Publications

2018

106. Tríbulo, Paula; Balzano-Nogueira, Leandro; Conesa, Ana; Siqueira, Luiz G; Hansen, Peter JChanges in the uterine metabolome of the cow during the first seven days after estrus Journal Article Molecular Reproduction and Development, 0 (ja), 2018.

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

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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, EmanuelGene 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.

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

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102. Arzalluz-Luque, Ángeles; Ana, ConesaSingle-cell RNAseq for the study of isoforms---how is that possible? Journal Article Genome Biology, 19 (1), pp. 110, 2018, ISSN: 1474-760X.

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101. Colli-Dula, Reyna Cristina; Fang, Xiefan; Moraga-Amador, David; Albornoz-Abud, Nacira; Zamora-Bustillos, Roberto; Conesa, Ana; Zapata-Perez, Omar; Moreno, Diego; Hernandez-Nuñez, EmanuelTranscriptome 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.

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100. 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.

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

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98. Delaye, Luis; Ruiz-Ruiz, Susana; Calderon, Enrique; Tarazona, Sonia; Conesa, Ana; Moya, AndrésEvidence 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.

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97. 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.

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96. 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.

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95. 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.

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94. Nueda, María José; Martorell-Marugan, Jordi; Martí, Cristina; Tarazona, Sonia; Conesa, AnaIdentification and visualization of differential isoform expression in RNA-seq time series Journal Article Bioinformatics, 34 (3), pp. 524-526, 2018.

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2017

93. Kaeding, N; Kaufhold, I; Mueller, C; Szaszak, M; Shima, K; Weinmaier, T; Lomas, R; Conesa, A; Schmitt-Kopplin, P; Rattei, T; Rupp, JGrowth of Chlamydia pneumoniae Is Enhanced in Cell swith Impaired Mitochondrial Function Journal Article FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY, 7 , 2017, ISSN: 2235-2988.

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92. Newman, J R B; Conesa, A; Mika, M; New, F N; Onengut-Gumuscu, S; Atkinson, M A; Rich, S S; McIntyre, L M; Concannon, PDisease-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.

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91. Conesa, A; Fernandez, M; Exposito, R; Campos, J; Lamua, Ramon J; del Navarro, Pilar M; Rubio-Munoz, P; Ahijado-Guzman, P; Gonzalez, C MCertolizumab Pegol Effectiveness and Retention Rate in Psoriatic Arthritis. Real Life Data Journal Article ARTHRITIS & RHEUMATOLOGY, 69 (10), 2017, ISSN: 2326-5191.

BibTeX

90. Hernandez-de-Diego, R; de Villiers, E P; Klingstrom, T; Gourle, H; Conesa, A; Bongcam-Rudloff, EThe eBioKit, a stand-alone educational platform for bioinformatics Journal Article PLOS COMPUTATIONAL BIOLOGY, 13 (9), 2017, ISSN: 1553-734X.

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89. Gomez-Cabrero, D; Marabita, F; Tarazona, S; Cano, I; Roca, J; Conesa, A; Sabatier, P; Tegner, JGuidelines 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.

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88. Ramirez, R N; El-Ali, N C; Mager, M A; Wyman, D; Conesa, A; Mortazavi, ADynamic Gene Regulatory Networks of Human Myeloid Differentiation Journal Article CELL SYSTEMS, 4 (4), pp. 416+, 2017, ISSN: 2405-4712.

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87. Sebastian-Leon, P; Conesa, A; Arnau, V; Remohi, J; Pellicer, A; Simon, C; Diaz-Gimeno, PNetwork 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, JIdentification 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.

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2016

85. Blaustein, R; Meyer, J; Conesa, A; Lorca, G; Teplitski, MImpacts 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. Furio-Tari, P; Conesa, A; Tarazona, SRGmatch: matching genomic regions to proximal genes in omics data integration Journal Article BMC BIOINFORMATICS, 17 (15), 2016, ISSN: 1471-2105.

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83. 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, GMaking 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.

