Publications

2021

145.

Tarazona, Sonia; Arzalluz-Luque, Angeles; Conesa, Ana

Undisclosed, unmet and neglected challenges in multi-omics studies Journal Article

In: Nature Computational Science, 1 (6), pp. 395-402, 2021, ISSN: 2662-8457.

Abstract | Links | BibTeX

144.

Lagani V Planell N, Sebastian-Leon P

STATegra: Multi-Omics Data Integration - A Conceptual Scheme With a Bioinformatics Pipeline Journal Article

In: Frontiers in Genetics, 12 , pp. 620453, 2021.

Abstract | Links | BibTeX

143.

Arzalluz-Luque, Angeles; Salguero, Pedro; Tarazona, Sonia; Conesa, Ana

Acorde: unraveling functionally-interpretable networks of isoform co-usage from single cell data Journal Article

In: bioRxiv, 2021.

BibTeX

142.

Nanni, Adalena V; Morse, Alison M; Newman, Jeremy RB; Choquette, Nicole E; Wedow, Jessica M; Liu, Zihao; Leakey, Andrew DB; Conesa, Ana; Ainsworth, Elizabeth A; McIntyre, Lauren

Ozone sensitivity of diverse maize genotypes is associated with differences in gene regulation, not gene content Journal Article

In: bioRxiv, 2021.

BibTeX

141.

no, Jes'us Rodr'iguez-Ba; Pachón, Jerónimo; Carratal`a, Jordi; Ryan, Pablo; Jarr'in, Inmaculada; Yllescas, Mar'ia; Arribas, José Ramón; Berenguer, Juan; noz, Esther Aznar Mu; Divasson, Pedro Gil; others,

Treatment with tocilizumab or corticosteroids for COVID-19 patients with hyperinflammatory state: a multicentre cohort study (SAM-COVID-19) Journal Article

In: Clinical Microbiology and Infection, 27 (2), pp. 244–252, 2021.

BibTeX

140.

Puig, Laura Sardón; Altintas, Ali; Casani, Salvador; Gabriel, Brendan M; Barres, Romain; Conesa, Ana; Chibalin, Alexander V; Naslund, Erik; Krook, Anna; Pillon, Nicolas J; others,

Circadian Transcriptomic and Epigenomic Remodeling in Response to Lipid Overload and Human Obesity Journal Article

In: bioRxiv, 2021.

BibTeX

139.

Rubio, Teresa; Felipo, Vicente; Tarazona, Sonia; Pastorelli, Roberta; Escudero-Garc'ia, Desamparados; Tosca, Joan; Urios, Amparo; Conesa, Ana; Montoliu, Carmina

Multi-omic analysis unveils biological pathways in peripheral immune system associated to minimal hepatic encephalopathy appearance in cirrhotic patients Journal Article

In: Scientific reports, 11 (1), pp. 1–14, 2021.

BibTeX

138.

Balzano-Nogueira, Leandro; Ramirez, Ricardo; Zamkovaya, Tatyana; Dailey, Jordan; Ardissone, Alexandria N; Chamala, Srikar; Serrano-Qu'ilez, Joan; Rubio, Teresa; Haller, Michael J; Concannon, Patrick; others,

Integrative analyses of TEDDY Omics data reveal lipid metabolism abnormalities, increased intracellular ROS and heightened inflammation prior to autoimmunity for type 1 diabetes Journal Article

In: Genome biology, 22 (1), pp. 1–27, 2021.

BibTeX

137.

Tarazona, Sonia; Carmona, Héctor; Conesa, Ana; Llansola, Marta; Felipo, Vicente

A multi-omic study for uncovering molecular mechanisms associated with hyperammonemia-induced cerebellar function impairment in rats Journal Article

In: Cell Biology and Toxicology, 37 (1), pp. 129–149, 2021.

BibTeX

136.

Zamkovaya, Tatyana; Foster, Jamie S; de Crécy-Lagard, Valérie; Conesa, Ana

A network approach to elucidate and prioritize microbial dark matter in microbial communities Journal Article

In: The ISME Journal, 15 (1), pp. 228–244, 2021.

BibTeX

2020

135.

Balzano-Nogueira L Tarazona S, Gómez-Cabrero D

Harmonization of quality metrics and power calculation in multi-omic studies Journal Article

In: Nature Communications, 11 (1), pp. 3092, 2020.

Abstract | Links | BibTeX

134.

Ugidos, Manuel; Tarazona, Sonia; Prats-Montalbán, José M; Ferrer, Alberto; Conesa, Ana

MultiBaC: A strategy to remove batch effects between different omic data types Journal Article

In: Statistical Methods in Medical Research, 0 (0), pp. 1-14, 2020, (PMID: 32131696).

Abstract | Links | BibTeX

133.

Nuño, Carme; Ugidos, Manuel; Tarazona, Sonia; Martín-Expósito, Manuel; Ferrer, Alberto; Rodríguez-Navarro, Susana; Conesa, Ana

A multi-omics dataset of heat-shock response in the yeast RNA binding protein Mip6 Journal Article

In: Scientific data, 7 (1), pp. 69-69, 2020, ISSN: 2052-4463, (32109230[pmid]).

Abstract | Links | BibTeX

132.

Nuño, Carme; Ugidos, Manuel; Tarazona, Sonia; Martín-Expósito, Manuel; Ferrer, Alberto; Rodríguez-Navarro, Susana; Conesa, Ana

A multi-omics dataset of heat-shock response in the yeast RNA binding protein Mip6 Journal Article

In: Scientific data, 7 (1), pp. 69-69, 2020, ISSN: 2052-4463, (32109230[pmid]).

Abstract | Links | BibTeX

131.

McIntyre, Lauren M; Huertas, Francisco; Moskalenko, Olexander; Llansola, Marta; Felipo, Vicente; Morse, Alison M; Conesa, Ana

GAIT-GM: Galaxy tools for modeling metabolite changes as a function of gene expression Journal Article

In: bioRxiv, 2020.

BibTeX

130.

Casan'i-Galdón, Salvador; Pereira, Cecile; Conesa, Ana

Padhoc: a computational pipeline for pathway reconstruction on the fly Journal Article

In: Bioinformatics, 36 (Supplement_2), pp. i795–i803, 2020.

BibTeX

129.

Ylla, Guillem; Liu, Tianyuan; Conesa, Ana

MirCure: a tool for quality control, filter and curation of microRNAs of animals and plants Journal Article

In: Bioinformatics, 36 (Supplement_2), pp. i618–i624, 2020.

BibTeX

128.

Bhattarai, Krishna; Conesa, Ana; Xiao, Shunyuan; Peres, Natalia A; Clark, David G; Parajuli, Saroj; Deng, Zhanao

Sequencing and analysis of gerbera daisy leaf transcriptomes reveal disease resistance and susceptibility genes differentially expressed and associated with powdery mildew resistance Journal Article

In: BMC plant biology, 20 (1), pp. 1–17, 2020.

BibTeX

127.

Liu, Tianyuan; Balzano-Nogueira, Leandro; Lleo, Ana; Conesa, Ana

Transcriptional differences for COVID-19 Disease Map genes between males and females indicate a different basal immunophenotype relevant to the disease Journal Article

In: Genes, 11 (12), pp. 1447, 2020.

BibTeX

126.

Gardner, Christopher L; da Silva, Danilo R; Pagliai, Fernando A; Pan, Lei; Padgett-Pagliai, Kaylie A; Blaustein, Ryan A; Merli, Marcelo L; Zhang, Dan; Pereira, Cécile; Teplitski, Max; others,

Assessment of unconventional antimicrobial compounds for the control of ‘Candidatus liberibacter asiaticus’, the causative agent of citrus greening disease Journal Article

In: Scientific reports, 10 (1), pp. 1–15, 2020.

BibTeX

125.

de la Fuente, Lorena; Arzalluz-Luque, Ángeles; Tardáguila, Manuel; Risco, Héctor Del; Mart'i, Cristina; Tarazona, Sonia; Salguero, Pedro; Scott, Raymond; Lerma, Alberto; Alastrue-Agudo, Ana; others,

tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing Journal Article

In: Genome biology, 21 , pp. 1–32, 2020.

