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• 2013
• Open Access A system-level , molecular evolutionary analysis of mammalian phototransduction. Brandon M. Invergo, Ludovica. Montanucci, Hafid. Laayouni, Jaume. Bertranpetit. (2013 ). Vol , Issue ,
• Contemporary paternal genetic landscape of Polish and German populations: from early medieval Slavic expansion to post-World War II resettlements. Krzysztof. Rębała, Begoña. Martínez-Cruz, Anke. Tönjes, Peter. Kovacs, Michael. Stumvoll, Iris. Lindner, Andreas. Büttner, H-Erich. Wichmann, Daniela. Siváková, Miroslav. Soták, Lluís. Quintana-Murci, Zofia. Szczerkowska, David. Comas. European journal of human genetics : EJHG (2013 Apr). Vol 21, Issue 4, 415-22 Link
• De Novo Assembly and Functional Annotation of the Olive (Olea europaea) Transcriptome. Antonio. Muñoz-Mérida, Juan José. González-Plaza, Andrés. Cañada, Ana María. Blanco, Maria Del Carmen. García-López, José Manuel. Rodríguez, Laia. Pedrola, M Dolores. Sicardo, M Luisa. Hernández, Raúl. De la Rosa, Angjelina. Belaj, Mayte. Gil-Borja, Francisco. Luque, José Manuel. Martínez-Rivas, David G. Pisano, Oswaldo. Trelles, Victoriano. Valpuesta, Carmen R. Beuzón, M. DelCarmenGarcía-López. DNA research : an international journal for rapid publication of reports on genes and genomes (2013 Jan). Vol 20, Issue 1, 93-108 Link
• Grape RNA-Seq analysis pipeline environment. David G. Knowles, Maik. Röder, Angelika. Merkel, Roderic. Guigó. Bioinformatics (Oxford, England) (2013 Mar). Vol 29, Issue 5, 614-21 Link
• Intron-centric estimation of alternative splicing from RNA-seq data. Dmitri D. Pervouchine, David G. Knowles, Roderic. Guigó. Bioinformatics (Oxford, England) (2013 Jan). Vol 29, Issue 2, 273-4 Link
• Accelerated exon evolution within primate segmental duplications. Belen. Lorente-Galdos, Jonathan. Bleyhl, Gabriel. Santpere, Laura. Vives, Oscar. Ramirez, Jessica. Hernandez, Roger. Anglada, Gregory M. Cooper, Arcadi. Navarro, Evan E. Eichler, Tomas. Marques-Bonet. Genome biology (2013 Jan). Vol 14, Issue 1, R9-R9 Link
• Identification of a functional variant in the KIF5A-CYP27B1-METTL1-FAM119B locus associated with multiple sclerosis. Antonio. Alcina, Maria. Fedetz, Oscar. Fernández, Albert. Saiz, Guillermo. Izquierdo, Miguel. Lucas, Laura. Leyva, Juan-Antonio. García-León, María Del Mar. Abad-Grau, Iraide. Alloza, Alfredo. Antigüedad, María J. Garcia-Barcina, Koen. Vandenbroeck, Jezabel. Varadé, Belén. de la Hera, Rafael. Arroyo, Manuel. Comabella, Xavier. Montalban, Natalia. Petit-Marty, Arcadi. Navarro, David. Otaegui, Javier. Olascoaga, Yolanda. Blanco, Elena. Urcelay, Fuencisla. Matesanz. Journal of medical genetics (2013 Jan). Vol 50, Issue 1, 25-33 Link
• MAPI: a software framework for distributed biomedical applications. Johan. Karlsson, Oswaldo. Trelles. Journal of biomedical semantics (2013 Jan). Vol 4, Issue 1, 4-4 Link
• The EU-ADR Web Platform: delivering advanced pharmacovigilance tools. José Luis. Oliveira, Pedro. Lopes, Tiago. Nunes, David. Campos, Scott. Boyer, Ernst. Ahlberg, Erik M. van Mulligen, Jan A. Kors, Bharat. Singh, Laura I. Furlong, Ferran. Sanz, Anna. Bauer-Mehren, Maria C. Carrascosa, Jordi. Mestres, Paul. Avillach, Gayo. Diallo, Carlos. Díaz Acedo, Johan. vanderLei. Pharmacoepidemiology and Drug Safety (2013 ). Vol 22, Issue 5, 459-467 Link
• 2012
• The protease MT1-MMP drives a combinatorial proteolytic program in activated endothelial cells. Agnieszka. Koziol, Pilar. Gonzalo, Alba. Mota, Ángela. Pollán, Cristina. Lorenzo, Nuria. Colomé, David. Montaner, Joaquín. Dopazo, Joaquín. Arribas, Francesc. Canals, AliciaG. Arroyo. FASEB journal : official publication of the Federation of American Societies for Experimental Biology (2012 Nov). Vol 26, Issue 11, 4481-94 Link