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

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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, AA survey of best practices for RNA-seq data analysis (vol 17, 13, 2016) Journal Article GENOME BIOLOGY, 17 , 2016, ISSN: 1474-760X.

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80. Furio-Tari, P; Tarazona, S; Gabaldon, T; Enright, A J; Conesa, AspongeScan: A web for detecting microRNA binding elements in lncRNA sequences Journal Article NUCLEIC ACIDS RESEARCH, 44 (W1), pp. W176-W180, 2016, ISSN: 0305-1048.

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

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78. 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, GMaking sense of big data in health research: Towards an EU action plan Journal Article GENOME MEDICINE, 8 , 2016, ISSN: 1756-994X.

Abstract | Links | BibTeX

77. Okonechnikov, K; Conesa, A; Garcia-Alcalde, FQualimap 2: advanced multi-sample quality control for high-throughput sequencing data Journal Article BIOINFORMATICS, 32 (2), pp. 292-294, 2016, ISSN: 1367-4803.

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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, AA survey of best practices for RNA-seq data analysis Journal Article GENOME BIOLOGY, 17 , 2016, ISSN: 1474-760X.

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2015

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

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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, AMethylome 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.

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

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72. Irmer, H; Tarazona, S; Sasse, C; Olbermann, P; Loeffler, J; Krappmann, S; Conesa, A; Braus, G HRNAseq analysis of Aspergillus fumigatus in blood reveals a just wait and see resting stage behavior Journal Article BMC GENOMICS, 16 , 2015, ISSN: 1471-2164.

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71.de la Fuente, L; Conesa, A; Lloret, A; Badenes, Luisa M; Rios, GGenome-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.

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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, VTwo independent epigenetic biomarkers predict survival in neuroblastoma Journal Article CLINICAL EPIGENETICS, 7 , 2015, ISSN: 1868-7083.

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2014

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

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68. Sebastian-Leon, P; Vidal, E; Minguez, P; Conesa, A; Tarazona, S; Amadoz, A; Armero, C; Salavert, F; Vidal-Puig, A; Montaner, D; Dopazo, JUnderstanding disease mechanisms with models of signaling pathway activities Journal Article BMC SYSTEMS BIOLOGY, 8 , 2014, ISSN: 1752-0509.

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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, LA 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.

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66. Nueda, M J; Tarazona, S; Conesa, ANext maSigPro: updating maSigPro bioconductor package for RNA-seq time series Journal Article BIOINFORMATICS, 30 (18), pp. 2598-2602, 2014, ISSN: 1367-4803.

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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, MAssessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures Journal Article NATURE COMMUNICATIONS, 5 , 2014, ISSN: 2041-1723.

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64. Sevilla, Turpin M; Carbonell-Munoz, R; Garcia-Solano, J; Torres-Moreno, D; Garcia-Garcia, F; Conesa, A; Perez-Guillermo, M; Conesa-Zamora, PDifferentially 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, MRelationship between genome and epigenome - challenges and requirements for future research Journal Article BMC GENOMICS, 15 , 2014, ISSN: 1471-2164.

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

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61. Gomez-Cabrero, D; Abugessaisa, I; Maier, D; Teschendorff, A; Merkenschlager, M; Gisel, A; Ballestar, E; Bongcam-Rudloff, E; Conesa, A; Tegner, JData integration in the era of omics: current and future challenges Journal Article BMC SYSTEMS BIOLOGY, 8 (2), 2014, ISSN: 1752-0509.

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60. Conesa, A; Mortazavi, AThe 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).

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

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

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

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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, PMethylation 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, PMethylation 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, CDefining the Genomic Signature of Totipotency and Pluripotency during Early Human Development Journal Article PLOS ONE, 8 (4), 2013, ISSN: 1932-6203.

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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, MExpression 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.

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2012

52. Yanez, Y; Grau, E; Canete, A; Conesa, A; Neira, Gonzalez A; Castel, VMETHYLATION STATUS IN NEUROBLASTOMA AND ITS PROGNOSTIC VALUE Journal Article PEDIATRIC BLOOD & CANCER, 59 (6, SI), pp. 1053-1054, 2012, ISSN: 1545-5009.