Abstract | Links | BibTeX

2019

124.

Jansen, Camden; Ramirez, Ricardo N.; El-Ali, Nicole C.; Gomez-Cabrero, David; Tegner, Jesper; Merkenschlager, Matthias; Conesa, Ana; Mortazavi, Ali

Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps Journal Article

In: PLOS Computational Biology, 15 (11), pp. e1006555, 2019, ISSN: 1553-7358.

Links | BibTeX

123.

Sana, T. G.; Lomas, R.; Gimenez, M. R.; Laubier, A.; Soscia, C.; Chauvet, C.; Conesa, A.; Voulhoux, R.; Ize, B.; Bleves, S.

Differential Modulation of Quorum Sensing Signaling through QslA in Pseudomonas aeruginosa Strains PAO1 and PA14 Journal Article

In: Journal of bacteriology, 201 (21), 2019, ISSN: 10985530.

Abstract | Links | BibTeX

122.

Jansen, Camden; Ramirez, Ricardo N; El-Ali, Nicole C; Gomez-Cabrero, David; Tegner, Jesper; Merkenschlager, Matthias; Conesa, Ana; Mortazavi, Ali

Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps Journal Article

In: PLOS Computational Biology, 15 (11), pp. e1006555, 2019, ISSN: 1553-7358.

Links | BibTeX

121.

Martín‐Expósito, Manuel; Gas, Maria‐Eugenia; Mohamad, Nada; Nuño‐Cabanes, Carme; Tejada‐Colón, Ana; Pascual‐García, Pau; Fuente, Lorena; Chaves‐Arquero, Belén; Merran, Jonathan; Corden, Jeffry; Conesa, Ana; Pérez‐Cañadillas, José Manuel; Bravo, Jerónimo; Rodríguez‐Navarro, Susana

Mip6 binds directly to the Mex67 UBA domain to maintain low levels of Msn2/4 stress‐dependent mRNAs Journal Article

In: EMBO reports, 2019, ISSN: 1469-221X.

Links | BibTeX

120.

Tarazona, Sonia; Bernabeu, Elena; Carmona, Héctor; Gómez-Giménez, Belén; García-Planells, Javier; Leonards, Pim E. G.; Jung, Stephan; Conesa, Ana; Felipo, Vicente; Llansola, Marta

A Multiomics Study to Unravel the Effects of Developmental Exposure to Endosulfan in Rats: Molecular Explanation for Sex-Dependent Effects Journal Article

In: ACS Chemical Neuroscience, 10 (10), pp. 4264–4279, 2019, ISSN: 19487193.

Abstract | Links | BibTeX

119.

Gomez-Cabrero, David; Tarazona, Sonia; Ferreirós-Vidal, Isabel; Ramirez, Ricardo N.; Company, Carlos; Schmidt, Andreas; Reijmers, Theo; von Saint Paul, Veronica; Marabita, Francesco; Rodríguez-Ubreva, Javier; Garcia-Gomez, Antonio; Carroll, Thomas; Cooper, Lee; Liang, Ziwei; Dharmalingam, Gopuraja; van der Kloet, Frans; Harms, Amy C.; Balzano-Nogueira, Leandro; Lagani, Vincenzo; Tsamardinos, Ioannis; Lappe, Michael; Maier, Dieter; Westerhuis, Johan A.; Hankemeier, Thomas; Imhof, Axel; Ballestar, Esteban; Mortazavi, Ali; Merkenschlager, Matthias; Tegner, Jesper; Conesa, Ana

STATegra, a comprehensive multi-omics dataset of B-cell differentiation in mouse Journal Article

In: Scientific data, 6 (1), pp. 256, 2019, ISSN: 20524463.

Abstract | Links | BibTeX

118.

García-Solano, José; del Carmen Turpin-Sevilla, María; García-García, Francisco; Carbonell-Muñoz, Rosa; Torres-Moreno, Daniel; Conesa, Ana; Conesa-Zamora, Pablo

Differences in gene expression profiling and biomarkers between histological colorectal carcinoma subsets from the serrated pathway Journal Article

In: Histopathology, 75 (4), pp. 496–507, 2019, ISSN: 13652559.

Abstract | Links | BibTeX

117.

Conesa, Ana; Beck, Stephan

Making multi-omics data accessible to researchers Journal Article

In: Scientific data, 6 (1), pp. 251, 2019, ISSN: 20524463.

Links | BibTeX

116.

Ferreirós-Vidal, Isabel; Carroll, Thomas; Zhang, Tianyi; Lagani, Vincenzo; Ramirez, Ricardo N.; Ing-Simmons, Elizabeth; Gómez-Valadés, Alicia G.; Cooper, Lee; Liang, Ziwei; Papoutsoglou, Georgios; Dharmalingam, Gopuraja; Guo, Ya; Tarazona, Sonia; Fernandes, Sunjay J.; Noori, Peri; Silberberg, Gilad; Fisher, Amanda G.; Tsamardinos, Ioannis; Mortazavi, Ali; Lenhard, Boris; Conesa, Ana; Tegner, Jesper; Merkenschlager, Matthias; Gomez-Cabrero, David

Feedforward regulation of Myc coordinates lineage-specific with housekeeping gene expression during B cell progenitor cell differentiation Journal Article

In: PLoS Biology, 17 (4), 2019, ISSN: 15457885.

Abstract | Links | BibTeX

115.

Brown, Peter; Conesa), RELISH Consortium (Ana; Zhou, Yaoqi

Large expert-curated database for benchmarking document similarity detection in biomedical literature search Journal Article

In: Database, 2019 , 2019, ISSN: 1758-0463, (baz085).

Abstract | Links | BibTeX

2018

114.

Duscher, Alexandrea A; Conesa, Ana; Bishop, Mary; Vroom, Madeline M; Zubizarreta, Sergio D; Foster, Jamie S

Transcriptional profiling of the mutualistic bacterium Vibrio fischeri and an hfq mutant under modeled microgravity Journal Article

In: npj Microgravity, 4 (1), pp. 25, 2018.

Links | BibTeX

113.

Sánchez-Gaya, Víctor; Casaní-Galdón, Salvador; Ugidos, Manuel; Kuang, Zheng; Mellor, Jane; Conesa, Ana; Tarazona, Sonia

Elucidating the Role of Chromatin State and Transcription Factors on the Regulation of the Yeast Metabolic Cycle: A Multi-Omic Integrative Approach Journal Article

In: Frontiers in Genetics, 9 , pp. 578, 2018, ISSN: 1664-8021.

Abstract | Links | BibTeX

112.

Solano, José García; Turpin, María C.; Torres-Moreno, Daniel; Huertas-López, Francisco; Tuomisto, Anne; Mäkinen, Markus J.; Conesa, Ana; Conesa-Zamora, Pablo

Two histologically colorectal carcinomas subsets from the serrated pathway show different methylome signatures and diagnostic biomarkers Journal Article

In: Clinical Epigenetics, 10 (1), pp. 141, 2018, ISSN: 1868-7083.

Abstract | Links | BibTeX

111.

Fábregas, Norma; Lozano-Elena, Fidel; Blasco-Escámez, David; Tohge, Takayuki; Martínez-Andújar, Cristina; Albacete, Alfonso; Osorio, Sonia; Bustamante, Mariana; Riechmann, José Luis; Nomura, Takahito; Conesa, Takao Yokota Ana; Alfocea, Francisco Pérez; Alisdair R. Fernie, 2; Caño-Delgado, Ana I.

Overexpression of the vascular brassinosteroid receptor BRL3 confers drought resistance without penalizing plant growth Journal Article

In: Nature communications, 9 (1), pp. 4680, 2018.

Links | BibTeX

110.

Tríbulo, Paula; Balzano-Nogueira, Leandro; Conesa, Ana; Siqueira, Luiz G.; Hansen, Peter J.

Changes in the uterine metabolome of the cow during the first seven days after estrus Journal Article

In: Molecular Reproduction and Development, 0 (ja), 2018.

Abstract | Links | BibTeX

109.