• Chimeras taking shape : Potential functions of proteins encoded by chimeric RNA transcripts. Milana. Frenkel-morgenstern, Vincent. Lacroix, Iakes. Ezkurdia, Yishai. Levin, Alexandra. Gabashvili, Jaime. Prilusky, Angela. Pozo, Michael. Tress, Rory. Johnson, Roderic. Guigo, Alfonso. Valencia, Claude. Bernard. (2012 ). Vol , Issue , 1231-1242
• Recombination gives a new insight in the effective population size and the history of the old world human populations. Marta. Melé, Asif. Javed, Marc. Pybus, Pierre. Zalloua, Marc. Haber, David. Comas, Mihai G. Netea, Oleg. Balanovsky, Elena. Balanovska, Li. Jin, Yajun. Yang, R M. Pitchappan, G. Arunkumar, Laxmi. Parida, Francesc. Calafell, Jaume. Bertranpetit. Molecular biology and evolution (2012 Jan). Vol 29, Issue 1, 25-30 Link
• Four new loci associations discovered by pathway-based and network analyses of the genome-wide variability profile of Hirschsprung's disease. Raquel Ma. Fernández, Marta. Bleda, Rocío. Núñez-Torres, Ignacio. Medina, Berta. Luzón-Toro, Luz. García-Alonso, Ana. Torroglosa, Martina. Marbà, Ma Valle. Enguix-Riego, David. Montaner, Guillermo. Antiñolo, Joaquín. Dopazo, Salud. Borrego. Orphanet journal of rare diseases (2012 Jan). Vol 7, Issue , 103-103 Link
• Evolutionary and functional evidence for positive selection at the human CD5 immune receptor gene. Elena. Carnero-Montoro, Lizette. Bonet, Johannes. Engelken, Torsten. Bielig, Mario. Martínez-Florensa, Francisco. Lozano, Elena. Bosch. Molecular biology and evolution (2012 Feb). Vol 29, Issue 2, 811-23 Link
• Genetic and genome-wide transcriptomic analyses identify co-regulation of oxidative response and hormone transcript abundance with vitamin C content in tomato fruit. Viviana. Lima-Silva, Abel. Rosado, Vitor. Amorim-Silva, Antonio. Muñoz-Mérida, Clara. Pons, Aureliano. Bombarely, Oswaldo. Trelles, Rafael. Fernández-Muñoz, Antonio. Granell, Victoriano. Valpuesta, MiguelÁngel. Botella. BMC genomics (2012 Jan). Vol 13, Issue , 187-187 Link
• Original article How to link ontologies and protein – protein interactions to literature : text-mining approaches and the BioCreative experience. Martin. Krallinger, Florian. Leitner, Miguel. Vazquez, David. Salgado, Christophe. Marcelle, Mike. Tyers, Alfonso. Valencia, Andrew. Chatr-aryamontri. (2012 ). Vol 2012, Issue , 1-12
• Chitinase 3-like 1 plasma levels are increased in patients with progressive forms of multiple sclerosis. E. Cantó, F. Reverter, C. Morcillo-Suárez, F. Matesanz, O. Fernández, G. Izquierdo, K. Vandenbroeck, A. Rodríguez-Antigüedad, E. Urcelay, R. Arroyo, D. Otaegui, J. Olascoaga, A. Saiz, A. Navarro, A. Sanchez, C. Domínguez, A. Caminero, A. Horga, M. Tintoré, X. Montalban, M. Comabella. Multiple Sclerosis Journal (2012 ). Vol 18, Issue 7, 983-990 Link
• Qualimap: evaluating next-generation sequencing alignment data. Fernando. García-Alcalde, Konstantin. Okonechnikov, José. Carbonell, Luis M. Cruz, Stefan. Götz, Sonia. Tarazona, Joaquín. Dopazo, Thomas F. Meyer, Ana. Conesa. Bioinformatics (Oxford, England) (2012 Oct). Vol 28, Issue 20, 2678-9 Link
• The tomato genome sequence provides insights into fleshy fruit evolution. The. Tomato, Genome. Consortium. Nature (2012 May). Vol 485, Issue 7400, 635-41 Link
• Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation. A. Gonzalez-Perez, J. Deu-Pons. Genome Medicine 2012 (2012 Nov). Vol 4, Issue 89, Pubmed.
• CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources. M. Bleda, J. Tarraga, A. de Maria, F. Salavert, L. Garcia-Alonso, M. Celma, A. Martin, J. Dopazo. Nucleic Acids Research (2012 Jun). Vol 40, Issue Web Server Issue, W609-W614 Pubmed.
• Inferring the regulatory network behind a gene expression experiment. Marta. Bleda, Ignacio. Medina, Roberto. Alonso, Alejandro. De Maria, Francisco. Salavert, Joaquin. Dopazo. Nucleic acids research (2012 Jul). Vol 40, Issue Web Server issue, W168-72 Link
• VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing. Ignacio. Medina, Alejandro. De Maria, Marta. Bleda, Francisco. Salavert, Roberto. Alonso, Cristina Y. Gonzalez, Joaquin. Dopazo. Nucleic acids research (2012 Jul). Vol 40, Issue Web Server issue, W54-8 Link
• Whole-genome bisulfite DNA sequencing of a DNMT3B mutant patient © 2012 Landes Bioscience . Enrique. Vidal, V. Jose, Ignacio. Medina, Maria R. Matarazzo, Joaquin. Dopazo. (2012 ). Vol 7, Issue 6, 542-550
• A map of human microRNA variation uncovers unexpectedly high levels of variability. José. Carbonell, Eva. Alloza, Pablo. Arce, Salud. Borrego, Javier. Santoyo, Macarena. Ruiz-Ferrer, Ignacio. Medina, Jorge. Jiménez-Almazán, Cristina. Méndez-Vidal, María. González-Del Pozo, Alicia. Vela, Shomi S. Bhattacharya, Guillermo. Antiñolo, Joaquín. Dopazo. Genome medicine (2012 Aug). Vol 4, Issue 8, 62-62 Link
• Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments. Luz. García-Alonso, Roberto. Alonso, Enrique. Vidal, Alicia. Amadoz, Alejandro. de María, Pablo. Minguez, Ignacio. Medina, Joaquín. Dopazo. Nucleic acids research (2012 Nov). Vol 40, Issue 20, e158-e158 Link
• Diversification of the expanded teleost-specific toll-like receptor family in Atlantic cod, Gadus morhua. Arvind Y M. Sundaram, Viswanath. Kiron, Joaquín. Dopazo, JorgeMO. Fernandes. BMC evolutionary biology (2012 Jan). Vol 12, Issue , 256-256 Link
• Cell-Dock: high-performance protein-protein docking. Carles. Pons, Daniel. Jiménez-González, Cecilia. González-Álvarez, Harald. Servat, Daniel. Cabrera-Benítez, Xavier. Aguilar, Juan. Fernández-Recio. Bioinformatics (Oxford, England) (2012 Sep). Vol 28, Issue 18, 2394-6 Link
• Human diseases through the lens of network biology. LauraI. Furlong. Trends in genetics : TIG (2012 Dec). Vol 29, Issue 3, 150-159 Link
• MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations. Adam. Hospital, Pau. Andrio, Carles. Fenollosa, Damjan. Cicin-Sain, Modesto. Orozco, JosepLluís. Gelpí. Bioinformatics (Oxford, England) (2012 May). Vol 28, Issue 9, 1278-9 Link