BibTeX

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

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50. 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, NDevelopment, 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.

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

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48. Garcia-Alcalde, F; Okonechnikov, K; Carbonell, J; Cruz, L M; Goetz, S; Tarazona, S; Dopazo, J; Meyer, T F; Conesa, AQualimap: evaluating next-generation sequencing alignment data Journal Article BIOINFORMATICS, 28 (20), pp. 2678-2679, 2012, ISSN: 1367-4803.

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47. Nueda, M J; Ferrer, A; Conesa, AARSyN: 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.

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46. 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, CIdentification of yeast genes that confer resistance to chitosan oligosaccharide (COS) using chemogenomics Journal Article BMC GENOMICS, 13 , 2012, ISSN: 1471-2164.

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45. Lin, C J; Irmer, H; Tarazona, S; Olbermann, P; Krappmann, S; Conesa, A; Braus, GRegulatory proteins in the opportunistic human pathogen Aspergillus fumigatus Journal Article MYCOSES, 55 (4, SI), pp. 135-136, 2012, ISSN: 0933-7407.

BibTeX

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

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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 LTranscriptome Profiling of the Intoxication Response of Tenebrio molitor Larvae to Bacillus thuringiensis Cry3Aa Protoxin Journal Article PLOS ONE, 7 (4), 2012, ISSN: 1932-6203.

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

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

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40. Tarazona, S; Prado-Lopez, S; Dopazo, J; Ferrer, A; Conesa, AVariable selection for multifactorial genomic data Journal Article CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS, 110 (1), pp. 113-122, 2012, ISSN: 0169-7439.

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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, MLarge-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.

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38. Tarazona, S; Garcia-Alcalde, F; Dopazo, J; Ferrer, A; Conesa, ADifferential expression in RNA-seq: A matter of depth Journal Article GENOME RESEARCH, 21 (12), pp. 2213-2223, 2011, ISSN: 1088-9051.

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37. Khalaf, A A; Gmitter, Jr.; Conesa, A; Dopazo, J; Moore, G AFortunella margarita Transcriptional Reprogramming Triggered by Xanthomonas citri subsp citri Journal Article BMC PLANT BIOLOGY, 11 , 2011, ISSN: 1471-2229.

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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 JProfiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencing Journal Article BMC GENOMICS, 12 , 2011, ISSN: 1471-2164.

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35. Goetz, S; Arnold, R; Sebastian-Leon, P; Martin-Rodriguez, S; Tischler, P; Jehl, M; Dopazo, J; Rattei, T; Conesa, AB2G-FAR, a species-centered GO annotation repository Journal Article BIOINFORMATICS, 27 (7), pp. 919-924, 2011, ISSN: 1367-4803.

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

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33. Garcia-Alcalde, F; Garcia-Lopez, F; Dopazo, J; Conesa, APaintomics: 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.

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2010

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

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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, JBabelomics: 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.

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

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29. Nemeth, A; Conesa, A; Santoyo-Lopez, J; Medina, I; Montaner, D; Peterfia, B; Solovei, I; Cremer, T; Dopazo, J; Laengst, GInitial Genomics of the Human Nucleolus Journal Article PLOS GENETICS, 6 (3), 2010, ISSN: 1553-7390.

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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, MHypoxia Promotes Efficient Differentiation of Human Embryonic Stem Cells to Functional Endothelium Journal Article STEM CELLS, 28 (3), pp. 407-418, 2010, ISSN: 1066-5099.

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

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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, MMembrane 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.

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25. Nueda, Jose M; Sebastian, P; Tarazona, S; Garcia-Garcia, F; Dopazo, J; Ferrer, A; Conesa, AFunctional 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, JDirect functional assessment of the composite phenotype through multivariate projection strategies Journal Article GENOMICS, 92 (6), pp. 373-383, 2008, ISSN: 0888-7543.

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23. Hoogerwerf, W A; Sinha, M; Conesa, A; Luxon, B A; Shahinian, V B; Cornelissen, G; Halberg, F; Bostwick, J; Timm, J; Cassone, V MTranscriptional Profiling of mRNA Expression in the Mouse Distal Colon Journal Article GASTROENTEROLOGY, 135 (6), pp. 2019-2029, 2008, ISSN: 0016-5085.

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

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21. Botton, A; Galla, G; Conesa, A; Bachem, C; Ramina, A; Barcaccia, GLarge-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology Journal Article BMC GENOMICS, 9 , 2008, ISSN: 1471-2164.

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

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, AHigh-throughput functional annotation and data mining with the Blast2GO suite Journal Article NUCLEIC ACIDS RESEARCH, 36 (10), pp. 3420-3435, 2008, ISSN: 0305-1048.

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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, MTime 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.

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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 BSpatial differentiation in the vegetative mycelium of Aspergillus niger Journal Article EUKARYOTIC CELL, 6 (12), pp. 2311-2322, 2007, ISSN: 1535-9778.

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15. Gandia, M; Conesa, A; Ancillo, G; Gadea, J; Forment, J; Pallas, V; Flores, R; Duran-Vila, N; Moreno, P; Guerri, JTranscriptional response of Citrus aurantifolia to infection by Citrus tristeza virus Journal Article VIROLOGY, 367 (2), pp. 298-306, 2007, ISSN: 0042-6822.

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14. Nueda, M J; Conesa, A; Westerhuis, J A; Hoefsloot, H C J; Smilde, A K; Talon, M; Ferrer, ADiscovering gene expression patterns in time course microarray experiments by ANOVA-SCA Journal Article BIOINFORMATICS, 23 (14), pp. 1792-1800, 2007, ISSN: 1367-4803.

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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, MAnalysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance Journal Article BMC GENOMICS, 8 , 2007, ISSN: 1471-2164.

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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 KDevelopment 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.

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11. Conesa, A; Nueda, M; Ferrer, A; Talon, MmaSigPro: 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.

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2005

10. Conesa, A; Gotz, S; Garcia-Gomez, J; Terol, J; Talon, M; Robles, MBlast2GO: a universal tool for annotation, visualization and analysis in functional genomics research Journal Article BIOINFORMATICS, 21 (18), pp. 3674-3676, 2005, ISSN: 1367-4803.

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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, VDevelopment 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.

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2003

8. Yi, X; Conesa, A; Punt, P; Hager, LExamining the role of glutamic acid 183 in chloroperoxidase catalysis Journal Article JOURNAL OF BIOLOGICAL CHEMISTRY, 278 (16), pp. 13855-13859, 2003, ISSN: 0021-9258.

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2002

7. Punt, P; van Biezen, N; Conesa, A; Albers, A; Mangnus, J; van den Hondel, CFilamentous fungi as cell factories for heterologous protein production Journal Article TRENDS IN BIOTECHNOLOGY, 20 (5), pp. 200-206, 2002, ISSN: 0167-7799.

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6. Conesa, A; Punt, P; van den Hondel, CFungal peroxidases: molecular aspects and applications Journal Article JOURNAL OF BIOTECHNOLOGY, 93 (2), pp. 143-158, 2002, ISSN: 0168-1656.

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5. Conesa, A; Jeenes, D; Archer, D; van den Hondel, C; Punt, PCalnexin overexpression increases manganese peroxidase production in Aspergillus niger Journal Article APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 68 (2), pp. 846-851, 2002, ISSN: 0099-2240.

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2001

4. Conesa, A; Punt, P; van Luijk, N; van den Hondel, CThe secretion pathway in filamentous fungi: A biotechnological view Journal Article FUNGAL GENETICS AND BIOLOGY, 33 (3), pp. 155-171, 2001, ISSN: 1087-1845.

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3. Conesa, A; Weelink, G; van den Hondel, C; Punt, PC-terminal propeptide of the Caldariomyces fumago chloroperoxidase: an intramolecular chaperone? Journal Article FEBS LETTERS, 503 (2-3), pp. 117-120, 2001, ISSN: 0014-5793.

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

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2000

1. Conesa, A; van den Hondel, C; Punt, PStudies 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