Arzalluz-Luque, Ángeles; Ana, Conesa
Single-cell RNAseq for the study of isoforms---how is that possible? Journal Article
In: Genome Biology, vol. 19, no. 1, pp. 110, 2018, ISSN: 1474-760X.
@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}
}
Colli-Dula, Reyna Cristina; Fang, Xiefan; Moraga-Amador, David; Albornoz-Abud, Nacira; Zamora-Bustillos, Roberto; Conesa, Ana; Zapata-Perez, Omar; Moreno, Diego; Hernandez-Nuñez, Emanuel
Transcriptome analysis reveals novel insights into the response of low-dose benzo(a)pyrene exposure in male tilapia Journal Article
In: Aquatic Toxicology, vol. 201, pp. 162 - 173, 2018, ISSN: 0166-445X.
@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}
}
Tarazona, Sonia; Balzano-Nogueira, Leandro; Conesa, Ana
Multiomics Data Integration in Time Series Experiments Journal Article
In: Comprehensive Analytical Chemistry, vol. 8, pp. 505-532, 2018.
@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},
journal = {Comprehensive Analytical Chemistry},
volume = {8},
pages = {505-532},
publisher = {Elsevier},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hernández-de-Diego, Rafael; Tarazona, Sonia; Martínez-Mira, Carlos; Balzano-Nogueira, Leandro; Furió-Tarí, Pedro; Jr Pappas, Georgios J; Conesa, Ana
PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data Journal Article
In: Nucleic Acids Research, pp. gky466, 2018.
@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}
}
Babilonia, Joany; Conesa, Ana; Casaburi, Giorgio; Pereira, Cecile; Louyakis, Artemis S.; Reid, R. Pamela; Foster, Jamie S.
Comparative Metagenomics Provides Insight Into the Ecosystem Functioning of the Shark Bay Stromatolites, Western Australia Journal Article
In: Frontiers in Microbiology, vol. 9, pp. 1359, 2018, ISSN: 1664-302X.
@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}
}
Delaye, Luis; Ruiz-Ruiz, Susana; Calderon, Enrique; Tarazona, Sonia; Conesa, Ana; Moya, Andrés
Evidence of the Red-Queen Hypothesis from Accelerated Rates of Evolution of Genes Involved in Biotic Interactions in Pneumocystis Journal Article
In: Genome Biology and Evolution, vol. 10, no. 6, pp. 1596-1606, 2018.
@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}
}
Zhu, Qile; Li, Xiaolin; Conesa, Ana; Pereira, Cécile
GRAM-CNN: a deep learning approach with local context for named entity recognition in biomedical text Journal Article
In: Bioinformatics, vol. 34, no. 9, pp. 1547-1554, 2018.
@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}
}
García-Molinero, Varinia; Garcíaa-Martínez, José; Reja, Rohit; Furió-Tarí, Pedro; Antúnez, Oreto; Vinayachandran, Vinesh; Conesa, Ana; Pugh, B. Franklin; Pérez-Ortín, José E.; Rodríguez-Navarro, Susana
The SAGA/TREX-2 subunit Sus1 binds widely to transcribed genes and affects mRNA turnover globally Journal Article
In: Epigenetics & Chromatin, vol. 11, no. 1, pp. 13, 2018.
@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}
}
Tardaguila, Manuel; de la Fuente, Lorena; Marti, Cristina; Pereira, Cécile; Pardo-Palacios, Francisco Jose; del Risco, Hector; Ferrell, Marc; Mellado, Maravillas; Macchietto, Marissa; Verheggen, Kenneth; Edelmann, Mariola; Ezkurdia, Iakes; Vazquez, Jesus; Tress, Michael; Mortazavi, Ali; Martens, Lennart; Rodriguez-Navarro, Susana; Moreno-Manzano, Victoria; Conesa, Ana
In: Genome Research, 2018.
@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}
}
Nueda, María José; Martorell-Marugan, Jordi; Martí, Cristina; Tarazona, Sonia; Conesa, Ana
Identification and visualization of differential isoform expression in RNA-seq time series Journal Article
In: Bioinformatics, vol. 34, no. 3, pp. 524-526, 2018.
