, integrated system that offers a
simple and effective way for experiment annotation and tracking of
analysis procedures.},
note = {High-Throughput Omics and Data Integration Workshop, Barcelona, SPAIN, FEB 13-15, 2013},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000331407000009,
title = {Molecular interactions between sugar beet and Polymyxa betae during its
life cycle},
author = { N. Desoignies and J. Carbonell and J. -S. Moreau and A. Conesa and J. Dopazo and A. Legreve},
url = {http://dx.doi.org/10.1111/aab.12095},
doi = {10.1111/aab.12095},
issn = {0003-4746},
year = {2014},
date = {2014-03-01},
journal = {ANNALS OF APPLIED BIOLOGY},
volume = {164},
number = {2},
pages = {244-256},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000331155800710,
title = {Methylation Microarray Analysis Identifies Differentially Methylated
Genes in Serrated Compared to Conventional Colorectal Carcinomas},
author = { J. Garcia-Solano and E. Alcaraz-Mateos and J. Wilce and D. Torres-Moreno and M. C. Turpin-Sevilla and C. Navarre and A. Conesa and A. Tuomisto and P. Sirnio and M. J. Makinen and M. Perez-Guillermo and P. Conesa-Zamora},
issn = {0023-6837},
year = {2014},
date = {2014-02-01},
journal = {LABORATORY INVESTIGATION},
volume = {94},
number = {1},
pages = {174A},
organization = {US & Canadian Acad Pathol; Dako; Biocare Med; Leica Biosystems; LabCorp
Specialty Testing Grp, Integrated Oncol; GenomOncology; Nephropath;
Ventana; Diagnost BioSystems},
note = {103rd Annual Meeting of the
United-States-and-Canadian-Academy-of-Pathology (USCAP), San Diego, CA, MAR 01-07, 2014},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000331502201024,
title = {Methylation Microarray Analysis Identifies Differentially Methylated
Genes in Serrated Compared to Conventional Colorectal Carcinomas},
author = { J. Garica-Solano and E. Alcaraz-Mateos and J. Wilce and D. Torres-Moreno and M. C. Turpin-Sevilla and C. Navarre and A. Conesa and A. Tuomisto and P. Sirnio and M. J. Makinen and M. Perez-Guillermo and P. Conesa-Zamora},
issn = {0893-3952},
year = {2014},
date = {2014-02-01},
journal = {MODERN PATHOLOGY},
volume = {27},
number = {2},
pages = {174A},
organization = {US & Canadian Acad Pathol; Dako; Biocare Med; Leica Biosystems; LabCorp
Specialty Testing Grp, Integrated Oncol; GenomOncology; Nephropath;
Ventana; Diagnost BioSystems},
note = {103rd Annual Meeting of the
United-States-and-Canadian-Academy-of-Pathology (USCAP), San Diego, CA, MAR 01-07, 2014},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000317907200122,
title = {Defining the Genomic Signature of Totipotency and Pluripotency during
Early Human Development},
author = { A. Galan and P. Diaz-Gimeno and M. Eugenia Poo and D. Valbuena and E. Sanchez and V. Ruiz and J. Dopazo and D. Montaner and A. Conesa and C. Simon},
url = {http://dx.doi.org/10.1371/journal.pone.0062135},
doi = {10.1371/journal.pone.0062135},
issn = {1932-6203},
year = {2013},
date = {2013-04-01},
journal = {PLOS ONE},
volume = {8},
number = {4},
abstract = {The genetic mechanisms governing human pre-implantation embryo
development and the in vitro counterparts, human embryonic stem cells
(hESCs), still remain incomplete. Previous global genome studies
demonstrated that totipotent blastomeres from day-3 human embryos and
pluripotent inner cell masses (ICMs) from blastocysts, display unique
and differing transcriptomes. Nevertheless, comparative gene expression
analysis has revealed that no significant differences exist between
hESCs derived from blastomeres versus those obtained from ICMs, suggesting that pluripotent hESCs involve a new developmental
progression. To understand early human stages evolution, we developed an
undifferentiation network signature (UNS) and applied it to a
differential gene expression profile between single blastomeres from
day-3 embryos, ICMs and hESCs. This allowed us to establish a unique
signature composed of highly interconnected genes characteristic of
totipotency (61 genes), in vivo pluripotency (20 genes), and in vitro
pluripotency (107 genes), and which are also proprietary according to
functional analysis. This systems biology approach has led to an
improved understanding of the molecular and signaling processes
governing human pre-implantation embryo development, as well as enabling
us to comprehend how hESCs might adapt to in vitro culture conditions.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000311383600015,
title = {Expression profiling shows differential molecular pathways and provides
potential new diagnostic biomarkers for colorectal serrated
adenocarcinoma},
author = { P. Conesa-Zamora and J. Garcia-Solano and F. Garcia-Garcia and M. del Carmen Turpin and J. Trujillo-Santos and D. Torres-Moreno and I. Oviedo-Ramirez and R. Carbonell-Munoz and E. Munoz-Delgado and E. Rodriguez-Braun and A. Conesa and M. Perez-Guillermo},
url = {http://dx.doi.org/10.1002/ijc.27674},
doi = {10.1002/ijc.27674},
issn = {0020-7136},
year = {2013},
date = {2013-01-01},
journal = {INTERNATIONAL JOURNAL OF CANCER},
volume = {132},
number = {2},
pages = {297-307},
abstract = {Serrated adenocarcinoma (SAC) is a recently recognized colorectal cancer
(CRC) subtype accounting for 7.5 to 8.7% of CRCs. It has been shown
that SAC has a poorer prognosis and has different molecular and
immunohistochemical features compared with conventional carcinoma (CC)
but, to date, only one previous study has analyzed its mRNA expression
profile by microarray. Using a different microarray platform, we have
studied the molecular signature of 11 SACs and compared it with that of
15 matched CC with the aim of discerning the functions which
characterize SAC biology and validating, at the mRNA and protein level, the most differentially expressed genes which were also tested using a
validation set of 70 SACs and 70 CCs to assess their diagnostic and
prognostic values. Microarray data showed a higher representation of
morphogenesis-, hypoxia-, cytoskeleton- and vesicle transport-related
functions and also an overexpression of fascin1 (actin-bundling protein
associated with invasion) and the antiapoptotic gene hippocalcin in SAC
all of which were validated both by quantitative real-time PCR (qPCR)
and immunohistochemistry. Fascin1 expression was statistically
associated with KRAS mutation with 88.6% sensitivity and 85.7%
specificity for SAC diagnosis and the positivity of fascin1 or hippocalcin was highly suggestive of SAC diagnosis (sensitivity =
100%). Evaluation of these markers in CRCs showing histological and
molecular characteristics of high-level microsatellite instability
(MSI-H) also helped to distinguish SACs from MSI-H CRCs. Molecular
profiling demonstrates that SAC shows activation of distinct signaling
pathways and that immunohistochemical fascin1 and hippocalcin expression
can be reliably used for its differentiation from other CRC subtypes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000309754300355,
title = {METHYLATION STATUS IN NEUROBLASTOMA AND ITS PROGNOSTIC VALUE},
author = { Y. Yanez and E. Grau and A. Canete and A. Conesa and A. Gonzalez Neira and V. Castel},
issn = {1545-5009},
year = {2012},
date = {2012-12-01},
journal = {PEDIATRIC BLOOD & CANCER},
volume = {59},
number = {6, SI},
pages = {1053-1054},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000310368300003,
title = {Early gene expression events in the laminar abscission zone of
abscission-promoted citrus leaves after a cycle of water
stress/rehydration: involvement of CitbHLH1},
author = { J. Agusti and J. Gimeno and P. Merelo and R. Serrano and M. Cercos and A. Conesa and M. Talon and F. R. Tadeo},
url = {http://dx.doi.org/10.1093/jxb/ers270},
doi = {10.1093/jxb/ers270},
issn = {0022-0957},
year = {2012},
date = {2012-10-01},
journal = {JOURNAL OF EXPERIMENTAL BOTANY},
volume = {63},
number = {17},
pages = {6079-6091},
abstract = {Leaf abscission is a common response of plants to drought stress. Some
species, such as citrus, have evolved a specific behaviour in this
respect, keeping their leaves attached to the plant body during water
stress until this is released by irrigation or rain. This study
successfully reproduced this phenomenon under controlled conditions (24h
of water stress followed by 24h of rehydration) and used it to construct
a suppression subtractive hybridization cDNA library enriched in genes
involved in the early stages of rehydration-promoted leaf abscission
after water stress. Sequencing of the library yielded 314 unigenes, which were spotted onto nylon membranes. Membrane hybridization with
petiole (Pet)- and laminar abscission zone (LAZ)-enriched RNA samples
corresponding to early steps in leaf abscission revealed an almost
exclusive preferential gene expression programme in the LAZ. The data
identified major processes such as protein metabolism, cell-wall
modification, signalling, control of transcription and vesicle
production, and transport as the main biological processes activated in
LAZs during the early steps of rehydration-promoted leaf abscission
after water stress. Based on these findings, a model for the early steps
of citrus leaf abscission is proposed. In addition, it is suggested that
CitbHLH1, the putative citrus orthologue of Arabidopsis BIGPETAL, may
play major roles in the control of abscission-related events in citrus
abscission zones.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000310262500003,
title = {Development, Characterization and Experimental Validation of a
Cultivated Sunflower (Helianthus annuus L.) Gene Expression
Oligonucleotide Microarray},
author = { P. Fernandez and M. Soria and D. Blesa and J. DiRienzo and S. Moschen and M. Rivarola and B. Jose Clavijo and S. Gonzalez and L. Peluffo and D. Principi and G. Dosio and L. Aguirrezabal and F. Garcia-Garcia and A. Conesa and E. Hopp and J. Dopazo and R. Amelia Heinz and N. Paniego},
url = {http://dx.doi.org/10.1371/journal.pone.0045899},
doi = {10.1371/journal.pone.0045899},
issn = {1932-6203},
year = {2012},
date = {2012-10-01},
journal = {PLOS ONE},
volume = {7},
number = {10},
abstract = {Oligonucleotide-based microarrays with accurate gene coverage represent
a key strategy for transcriptional studies in orphan species such as
sunflower, H. annuus L., which lacks full genome sequences. The goal of
this study was the development and functional annotation of a
comprehensive sunflower unigene collection and the design and validation
of a custom sunflower oligonucleotide-based microarray. A large scale
EST (>130,000 ESTs) curation, assembly and sequence annotation was
performed using Blast2GO (www.blast2go.de). The EST assembly comprises
41,013 putative transcripts (12,924 contigs and 28,089 singletons). The
resulting Sunflower Unigen Resource (SUR version 1.0) was used to design
an oligonucleotide-based Agilent microarray for cultivated sunflower.
This microarray includes a total of 42,326 features: 1,417 Agilent
controls, 74 control probes for sunflower replicated 10 times (740
controls) and 40,169 different non-control probes. Microarray
performance was validated using a model experiment examining the
induction of senescence by water deficit. Pre-processing and
differential expression analysis of Agilent microarrays was performed
using the Bioconductor limma package. The analyses based on p-values
calculated by eBayes (p<0.01) allowed the detection of 558
differentially expressed genes between water stress and control
conditions; from these, ten genes were further validated by qPCR.
Over-represented ontologies were identified using FatiScan in the
Babelomics suite. This work generated a curated and trustable sunflower
unigene collection, and a custom, validated sunflower
oligonucleotide-based microarray using Agilent technology. Both the
curated unigene collection and the validated oligonucleotide microarray
provide key resources for sunflower genome analysis, transcriptional
studies, and molecular breeding for crop improvement.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000308289400005,
title = {Microarray analysis of Etrog citron (Citrus medica L.) reveals changes
in chloroplast, cell wall, peroxidase and symporter activities in
response to viroid infection},
author = { S. Rizza and A. Conesa and J. Juarez and A. Catara and L. Navarro and N. Duran-Vila and G. Ancillo},
url = {http://dx.doi.org/10.1111/j.1364-3703.2012.00794.x},
doi = {10.1111/j.1364-3703.2012.00794.x},
issn = {1464-6722},
year = {2012},
date = {2012-10-01},
journal = {MOLECULAR PLANT PATHOLOGY},
volume = {13},
number = {8},
pages = {852-864},
abstract = {Viroids are small (246401 nucleotides), single-stranded, circular RNA
molecules that infect several crop plants and can cause diseases of
economic importance. Citrus are the hosts in which the largest number of
viroids have been identified. Citrus exocortis viroid (CEVd), the causal
agent of citrus exocortis disease, induces considerable losses in citrus
crops. Changes in the gene expression profile during the early
(pre-symptomatic) and late (post-symptomatic) stages of Etrog citron
infected with CEVd were investigated using a citrus cDNA microarray.
MaSigPro analysis was performed and, on the basis of gene expression
profiles as a function of the time after infection, the differentially
expressed genes were classified into five clusters. FatiScan analysis
revealed significant enrichment of functional categories for each
cluster, indicating that viroid infection triggers important changes in
chloroplast, cell wall, peroxidase and symporter activities.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000309881200016,
title = {Qualimap: evaluating next-generation sequencing alignment data},
author = { F. Garcia-Alcalde and K. Okonechnikov and J. Carbonell and L. M. Cruz and S. Goetz and S. Tarazona and J. Dopazo and T. F. Meyer and A. Conesa},
url = {http://dx.doi.org/10.1093/bioinformatics/bts503},
doi = {10.1093/bioinformatics/bts503},
issn = {1367-4803},
year = {2012},
date = {2012-10-01},
journal = {BIOINFORMATICS},
volume = {28},
number = {20},
pages = {2678-2679},
abstract = {Motivation: The sequence alignment/map (SAM) and the binary
alignment/map (BAM) formats have become the standard method of
representation of nucleotide sequence alignments for next-generation
sequencing data. SAM/BAM files usually contain information from tens to
hundreds of millions of reads. Often, the sequencing technology, protocol and/or the selected mapping algorithm introduce some unwanted
biases in these data. The systematic detection of such biases is a
non-trivial task that is crucial to drive appropriate downstream
analyses.
Results: We have developed Qualimap, a Java application that supports
user-friendly quality control of mapping data, by considering sequence
features and their genomic properties. Qualimap takes sequence alignment
data and provides graphical and statistical analyses for the evaluation
of data. Such quality-control data are vital for highlighting problems
in the sequencing and/or mapping processes, which must be addressed
prior to further analyses.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000305420000014,
title = {ARSyN: a method for the identification and removal of systematic noise
in multifactorial time course microarray experiments},
author = { M. J. Nueda and A. Ferrer and A. Conesa},
url = {http://dx.doi.org/10.1093/biostatistics/kxr042},
doi = {10.1093/biostatistics/kxr042},
issn = {1465-4644},
year = {2012},
date = {2012-07-01},
journal = {BIOSTATISTICS},
volume = {13},
number = {3},
pages = {553-566},
abstract = {Transcriptomic profiling experiments that aim to the identification of
responsive genes in specific biological conditions are commonly set up
under defined experimental designs that try to assess the effects of
factors and their interactions on gene expression. Data from these
controlled experiments, however, may also contain sources of unwanted
noise that can distort the signal under study, affect the residuals of
applied statistical models, and hamper data analysis. Commonly, normalization methods are applied to transcriptomics data to remove
technical artifacts, but these are normally based on general assumptions
of transcript distribution and greatly ignore both the characteristics
of the experiment under consideration and the coordinative nature of
gene expression. In this paper, we propose a novel methodology, ARSyN, for the preprocessing of microarray data that takes into account these 2
last aspects. By combining analysis of variance (ANOVA) modeling of gene
expression values and multivariate analysis of estimated effects, the
method identifies the nonstructured part of the signal associated to the
experimental factors (the noise within the signal) and the structured
variation of the ANOVA errors (the signal of the noise). By removing
these noise fractions from the original data, we create a filtered data
set that is rich in the information of interest and includes only the
random noise required for inferential analysis. In this work, we focus
on multifactorial time course microarray (MTCM) experiments with 2
factors: one quantitative such as time or dosage and the other
qualitative, as tissue, strain, or treatment. However, the method can be
used in other situations such as experiments with only one factor or
more complex designs with more than 2 factors. The filtered data
obtained after applying ARSyN can be further analyzed with the
appropriate statistical technique to obtain the biological information
required. To evaluate the performance of the filtering strategy, we have
applied different statistical approaches for MTCM analysis to several
real and simulated data sets, studying also the efficiency of these
techniques. By comparing the results obtained with the original and
ARSyN filtered data and also with other filtering techniques, we can
conclude that the proposed method increases the statistical power to
detect biological signals, especially in cases where there are high
levels of structural noise. Software for ARSyN is freely available at
http://www.ua.es/personal/mj.nueda.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000311518100001,
title = {Identification of yeast genes that confer resistance to chitosan
oligosaccharide (COS) using chemogenomics},
author = { M. D. L. A. Jaime and L. Vicente Lopez-Llorca and A. Conesa and A. Y. Lee and M. Proctor and L. E. Heisler and M. Gebbia and G. Giaever and J. T. Westwood and C. Nislow},
url = {http://dx.doi.org/10.1186/1471-2164-13-267},
doi = {10.1186/1471-2164-13-267},
issn = {1471-2164},
year = {2012},
date = {2012-06-01},
journal = {BMC GENOMICS},
volume = {13},
abstract = {Background: Chitosan oligosaccharide (COS), a deacetylated derivative of
chitin, is an abundant, and renewable natural polymer. COS has higher
antimicrobial properties than chitosan and is presumed to act by
disrupting/permeabilizing the cell membranes of bacteria, yeast and
fungi. COS is relatively non-toxic to mammals. By identifying the
molecular and genetic targets of COS, we hope to gain a better
understanding of the antifungal mode of action of COS.
Results: Three different chemogenomic fitness assays, haploinsufficiency
(HIP), homozygous deletion (HOP), and multicopy suppression (MSP)
profiling were combined with a transcriptomic analysis to gain insight
in to the mode of action and mechanisms of resistance to chitosan
oligosaccharides. The fitness assays identified 39 yeast deletion
strains sensitive to COS and 21 suppressors of COS sensitivity. The
genes identified are involved in processes such as RNA biology
(transcription, translation and regulatory mechanisms), membrane
functions (e.g. signalling, transport and targeting), membrane
structural components, cell division, and proteasome processes. The
transcriptomes of control wild type and 5 suppressor strains
overexpressing ARL1, BCK2, ERG24, MSG5, or RBA50, were analyzed in the
presence and absence of COS. Some of the up-regulated transcripts in the
suppressor overexpressing strains exposed to COS included genes involved
in transcription, cell cycle, stress response and the Ras signal
transduction pathway. Down-regulated transcripts included those encoding
protein folding components and respiratory chain proteins. The
COS-induced transcriptional response is distinct from previously
described environmental stress responses (i.e. thermal, salt, osmotic
and oxidative stress) and pre-treatment with these well characterized
environmental stressors provided little or any resistance to COS.
Conclusions: Overexpression of the ARL1 gene, a member of the Ras
superfamily that regulates membrane trafficking, provides protection
against COS-induced cell membrane permeability and damage. We found that
the ARL1 COS-resistant over-expression strain was as sensitive to
Amphotericin B, Fluconazole and Terbinafine as the wild type cells and
that when COS and Fluconazole are used in combination they act in a
synergistic fashion. The gene targets of COS identified in this study
indicate that COS's mechanism of action is different from other commonly
studied fungicides that target membranes, suggesting that COS may be an
effective fungicide for drug-resistant fungal pathogens.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000305069800421,
title = {Regulatory proteins in the opportunistic human pathogen Aspergillus
fumigatus},
author = { C. J. Lin and H. Irmer and S. Tarazona and P. Olbermann and S. Krappmann and A. Conesa and G. Braus},
issn = {0933-7407},
year = {2012},
date = {2012-06-01},
journal = {MYCOSES},
volume = {55},
number = {4, SI},
pages = {135-136},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000301295900020,
title = {Mining of miRNAs and potential targets from gene oriented clusters of
transcripts sequences of the anti-malarial plant, Artemisia annua},
author = { A. L. Perez-Quintero and G. Sablok and T. V. Tatarinova and A. Conesa and J. Kuo and C. Lopez},
url = {http://dx.doi.org/10.1007/s10529-011-0808-0},
doi = {10.1007/s10529-011-0808-0},
issn = {0141-5492},
year = {2012},
date = {2012-04-01},
journal = {BIOTECHNOLOGY LETTERS},
volume = {34},
number = {4},
pages = {737-745},
abstract = {miRNAs involved in the biosynthesis of artemisinin, an anti-malarial
compound form the plant Artemisia annua, have been identified using
computational approaches to find conserved pre-miRNAs in available A.
annua UniGene collections. Eleven pre-miRNAs were found from nine
families. Targets predicted for these miRNAs were mainly transcription
factors for conserved miRNAs. No target genes involved in artemisinin
biosynthesis were found. However, miR390 was predicted to target a gene
involved in the trichome development, which is the site of synthesis of
artemisinin and could be a candidate for genetic transformation aiming
to increase the content of artemisinin. Phylogenetic analyses were
carried out to determinate the relation between A. annua and other plant
pre-miRNAs: the pre-miRNA-based phylogenetic trees failed to correspond
to known phylogenies, suggesting that pre-miRNA primary sequences may be
too variable to accurately predict phylogenetic relations.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000305345200011,
title = {Transcriptome Profiling of the Intoxication Response of Tenebrio molitor
Larvae to Bacillus thuringiensis Cry3Aa Protoxin},
author = { B. Oppert and S. E. Dowd and P. Bouffard and L. Li and A. Conesa and M. D. Lorenzen and M. Toutges and J. Marshall and D. L. Huestis and J. Fabrick and C. Oppert and J. L. Jurat-Fuentes},
url = {http://dx.doi.org/10.1371/journal.pone.0034624},
doi = {10.1371/journal.pone.0034624},
issn = {1932-6203},
year = {2012},
date = {2012-04-01},
journal = {PLOS ONE},
volume = {7},
number = {4},
abstract = {Bacillus thuringiensis (Bt) crystal (Cry) proteins are effective against
a select number of insect pests, but improvements are needed to increase
efficacy and decrease time to mortality for coleopteran pests. To gain
insight into the Bt intoxication process in Coleoptera, we performed
RNA-Seq on cDNA generated from the guts of Tenebrio molitor larvae that
consumed either a control diet or a diet containing Cry3Aa protoxin.
Approximately 134,090 and 124,287 sequence reads from the control and
Cry3Aa-treated groups were assembled into 1,318 and 1,140 contigs, respectively. Enrichment analyses indicated that functions associated
with mitochondrial respiration, signalling, maintenance of cell
structure, membrane integrity, protein recycling/synthesis, and glycosyl
hydrolases were significantly increased in Cry3Aa-treated larvae, whereas functions associated with many metabolic processes were reduced, especially glycolysis, tricarboxylic acid cycle, and fatty acid
synthesis. Microarray analysis was used to evaluate temporal changes in
gene expression after 6, 12 or 24 h of Cry3Aa exposure. Overall, microarray analysis indicated that transcripts related to allergens, chitin-binding proteins, glycosyl hydrolases, and tubulins were induced, and those related to immunity and metabolism were repressed in
Cry3Aa-intoxicated larvae. The 24 h microarray data validated most of
the RNA-Seq data. Of the three intoxication intervals, larvae
demonstrated more differential expression of transcripts after 12 h
exposure to Cry3Aa. Gene expression examined by three different methods
in control vs. Cry3Aa-treated larvae at the 24 h time point indicated
that transcripts encoding proteins with chitin-binding domain 3 were the
most differentially expressed in Cry3Aa-intoxicated larvae. Overall, the
data suggest that T. molitor larvae mount a complex response to Cry3Aa
during the initial 24 h of intoxication. Data from this study represent
the largest genetic sequence dataset for T. molitor to date.
Furthermore, the methods in this study are useful for comparative
analyses in organisms lacking a sequenced genome.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000209459000044,
title = {Transdifferentiation of MALME-3M and MCF-7 Cells toward Adipocyte-like
Cells is Dependent on Clathrin-mediated Endocytosis},
author = { J. Carcel-Trullols and C. Aguilar-Gallardo and F. Garcia-Alcalde and M. Angel Pardo-Cea and J. Dopazo and A. Conesa and C. Simon},
url = {http://dx.doi.org/10.1186/2193-1801-1-44},
doi = {10.1186/2193-1801-1-44},
issn = {2193-1801},
year = {2012},
date = {2012-01-01},
journal = {SPRINGERPLUS},
volume = {1},
abstract = {Enforced cell transdifferentiation of human cancer cells is a promising
alternative to conventional chemotherapy. We previously identified
albumin-associated lipid-and, more specifically, saturated fatty
acid-induced transdifferentiation programs in human cancer cells
(HCCLs). In this study, we further characterized the adipocyte-like
cells, resulting from the transdifferentiation of human cancer cell
lines MCF-7 and MALME-3M, and proposed a common mechanistic approach for
these transdifferentiating programs. We showed the loss of pigmentation
in MALME-3M cells treated with albumin-associated lipids, based on
electron microscopic analysis, and the overexpression of perilipin 2
(PLIN2) by western blotting in MALME-3M and MCF-7 cells treated with
unsaturated fatty acids. Comparing the gene expression profiles of naive
melanoma MALME-3M cells and albumin-associated lipid-treated cells, based on RNA sequencing, we confirmed the transcriptional upregulation
of some key adipogenic gene markers and also an alternative splicing of
the adipogenic master regulator PPARG, that is probably related to the
reported up regulated expression of the protein. Most importantly, these
results also showed the upregulation of genes responsible for Clathrin
(CLTC) and other adaptor-related proteins. An increase in CLTC
expression in the transdifferentiated cells was confirmed by western
blotting. Inactivation of CLTC by chlorpromazine (CHP), an inhibitor of
CTLC mediated endocytosis (CME), and gene silencing by siRNAs, partially
reversed the accumulation of neutral lipids observed in the
transdifferentiated cells. These findings give a deeper insight into the
phenotypic changes observed in HCCL to adipocyte-like
transdifferentiation and point towards CME as a key pathway in distinct
transdifferentiation programs.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000298300800012,
title = {Histone modifications and expression of DAM6 gene in peach are modulated
during bud dormancy release in a cultivar-dependent manner},
author = { C. Leida and A. Conesa and G. Llacer and M. Luisa Badenes and G. Rios},
url = {http://dx.doi.org/10.1111/j.1469-8137.2011.03863.x},
doi = {10.1111/j.1469-8137.2011.03863.x},
issn = {0028-646X},
year = {2012},
date = {2012-01-01},
journal = {NEW PHYTOLOGIST},
volume = {193},
number = {1},
pages = {67-80},
abstract = {Bud dormancy release in many woody perennial plants responds to the
seasonal accumulation of chilling stimulus. MADS-box transcription
factors encoded by DORMANCY ASSOCIATED MADS-box (DAM) genes in peach
(Prunus persica) are implicated in this pathway, but other regulatory
factors remain to be identified. In addition, the regulation of DAM gene
expression is not well known at the molecular level. A microarray
hybridization approach was performed to identify genes whose expression
correlates with the bud dormancy-related behaviour in 10 different peach
cultivars. Histone modifications in DAM6 gene were investigated by
chromatin immunoprecipitation in two different cultivars. The expression
of DAM4DAM6 and several genes related to abscisic acid and drought
stress response correlated with the dormancy behaviour of peach
cultivars. The trimethylation of histone H3 at K27 in the DAM6 promoter, coding region and the second large intron was preceded by a decrease in
acetylated H3 and trimethylated H3K4 in the region of translation start, coinciding with repression of DAM6 during dormancy release. Analysis of
chromatin modifications reinforced the role of epigenetic mechanisms in
DAM6 regulation and bud dormancy release, and highlighted common
features with the vernalization process in Arabidopsis thaliana and
cereals.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000299712500014,
title = {Variable selection for multifactorial genomic data},
author = { S. Tarazona and S. Prado-Lopez and J. Dopazo and A. Ferrer and A. Conesa},
url = {http://dx.doi.org/10.1016/j.chemolab.2011.10.012},
doi = {10.1016/j.chemolab.2011.10.012},
issn = {0169-7439},
year = {2012},
date = {2012-01-01},
journal = {CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS},
volume = {110},
number = {1},
pages = {113-122},
abstract = {Dimension reduction techniques are used to explore genomic data. Due to
the large number of variables (genes) included in this kind of studies, variable selection methods are needed to identify the most responsive
genes in order to get a better interpretation of the results or to
conduct more specific experiments. These methods should be consistent
with the amount of signal in the data. For this purpose, we introduce a
novel selection strategy called minAS and also adapt other existing
strategies, such us Gamma approximation, resampling techniques, etc. All
of them are based on studying the distribution of statistics measuring
the importance of the variables in the model. These strategies have been
applied to the ASCA-genes analysis framework and more generally to
dimension reduction techniques as PCA. The performance of the different
strategies was evaluated using simulated data. The best performing
methods were then applied on an experimental dataset containing the
transcriptomic profiles of human embryonic stem cells cultured under
different oxygen concentrations. The ability of the methods to extract
relevant biological information from the data is discussed. (C) 2011
Elsevier B.V. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000297242100015,
title = {Large-scale transcriptional profiling and functional assays reveal
important roles for Rho-GTPase signalling and SCL during haematopoietic
differentiation of human embryonic stem cells},
author = { S. Yung and M. Ledran and I. Moreno-Gimeno and A. Conesa and D. Montaner and J. Dopazo and I. Dimmick and N. J. Slater and L. Marenah and P. J. Real and I. Paraskevopoulou and V. Bisbal and D. Burks and M. Santibanez-Koref and R. Moreno and J. Mountford and P. Menendez and L. Armstrong and M. Lako},
url = {http://dx.doi.org/10.1093/hmg/ddr431},
doi = {10.1093/hmg/ddr431},
issn = {0964-6906},
year = {2011},
date = {2011-12-01},
journal = {HUMAN MOLECULAR GENETICS},
volume = {20},
number = {24},
pages = {4932-4946},
abstract = {Understanding the transcriptional cues that direct differentiation of
human embryonic stem cells (hESCs) and human-induced pluripotent stem
cells to defined and functional cell types is essential for future
clinical applications. In this study, we have compared transcriptional
profiles of haematopoietic progenitors derived from hESCs at various
developmental stages of a feeder-and serum-free differentiation method
and show that the largest transcriptional changes occur during the first
4 days of differentiation. Data mining on the basis of molecular
function revealed Rho-GTPase signalling as a key regulator of
differentiation. Inhibition of this pathway resulted in a significant
reduction in the numbers of emerging haematopoietic progenitors
throughout the differentiation window, thereby uncovering a previously
unappreciated role for Rho-GTPase signalling during human haematopoietic
development. Our analysis indicated that SCL was the 11th most
upregulated transcript during the first 4 days of the hESC
differentiation process. Overexpression of SCL in hESCs promoted
differentiation to meso-endodermal lineages, the emergence of
haematopoietic and erythro-megakaryocytic progenitors and accelerated
erythroid differentiation. Importantly, intrasplenic transplantation of
SCL-overexpressing hESC-derived haematopoietic cells enhanced recovery
from induced acute anaemia without significant cell engraftment, suggesting a paracrine-mediated effect.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000297918600020,
title = {Differential expression in RNA-seq: A matter of depth},
author = { S. Tarazona and F. Garcia-Alcalde and J. Dopazo and A. Ferrer and A. Conesa},
url = {http://dx.doi.org/10.1101/gr.124321.111},
doi = {10.1101/gr.124321.111},
issn = {1088-9051},
year = {2011},
date = {2011-12-01},
journal = {GENOME RESEARCH},
volume = {21},
number = {12},
pages = {2213-2223},
abstract = {Next-generation sequencing (NGS) technologies are revolutionizing genome
research, and in particular, their application to transcriptomics
(RNA-seq) is increasingly being used for gene expression profiling as a
replacement for microarrays. However, the properties of RNA-seq data
have not been yet fully established, and additional research is needed
for understanding how these data respond to differential expression
analysis. In this work, we set out to gain insights into the
characteristics of RNA-seq data analysis by studying an important
parameter of this technology: the sequencing depth. We have analyzed how
sequencing depth affects the detection of transcripts and their
identification as differentially expressed, looking at aspects such as
transcript biotype, length, expression level, and fold-change. We have
evaluated different algorithms available for the analysis of RNA-seq and
proposed a novel approach-NOISeq-that differs from existing methods in
that it is data-adaptive and nonparametric. Our results reveal that most
existing methodologies suffer from a strong dependency on sequencing
depth for their differential expression calls and that this results in a
considerable number of false positives that increases as the number of
reads grows. In contrast, our proposed method models the noise
distribution from the actual data, can therefore better adapt to the
size of the data set, and is more effective in controlling the rate of
false discoveries. This work discusses the true potential of RNA-seq for
studying regulation at low expression ranges, the noise within RNA-seq
data, and the issue of replication.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000297983800001,
title = {Fortunella margarita Transcriptional Reprogramming Triggered by
Xanthomonas citri subsp citri},
author = { A. A. Khalaf and Jr. Gmitter and A. Conesa and J. Dopazo and G. A. Moore},
url = {http://dx.doi.org/10.1186/1471-2229-11-159},
doi = {10.1186/1471-2229-11-159},
issn = {1471-2229},
year = {2011},
date = {2011-11-01},
journal = {BMC PLANT BIOLOGY},
volume = {11},
abstract = {Background: Citrus canker disease caused by the bacterial pathogen
Xanthomonas citri subsp. citri (Xcc) has become endemic in areas where
high temperature, rain, humidity, and windy conditions provide a
favourable environment for the dissemination of the bacterium. Xcc is
pathogenic on many commercial citrus varieties but appears to elicit an
incompatible reaction on the citrus relative Fortunella margarita Swing
(kumquat), in the form of a very distinct delayed necrotic response. We
have developed subtractive libraries enriched in sequences expressed in
kumquat leaves during both early and late stages of the disease. The
isolated differentially expressed transcripts were subsequently
sequenced. Our results demonstrate how the use of microarray expression
profiling can help assign roles to previously uncharacterized genes and
elucidate plant pathogenesis-response related mechanisms. This can be
considered to be a case study in a citrus relative where high throughput
technologies were utilized to understand defence mechanisms in
Fortunella and citrus at the molecular level.
Results: cDNAs from sequenced kumquat libraries (ESTs) made from
subtracted RNA populations, healthy vs. infected, were used to make this
microarray. Of 2054 selected genes on a customized array, 317 were
differentially expressed (P < 0.05) in Xcc challenged kumquat plants
compared to mock-inoculated ones. This study identified components of
the incompatible interaction such as reactive oxygen species (ROS) and
programmed cell death (PCD). Common defence mechanisms and a number of
resistance genes were also identified. In addition, there were a
considerable number of differentially regulated genes that had no
homologues in the databases. This could be an indication of either a
specialized set of genes employed by kumquat in response to canker
disease or new defence mechanisms in citrus.
Conclusion: Functional categorization of kumquat Xcc-responsive genes
revealed an enhanced defence-related metabolism as well as a number of
resistant response-specific genes in the kumquat transcriptome in
response to Xcc inoculation. Gene expression profile(s) were analyzed to
assemble a comprehensive and inclusive image of the molecular
interaction in the kumquat/Xcc system. This was done in order to
elucidate molecular mechanisms associated with the development of the
hypersensitive response phenotype in kumquat leaves. These data will be
used to perform comparisons among citrus species to evaluate means to
enhance the host immune responses against bacterial diseases.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000292249800002,
title = {Profiling the venom gland transcriptomes of Costa Rican snakes by 454
pyrosequencing},
author = { J. Durban and P. Juarez and Y. Angulo and B. Lomonte and M. Flores-Diaz and A. Alape-Giron and M. Sasa and L. Sanz and J. M. Gutierrez and J. Dopazo and A. Conesa and J. J. Calvete},
url = {http://dx.doi.org/10.1186/1471-2164-12-259},
doi = {10.1186/1471-2164-12-259},
issn = {1471-2164},
year = {2011},
date = {2011-05-01},
journal = {BMC GENOMICS},
volume = {12},
abstract = {Background: A long term research goal of venomics, of applied importance
for improving current antivenom therapy, but also for drug discovery, is
to understand the pharmacological potential of venoms. Individually or
combined, proteomic and transcriptomic studies have demonstrated their
feasibility to explore in depth the molecular diversity of venoms. In
the absence of genome sequence, transcriptomes represent also valuable
searchable databases for proteomic projects.
Results: The venom gland transcriptomes of 8 Costa Rican taxa from 5
genera (Crotalus, Bothrops, Atropoides, Cerrophidion, and Bothriechis)
of pitvipers were investigated using high-throughput 454 pyrosequencing.
100,394 out of 330,010 masked reads produced significant hits in the
available databases. 5.165,220 nucleotides (8.27%) were masked by
RepeatMasker, the vast majority of which corresponding to class I
(retroelements) and class II (DNA transposons) mobile elements. BLAST
hits included 79,991 matches to entries of the taxonomic suborder
Serpentes, of which 62,433 displayed similarity to documented venom
proteins. Strong discrepancies between the transcriptome-computed and
the proteome-gathered toxin compositions were obvious at first sight.
Although the reasons underlaying this discrepancy are elusive, since no
clear trend within or between species is apparent, the data indicate
that individual mRNA species may be translationally controlled in a
species-dependent manner. The minimum number of genes from each toxin
family transcribed into the venom gland transcriptome of each species
was calculated from multiple alignments of reads matched to a
full-length reference sequence of each toxin family. Reads encoding ORF
regions of Kazal-type inhibitor-like proteins were uniquely found in
Bothriechis schlegelii and B. lateralis transcriptomes, suggesting a
genus-specific recruitment event during the early-Middle Miocene. A
transcriptome-based cladogram supports the large divergence between A.
mexicanus and A. picadoi, and a closer kinship between A. mexicanus and
C. godmani.
Conclusions: Our comparative next-generation sequencing (NGS) analysis
reveals taxon-specific trends governing the formulation of the venom
arsenal. Knowledge of the venom proteome provides hints on the
translation efficiency of toxin-coding transcripts, contributing thereby
to a more accurate interpretation of the transcriptome. The application
of NGS to the analysis of snake venom transcriptomes, may represent the
tool for opening the door to systems venomics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000289162000005,
title = {B2G-FAR, a species-centered GO annotation repository},
author = { S. Goetz and R. Arnold and P. Sebastian-Leon and S. Martin-Rodriguez and P. Tischler and M. Jehl and J. Dopazo and T. Rattei and A. Conesa},
url = {http://dx.doi.org/10.1093/bioinformatics/btr059},
doi = {10.1093/bioinformatics/btr059},
issn = {1367-4803},
year = {2011},
date = {2011-04-01},
journal = {BIOINFORMATICS},
volume = {27},
number = {7},
pages = {919-924},
abstract = {Motivation: Functional genomics research has expanded enormously in the
last decade thanks to the cost reduction in high-throughput technologies
and the development of computational tools that generate, standardize
and share information on gene and protein function such as the Gene
Ontology ( GO). Nevertheless, many biologists, especially working with
non-model organisms, still suffer from non-existing or low-coverage
functional annotation, or simply struggle retrieving, summarizing and
querying these data.
Results: The Blast2GO Functional Annotation Repository (B2G-FAR) is a
bioinformatics resource envisaged to provide functional information for
otherwise uncharacterized sequence data and offers data mining tools to
analyze a larger repertoire of species than currently available. This
new annotation resource has been created by applying the Blast2GO
functional annotation engine in a strongly high-throughput manner to the
entire space of public available sequences. The resulting repository
contains GO term predictions for over 13.2 million non-redundant protein
sequences based on BLAST search alignments from the SIMAP database. We
generated GO annotation for approximately 150 000 different taxa making
available 2000 species with the highest coverage through B2G-FAR. A
second section within B2G-FAR holds functional annotations for 17
non-model organism Affymetrix GeneChips.
Conclusions: B2G-FAR provides easy access to exhaustive functional
annotation for 2000 species offering a good balance between quality and
quantity, thereby supporting functional genomics research especially in
the case of non-model organisms.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000288020600040,
title = {Modeling Human Endometrial Decidualization from the Interaction between
Proteome and Secretome},
author = { T. Garrido-Gomez and F. Dominguez and J. Antonio Lopez and E. Camafeita and A. Quinonero and J. Antonio Martinez-Conejero and A. Pellicer and A. Conesa and C. Simon},
url = {http://dx.doi.org/10.1210/jc.2010-1825},
doi = {10.1210/jc.2010-1825},
issn = {0021-972X},
year = {2011},
date = {2011-03-01},
journal = {JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM},
volume = {96},
number = {3},
pages = {706-716},
abstract = {Context: Decidualization of the human endometrium, which involves
morphological and biochemical modifications of the endometrial stromal
cells (ESCs), is a prerequisite for adequate trophoblast invasion and
placenta formation.
Objective: This study aims to investigate the proteome and secretome of
in vitro decidualized ESCs. These data were combined with published
genomic information and integrated to model the human decidualization
interactome.
Design: Prospective experimental case-control study.
Setting: A private research foundation.
Patients: Sixteen healthy volunteer ovum donors.
Intervention: Endometrial samples were obtained, and ESCs were isolated
and decidualized in vitro.
Main Outcome Measures: Two-dimensional difference in-gel
electrophoresis, matrix-assisted laser
desorption/ionization-time-of-flight mass spectrometry, Western blot, human protein cytokine array, ELISA, and bioinformatics analysis were
performed.
Results: The proteomic analysis revealed 60 differentially expressed
proteins (36 over-and 24 underexpressed) in decidualized versus control
ESCs, including known decidualization markers (cathepsin B) and new
biomarkers (transglutaminase 2, peroxiredoxin 4, and the ACTB protein).
In the secretomic analysis, a total of 13 secreted proteins (11 up-and 2
down-regulated) were identified, including well-recognized markers (IGF
binding protein-1 and prolactin) and novel ones (myeloid progenitor
inhibitory factor-1 and platelet endothelial cell adhesion molecule-1).
These proteome/secretome profiles have been integrated into a
decidualization interactome model.
Conclusions: Proteomic and secretomic have been used as hypothesis-free
approaches together with complex bioinformatics to model the human
decidual interactome for the first time. We confirm previous knowledge, describe new molecules, and we have built up a model for human in vitro
decidualization as invaluable tool for the diagnosis, therapy, and
interpretation of biological phenomena. (J Clin Endocrinol Metab 96:
706-716, 2011)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000285626300021,
title = {Paintomics: a web based tool for the joint visualization of
transcriptomics and metabolomics data},
author = { F. Garcia-Alcalde and F. Garcia-Lopez and J. Dopazo and A. Conesa},
url = {http://dx.doi.org/10.1093/bioinformatics/btq594},
doi = {10.1093/bioinformatics/btq594},
issn = {1367-4803},
year = {2011},
date = {2011-01-01},
journal = {BIOINFORMATICS},
volume = {27},
number = {1},
pages = {137-139},
abstract = {Motivation: The development of the omics technologies such as
transcriptomics, proteomics and metabolomics has made possible the
realization of systems biology studies where biological systems are
interrogated at different levels of biochemical activity (gene
expression, protein activity and/or metabolite concentration). An
effective approach to the analysis of these complex datasets is the
joined visualization of the disparate biomolecular data on the framework
of known biological pathways.
Results: We have developed the Paintomics web server as an easy-to-use
bioinformatics resource that facilitates the integrated visual analysis
of experiments where transcriptomics and metabolomics data have been
measured on different conditions for the same samples. Basically, Paintomics takes complete transcriptomics and metabolomics datasets, together with lists of significant gene or metabolite changes, and
paints this information on KEGG pathway maps.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000284658300011,
title = {A multiway approach to data integration in systems biology based on
Tucker3 and N-PLS},
author = { A. Conesa and J. M. Prats-Montalban and S. Tarazona and M. Jose Nueda and A. Ferrer},
url = {http://dx.doi.org/10.1016/j.chemolab.2010.06.004},
doi = {10.1016/j.chemolab.2010.06.004},
issn = {0169-7439},
year = {2010},
date = {2010-11-01},
journal = {CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS},
volume = {104},
number = {1, SI},
pages = {101-111},
abstract = {This paper discusses the potential of multi-way projection methods for
analysing multifactorial data structures to identify underlying
components of variability that interconnect different blocks of omics
variables. We explore their suitability for explorative and variable
selection analysis of systems biology data where different types of
biological parameters are studied together. These methodologies were
applied to the integrative analysis of a functional genomics dataset
where transcriptomics, metabolomics and physiological data are
available. Our results show that multiway methods are suited to
accommodate multifactorial omics experiments and to analyse
relationships between different biochemical layers. Additionally, strategies are presented for variable selection in the context of omics
data and for interpreting results at the level of cellular pathways. (C)
2010 Elsevier B.V. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000284148900034,
title = {Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling},
author = { I. Medina and J. Carbonell and L. Pulido and S. C. Madeira and S. Goetz and A. Conesa and J. Tarraga and A. Pascual-Montano and R. Nogales-Cadenas and J. Santoyo and F. Garcia and M. Marba and D. Montaner and J. Dopazo},
url = {http://dx.doi.org/10.1093/nar/gkq388},
doi = {10.1093/nar/gkq388},
issn = {0305-1048},
year = {2010},
date = {2010-07-01},
journal = {NUCLEIC ACIDS RESEARCH},
volume = {38},
number = {2},
pages = {W210-W213},
abstract = {Babelomics is a response to the growing necessity of integrating and
analyzing different types of genomic data in an environment that allows
an easy functional interpretation of the results. Babelomics includes a
complete suite of methods for the analysis of gene expression data that
include normalization (covering most commercial platforms), pre-processing, differential gene expression (case-controls, multiclass, survival or continuous values), predictors, clustering; large-scale
genotyping assays (case controls and TDTs, and allows population
stratification analysis and correction). All these genomic data analysis
facilities are integrated and connected to multiple options for the
functional interpretation of the experiments. Different methods of
functional enrichment or gene set enrichment can be used to understand
the functional basis of the experiment analyzed. Many sources of
biological information, which include functional (GO, KEGG, Biocarta, Reactome, etc.), regulatory (Transfac, Jaspar, ORegAnno, miRNAs, etc.), text-mining or protein-protein interaction modules can be used for this
purpose. Finally a tool for the de novo functional annotation of
sequences has been included in the system. This provides support for the
functional analysis of non-model species. Mirrors of Babelomics or
command line execution of their individual components are now possible.
Babelomics is available at http://www.babelomics.org.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000284148900039,
title = {Serial Expression Analysis: a web tool for the analysis of serial gene
expression data},
author = { M. Jose Nueda and J. Carbonell and I. Medina and J. Dopazo and A. Conesa},
url = {http://dx.doi.org/10.1093/nar/gkq488},
doi = {10.1093/nar/gkq488},
issn = {0305-1048},
year = {2010},
date = {2010-07-01},
journal = {NUCLEIC ACIDS RESEARCH},
volume = {38},
number = {2},
pages = {W239-W245},
abstract = {Serial transcriptomics experiments investigate the dynamics of gene
expression changes associated with a quantitative variable such as time
or dosage. The statistical analysis of these data implies the study of
global and gene-specific expression trends, the identification of
significant serial changes, the comparison of expression profiles and
the assessment of transcriptional changes in terms of cellular
processes. We have created the SEA (Serial Expression Analysis) suite to
provide a complete web-based resource for the analysis of serial
transcriptomics data. SEA offers five different algorithms based on
univariate, multivariate and functional profiling strategies framed
within a user-friendly interface and a project-oriented architecture to
facilitate the analysis of serial gene expression data sets from
different perspectives. SEA is available at sea.bioinfo.cipf.es.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000276311400004,
title = {Initial Genomics of the Human Nucleolus},
author = { A. Nemeth and A. Conesa and J. Santoyo-Lopez and I. Medina and D. Montaner and B. Peterfia and I. Solovei and T. Cremer and J. Dopazo and G. Laengst},
url = {http://dx.doi.org/10.1371/journal.pgen.1000889},
doi = {10.1371/journal.pgen.1000889},
issn = {1553-7390},
year = {2010},
date = {2010-03-01},
journal = {PLOS GENETICS},
volume = {6},
number = {3},
abstract = {We report for the first time the genomics of a nuclear compartment of
the eukaryotic cell. 454 sequencing and microarray analysis revealed the
pattern of nucleolus-associated chromatin domains (NADs) in the linear
human genome and identified different gene families and certain
satellite repeats as the major building blocks of NADs, which constitute
about 4% of the genome. Bioinformatic evaluation showed that
NAD-localized genes take part in specific biological processes, like the
response to other organisms, odor perception, and tissue development. 3D
FISH and immunofluorescence experiments illustrated the spatial
distribution of NAD-specific chromatin within interphase nuclei and its
alteration upon transcriptional changes. Altogether, our findings
describe the nature of DNA sequences associated with the human nucleolus
and provide insights into the function of the nucleolus in genome
organization and establishment of nuclear architecture.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000277093700004,
title = {Hypoxia Promotes Efficient Differentiation of Human Embryonic Stem Cells
to Functional Endothelium},
author = { S. Prado-Lopez and A. Conesa and A. Arminan and M. Martinez-Losa and C. Escobedo-Lucea and C. Gandia and S. Tarazona and D. Melguizo and D. Blesa and D. Montaner and S. Sanz-Gonzalez and P. Sepulveda and S. Goetz and J. Enrique O'Connor and R. Moreno and J. Dopazo and D. J. Burks and M. Stojkovic},
url = {http://dx.doi.org/10.1002/stem.295},
doi = {10.1002/stem.295},
issn = {1066-5099},
year = {2010},
date = {2010-03-01},
journal = {STEM CELLS},
volume = {28},
number = {3},
pages = {407-418},
abstract = {Early development of mammalian embryos occurs in an environment of
relative hypoxia. Nevertheless, human embryonic stem cells (hESC), which
are derived from the inner cell mass of blastocyst, are routinely
cultured under the same atmospheric conditions (21% O(2)) as somatic
cells. We hypothesized that O2 levels modulate gene expression and
differentiation potential of hESC, and thus, we performed gene profiling
of hESC maintained under normoxic or hypoxic (1% or 5% O(2))
conditions. Our analysis revealed that hypoxia downregulates expression
of pluripotency markers in hESC but increases significantly the
expression of genes associated with angio-and vasculogenesis including
vascular endothelial growth factor and angiopoitein-like proteins.
Consequently, we were able to efficiently differentiate hESC to
functional endothelial cells (EC) by varying O(2) levels; after 24 hours
at 5% O(2), more than 50% of cells were CD34+. Transplantation of
resulting endothelial-like cells improved both systolic function and
fractional shortening in a rodent model of myocardial infarction.
Moreover, analysis of the infarcted zone revealed that transplanted EC
reduced the area of fibrous scar tissue by 50%. Thus, use of hypoxic
conditions to specify the endothelial lineage suggests a novel strategy
for cellular therapies aimed at repair of damaged vasculature in
pathologies such as cerebral ischemia and myocardial infarction. STEM
CELLS 2010; 28: 407-418},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000276399100033,
title = {SIMAP-a comprehensive database of pre-calculated protein sequence
similarities, domains, annotations and clusters},
author = { T. Rattei and P. Tischler and S. Goetz and M. Jehl and J. Hoser and R. Arnold and A. Conesa and H. Mewes},
url = {http://dx.doi.org/10.1093/nar/gkp949},
doi = {10.1093/nar/gkp949},
issn = {0305-1048},
year = {2010},
date = {2010-01-01},
journal = {NUCLEIC ACIDS RESEARCH},
volume = {38},
number = {1},
pages = {D223-D226},
abstract = {The prediction of protein function as well as the reconstruction of
evolutionary genesis employing sequence comparison at large is still the
most powerful tool in sequence analysis. Due to the exponential growth
of the number of known protein sequences and the subsequent quadratic
growth of the similarity matrix, the computation of the Similarity
Matrix of Proteins (SIMAP) becomes a computational intensive task. The
SIMAP database provides a comprehensive and up-to-date precalculation of
the protein sequence similarity matrix, sequence-based features and
sequence clusters. As of September 2009, SIMAP covers 48 million
proteins and more than 23 million non-redundant sequences. Novel
features of SIMAP include the expansion of the sequence space by
including databases such as ENSEMBL as well as the integration of
metagenomes based on their consistent processing and annotation.
Furthermore, protein function predictions by Blast2GO are pre-calculated
for all sequences in SIMAP and the data access and query functions have
been improved. SIMAP assists biologists to query the up-to-date sequence
space systematically and facilitates large-scale downstream projects in
computational biology. Access to SIMAP is freely provided through the
web portal for individuals (http://mips.gsf.de/simap/) and for
programmatic access through DAS (http://webclu.bio.wzw.tum.de/das/) and
Web-Service
(http://mips.gsf.de/webservices/services/SimapService2.0?wsdl).},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000267339600003,
title = {Membrane transporters and carbon metabolism implicated in chloride
homeostasis differentiate salt stress responses in tolerant and
sensitive Citrus rootstocks},
author = { J. Brumos and J. M. Colmenero-Flores and A. Conesa and P. Izquierdo and G. Sanchez and D. J. Iglesias and M. F. Lopez-Climent and A. Gomez-Cadenas and M. Talon},
url = {http://dx.doi.org/10.1007/s10142-008-0107-6},
doi = {10.1007/s10142-008-0107-6},
issn = {1438-793X},
year = {2009},
date = {2009-08-01},
journal = {FUNCTIONAL & INTEGRATIVE GENOMICS},
volume = {9},
number = {3},
pages = {293-309},
abstract = {Salinity tolerance in Citrus is strongly related to leaf chloride
accumulation. Both chloride homeostasis and specific genetic responses
to Cl(-) toxicity are issues scarcely investigated in plants. To
discriminate the transcriptomic network related to Cl(-) toxicity and
salinity tolerance, we have used two Cl(-) salt treatments (NaCl and
KCl) to perform a comparative microarray approach on two Citrus
genotypes, the salt-sensitive Carrizo citrange, a poor Cl(-) excluder, and the tolerant Cleopatra mandarin, an efficient Cl(-) excluder. The
data indicated that Cl(-) toxicity, rather than Na(+) toxicity and/or
the concomitant osmotic perturbation, is the primary factor involved in
the molecular responses of citrus plant leaves to salinity. A number of
uncharacterized membrane transporter genes, like NRT1-2, were
differentially regulated in the tolerant and the sensitive genotypes, suggesting its potential implication in Cl(-) homeostasis. Analyses of
enriched functional categories showed that the tolerant rootstock
induced wider stress responses in gene expression while repressing
central metabolic processes such as photosynthesis and carbon
utilization. These features were in agreement with phenotypic changes in
the patterns of photosynthesis, transpiration, and stomatal conductance
and support the concept that regulation of transpiration and its
associated metabolic adjustments configure an adaptive response to
salinity that reduces Cl(-) accumulation in the tolerant genotype.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000267522200009,
title = {Functional assessment of time course microarray data},
author = { M. Jose Nueda and P. Sebastian and S. Tarazona and F. Garcia-Garcia and J. Dopazo and A. Ferrer and A. Conesa},
url = {http://dx.doi.org/10.1186/1471-2105-10-S6-S9},
doi = {10.1186/1471-2105-10-S6-S9},
issn = {1471-2105},
year = {2009},
date = {2009-01-01},
journal = {BMC BIOINFORMATICS},
volume = {10},
abstract = {Motivation: Time-course microarray experiments study the progress of
gene expression along time across one or several experimental
conditions. Most developed analysis methods focus on the clustering or
the differential expression analysis of genes and do not integrate
functional information. The assessment of the functional aspects of
time-course transcriptomics data requires the use of approaches that
exploit the activation dynamics of the functional categories to where
genes are annotated.
Methods: We present three novel methodologies for the functional
assessment of time-course microarray data. i) maSigFun derives from the
maSigPro method, a regression-based strategy to model time-dependent
expression patterns and identify genes with differences across series.
maSigFun fits a regression model for groups of genes labeled by a
functional class and selects those categories which have a significant
model. ii) PCA-maSigFun fits a PCA model of each functional
class-defined expression matrix to extract orthogonal patterns of
expression change, which are then assessed for their fit to a
time-dependent regression model. iii) ASCA-functional uses the ASCA
model to rank genes according to their correlation to principal time
expression patterns and assess functional enrichment on a GSA fashion.
We used simulated and experimental datasets to study these novel
approaches. Results were compared to alternative methodologies.
Results: Synthetic and experimental data showed that the different
methods are able to capture different aspects of the relationship
between genes, functions and co-expression that are biologically
meaningful. The methods should not be considered as competitive but they
provide different insights into the molecular and functional dynamic
events taking place within the biological system under study.},
note = {European Molecular Biology Network Conference, Martina, ITALY, SEP
18-20, 2008},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000261460100001,
title = {Direct functional assessment of the composite phenotype through
multivariate projection strategies},
author = { A. Conesa and R. Bro and F. Garcia-Garcia and J. M. Prats and S. Gotz and K. Kjeldahl and D. Montaner and J. Dopazo},
url = {http://dx.doi.org/10.1016/j.ygeno.2008.05.015},
doi = {10.1016/j.ygeno.2008.05.015},
issn = {0888-7543},
year = {2008},
date = {2008-12-01},
journal = {GENOMICS},
volume = {92},
number = {6},
pages = {373-383},
abstract = {We present a novel approach for the analysis of transcriptomics; data
that integrates functional annotation of gene sets with expression
values in a multivariate fashion, and directly assesses the relation of
functional features to a multivariate space of response phenotypical
variables. Multivariate projection methods are used to obtain new
correlated variables for a set of genes that share a given function.
These new functional variables are then related to the response
variables of interest. The analysis of the principal directions of the
multivariate regression allows for the identification of gene function
features correlated with the phenotype. Two different transcriptomics
studies are used to illustrate the statistical and interpretative
aspects of the methodology. We demonstrate the superiority of the
proposed method over equivalent approaches. (C) 2008 Elsevier Inc. All
rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000261762200064,
title = {Transcriptional Profiling of mRNA Expression in the Mouse Distal Colon},
author = { W. A. Hoogerwerf and M. Sinha and A. Conesa and B. A. Luxon and V. B. Shahinian and G. Cornelissen and F. Halberg and J. Bostwick and J. Timm and V. M. Cassone},
url = {http://dx.doi.org/10.1053/j.gastro.2008.08.048},
doi = {10.1053/j.gastro.2008.08.048},
issn = {0016-5085},
year = {2008},
date = {2008-12-01},
journal = {GASTROENTEROLOGY},
volume = {135},
number = {6},
pages = {2019-2029},
abstract = {Background & Aims: intestinal epithelial cells and the myenteric plexus
of the mouse gastrointestinal tract contain a circadian clock-based
intrinsic timekeeping system. Because disruption of the biological clock
has been associated with increased susceptibility to colon cancer and
gastrointestinal symptoms, we aimed to identify rhythmically expressed
genes in the mouse distal colon. Methods: Microarray analysis was used
to identify genes that were rhythmically expressed over a 24-hour
light/dark cycle. The transcripts were then classified according to
expression pattern, function, and association with physiologic and
pathophysiologic processes of the colon. Results: A circadian gene
expression pattern was detected in approximately 3.7% of distal.
colonic genes. A large percentage of these genes were involved in cell
signaling, differentiation, and proliferation and cell death. Of all the
rhythmically expressed genes in the mouse colon, approximately 7%
(64/906) have been associated with colorectal cancer formation (eg, B-cell leukemia/lymphoma-2 [Bcl2]) and 1.8% (18/906) with various
colonic functions such as motility and secretion (eg, vasoactive
intestinal polypeptide, cystic fibrosis transmembrane conductance
regulator). Conclusions: A subset of genes in the murine colon follows a
rhythmic expression pattern. These findings may have significant
implications for colonic physiology and pathophysiology.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000258440100004,
title = {Transcriptome analysis provides new insights into liver changes induced
in the rat upon dietary administration of the food additives butylated
hydroxytoluene, curcumin, propyl gallate and thiabendazole},
author = { R. Stierum and A. Conesa and W. Heijne and B. van Ommen and K. Junker and M. P. Scott and R. J. Price and C. Meredith and B. G. Lake and J. Groten},
url = {http://dx.doi.org/10.1016/j.fct.2008.04.019},
doi = {10.1016/j.fct.2008.04.019},
issn = {0278-6915},
year = {2008},
date = {2008-08-01},
journal = {FOOD AND CHEMICAL TOXICOLOGY},
volume = {46},
number = {8},
pages = {2616-2628},
abstract = {Transcriptomics was performed to gain insight into mechanisms of food
additives butylated hydroxytoluene (BHT), curcumin (CC), propyl gallate
(PG), and thiabendazole (TB), additives for which interactions in the
liver can not be excluded. Additives were administered in diets for 28
days to Sprague-Dawley rats and cDNA microarray experiments were
performed on hepatic RNA. BHT induced changes in the expression of 10
genes, including phase I (CYP2B1/2: CYP3A9; CYP2C6) and phase II
metabolism (GST mu 2). The CYP2B1/2 and GST expression findings were
confirmed by real time RT-PCR, western blotting, and increased GST
activity towards DCNB. CC altered the expression of 12 genes. Three out
of these were related to peroxisomes (phytanoyl-CoA dioxygenase, enoyl-CoA hydratase; CYP4A3). Increased cyanide insensitive
palmitoyl-CoA oxidation was observed, suggesting that CC is a weak
peroxisome proliferator. TB changed the expression of 12 genes, including CYP1A2. In line, CYP1A2 protein expression was increased. The
expression level of five genes, associated with p53 was found to change
upon TB treatment, including p53 itself, GADD45 alpha, DN-7, protein
kinase C beta and serum albumin. These array experiments led to the
novel finding that TB is capable of inducing p53 at the protein level, at least at the highest dose levels employed above the current NOAEL.
The expression of eight genes changed upon PG administration. This study
shows the value of gene expression profiling in food toxicology in terms
of generating novel hypotheses on the mechanisms of action of food
additives in relation to pathology. (C) 2008 Elsevier Ltd. All rights
reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000258552300001,
title = {Large-scale Gene Ontology analysis of plant transcriptome-derived
sequences retrieved by AFLP technology},
author = { A. Botton and G. Galla and A. Conesa and C. Bachem and A. Ramina and G. Barcaccia},
url = {http://dx.doi.org/10.1186/1471-2164-9-347},
doi = {10.1186/1471-2164-9-347},
issn = {1471-2164},
year = {2008},
date = {2008-07-01},
journal = {BMC GENOMICS},
volume = {9},
abstract = {Background: After 10-year-use of AFLP (Amplified Fragment Length
Polymorphism) technology for DNA fingerprinting and mRNA profiling, large repertories of genome- and transcriptome-derived sequences are
available in public databases for model, crop and tree species. AFLP
marker systems have been and are being extensively exploited for genome
scanning and gene mapping, as well as cDNA-AFLP for transcriptome
profiling and differentially expressed gene cloning. The evaluation, annotation and classification of genomic markers and expressed
transcripts would be of great utility for both functional genomics and
systems biology research in plants. This may be achieved by means of the
Gene Ontology (GO), consisting in three structured vocabularies (i.e.
ontologies) describing genes, transcripts and proteins of any organism
in terms of their associated cellular component, biological process and
molecular function in a species-independent manner. In this paper, the
functional annotation of about 8,000 AFLP-derived ESTs retrieved in the
NCBI databases was carried out by using GO terminology.
Results: Descriptive statistics on the type, size and nature of gene
sequences obtained by means of AFLP technology were calculated. The gene
products associated with mRNA transcripts were then classified according
to the three main GO vocabularies. A comparison of the functional
content of cDNA-AFLP records was also performed by splitting the
sequence dataset into monocots and dicots and by comparing them to all
annotated ESTs of Arabidopsis and rice, respectively. On the whole, the
statistical parameters adopted for the in silico AFLP-derived
transcriptome-anchored sequence analysis proved to be critical for
obtaining reliable GO results. Such an exhaustive annotation may offer a
suitable platform for functional genomics, particularly useful in
non-model species.
Conclusion: Reliable GO annotations of AFLP-derived sequences can be
gathered through the optimization of the experimental steps and the
statistical parameters adopted. The Blast2GO software was shown to
represent a comprehensive bioinformatics solution for an
annotation-based functional analysis. According to the whole set of GO
annotations, the AFLP technology generates thorough information for
angiosperm gene products and shares common features across angiosperm
species and families. The utility of this technology for structural and
functional genomics in plants can be implemented by serial annotation
analyses of genome- anchored fragments and organ/tissue-specific
repertories of transcriptome-derived fragments.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000258142300064,
title = {Babelomics: advanced functional profiling of transcriptomics, proteomics
and genomics experiments},
author = { F. Al-Shahrour and J. Carbonell and P. Minguez and S. Goetz and A. Conesa and J. Tarrraga and I. Medina and E. Alloza and D. Montaner and J. Dopazo},
url = {http://dx.doi.org/10.1093/nar/gkn318},
doi = {10.1093/nar/gkn318},
issn = {0305-1048},
year = {2008},
date = {2008-07-01},
journal = {NUCLEIC ACIDS RESEARCH},
volume = {36},
number = {S},
pages = {W341-W346},
abstract = {We present a new version of Babelomics, a complete suite of web tools
for the functional profiling of genome scale experiments, with new and
improved methods as well as more types of functional definitions.
Babelomics includes different flavours of conventional functional
enrichment methods as well as more advanced gene set analysis methods
that makes it a unique tool among the similar resources available. In
addition to the well-known functional definitions (GO, KEGG), Babelomics
includes new ones such as Biocarta pathways or text mining-derived
functional terms. Regulatory modules implemented include transcriptional
control (Transfac, CisRed) and other levels of regulation such as
miRNA-mediated interference. Moreover, Babelomics allows for
sub-selection of terms in order to test more focused hypothesis. Also
gene annotation correspondence tables can be imported, which allows
testing with user-defined functional modules. Finally, a tool for the de
novo functional annotation of sequences has been included in the system.
This allows using yet unannotated organisms in the program. Babelomics
has been extensively re-engineered and now it includes the use of web
services and Web 2.0 technology features, a new user interface with
persistent sessions and a new extended database of gene identifiers.
Babelomics is available at http://www.babelomics.org.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000258142300058,
title = {GEPAS, a web-based tool for microarray data analysis and interpretation},
author = { J. Tarraga and I. Medina and J. Carbonell and J. Huerta-Cepas and P. Minguez and E. Alloza and F. Al-Shahrour and S. Vegas-Azcarate and S. Goetz and P. Escobar and F. Garcia-Garcia and A. Conesa and D. Montaner and J. Dopazo},
url = {http://dx.doi.org/10.1093/nar/gkn303},
doi = {10.1093/nar/gkn303},
issn = {0305-1048},
year = {2008},
date = {2008-07-01},
journal = {NUCLEIC ACIDS RESEARCH},
volume = {36},
number = {S},
pages = {W308-W314},
abstract = {Gene Expression Profile Analysis Suite (GEPAS) is one of the most
complete and extensively used web-based packages for microarray data
analysis. During its more than 5 years of activity it has continuously
been updated to keep pace with the state-of-the-art in the changing
microarray data analysis arena. GEPAS offers diverse analysis options
that include well established as well as novel algorithms for
normalization, gene selection, class prediction, clustering and
functional profiling of the experiment. New options for time-course (or
dose-response) experiments, microarray-based class prediction, new
clustering methods and new tests for differential expression have been
included. The new pipeliner module allows automating the execution of
sequential analysis steps by means of a simple but powerful graphic
interface. An extensive re-engineering of GEPAS has been carried out
which includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended
database of gene identifiers. GEPAS is nowadays the most quoted web tool
in its field and it is extensively used by researchers of many countries
and its records indicate an average usage rate of 500 experiments per
day. GEPAS, is available at http://www.gepas.org.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000257183200025,
title = {High-throughput functional annotation and data mining with the Blast2GO
suite},
author = { S. Gotz and J. M. Garcia-Gomez and J. Terol and T. D. Williams and S. H. Nagaraj and M. J. Nueda and M. Robles and M. Talon and J. Dopazo and A. Conesa},
url = {http://dx.doi.org/10.1093/nar/gkn176},
doi = {10.1093/nar/gkn176},
issn = {0305-1048},
year = {2008},
date = {2008-06-01},
journal = {NUCLEIC ACIDS RESEARCH},
volume = {36},
number = {10},
pages = {3420-3435},
abstract = {Functional genomics technologies have been widely adopted in the
biological research of both model and non-model species. An efficient
functional annotation of DNA or protein sequences is a major requirement
for the successful application of these approaches as functional
information on gene products is often the key to the interpretation of
experimental results. Therefore, there is an increasing need for
bioinformatics resources which are able to cope with large amount of
sequence data, produce valuable annotation results and are easily
accessible to laboratories where functional genomics projects are being
undertaken. We present the Blast2GO suite as an integrated and
biologist-oriented solution for the high-throughput and automatic
functional annotation of DNA or protein sequences based on the Gene
Ontology vocabulary. The most outstanding Blast2GO features are: (i) the
combination of various annotation strategies and tools controlling type
and intensity of annotation, (ii) the numerous graphical features such
as the interactive GO-graph visualization for gene-set function
profiling or descriptive charts, (iii) the general sequence management
features and (iv) high-throughput capabilities. We used the Blast2GO
framework to carry out a detailed analysis of annotation behaviour
through homology transfer and its impact in functional genomics
research. Our aim is to offer biologists useful information to take into
account when addressing the task of functionally characterizing their
sequence data.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000257750100001,
title = {Time course profiling of the retinal transcriptome after optic nerve
transection and optic nerve crush},
author = { M. Agudo and M. C. Perez-Marin and U. Loenngren and P. Sobrado and A. Conesa and I. Canovas and M. Salinas-Navarro and J. Miralles-Imperial and F. Hallbook and M. Vidal-Sanz},
issn = {1090-0535},
year = {2008},
date = {2008-06-01},
journal = {MOLECULAR VISION},
volume = {14},
number = {126},
pages = {1050-1063},
abstract = {Purpose: A time-course analysis of gene regulation in the adult rat
retina after intraorbital nerve crush (IONC) and intraorbital nerve
transection (IONT).
Methods: RNA was extracted from adult rat retinas undergoing either IONT
or IONC at increasing times post-lesion. Affymetrix RAE230.2 arrays were
hybridized and analyzed. Statistically regulated genes were annotated
and functionally clustered. Arrays were validated by means of quantative
reverse transcription polymerase chain reaction (qRT-PCR) on ten
regulated genes at two times post-lesion. Western blotting and
immunohistofluorescence for four pro-apoptotic proteins were performed
on naive and injured retinas. Finally, custom signaling maps for IONT-
and IONC-induced death response were generated (MetaCore, Genego Inc.).
Results: Here we show that over time, 3,219 sequences were regulated
after IONT and 1,996 after IONC. Out of the total of regulated
sequences, 1,078 were commonly regulated by both injuries.
Interestingly, while IONT mainly triggers a gene upregulation-sustained
over time, IONC causes a transitory downregulation. Functional
clustering identified the regulation of high interest biologic
processes, most importantly cell death wherein apoptosis was the most
significant cluster. Ten death-related genes upregulated by both
injuries were used for array validation by means of qRT-PCR. In
addition, western blotting and immunohistofluorescence of total and
active Caspase 3 (Casp3), tumor necrosis factor receptor type 1
associated death domain (TRADD), tumor necrosis factor receptor
superfamily member 1a (TNFR1a), and c-fos were performed to confirm
their protein regulation and expression pattern in nave and injured
retinas. These analyses demonstrated that for these genes, protein
regulation followed transcriptional regulation and that these
proapoptotic proteins were expressed by retinal ganglion cells (RGCs).
MetaCore-based death-signaling maps show that several apoptotic cascades
were regulated in the retina following optic nerve injury and highlight
the similarities and differences between IONT and IONC in cell death
profiling.
Conclusions: This comprehensive time course retinal transcriptome study
comparing IONT and IONC lesions provides a unique valuable tool to
understand the molecular mechanisms underlying optic nerve injury and to
design neuroprotective protocols.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000251896100016,
title = {Spatial differentiation in the vegetative mycelium of Aspergillus niger},
author = { A. M. Levin and R. P. de Vries and A. Conesa and C. de Bekker and M. Talon and H. H. Menke and N. N. M. E. van Peij and H. A. B. Wosten},
url = {http://dx.doi.org/10.1128/EC.00244-07},
doi = {10.1128/EC.00244-07},
issn = {1535-9778},
year = {2007},
date = {2007-12-01},
journal = {EUKARYOTIC CELL},
volume = {6},
number = {12},
pages = {2311-2322},
abstract = {Fungal mycelia are exposed to heterogenic substrates. The substrate in
the central part of the colony has been (partly) degraded, whereas it is
still unexplored at the periphery of the mycelium. We here assessed
whether substrate heterogeneity is a main determinant of spatial gene
expression in colonies of Aspergillus niger. This question was addressed
by analyzing whole-genome gene expression in five concentric zones of
7-day-old maltose- and xylose-grown colonies. Expression profiles at the
periphery and the center were clearly different. More than 25% of the
active genes showed twofold differences in expression between the inner
and outermost zones of the colony. Moreover, 9% of the genes were
expressed in only one of the five concentric zones, showing that a
considerable part of the genome is active in a restricted part of the
colony only. Statistical analysis of expression profiles of colonies
that had either been or not been transferred to fresh xylose-containing
medium showed that differential expression in a colony is due to the
heterogeneity of the medium (e.g., genes involved in secretion, genes
encoding proteases, and genes involved in xylose metabolism) as well as
to medium-independent mechanisms (e.g., genes involved in nitrate
metabolism and genes involved in cell wall synthesis and modification).
Thus, we conclude that the mycelia of 7-day-old colonies of A. niger are
highly differentiated. This conclusion is also indicated by the fact
that distinct zones of the colony grow and secrete proteins, even after
transfer to fresh medium.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000250162900007,
title = {Transcriptional response of Citrus aurantifolia to infection by Citrus
tristeza virus},
author = { M. Gandia and A. Conesa and G. Ancillo and J. Gadea and J. Forment and V. Pallas and R. Flores and N. Duran-Vila and P. Moreno and J. Guerri},
url = {http://dx.doi.org/10.1016/j.virol.2007.05.025},
doi = {10.1016/j.virol.2007.05.025},
issn = {0042-6822},
year = {2007},
date = {2007-10-01},
journal = {VIROLOGY},
volume = {367},
number = {2},
pages = {298-306},
abstract = {Changes in gene expression of Mexican lime plants in response to
infection with a severe (T305) or a mild (T385) isolate of Citrus
tristeza virus (CTV) were analyzed using a cDNA microarray containing
12,672 probes to 6875 different citrus genes. Statistically significant
(P < 0.01) expression changes of 334 genes were detected in response to
infection with isolate T305, whereas infection with T385 induced no
significant change. Induced genes included 145 without significant
similarity with known sequences and 189 that were classified in seven
functional categories. Genes related with response to stress and defense
were the main category and included 28% of the genes induced. Selected
transcription changes detected by microarray analysis were confirmed by
quantitative real-time RT-PCR. Changes detected in the transcriptome
upon infecting lime with T305 may be associated either with symptom
expression, with a strain-specific defense mechanism, or with a general
response to stress. (c) 2007 Elsevier Inc. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000249248300011,
title = {Discovering gene expression patterns in time course microarray
experiments by ANOVA-SCA},
author = { M. J. Nueda and A. Conesa and J. A. Westerhuis and H. C. J. Hoefsloot and A. K. Smilde and M. Talon and A. Ferrer},
url = {http://dx.doi.org/10.1093/bioinformatics/btm251},
doi = {10.1093/bioinformatics/btm251},
issn = {1367-4803},
year = {2007},
date = {2007-07-01},
journal = {BIOINFORMATICS},
volume = {23},
number = {14},
pages = {1792-1800},
abstract = {Motivation: Designed microarray experiments are used to investigate the
effects that controlled experimental factors have on gene expression and
learn about the transcriptional responses associated with external
variables. In these datasets, signals of interest coexist with varying
sources of unwanted noise in a framework of (co)relation among the
measured variables and with the different levels of the studied factors.
Discovering experimentally relevant transcriptional changes require
methodologies that take all these elements into account.
Results: In this work, we develop the application of the Analysis of
variance-simultaneous component analysis (ANOVA-SCA) Smilde et al, Bioinformatics, (2005) to the analysis of multiple series time course
microarray data as an example of multifactorial gene expression
profiling experiments. We denoted this implementation as ASCA-genes. We
show how the combination of ANOVA-modeling and a dimension reduction
technique is effective in extracting targeted signals from data
by-passing structural noise. The methodology is valuable for identifying
main and secondary responses associated with the experimental factors
and spotting relevant experimental conditions. We additionally propose a
novel approach for gene selection in the context of the relation of
individual transcriptional patterns to global gene expression signals.
We demonstrate the methodology on both real and synthetic datasets.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000244326200001,
title = {Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance},
author = { J. Terol and A. Conesa and J. M. Colmenero and M. Cercos and F. Tadeo and J. Agusti and E. Alos and F. Andres and G. Soler and J. Brumos and D. J. Iglesias and S. Gotz and F. Legaz and X. Argout and B. Courtois and P. Ollitrault and C. Dossat and P. Wincker and R. Morillon and M. Talon},
url = {http://dx.doi.org/10.1186/1471-2164-8-31},
doi = {10.1186/1471-2164-8-31},
issn = {1471-2164},
year = {2007},
date = {2007-01-01},
journal = {BMC GENOMICS},
volume = {8},
abstract = {Background: Improvement of Citrus, the most economically important fruit
crop in the world, is extremely slow and inherently costly because of
the long-term nature of tree breeding and an unusual combination of
reproductive characteristics. Aside from disease resistance, major
commercial traits in Citrus are improved fruit quality, higher yield and
tolerance to environmental stresses, especially salinity.
Results: A normalized full length and 9 standard cDNA libraries were
generated, representing particular treatments and tissues from selected
varieties ( Citrus clementina and C. sinensis) and rootstocks ( C.
reshni, and C. sinenis x Poncirus trifoliata) differing in fruit
quality, resistance to abscission, and tolerance to salinity. The goal
of this work was to provide a large expressed sequence tag ( EST)
collection enriched with transcripts related to these well appreciated
agronomical traits. Towards this end, more than 54000 ESTs derived from
these libraries were analyzed and annotated. Assembly of 52626 useful
sequences generated 15664 putative transcription units distributed in
7120 contigs, and 8544 singletons. BLAST annotation produced significant
hits for more than 80% of the hypothetical transcription units and
suggested that 647 of these might be Citrus specific unigenes. The
unigene set, composed of similar to 13000 putative different
transcripts, including more than 5000 novel Citrus genes, was assigned
with putative functions based on similarity, GO annotations and protein
domains.
Conclusion: Comparative genomics with Arabidopsis revealed the presence
of putative conserved orthologs and single copy genes in Citrus and also
the occurrence of both gene duplication events and increased number of
genes for specific pathways. In addition, phylogenetic analysis
performed on the ammonium transporter family and glycosyl transferase
family 20 suggested the existence of Citrus paralogs. Analysis of the
Citrus gene space showed that the most important metabolic pathways
known to affect fruit quality were represented in the unigene set.
Overall, the similarity analyses indicated that the sequences of the
genes belonging to these varieties and rootstocks were essentially
identical, suggesting that the differential behaviour of these species
cannot be attributed to major sequence divergences. This Citrus EST
assembly contributes both crucial information to discover genes of
agronomical interest and tools for genetic and genomic analyses, such as
the development of new markers and microarrays.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}