Sánchez-Gaya, Víctor; Casaní-Galdón, Salvador; Ugidos, Manuel; Kuang, Zheng; Mellor, Jane; Conesa, Ana; Tarazona, Sonia

Elucidating the Role of Chromatin State and Transcription Factors on the Regulation of the Yeast Metabolic Cycle: A Multi-Omic Integrative Approach Journal Article

In: Frontiers in Genetics, 9 , 2018, ISSN: 1664-8021.

Abstract | Links | BibTeX

108.

Arroyo-Crespo, Juan J.; Armiñán, Ana; Charbonnier, David; Balzano-Nogueira, Leandro; Huertas-López, Francisco; Martí, Cristina; Tarazona, Sonia; Forteza, Jerónimo; Conesa, Ana; Vicent, María J.

Tumor microenvironment-targeted poly-L-glutamic acid-based combination conjugate for enhanced triple negative breast cancer treatment Journal Article

In: Biomaterials, 186 , pp. 8 - 21, 2018, ISSN: 0142-9612.

Links | BibTeX

107.

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

Gene expression profile and molecular pathway datasets resulting from benzo(a)pyrene exposure in the liver and testis of adult tilapia Journal Article

In: Data in Brief, 20 , pp. 1500 - 1509, 2018, ISSN: 2352-3409.

Links | BibTeX

106.

Newman, Jeremy R. B.; Concannon, Patrick; Tardaguila, Manuel; Conesa, Ana; McIntyre, Lauren M.

Event Analysis: Using Transcript Events To Improve Estimates of Abundance in RNA-seq Data Journal Article

In: G3: Genes, Genomes, Genetics, 8 (9), pp. 2923–2940, 2018.

Abstract | Links | BibTeX

105.

Arzalluz-Luque, Ángeles; Ana, Conesa

Single-cell RNAseq for the study of isoforms---how is that possible? Journal Article

In: Genome Biology, 19 (1), pp. 110, 2018, ISSN: 1474-760X.

Abstract | Links | BibTeX

104.

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, 201 , pp. 162 - 173, 2018, ISSN: 0166-445X.

Links | BibTeX

103.

Tarazona, Sonia; Balzano-Nogueira, Leandro; Conesa, Ana

Multiomics Data Integration in Time Series Experiments Journal Article

In: Comprehensive Analytical Chemistry, 8 , pp. 505-532, 2018.

Links | BibTeX

102.

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.

Links | BibTeX

101.

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, 9 , pp. 1359, 2018, ISSN: 1664-302X.

Abstract | Links | BibTeX

100.

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, 10 (6), pp. 1596-1606, 2018.

Links | BibTeX

99.

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, 34 (9), pp. 1547-1554, 2018.

Links | BibTeX

98.

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, 11 (1), pp. 13, 2018.

Abstract | Links | BibTeX

97.

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

SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification Journal Article

In: Genome Research, 2018.

Abstract | Links | BibTeX

96.

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, 34 (3), pp. 524-526, 2018.

Links | BibTeX

95.

Martínez-Mira, Carlos; Conesa, Ana; Tarazona, Sonia

MOSim: Multi-Omics Simulation in R Journal Article Forthcoming

In: bioRxiv, pp. 421834, Forthcoming.

Links | BibTeX

2017

94.

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, 7 , 2017, ISSN: 2235-2988.

Abstract | Links | BibTeX

93.

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.

Disease-specific biases in alternative splicing and tissue-specific dysregulation revealed by multitissue profiling of lymphocyte gene expression in type 1 diabetes Journal Article

In: GENOME RESEARCH, 27 (11), pp. 1807-1815, 2017, ISSN: 1088-9051.

Abstract | Links | BibTeX

92.

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.

Links | BibTeX

91.

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, 69 (10), 2017, ISSN: 2326-5191.

BibTeX

90.

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, 5 (3), pp. 168-175, 2017, ISSN: 2405-4712.

Abstract | Links | BibTeX

89.

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, 13 (9), 2017, ISSN: 1553-734X.

Abstract | Links | BibTeX

88.

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, 4 (4), pp. 416+, 2017, ISSN: 2405-4712.

Abstract | Links | BibTeX

87.

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, 24 (1), pp. 162A, 2017, ISSN: 1933-7191, (64th Annual Scientific Meeting of the Society-for-Reproductive-Investigation (SRI), Orlando, FL, MAR 15-18, 2017).

BibTeX

86.

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, 66 , pp. 26-35, 2017, ISSN: 1476-9271.

Abstract | Links | BibTeX

2016

85.

Blaustein, R.; Meyer, J.; Conesa, A.; Lorca, G.; Teplitski, M.

Impacts of abundance of Candidatus Liberibacter on the citrus phyto-microbiome Journal Article

In: PHYTOPATHOLOGY, 106 (12, S), pp. 25-26, 2016, ISSN: 0031-949X, (Annual Meeting of the American-Phytopathological-Society (APS), Tampa, FL, JUL 30-AUG 03, 2016).

BibTeX

84.

Auffray, C.; Balling, R.; Barroso, I.; Bencze, L.; Benson, M.; Bergeron, J.; Bernal-Delgado, E.; Blomberg, N.; Bock, C.; Conesa, A.; Signore, S. Del; Delogne, C.; Devilee, P.; Meglio, A. Di; Eijkemans, M.; Flicek, P.; Graf, N.; Grimm, V.; Guchelaar, H.; Guo, Y.; Gut, I. G.; Hanbury, A.; Hanif, S.; Hilgers, R.; Honrado, A.; Hose, D. R.; Houwing-Duistermaat, J.; Hubbard, T.; Janacek, S. H.; Karanikas, H.; Kievits, T.; Kohler, M.; Kremer, A.; Lanfear, J.; Lengauer, T.; Maes, E.; Meert, T.; Muller, W.; Nickel, D.; Oledzki, P.; Pedersen, B.; Petkovic, M.; Pliakos, K.; Rattray, M.; i Mas, J. Redon; Schneider, R.; Sengstag, T.; Serra-Picamal, X.; Spek, W.; Vaas, L. A. I.; van Batenburg, O.; Vandelaer, M.; Varnai, P.; Villoslada, P.; Vizcaino, J. A.; Wubbe, J. P. M.; Zanetti, G.

Making sense of big data in health research: towards an EU action plan (vol 8, pg 71, 2016) Journal Article

In: GENOME MEDICINE, 8 , 2016, ISSN: 1756-994X.

Links | BibTeX

83.

Furio-Tari, P.; Conesa, A.; Tarazona, S.

RGmatch: matching genomic regions to proximal genes in omics data integration Journal Article

In: BMC BIOINFORMATICS, 17 (15), 2016, ISSN: 1471-2105.

Abstract | Links | BibTeX

82.

Panis, D. N. De; Padro, J.; Furio-Tari, P.; Tarazona, S.; Carmona, P. S. Milla; Soto, I. M.; Dopazo, H.; Conesa, A.; Hasson, E.

Transcriptome modulation during host shift is driven by secondary metabolites in desert Drosophila Journal Article

In: MOLECULAR ECOLOGY, 25 (18), pp. 4534-4550, 2016, ISSN: 0962-1083.

Abstract | Links | BibTeX

81.

Conesa, A.; Madrigal, P.; Tarazona, S.; Gomez-Cabrero, D.; Cervera, A.; McPherson, A.; Szczesniak, M. W.; Gaffney, D. J.; Elo, L. L.; Zhang, X.; Mortazavi, A.

A survey of best practices for RNA-seq data analysis (vol 17, 13, 2016) Journal Article

In: GENOME BIOLOGY, 17 , 2016, ISSN: 1474-760X.

Links | BibTeX

80.

Furio-Tari, P.; Tarazona, S.; Gabaldon, T.; Enright, A. J.; Conesa, A.

spongeScan: A web for detecting microRNA binding elements in lncRNA sequences Journal Article

In: NUCLEIC ACIDS RESEARCH, 44 (W1), pp. W176-W180, 2016, ISSN: 0305-1048.

Abstract | Links | BibTeX

79.

Auffray, C.; Balling, R.; Barroso, I.; Bencze, L.; Benson, M.; Bergeron, J.; Bernal-Delgado, E.; Blomberg, N.; Bock, C.; Conesa, A.; Signore, S. Del; Delogne, C.; Devilee, P.; Meglio, A. Di; Eijkemans, M.; Flicek, P.; Graf, N.; Grimm, V.; Guchelaar, H.; Guo, Y.; Gut, I. G.; Hanbury, A.; Hanif, S.; Hilgers, R.; Honrado, A.; Hose, D. R.; Houwing-Duistermaat, J.; Hubbard, T.; Janacek, S. H.; Karanikas, H.; Kievits, T.; Kohler, M.; Kremer, A.; Lanfear, J.; Lengauer, T.; Maes, E.; Meert, T.; Mueller, W.; Nickel, D.; Oledzki, P.; Pedersen, B.; Petkovic, M.; Pliakos, K.; Rattray, M.; i Mas, J. Redon; Schneider, R.; Sengstag, T.; Serra-Picamal, X.; Spek, W.; Vaas, L. A. I.; van Batenburg, O.; Vandelaer, M.; Varnai, P.; Villoslada, P.; Vizcaino, J. A.; Wubbe, J. P. M.; Zanetti, G.

Making sense of big data in health research: Towards an EU action plan Journal Article

In: GENOME MEDICINE, 8 , 2016, ISSN: 1756-994X.

Abstract | Links | BibTeX

78.

van der Kloet, F. M.; Sebastian-Leon, P.; Conesa, A.; Smilde, A. K.; Westerhuis, J. A.

Separating common from distinctive variation Journal Article

In: BMC BIOINFORMATICS, 17 (5), 2016, ISSN: 1471-2105, (Conference on Statistical Methods for Omics Data Integration and Analysis, Heraklion, GREECE, NOV 10-12, 2014).

Abstract | Links | BibTeX

77.

Okonechnikov, K.; Conesa, A.; Garcia-Alcalde, F.

Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data Journal Article

In: BIOINFORMATICS, 32 (2), pp. 292-294, 2016, ISSN: 1367-4803.

Abstract | Links | BibTeX

76.

Conesa, A.; Madrigal, P.; Tarazona, S.; Gomez-Cabrero, D.; Cervera, A.; McPherson, A.; Szczesniak, M. W.; Gaffney, D. J.; Elo, L. L.; Zhang, X.; Mortazavi, A.

A survey of best practices for RNA-seq data analysis Journal Article

In: GENOME BIOLOGY, 17 , 2016, ISSN: 1474-760X.

Abstract | Links | BibTeX

2015

75.

Tarazona, S.; Furio-Tari, P.; Turra, D.; Pietro, A. Di; Nueda, M. Jose; Ferrer, A.; Conesa, A.

Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package Journal Article

In: NUCLEIC ACIDS RESEARCH, 43 (21), 2015, ISSN: 0305-1048.

Abstract | Links | BibTeX

74.

Conesa-Zamora, P.; Garcia-Solano, J.; del Carmen Turpin, M.; Sebastian-Leon, P.; Torres-Moreno, D.; Estrada, E.; Tuomisto, A.; Wilce, J.; Maekinen, M. J.; Perez-Guillermo, M.; Conesa, A.

Methylome profiling reveals functions and genes which are differentially methylated in serrated compared to conventional colorectal carcinoma Journal Article

In: CLINICAL EPIGENETICS, 7 , 2015, ISSN: 1868-7083.

Abstract | Links | BibTeX

73.

Morin-Adeline, V.; Mueller, K.; Conesa, A.; Slapeta, J.

Comparative RNA-seq analysis of the Tritrichomonas foetus PIG30/1 isolate from pigs reveals close association with Tritrichomonas foetus BP-4 isolate `bovine genotype' Journal Article

In: VETERINARY PARASITOLOGY, 212 (3-4), pp. 111-117, 2015, ISSN: 0304-4017.

Abstract | Links | BibTeX

72.

Irmer, H.; Tarazona, S.; Sasse, C.; Olbermann, P.; Loeffler, J.; Krappmann, S.; Conesa, A.; Braus, G. H.

RNAseq analysis of Aspergillus fumigatus in blood reveals a just wait and see resting stage behavior Journal Article

In: BMC GENOMICS, 16 , 2015, ISSN: 1471-2164.

Abstract | Links | BibTeX

71.

de la Fuente, L.; Conesa, A.; Lloret, A.; Badenes, M. Luisa; Rios, G.

Genome-wide changes in histone H3 lysine 27 trimethylation associated with bud dormancy release in peach Journal Article

In: TREE GENETICS & GENOMES, 11 (3), 2015, ISSN: 1614-2942.

Abstract | Links | BibTeX

70.

Yanez, Y.; Grau, E.; Rodriguez-Cortez, V. C.; Hervas, D.; Vidal, E.; Noguera, R.; Hernandez, M.; Segura, V.; Canete, A.; Conesa, A.; de Mora, J. Font; Castel, V.

Two independent epigenetic biomarkers predict survival in neuroblastoma Journal Article

In: CLINICAL EPIGENETICS, 7 , 2015, ISSN: 1868-7083.

Abstract | Links | BibTeX

2014

69.

Morin-Adeline, V.; Lomas, R.; O'Meally, D.; Stack, C.; Conesa, A.; Slapeta, J.

Comparative transcriptomics reveals striking similarities between the bovine and feline isolates of Tritrichomonas foetus: consequences for in silico drug-target identification Journal Article

In: BMC GENOMICS, 15 , 2014, ISSN: 1471-2164.

Abstract | Links | BibTeX

68.

Sebastian-Leon, P.; Vidal, E.; Minguez, P.; Conesa, A.; Tarazona, S.; Amadoz, A.; Armero, C.; Salavert, F.; Vidal-Puig, A.; Montaner, D.; Dopazo, J.

Understanding disease mechanisms with models of signaling pathway activities Journal Article

In: BMC SYSTEMS BIOLOGY, 8 , 2014, ISSN: 1752-0509.

Abstract | Links | BibTeX

67.

Su, Z.; Labaj, P. P.; Li, S.; Thierry-Mieg, J.; Thierry-Mieg, D.; Shi, W.; Wang, C.; Schroth, G. P.; Setterquist, R. A.; Thompson, J. F.; Jones, W. D.; Xiao, W.; Xu, W.; Jensen, R. V.; Kelly, R.; Xu, J.; Conesa, A.; Furlanello, C.; Gao, H.; Hong, H.; Jafari, N.; Letovsky, S.; Liao, Y.; Lu, F.; Oakeley, E. J.; Peng, Z.; Praul, C. A.; Santoyo-Lopez, J.; Scherer, A.; Shi, T.; Smyth, G. K.; Staedtler, F.; Sykacek, P.; Tan, X.; Thompson, E. A.; Vandesompele, J.; Wang, M. D.; Wang, J.; Wolfinger, R. D.; Zavadil, J.; Auerbach, S. S.; Bao, W.; Binder, H.; Blomquist, T.; Brilliant, M. H.; Bushel, P. R.; Cain, W.; Catalano, J. G.; Chang, C.; Chen, T.; Chen, G.; Chen, R.; Chierici, M.; Chu, T.; Clevert, D.; Deng, Y.; Derti, A.; Devanarayan, V.; Dong, Z.; Dopazo, J.; Du, T.; Fang, H.; Fang, Y.; Fasold, M.; Fernandez, A.; Fischer, M.; Furio-Tari, P.; Fuscoe, J. C.; Caiment, F.; Gaj, S.; Gandara, J.; Gao, H.; Ge, W.; Gondo, Y.; Gong, B.; Gong, M.; Gong, Z.; Green, B.; Guo, C.; Guo, L.; Guo, L.; Hadfield, J.; Hellemans, J.; Hochreiter, S.; Jia, M.; Jian, M.; Johnson, C. D.; Kay, S.; Kleinjans, J.; Lababidi, S.; Levy, S.; Li, Q.; Li, L.; Li, L.; Li, P.; Li, Y.; Li, H.; Li, J.; Li, S.; Lin, S. M.; Lopez, F. J.; Lu, X.; Luo, H.; Ma, X.; Meehan, J.; Megherbi, D. B.; Mei, N.; Mu, B.; Ning, B.; Pandey, A.; Perez-Florido, J.; Perkins, R. G.; Peters, R.; Phan, J. H.; Pirooznia, M.; Qian, F.; Qing, T.; Rainbow, L.; Rocca-Serra, P.; Sambourg, L.; Sansone, S.; Schwartz, S.; Shah, R.; Shen, J.; Smith, T. M.; Stegle, O.; Stralis-Pavese, N.; Stupka, E.; Suzuki, Y.; Szkotnicki, L. T.; Tinning, M.; Tu, B.; van Deft, J.; Vela-Boza, A.; Venturini, E.; Walker, S. J.; Wan, L.; Wang, W.; Wang, J.; Wang, J.; Wieben, E. D.; Willey, J. C.; Wu, P.; Xuan, J.; Yang, Y.; Ye, Z.; Yin, Y.; Yu, Y.; Yuan, Y.; Zhang, J.; Zhang, K. K.; Zhang, W.; Zhang, W.; Zhang, Y.; Zhao, C.; Zheng, Y.; Zhou, Y.; Zumbo, P.; Tong, W.; Kreil, D. P.; Mason, C. E.; Shi, L.

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium Journal Article

In: NATURE BIOTECHNOLOGY, 32 (9), pp. 903-914, 2014, ISSN: 1087-0156.

Abstract | Links | BibTeX

66.

Nueda, M. J.; Tarazona, S.; Conesa, A.

Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series Journal Article

In: BIOINFORMATICS, 30 (18), pp. 2598-2602, 2014, ISSN: 1367-4803.

Abstract | Links | BibTeX

65.

Munro, S. A.; Lund, S. P.; Pine, P. S.; Binder, H.; Clevert, D.; Conesa, A.; Dopazo, J.; Fasold, M.; Hochreiter, S.; Hong, H.; Jafari, N.; Kreil, D. P.; Labaj, P. P.; Li, S.; Liao, Y.; Lin, S. M.; Meehan, J.; Mason, C. E.; Santoyo-Lopez, J.; Setterquist, R. A.; Shi, L.; Shi, W.; Smyth, G. K.; Stralis-Pavese, N.; Su, Z.; Tong, W.; Wang, C.; Wang, J.; Xu, J.; Ye, Z.; Yang, Y.; Yu, Y.; Salit, M.

Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures Journal Article

In: NATURE COMMUNICATIONS, 5 , 2014, ISSN: 2041-1723.

Abstract | Links | BibTeX

64.

Sevilla, M. Turpin; Carbonell-Munoz, R.; Garcia-Solano, J.; Torres-Moreno, D.; Garcia-Garcia, F.; Conesa, A.; Perez-Guillermo, M.; Conesa-Zamora, P.

Differentially expressed functions and genes between serrated adenocarcinoma and sporadic colorectal carcinoma showing histological and molecular features of high level of microsatellite instability Journal Article

In: EUROPEAN JOURNAL OF CANCER, 50 (5), pp. S219, 2014, ISSN: 0959-8049.

BibTeX

63.

Almouzni, G.; Altucci, L.; Amati, B.; Ashley, N.; Baulcombe, D.; Beaujean, N.; Bock, C.; Bongcam-Rudloff, E.; Bousquet, J.; Braun, S.; Paillerets, B. Bressac-de; Bussemakers, M.; Clarke, L.; Conesa, A.; Estivill, X.; Fazeli, A.; Grgurevic, N.; Gut, I.; Heijmans, B. T.; Hermouet, S.; Houwing-Duistermaat, J.; Iacobucci, I.; Ilas, J.; Kandimalla, R.; Krauss-Etschmann, S.; Lasko, P.; Lehmann, S.; Lindroth, A.; Majdic, G.; Marcotte, E.; Martinelli, G.; Martinet, N.; Meyer, E.; Miceli, C.; Mills, K.; Moreno-Villanueva, M.; Morvan, G.; Nickel, D.; Niesler, B.; Nowacki, M.; Nowak, J.; Ossowski, S.; Pelizzola, M.; Pochet, R.; Potocnik, U.; Radwanska, M.; Raes, J.; Rattray, M.; Robinson, M. D.; Roelen, B.; Sauer, S.; Schinzer, D.; Slagboom, E.; Spector, T.; Stunnenberg, H. G.; Tiligada, E.; Torres-Padilla, M.; Tsonaka, R.; Soom, A. Van; Vidakovic, M.; Widschwendter, M.

Relationship between genome and epigenome - challenges and requirements for future research Journal Article

In: BMC GENOMICS, 15 , 2014, ISSN: 1471-2164.

Abstract | Links | BibTeX

62.

Larriba, E.; Jaime, M. D. L. A.; Carbonell-Caballero, J.; Conesa, A.; Dopazo, J.; Nislow, C.; Martin-Nieto, J.; Lopez-Llorca, L. Vicente

Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia Journal Article

In: FUNGAL GENETICS AND BIOLOGY, 65 , pp. 69-80, 2014, ISSN: 1087-1845.

Abstract | Links | BibTeX

61.

Desoignies, N.; Carbonell, J.; Moreau, J. -S.; Conesa, A.; Dopazo, J.; Legreve, A.

Molecular interactions between sugar beet and Polymyxa betae during its life cycle Journal Article

In: ANNALS OF APPLIED BIOLOGY, 164 (2), pp. 244-256, 2014, ISSN: 0003-4746.

Links | BibTeX

60.

Gomez-Cabrero, D.; Abugessaisa, I.; Maier, D.; Teschendorff, A.; Merkenschlager, M.; Gisel, A.; Ballestar, E.; Bongcam-Rudloff, E.; Conesa, A.; Tegner, J.

Data integration in the era of omics: current and future challenges Journal Article

In: BMC SYSTEMS BIOLOGY, 8 (2), 2014, ISSN: 1752-0509.

Abstract | Links | BibTeX

59.

Conesa, A.; Mortazavi, A.

The common ground of genomics and systems biology Journal Article

In: BMC SYSTEMS BIOLOGY, 8 (2), 2014, ISSN: 1752-0509, (High-Throughput Omics and Data Integration Workshop, Barcelona, SPAIN, FEB 13-15, 2013).

Abstract | Links | BibTeX

58.

Ponzoni, I.; Nueda, M. J.; Tarazona, S.; Goetz, S.; Montaner, D.; Dussaut, J. S.; Dopazo, J.; Conesa, A.

Pathway network inference from gene expression data Journal Article

In: BMC SYSTEMS BIOLOGY, 8 (2), 2014, ISSN: 1752-0509, (High-Throughput Omics and Data Integration Workshop, Barcelona, SPAIN, FEB 13-15, 2013).

Abstract | Links | BibTeX

57.

de Diego, R. Hernandez; Boix-Chova, N.; Gomez-Cabrero, D.; Tegner, J.; Abugessaisa, I.; Conesa, A.

STATegra EMS: an Experiment Management System for complex next-generation omics experiments Journal Article

In: BMC SYSTEMS BIOLOGY, 8 (2), 2014, ISSN: 1752-0509, (High-Throughput Omics and Data Integration Workshop, Barcelona, SPAIN, FEB 13-15, 2013).

Abstract | Links | BibTeX

56.

Garcia-Solano, J.; Alcaraz-Mateos, E.; Wilce, J.; Torres-Moreno, D.; Turpin-Sevilla, M. C.; Navarre, C.; Conesa, A.; Tuomisto, A.; Sirnio, P.; Makinen, M. J.; Perez-Guillermo, M.; Conesa-Zamora, P.

Methylation Microarray Analysis Identifies Differentially Methylated Genes in Serrated Compared to Conventional Colorectal Carcinomas Journal Article

In: LABORATORY INVESTIGATION, 94 (1), pp. 174A, 2014, ISSN: 0023-6837, (103rd Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology (USCAP), San Diego, CA, MAR 01-07, 2014).

BibTeX

55.

Garica-Solano, J.; Alcaraz-Mateos, E.; Wilce, J.; Torres-Moreno, D.; Turpin-Sevilla, M. C.; Navarre, C.; Conesa, A.; Tuomisto, A.; Sirnio, P.; Makinen, M. J.; Perez-Guillermo, M.; Conesa-Zamora, P.

Methylation Microarray Analysis Identifies Differentially Methylated Genes in Serrated Compared to Conventional Colorectal Carcinomas Journal Article

In: MODERN PATHOLOGY, 27 (2), pp. 174A, 2014, ISSN: 0893-3952, (103rd Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology (USCAP), San Diego, CA, MAR 01-07, 2014).

BibTeX

2013

54.

Galan, A.; Diaz-Gimeno, P.; Poo, M. Eugenia; Valbuena, D.; Sanchez, E.; Ruiz, V.; Dopazo, J.; Montaner, D.; Conesa, A.; Simon, C.

Defining the Genomic Signature of Totipotency and Pluripotency during Early Human Development Journal Article

In: PLOS ONE, 8 (4), 2013, ISSN: 1932-6203.

Abstract | Links | BibTeX

53.

Conesa-Zamora, P.; Garcia-Solano, J.; Garcia-Garcia, F.; del Carmen Turpin, M.; Trujillo-Santos, J.; Torres-Moreno, D.; Oviedo-Ramirez, I.; Carbonell-Munoz, R.; Munoz-Delgado, E.; Rodriguez-Braun, E.; Conesa, A.; Perez-Guillermo, M.

Expression profiling shows differential molecular pathways and provides potential new diagnostic biomarkers for colorectal serrated adenocarcinoma Journal Article

In: INTERNATIONAL JOURNAL OF CANCER, 132 (2), pp. 297-307, 2013, ISSN: 0020-7136.

Abstract | Links | BibTeX

2012

52.

Yanez, Y.; Grau, E.; Canete, A.; Conesa, A.; Neira, A. Gonzalez; Castel, V.

METHYLATION STATUS IN NEUROBLASTOMA AND ITS PROGNOSTIC VALUE Journal Article

In: PEDIATRIC BLOOD & CANCER, 59 (6, SI), pp. 1053-1054, 2012, ISSN: 1545-5009.

BibTeX

51.

Rizza, S.; Conesa, A.; Juarez, J.; Catara, A.; Navarro, L.; Duran-Vila, N.; Ancillo, G.

Microarray analysis of Etrog citron (Citrus medica L.) reveals changes in chloroplast, cell wall, peroxidase and symporter activities in response to viroid infection Journal Article

In: MOLECULAR PLANT PATHOLOGY, 13 (8), pp. 852-864, 2012, ISSN: 1464-6722.

Abstract | Links | BibTeX

50.

Garcia-Alcalde, F.; Okonechnikov, K.; Carbonell, J.; Cruz, L. M.; Goetz, S.; Tarazona, S.; Dopazo, J.; Meyer, T. F.; Conesa, A.

Qualimap: evaluating next-generation sequencing alignment data Journal Article

In: BIOINFORMATICS, 28 (20), pp. 2678-2679, 2012, ISSN: 1367-4803.

Abstract | Links | BibTeX

49.

Fernandez, P.; Soria, M.; Blesa, D.; DiRienzo, J.; Moschen, S.; Rivarola, M.; Clavijo, B. Jose; Gonzalez, S.; Peluffo, L.; Principi, D.; Dosio, G.; Aguirrezabal, L.; Garcia-Garcia, F.; Conesa, A.; Hopp, E.; Dopazo, J.; Heinz, R. Amelia; Paniego, N.

Development, Characterization and Experimental Validation of a Cultivated Sunflower (Helianthus annuus L.) Gene Expression Oligonucleotide Microarray Journal Article

In: PLOS ONE, 7 (10), 2012, ISSN: 1932-6203.

Abstract | Links | BibTeX

48.

Agusti, J.; Gimeno, J.; Merelo, P.; Serrano, R.; Cercos, M.; Conesa, A.; Talon, M.; Tadeo, F. R.

Early gene expression events in the laminar abscission zone of abscission-promoted citrus leaves after a cycle of water stress/rehydration: involvement of CitbHLH1 Journal Article

In: JOURNAL OF EXPERIMENTAL BOTANY, 63 (17), pp. 6079-6091, 2012, ISSN: 0022-0957.

Abstract | Links | BibTeX

47.

Nueda, M. J.; Ferrer, A.; Conesa, A.

ARSyN: a method for the identification and removal of systematic noise in multifactorial time course microarray experiments Journal Article

In: BIOSTATISTICS, 13 (3), pp. 553-566, 2012, ISSN: 1465-4644.

Abstract | Links | BibTeX

46.

Lin, C. J.; Irmer, H.; Tarazona, S.; Olbermann, P.; Krappmann, S.; Conesa, A.; Braus, G.

Regulatory proteins in the opportunistic human pathogen Aspergillus fumigatus Journal Article

In: MYCOSES, 55 (4, SI), pp. 135-136, 2012, ISSN: 0933-7407.

BibTeX

45.

Jaime, M. D. L. A.; Lopez-Llorca, L. Vicente; Conesa, A.; Lee, A. Y.; Proctor, M.; Heisler, L. E.; Gebbia, M.; Giaever, G.; Westwood, J. T.; Nislow, C.

Identification of yeast genes that confer resistance to chitosan oligosaccharide (COS) using chemogenomics Journal Article

In: BMC GENOMICS, 13 , 2012, ISSN: 1471-2164.

Abstract | Links | BibTeX

44.

Perez-Quintero, A. L.; Sablok, G.; Tatarinova, T. V.; Conesa, A.; Kuo, J.; Lopez, C.

Mining of miRNAs and potential targets from gene oriented clusters of transcripts sequences of the anti-malarial plant, Artemisia annua Journal Article

In: BIOTECHNOLOGY LETTERS, 34 (4), pp. 737-745, 2012, ISSN: 0141-5492.

Abstract | Links | BibTeX

43.

Oppert, B.; Dowd, S. E.; Bouffard, P.; Li, L.; Conesa, A.; Lorenzen, M. D.; Toutges, M.; Marshall, J.; Huestis, D. L.; Fabrick, J.; Oppert, C.; Jurat-Fuentes, J. L.

Transcriptome Profiling of the Intoxication Response of Tenebrio molitor Larvae to Bacillus thuringiensis Cry3Aa Protoxin Journal Article

In: PLOS ONE, 7 (4), 2012, ISSN: 1932-6203.

Abstract | Links | BibTeX

42.

Carcel-Trullols, J.; Aguilar-Gallardo, C.; Garcia-Alcalde, F.; Pardo-Cea, M. Angel; Dopazo, J.; Conesa, A.; Simon, C.

Transdifferentiation of MALME-3M and MCF-7 Cells toward Adipocyte-like Cells is Dependent on Clathrin-mediated Endocytosis Journal Article

In: SPRINGERPLUS, 1 , 2012, ISSN: 2193-1801.

Abstract | Links | BibTeX

41.

Leida, C.; Conesa, A.; Llacer, G.; Badenes, M. Luisa; Rios, G.

Histone modifications and expression of DAM6 gene in peach are modulated during bud dormancy release in a cultivar-dependent manner Journal Article

In: NEW PHYTOLOGIST, 193 (1), pp. 67-80, 2012, ISSN: 0028-646X.

Abstract | Links | BibTeX

40.

Tarazona, S.; Prado-Lopez, S.; Dopazo, J.; Ferrer, A.; Conesa, A.

Variable selection for multifactorial genomic data Journal Article

In: CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS, 110 (1), pp. 113-122, 2012, ISSN: 0169-7439.

Abstract | Links | BibTeX

2011

39.

Yung, S.; Ledran, M.; Moreno-Gimeno, I.; Conesa, A.; Montaner, D.; Dopazo, J.; Dimmick, I.; Slater, N. J.; Marenah, L.; Real, P. J.; Paraskevopoulou, I.; Bisbal, V.; Burks, D.; Santibanez-Koref, M.; Moreno, R.; Mountford, J.; Menendez, P.; Armstrong, L.; Lako, M.

Large-scale transcriptional profiling and functional assays reveal important roles for Rho-GTPase signalling and SCL during haematopoietic differentiation of human embryonic stem cells Journal Article

In: HUMAN MOLECULAR GENETICS, 20 (24), pp. 4932-4946, 2011, ISSN: 0964-6906.

Abstract | Links | BibTeX

38.

Tarazona, S.; Garcia-Alcalde, F.; Dopazo, J.; Ferrer, A.; Conesa, A.

Differential expression in RNA-seq: A matter of depth Journal Article

In: GENOME RESEARCH, 21 (12), pp. 2213-2223, 2011, ISSN: 1088-9051.

Abstract | Links | BibTeX

37.

Khalaf, A. A.; Gmitter, Jr.; Conesa, A.; Dopazo, J.; Moore, G. A.

Fortunella margarita Transcriptional Reprogramming Triggered by Xanthomonas citri subsp citri Journal Article

In: BMC PLANT BIOLOGY, 11 , 2011, ISSN: 1471-2229.

Abstract | Links | BibTeX

36.

Durban, J.; Juarez, P.; Angulo, Y.; Lomonte, B.; Flores-Diaz, M.; Alape-Giron, A.; Sasa, M.; Sanz, L.; Gutierrez, J. M.; Dopazo, J.; Conesa, A.; Calvete, J. J.

Profiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencing Journal Article

In: BMC GENOMICS, 12 , 2011, ISSN: 1471-2164.

Abstract | Links | BibTeX

35.

Goetz, S.; Arnold, R.; Sebastian-Leon, P.; Martin-Rodriguez, S.; Tischler, P.; Jehl, M.; Dopazo, J.; Rattei, T.; Conesa, A.

B2G-FAR, a species-centered GO annotation repository Journal Article

In: BIOINFORMATICS, 27 (7), pp. 919-924, 2011, ISSN: 1367-4803.

Abstract | Links | BibTeX

34.

Garrido-Gomez, T.; Dominguez, F.; Lopez, J. Antonio; Camafeita, E.; Quinonero, A.; Martinez-Conejero, J. Antonio; Pellicer, A.; Conesa, A.; Simon, C.

Modeling Human Endometrial Decidualization from the Interaction between Proteome and Secretome Journal Article

In: JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM, 96 (3), pp. 706-716, 2011, ISSN: 0021-972X.

Abstract | Links | BibTeX

33.

Garcia-Alcalde, F.; Garcia-Lopez, F.; Dopazo, J.; Conesa, A.

Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data Journal Article

In: BIOINFORMATICS, 27 (1), pp. 137-139, 2011, ISSN: 1367-4803.

Abstract | Links | BibTeX

2010

32.

Conesa, A.; Prats-Montalban, J. M.; Tarazona, S.; Nueda, M. Jose; Ferrer, A.

A multiway approach to data integration in systems biology based on Tucker3 and N-PLS Journal Article

In: CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS, 104 (1, SI), pp. 101-111, 2010, ISSN: 0169-7439.

Abstract | Links | BibTeX

31.

Medina, I.; Carbonell, J.; Pulido, L.; Madeira, S. C.; Goetz, S.; Conesa, A.; Tarraga, J.; Pascual-Montano, A.; Nogales-Cadenas, R.; Santoyo, J.; Garcia, F.; Marba, M.; Montaner, D.; Dopazo, J.

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling Journal Article

In: NUCLEIC ACIDS RESEARCH, 38 (2), pp. W210-W213, 2010, ISSN: 0305-1048.

Abstract | Links | BibTeX

30.

Nueda, M. Jose; Carbonell, J.; Medina, I.; Dopazo, J.; Conesa, A.

Serial Expression Analysis: a web tool for the analysis of serial gene expression data Journal Article

In: NUCLEIC ACIDS RESEARCH, 38 (2), pp. W239-W245, 2010, ISSN: 0305-1048.

Abstract | Links | BibTeX

29.

Nemeth, A.; Conesa, A.; Santoyo-Lopez, J.; Medina, I.; Montaner, D.; Peterfia, B.; Solovei, I.; Cremer, T.; Dopazo, J.; Laengst, G.

Initial Genomics of the Human Nucleolus Journal Article

In: PLOS GENETICS, 6 (3), 2010, ISSN: 1553-7390.

Abstract | Links | BibTeX

28.

Prado-Lopez, S.; Conesa, A.; Arminan, A.; Martinez-Losa, M.; Escobedo-Lucea, C.; Gandia, C.; Tarazona, S.; Melguizo, D.; Blesa, D.; Montaner, D.; Sanz-Gonzalez, S.; Sepulveda, P.; Goetz, S.; O'Connor, J. Enrique; Moreno, R.; Dopazo, J.; Burks, D. J.; Stojkovic, M.

Hypoxia Promotes Efficient Differentiation of Human Embryonic Stem Cells to Functional Endothelium Journal Article

In: STEM CELLS, 28 (3), pp. 407-418, 2010, ISSN: 1066-5099.

Abstract | Links | BibTeX

27.

Rattei, T.; Tischler, P.; Goetz, S.; Jehl, M.; Hoser, J.; Arnold, R.; Conesa, A.; Mewes, H.

SIMAP-a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters Journal Article

In: NUCLEIC ACIDS RESEARCH, 38 (1), pp. D223-D226, 2010, ISSN: 0305-1048.

Abstract | Links | BibTeX

2009

26.

Brumos, J.; Colmenero-Flores, J. M.; Conesa, A.; Izquierdo, P.; Sanchez, G.; Iglesias, D. J.; Lopez-Climent, M. F.; Gomez-Cadenas, A.; Talon, M.

Membrane transporters and carbon metabolism implicated in chloride homeostasis differentiate salt stress responses in tolerant and sensitive Citrus rootstocks Journal Article

In: FUNCTIONAL & INTEGRATIVE GENOMICS, 9 (3), pp. 293-309, 2009, ISSN: 1438-793X.

Abstract | Links | BibTeX

25.

Nueda, M. Jose; Sebastian, P.; Tarazona, S.; Garcia-Garcia, F.; Dopazo, J.; Ferrer, A.; Conesa, A.

Functional assessment of time course microarray data Journal Article

In: BMC BIOINFORMATICS, 10 , 2009, ISSN: 1471-2105, (European Molecular Biology Network Conference, Martina, ITALY, SEP 18-20, 2008).

Abstract | Links | BibTeX

2008

24.

Conesa, A.; Bro, R.; Garcia-Garcia, F.; Prats, J. M.; Gotz, S.; Kjeldahl, K.; Montaner, D.; Dopazo, J.

Direct functional assessment of the composite phenotype through multivariate projection strategies Journal Article

In: GENOMICS, 92 (6), pp. 373-383, 2008, ISSN: 0888-7543.

Abstract | Links | BibTeX

23.

Hoogerwerf, W. A.; Sinha, M.; Conesa, A.; Luxon, B. A.; Shahinian, V. B.; Cornelissen, G.; Halberg, F.; Bostwick, J.; Timm, J.; Cassone, V. M.

Transcriptional Profiling of mRNA Expression in the Mouse Distal Colon Journal Article

In: GASTROENTEROLOGY, 135 (6), pp. 2019-2029, 2008, ISSN: 0016-5085.

Abstract | Links | BibTeX

22.

Stierum, R.; Conesa, A.; Heijne, W.; van Ommen, B.; Junker, K.; Scott, M. P.; Price, R. J.; Meredith, C.; Lake, B. G.; Groten, J.

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 Journal Article

In: FOOD AND CHEMICAL TOXICOLOGY, 46 (8), pp. 2616-2628, 2008, ISSN: 0278-6915.

Abstract | Links | BibTeX

21.

Tarraga, J.; Medina, I.; Carbonell, J.; Huerta-Cepas, J.; Minguez, P.; Alloza, E.; Al-Shahrour, F.; Vegas-Azcarate, S.; Goetz, S.; Escobar, P.; Garcia-Garcia, F.; Conesa, A.; Montaner, D.; Dopazo, J.

GEPAS, a web-based tool for microarray data analysis and interpretation Journal Article

In: NUCLEIC ACIDS RESEARCH, 36 (S), pp. W308-W314, 2008, ISSN: 0305-1048.

Abstract | Links | BibTeX

20.

Al-Shahrour, F.; Carbonell, J.; Minguez, P.; Goetz, S.; Conesa, A.; Tarrraga, J.; Medina, I.; Alloza, E.; Montaner, D.; Dopazo, J.

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments Journal Article

In: NUCLEIC ACIDS RESEARCH, 36 (S), pp. W341-W346, 2008, ISSN: 0305-1048.

Abstract | Links | BibTeX

19.

Botton, A.; Galla, G.; Conesa, A.; Bachem, C.; Ramina, A.; Barcaccia, G.

Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology Journal Article

In: BMC GENOMICS, 9 , 2008, ISSN: 1471-2164.

Abstract | Links | BibTeX

18.

Gotz, S.; Garcia-Gomez, J. M.; Terol, J.; Williams, T. D.; Nagaraj, S. H.; Nueda, M. J.; Robles, M.; Talon, M.; Dopazo, J.; Conesa, A.

High-throughput functional annotation and data mining with the Blast2GO suite Journal Article

In: NUCLEIC ACIDS RESEARCH, 36 (10), pp. 3420-3435, 2008, ISSN: 0305-1048.

Abstract | Links | BibTeX

17.

Agudo, M.; Perez-Marin, M. C.; Loenngren, U.; Sobrado, P.; Conesa, A.; Canovas, I.; Salinas-Navarro, M.; Miralles-Imperial, J.; Hallbook, F.; Vidal-Sanz, M.

Time course profiling of the retinal transcriptome after optic nerve transection and optic nerve crush Journal Article

In: MOLECULAR VISION, 14 (126), pp. 1050-1063, 2008, ISSN: 1090-0535.

Abstract | BibTeX

2007

16.

Levin, A. M.; de Vries, R. P.; Conesa, A.; de Bekker, C.; Talon, M.; Menke, H. H.; van Peij, N. N. M. E.; Wosten, H. A. B.

Spatial differentiation in the vegetative mycelium of Aspergillus niger Journal Article

In: EUKARYOTIC CELL, 6 (12), pp. 2311-2322, 2007, ISSN: 1535-9778.

Abstract | Links | BibTeX

15.

Gandia, M.; Conesa, A.; Ancillo, G.; Gadea, J.; Forment, J.; Pallas, V.; Flores, R.; Duran-Vila, N.; Moreno, P.; Guerri, J.

Transcriptional response of Citrus aurantifolia to infection by Citrus tristeza virus Journal Article

In: VIROLOGY, 367 (2), pp. 298-306, 2007, ISSN: 0042-6822.

Abstract | Links | BibTeX

14.

Nueda, M. J.; Conesa, A.; Westerhuis, J. A.; Hoefsloot, H. C. J.; Smilde, A. K.; Talon, M.; Ferrer, A.

Discovering gene expression patterns in time course microarray experiments by ANOVA-SCA Journal Article

In: BIOINFORMATICS, 23 (14), pp. 1792-1800, 2007, ISSN: 1367-4803.

Abstract | Links | BibTeX

13.

Terol, J.; Conesa, A.; Colmenero, J. M.; Cercos, M.; Tadeo, F.; Agusti, J.; Alos, E.; Andres, F.; Soler, G.; Brumos, J.; Iglesias, D. J.; Gotz, S.; Legaz, F.; Argout, X.; Courtois, B.; Ollitrault, P.; Dossat, C.; Wincker, P.; Morillon, R.; Talon, M.

Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance Journal Article

In: BMC GENOMICS, 8 , 2007, ISSN: 1471-2164.

Abstract | Links | BibTeX

2006

12.

Williams, T. D.; Diab, A. M.; George, S. G.; Godfrey, R. E.; Sabine, V.; Conesa, A.; Minchin, S. D.; Watts, P. C.; Chipman, J. K.

Development of the GENIPOL European flounder (Platichthys flesus) microarray and determination of temporal transcriptional responses to cadmium at low dose. Journal Article

In: ENVIRONMENTAL SCIENCE & TECHNOLOGY, 40 (20), pp. 6479-6488, 2006, ISSN: 0013-936X.

Abstract | Links | BibTeX

11.

Conesa, A.; Nueda, M.; Ferrer, A.; Talon, M.

maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments Journal Article

In: BIOINFORMATICS, 22 (9), pp. 1096-1102, 2006, ISSN: 1367-4803.

Abstract | Links | BibTeX

2005

10.

Conesa, A.; Gotz, S.; Garcia-Gomez, J.; Terol, J.; Talon, M.; Robles, M.

Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research Journal Article

In: BIOINFORMATICS, 21 (18), pp. 3674-3676, 2005, ISSN: 1367-4803.

Abstract | Links | BibTeX

9.

Forment, J.; Gadea, J.; Huerta, L.; Abizanda, L.; Agusti, J.; Alamar, S.; Alos, E.; Andres, F.; Arribas, R.; Beltran, J.; Berbel, A.; Blazquez, M.; Brumos, J.; Canas, L.; Cercos, M.; Colmenero-Flores, J.; Conesa, A.; Estables, B.; Gandia, M.; Garcia-Martinez, J.; Gimeno, J.; Gisbert, A.; Gomez, G.; Gonzalez-Candelas, L.; Granell, A.; Guerri, J.; Lafuente, M.; Madueno, F.; Marcos, J.; Marques, M.; Martinez, F.; Martinez-Godoy, M.; Miralles, S.; Moreno, P.; Navarro, L.; Pallas, V.; Perez-Amador, M.; Perez-Valle, J.; Pons, C.; Rodrigo, I.; Rodriguez, P.; Royo, C.; Serrano, R.; Soler, G.; Tadeo, F.; Talon, M.; Terol, J.; Trenor, M.; Vaello, L.; Vicente, O.; Vidal, C.; Zacarias, L.; Conejero, V.

Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies Journal Article

In: PLANT MOLECULAR BIOLOGY, 57 (3), pp. 375-391, 2005, ISSN: 0167-4412.

Abstract | Links | BibTeX

2003

8.

Yi, X.; Conesa, A.; Punt, P.; Hager, L.

Examining the role of glutamic acid 183 in chloroperoxidase catalysis Journal Article

In: JOURNAL OF BIOLOGICAL CHEMISTRY, 278 (16), pp. 13855-13859, 2003, ISSN: 0021-9258.

Abstract | Links | BibTeX

2002

7.

Punt, P.; van Biezen, N.; Conesa, A.; Albers, A.; Mangnus, J.; van den Hondel, C.

Filamentous fungi as cell factories for heterologous protein production Journal Article

In: TRENDS IN BIOTECHNOLOGY, 20 (5), pp. 200-206, 2002, ISSN: 0167-7799.

Abstract | Links | BibTeX

6.

Conesa, A.; Punt, P.; van den Hondel, C.

Fungal peroxidases: molecular aspects and applications Journal Article

In: JOURNAL OF BIOTECHNOLOGY, 93 (2), pp. 143-158, 2002, ISSN: 0168-1656.

Abstract | Links | BibTeX

5.

Conesa, A.; Jeenes, D.; Archer, D.; van den Hondel, C.; Punt, P.

Calnexin overexpression increases manganese peroxidase production in Aspergillus niger Journal Article

In: APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 68 (2), pp. 846-851, 2002, ISSN: 0099-2240.

Abstract | Links | BibTeX

2001

4.

Conesa, A.; Punt, P.; van Luijk, N.; van den Hondel, C.

The secretion pathway in filamentous fungi: A biotechnological view Journal Article

In: FUNGAL GENETICS AND BIOLOGY, 33 (3), pp. 155-171, 2001, ISSN: 1087-1845.

Abstract | Links | BibTeX

3.

Conesa, A.; Weelink, G.; van den Hondel, C.; Punt, P.

C-terminal propeptide of the Caldariomyces fumago chloroperoxidase: an intramolecular chaperone? Journal Article

In: FEBS LETTERS, 503 (2-3), pp. 117-120, 2001, ISSN: 0014-5793.

Abstract | Links | BibTeX

2.

Conesa, A.; van de Velde, F.; van Rantwijk, F.; Sheldon, R.; van den Hondel, C.; Punt, P.

Expression of the Caldariomyces fumago chloroperoxidase in Aspergillus niger and characterization of the recombinant enzyme Journal Article

In: JOURNAL OF BIOLOGICAL CHEMISTRY, 276 (21), pp. 17635-17640, 2001, ISSN: 0021-9258.

Abstract | Links | BibTeX

2000

1.

Conesa, A.; van den Hondel, C.; Punt, P.

Studies on the production of fungal peroxidases in Aspergillus niger Journal Article

In: APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 66 (7), pp. 3016-3023, 2000, ISSN: 0099-2240.

Abstract | Links | BibTeX