@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}
}
Martínez-Mira, Carlos; Conesa, Ana; Tarazona, Sonia
MOSim: Multi-Omics Simulation in R Journal Article Forthcoming
In: bioRxiv, pp. 421834, Forthcoming.
@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}
}
Kaeding, N.; Kaufhold, I.; Mueller, C.; Szaszak, M.; Shima, K.; Weinmaier, T.; Lomas, R.; Conesa, A.; Schmitt-Kopplin, P.; Rattei, T.; Rupp, J.
Growth of Chlamydia pneumoniae Is Enhanced in Cell swith Impaired Mitochondrial Function Journal Article
In: FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY, vol. 7, 2017, ISSN: 2235-2988.
@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}
}
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.
Newman, J. R. B.; Conesa, A.; Mika, M.; New, F. N.; Onengut-Gumuscu, S.; Atkinson, M. A.; Rich, S. S.; McIntyre, L. M.; Concannon, P.
In: GENOME RESEARCH, vol. 27, no. 11, pp. 1807-1815, 2017, ISSN: 1088-9051.
@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}
}
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.
Merino, Gabriela A.; Conesa, Ana; Fernández, Elmer A.
A benchmarking of workflows for detecting differential splicing and differential expression at isoform level in human RNA-seq studies Journal Article
In: Briefings in Bioinformatics, pp. bbx122, 2017.
@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}
}
Conesa, A.; Fernandez, M.; Exposito, R.; Campos, J.; Lamua, J. Ramon; del Pilar Navarro, M.; Rubio-Munoz, P.; Ahijado-Guzman, P.; Gonzalez, C. M.
Certolizumab Pegol Effectiveness and Retention Rate in Psoriatic Arthritis. Real Life Data Journal Article
In: ARTHRITIS & RHEUMATOLOGY, vol. 69, no. 10, 2017, ISSN: 2326-5191.
@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}
}
Gomez-Cabrero, D.; Marabita, F.; Tarazona, S.; Cano, I.; Roca, J.; Conesa, A.; Sabatier, P.; Tegner, J.
Guidelines for Developing Successful Short Advanced Courses in Systems Medicine and Systems Biology Journal Article
In: CELL SYSTEMS, vol. 5, no. 3, pp. 168-175, 2017, ISSN: 2405-4712.
@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}
}
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.
Hernandez-de-Diego, R.; de Villiers, E. P.; Klingstrom, T.; Gourle, H.; Conesa, A.; Bongcam-Rudloff, E.
The eBioKit, a stand-alone educational platform for bioinformatics Journal Article
In: PLOS COMPUTATIONAL BIOLOGY, vol. 13, no. 9, 2017, ISSN: 1553-734X.
@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}
}
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.
Ramirez, R. N.; El-Ali, N. C.; Mager, M. A.; Wyman, D.; Conesa, A.; Mortazavi, A.
Dynamic Gene Regulatory Networks of Human Myeloid Differentiation Journal Article
In: CELL SYSTEMS, vol. 4, no. 4, pp. 416+, 2017, ISSN: 2405-4712.
@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}
}
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.
Sebastian-Leon, P.; Conesa, A.; Arnau, V.; Remohi, J.; Pellicer, A.; Simon, C.; Diaz-Gimeno, P.
Network Biology of Menstrual Cycle to Understand the Key Drivers of Endometrial Receptivity. Journal Article
In: REPRODUCTIVE SCIENCES, vol. 24, no. 1, pp. 162A, 2017, ISSN: 1933-7191, (64th Annual Scientific Meeting of the Society-for-Reproductive-Investigation (SRI), Orlando, FL, MAR 15-18, 2017).
@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}
}
Ordonez-Baquera, P. Lucia; Gonzalez-Rodriguez, E.; Aguado-Santacruz, G. Armando; Rascon-Cruz, Q.; Conesa, A.; Moreno-Brito, V.; Echavarria, R.; Dominguez-Viveros, J.
Identification of miRNA from Bouteloua gracilis, a drought tolerant grass, by deep sequencing and their in silico analysis Journal Article
In: COMPUTATIONAL BIOLOGY AND CHEMISTRY, vol. 66, pp. 26-35, 2017, ISSN: 1476-9271.
@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}
}
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.