• Landscape of transcription in human cells. Sarah. Djebali, Carrie a. Davis, Angelika. Merkel, Alex. Dobin, Timo. Lassmann, Ali. Mortazavi, Andrea. Tanzer, Julien. Lagarde, Wei. Lin, Felix. Schlesinger, Chenghai. Xue, Georgi K. Marinov, Jainab. Khatun, Brian a. Williams, Chris. Zaleski, Joel. Rozowsky, Maik. Röder, Felix. Kokocinski, Rehab F. Abdelhamid, Tyler. Alioto, Igor. Antoshechkin, Michael T. Baer, Nadav S. Bar, Philippe. Batut, Kimberly. Bell, Ian. Bell, Sudipto. Chakrabortty, Xian. Chen, Jacqueline. Chrast, Joao. Curado, Thomas. Derrien, Jorg. Drenkow, Erica. Dumais, Jacqueline. Dumais, Radha. Duttagupta, Emilie. Falconnet, Meagan. Fastuca, Kata. Fejes-Toth, Pedro. Ferreira, Sylvain. Foissac, Melissa J. Fullwood, Hui. Gao, David. Gonzalez, Assaf. Gordon, Harsha. Gunawardena, Cedric. Howald, Sonali. Jha, Rory. Johnson, Philipp. Kapranov, Brandon. King, Colin. Kingswood, Oscar J. Luo, Eddie. Park, Kimberly. Persaud, Jonathan B. Preall, Paolo. Ribeca, Brian. Risk, Daniel. Robyr, Michael. Sammeth, Lorian. Schaffer, Lei-Hoon. See, Atif. Shahab, Jorgen. Skancke, Ana Maria. Suzuki, Hazuki. Takahashi, Hagen. Tilgner, Diane. Trout, Nathalie. Walters, Huaien. Wang, John. Wrobel, Yanbao. Yu, Xiaoan. Ruan, Yoshihide. Hayashizaki, Jennifer. Harrow, Mark. Gerstein, Tim. Hubbard, Alexandre. Reymond, Stylianos E. Antonarakis, Gregory. Hannon, Morgan C. Giddings, Yijun. Ruan, Barbara. Wold, Piero. Carninci, Roderic. Guigó, ThomasR. Gingeras. Nature (2012 Sep). Vol 489, Issue 7414, 101-8 Link
• H-bond network optimization in protein-protein complexes: are all-atom force field scores enough?. Diego. Masone, Israel Cabeza De. Vaca, Carles. Pons, Juan Fernandez. Recio, Victor. Guallar. Proteins (2012 Mar). Vol 80, Issue 3, 818-24 Link
• Evolutionary Genomics of Genes Involved in Olfactory Behavior in the Drosophila melanogaster Species Group. Nicolás. Lavagnino, François. Serra, Leonardo. Arbiza, Hernán. Dopazo, Esteban. Hasson. Evolutionary bioinformatics online (2012 Jan). Vol 8, Issue , 89-104 Link
• Getting personalized cancer genome analysis into the clinic: the challenges in bioinformatics. Alfonso. Valencia, Manuel. Hidalgo. Genome medicine (2012 Jul). Vol 4, Issue 7, 61-61 Link
• GENCODE: the reference human genome annotation for The ENCODE Project. Jennifer. Harrow, Adam. Frankish, Jose M. Gonzalez, Electra. Tapanari, Mark. Diekhans, Felix. Kokocinski, Bronwen L. Aken, Daniel. Barrell, Amonida. Zadissa, Stephen. Searle, If. Barnes, Alexandra. Bignell, Veronika. Boychenko, Toby. Hunt, Mike. Kay, Gaurab. Mukherjee, Jeena. Rajan, Gloria. Despacio-Reyes, Gary. Saunders, Charles. Steward, Rachel. Harte, Michael. Lin, Cédric. Howald, Andrea. Tanzer, Thomas. Derrien, Jacqueline. Chrast, Nathalie. Walters, Suganthi. Balasubramanian, Baikang. Pei, Michael. Tress, Jose Manuel. Rodriguez, Iakes. Ezkurdia, Jeltje. van Baren, Michael. Brent, David. Haussler, Manolis. Kellis, Alfonso. Valencia, Alexandre. Reymond, Mark. Gerstein, Roderic. Guigó, TimJ. Hubbard. Genome research (2012 Sep). Vol 22, Issue 9, 1760-74 Link
• Transcriptome profiling of the intoxication response of Tenebrio molitor larvae to Bacillus thuringiensis Cry3Aa protoxin. Brenda. Oppert, Scot E. Dowd, Pascal. Bouffard, Lewyn. Li, Ana. Conesa, Marcé D. Lorenzen, Michelle. Toutges, Jeremy. Marshall, Diana L. Huestis, Jeff. Fabrick, Cris. Oppert, JuanLuis. Jurat-Fuentes. PloS one (2012 Jan). Vol 7, Issue 4, e34624-e34624 Link
• Reconstructing the population history of European Romani from genome-wide data. Isabel. Mendizabal, Oscar. Lao, Urko M. Marigorta, Andreas. Wollstein, Leonor. Gusmão, Vladimir. Ferak, Mihai. Ioana, Albena. Jordanova, Radka. Kaneva, Anastasia. Kouvatsi, Vaidutis. Kučinskas, Halyna. Makukh, Andres. Metspalu, Mihai G. Netea, Rosario. de Pablo, Horolma. Pamjav, Dragica. Radojkovic, Sarah J H. Rolleston, Jadranka. Sertic, Milan. Macek, David. Comas, Manfred. Kayser. Current biology : CB (2012 Dec). Vol 22, Issue 24, 2342-9 Link
• Automatic Filtering and Substantiation of Drug Safety Signals. A. Bauer-Mehren, E.M. van Mullingen, P. Avillach, M.C. Carrascosa, R. Garcia-Serna, J. Piñero, B. Singh, P. Lopes, J.L. Oliveira, G. Diallo, E.A. Helgee, S. Boyer, J. Mestres, F. Sanz, J.A. Kors. PLoS Computational Biology (2012 Apr). Vol 8, Issue 4,
• Network-level and population genetics analysis of the insulin/TOR signal transduction pathway across human populations. Pierre. Luisi, David. Alvarez-Ponce, Giovanni Marco. Dall'Olio, Martin. Sikora, Jaume. Bertranpetit, Hafid. Laayouni. Molecular biology and evolution (2012 May). Vol 29, Issue 5, 1379-92 Link
• An integrated encyclopedia of DNA elements in the human genome. Ian. Dunham, Anshul. Kundaje, Shelley F.. Aldred, Patrick J.. Collins, Carrie a.. Davis, Francis. Doyle, Charles B.. Epstein, Seth. Frietze, Jennifer. Harrow, Rajinder. Kaul, Jainab. Khatun, Bryan R.. Lajoie, Stephen G.. Landt, Bum-Kyu. Lee, Florencia. Pauli, Kate R.. Rosenbloom, Peter. Sabo, Alexias. Safi, Amartya. Sanyal, Noam. Shoresh, Jeremy M.. Simon, Lingyun. Song, Nathan D.. Trinklein, Robert C.. Altshuler, Ewan. Birney, James B.. Brown, Chao. Cheng, Sarah. Djebali, Xianjun. Dong, Jason. Ernst, Terrence S.. Furey, Mark. Gerstein, Belinda. Giardine, Melissa. Greven, Ross C.. Hardison, Robert S.. Harris, Javier. Herrero, Michael M.. Hoffman, Sowmya. Iyer, Manolis. Kellis, Pouya. Kheradpour, Timo. Lassmann, Qunhua. Li, Xinying. Lin, Georgi K.. Marinov, Angelika. Merkel, Ali. Mortazavi, Stephen C. J.. Parker, Timothy E.. Reddy, Joel. Rozowsky, Felix. Schlesinger, Robert E.. Thurman, Jie. Wang, Lucas D.. Ward, Troy W.. Whitfield, Steven P.. Wilder, Weisheng. Wu, Hualin S.. Xi, Kevin Y.. Yip, Jiali. Zhuang, Bradley E.. Bernstein, Eric D.. Green, Chris. Gunter, Michael. Snyder, Michael J.. Pazin, Rebecca F.. Lowdon, Laura a. L.. Dillon, Leslie B.. Adams, Caroline J.. Kelly, Julia. Zhang, Judith R.. Wexler, Peter J.. Good, Elise a.. Feingold, Gregory E.. Crawford, Job. Dekker, Laura. Elnitski, Peggy J.. Farnham, Morgan C.. Giddings, Thomas R.. Gingeras, Roderic. Guigó, Timothy J.. Hubbard, W.. James Kent, Jason D.. Lieb, Elliott H.. Margulies, Richard M.. Myers, John a.. Stamatoyannopoulos, Scott a.. Tenenbaum, Zhiping. Weng, Kevin P.. White, Barbara. Wold, Yanbao. Yu, John. Wrobel, Brian a.. Risk, Harsha P.. Gunawardena, Heather C.. Kuiper, Christopher W.. Maier, Ling. Xie, Xian. Chen, Tarjei S.. Mikkelsen, Shawn. Gillespie, Alon. Goren, Oren. Ram, Xiaolan. Zhang, Li. Wang, Robbyn. Issner, Michael J.. Coyne, Timothy. Durham, Manching. Ku, Thanh. Truong, Matthew L.. Eaton, Alex. Dobin, Andrea. Tanzer, Julien. Lagarde, Wei. Lin, Chenghai. Xue, Brian a.. Williams, Chris. Zaleski, Maik. Röder, Felix. Kokocinski, Rehab F.. Abdelhamid, Tyler. Alioto, Igor. Antoshechkin, Michael T.. Baer, Philippe. Batut, Ian. Bell, Kimberly. Bell, Sudipto. Chakrabortty, Jacqueline. Chrast, Joao. Curado, Thomas. Derrien, Jorg. Drenkow, Erica. Dumais, Jackie. Dumais, Radha. Duttagupta, Megan. Fastuca, Kata. Fejes-Toth, Pedro. Ferreira, Sylvain. Foissac, Melissa J.. Fullwood, Hui. Gao, David. Gonzalez, Assaf. Gordon, Cédric. Howald, Sonali. Jha, Rory. Johnson, Philipp. Kapranov, Brandon. King, Colin. Kingswood, Guoliang. Li, Oscar J.. Luo, Eddie. Park, Jonathan B.. Preall, Kimberly. Presaud, Paolo. Ribeca, Daniel. Robyr, Xiaoan. Ruan, Michael. Sammeth, Kuljeet. Singh Sandhu, Lorain. Schaeffer, Lei-Hoon. See, Atif. Shahab, Jorgen. Skancke, Ana. Maria Suzuki, Hazuki. Takahashi, Hagen. Tilgner, Diane. Trout, Nathalie. Walters, Huaien. Wang, Yoshihide. Hayashizaki, Alexandre. Reymond, Stylianos E.. Antonarakis, Gregory J.. Hannon, Yijun. Ruan, Piero. Carninci, Cricket a.. Sloan, Katrina. Learned, Venkat S.. Malladi, Matthew C.. Wong, Galt P.. Barber, Melissa S.. Cline, Timothy R.. Dreszer, Steven G.. Heitner, Donna. Karolchik, Vanessa M.. Kirkup, Laurence R.. Meyer, Jeffrey C.. Long, Morgan. Maddren, Brian J.. Raney, Linda L.. Grasfeder, Paul G.. Giresi, Anna. Battenhouse, Nathan C.. Sheffield, Kimberly a.. Showers, Darin. London, Akshay a.. Bhinge, Christopher. Shestak, Matthew R.. Schaner, Seul. Ki Kim, Zhuzhu Z.. Zhang, Piotr a.. Mieczkowski, Joanna O.. Mieczkowska, Zheng. Liu, Ryan M.. McDaniell, Yunyun. Ni, Naim U.. Rashid, Min. Jae Kim, Sheera. Adar, Zhancheng. Zhang, Tianyuan. Wang, Deborah. Winter, Damian. Keefe, Vishwanath R.. Iyer, Meizhen. Zheng, Ping. Wang, Jason. Gertz, Jost. Vielmetter, E.. Christopher Partridge, Katherine E.. Varley, Clarke. Gasper, Anita. Bansal, Shirley. Pepke, Preti. Jain, Henry. Amrhein, Kevin M.. Bowling, Michael. Anaya, Marie K.. Cross, Michael a.. Muratet, Kimberly M.. Newberry, Kenneth. McCue, Amy S.. Nesmith, Katherine I.. Fisher-Aylor, Barbara. Pusey, Gilberto. DeSalvo, Stephanie L.. Parker, Sreeram. Balasubramanian, Nicholas S.. Davis, Sarah K.. Meadows, Tracy. Eggleston, J.. Scott Newberry, Shawn E.. Levy, Devin M.. Absher, Wing H.. Wong, Matthew J.. Blow, Axel. Visel, Len a.. Pennachio, Hanna M.. Petrykowska, Alexej. Abyzov, Bronwen. Aken, Daniel. Barrell, Gemma. Barson, Andrew. Berry, Alexandra. Bignell, Veronika. Boychenko, Giovanni. Bussotti, Claire. Davidson, Gloria. Despacio-Reyes, Mark. Diekhans, Iakes. Ezkurdia, Adam. Frankish, James. Gilbert, Jose. Manuel Gonzalez, Ed. Griffiths, Rachel. Harte, David a.. Hendrix, Toby. Hunt, Irwin. Jungreis, Mike. Kay, Ekta. Khurana, Jing. Leng, Michael F.. Lin, Jane. Loveland, Zhi. Lu, Deepa. Manthravadi, Marco. Mariotti, Jonathan. Mudge, Gaurab. Mukherjee, Cedric. Notredame, Baikang. Pei, Jose. Manuel Rodriguez, Gary. Saunders, Andrea. Sboner, Stephen. Searle, Cristina. Sisu, Catherine. Snow, Charlie. Steward, Electra. Tapanari, Michael L.. Tress, Marijke J.. van Baren, Stefan. Washietl, Laurens. Wilming, Amonida. Zadissa, Zhengdong. Zhang, Michael. Brent, David. Haussler, Alfonso. Valencia, Nick. Addleman, Roger P.. Alexander, Raymond K.. Auerbach, Suganthi. Balasubramanian, Keith. Bettinger, Nitin. Bhardwaj, Alan P.. Boyle, Alina R.. Cao, Philip. Cayting, Alexandra. Charos, Yong. Cheng, Catharine. Eastman, Ghia. Euskirchen, Joseph D.. Fleming, Fabian. Grubert, Lukas. Habegger, Manoj. Hariharan, Arif. Harmanci, Sushma. Iyengar, Victor X.. Jin, Konrad J.. Karczewski, Maya. Kasowski, Phil. Lacroute, Hugo. Lam, Nathan. Lamarre-Vincent, Jin. Lian, Marianne. Lindahl-Allen, Renqiang. Min, Benoit. Miotto, Hannah. Monahan, Zarmik. Moqtaderi, Xinmeng J.. Mu, Henriette. O’Geen, Zhengqing. Ouyang, Dorrelyn. Patacsil, Debasish. Raha, Lucia. Ramirez, Brian. Reed, Minyi. Shi, Teri. Slifer, Heather. Witt, Linfeng. Wu, Xiaoqin. Xu, Koon-Kiu. Yan, Xinqiong. Yang, Kevin. Struhl, Sherman M.. Weissman, Luiz O.. Penalva, Subhradip. Karmakar, Raj R.. Bhanvadia, Alina. Choudhury, Marc. Domanus, Lijia. Ma, Jennifer. Moran, Alec. Victorsen, Thomas. Auer, Lazaro. Centanin, Michael. Eichenlaub, Franziska. Gruhl, Stephan. Heermann, Burkhard. Hoeckendorf, Daigo. Inoue, Tanja. Kellner, Stephan. Kirchmaier, Claudia. Mueller, Robert. Reinhardt, Lea. Schertel, Stephanie. Schneider, Rebecca. Sinn, Beate. Wittbrodt, Jochen. Wittbrodt, Gaurav. Jain, Gayathri. Balasundaram, Daniel L.. Bates, Rachel. Byron, Theresa K.. Canfield, Morgan J.. Diegel, Douglas. Dunn, Abigail K.. Ebersol, Tristan. Frum, Kavita. Garg, Erica. Gist, R.. Scott Hansen, Lisa. Boatman, Eric. Haugen, Richard. Humbert, Audra K.. Johnson, Ericka M.. Johnson, Tattyana V.. Kutyavin, Kristen. Lee, Dimitra. Lotakis, Matthew T.. Maurano, Shane J.. Neph, Fiedencio V.. Neri, Eric D.. Nguyen, Hongzhu. Qu, Alex P.. Reynolds, Vaughn. Roach, Eric. Rynes, Minerva E.. Sanchez, Richard S.. Sandstrom, Anthony O.. Shafer, Andrew B.. Stergachis, Sean. Thomas, Benjamin. Vernot, Jeff. Vierstra, Shinny. Vong, Hao. Wang, Molly a.. Weaver, Yongqi. Yan, Miaohua. Zhang, Joshua M.. Akey, Michael. Bender, