Publications

2021

144.

van der Planell N Lagani V, Sebastian-Leon Kloet Ewing Karathanasis Urdangarin Arozarena Jagodic Tsamardinos Tarazona Conesa Tegner Gomez-Cabrero P F E N A I M I S A J D

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

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)

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)

bioRxiv, 2021.

(BibTeX)

141.

~n, Jes{'u}s Rodr{'i}guez-Ba; Pachón, Jerónimo; `a, Jordi Carratal; Ryan, Pablo; 'i, Inmaculada Jarr; 'i, Mar; Arribas, José Ramón; Berenguer, Juan; ~n, 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)

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)

bioRxiv, 2021.

(BibTeX)

139.

Rubio, Teresa; Felipo, Vicente; Tarazona, Sonia; Pastorelli, Roberta; 'i, Desamparados Escudero-Garc; 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)

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

(BibTeX)

138.

Balzano-Nogueira, Leandro; Ramirez, Ricardo; Zamkovaya, Tatyana; Dailey, Jordan; Ardissone, Alexandria N; Chamala, Srikar; 'i, Joan Serrano-Qu; 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)

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)

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)

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

(BibTeX)

2020

135.

Tarazona S Balzano-Nogueira L, Gómez-Cabrero Schmidt Imhof Hankemeier Tegnér Westerhuis JA Conesa D A A T J A

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

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)

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)

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)

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)

bioRxiv, 2020.

(BibTeX)

130.

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

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

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)

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)

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)

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)

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

(BibTeX)

125.

de la Fuente, Lorena; Arzalluz-Luque, Ángeles; Tardáguila, Manuel; Risco, Héctor Del; 'i, Cristina Mart; 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)

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)

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)

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)

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)

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)

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 Paul, Veronica Saint; 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)

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

(Abstract | Links | BibTeX)

118.

García-Solano, José; del Turpin-Sevilla, María Carmen; 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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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 ; Pappas Jr, Georgios J; Conesa, Ana

PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data (Journal Article)

Nucleic Acids Research, pp. gky466, 2018.

(Links | BibTeX)

101.

Babilonia, Joany; Conesa, Ana; Casaburi, Giorgio; Pereira, Cecile; Louyakis, Artemis S; Reid, Pamela R; Foster, Jamie S

Comparative Metagenomics Provides Insight Into the Ecosystem Functioning of the Shark Bay Stromatolites, Western Australia (Journal Article)

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)

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)

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, Franklin B; 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)

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)

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)

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)

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)

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)

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)

Briefings in Bioinformatics, pp. bbx122, 2017.

(Links | BibTeX)

91.

Conesa, A; Fernandez, M; Exposito, R; Campos, J; Lamua, Ramon J; del Navarro, Pilar M; Rubio-Munoz, P; Ahijado-Guzman, P; Gonzalez, C M

Certolizumab Pegol Effectiveness and Retention Rate in Psoriatic Arthritis. Real Life Data (Journal Article)

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)

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)

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)

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)

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, Lucia P; Gonzalez-Rodriguez, E; Aguado-Santacruz, Armando G; 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)

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)

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, Del S; Delogne, C; Devilee, P; Meglio, Di A; 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, Redon J; 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)

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)

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

(Abstract | Links | BibTeX)

82.

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

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

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)

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)

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, Del S; Delogne, C; Devilee, P; Meglio, Di A; 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, Redon J; 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)

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)

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)

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)

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

(Abstract | Links | BibTeX)

2015

75.

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

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

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

(Abstract | Links | BibTeX)

74.

Conesa-Zamora, P; Garcia-Solano, J; del Turpin, Carmen 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)

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)

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)

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

(Abstract | Links | BibTeX)

71.

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

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

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, Font J; Castel, V

Two independent epigenetic biomarkers predict survival in neuroblastoma (Journal Article)

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)

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)

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)

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)

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)

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

(Abstract | Links | BibTeX)

64.

Sevilla, Turpin M; 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)

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, Bressac-de B; 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, Van A; Vidakovic, M; Widschwendter, M

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

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, Vicente L

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

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)

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)

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)

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)

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, Hernandez R; 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)

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)

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)

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, Eugenia M; 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)

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

(Abstract | Links | BibTeX)

53.

Conesa-Zamora, P; Garcia-Solano, J; Garcia-Garcia, F; del Turpin, Carmen 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)

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, Gonzalez A; Castel, V

METHYLATION STATUS IN NEUROBLASTOMA AND ITS PROGNOSTIC VALUE (Journal Article)

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)

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)

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, Jose B; Gonzalez, S; Peluffo, L; Principi, D; Dosio, G; Aguirrezabal, L; Garcia-Garcia, F; Conesa, A; Hopp, E; Dopazo, J; Heinz, Amelia R; Paniego, N

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

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)

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)

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)

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

(BibTeX)

45.

Jaime, M D L A; Lopez-Llorca, Vicente L; 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)

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)

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)

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

(Abstract | Links | BibTeX)

42.

Carcel-Trullols, J; Aguilar-Gallardo, C; Garcia-Alcalde, F; Pardo-Cea, Angel M; 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)

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

(Abstract | Links | BibTeX)

41.

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

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

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)

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)

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)

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)

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)

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)

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

(Abstract | Links | BibTeX)

34.

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

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

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)

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

(Abstract | Links | BibTeX)

2010

32.

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

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

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)

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

(Abstract | Links | BibTeX)

30.

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

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

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)

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, Enrique J; Moreno, R; Dopazo, J; Burks, D J; Stojkovic, M

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

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)

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)

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

(Abstract | Links | BibTeX)

25.

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

Functional assessment of time course microarray data (Journal Article)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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

(Abstract | Links | BibTeX)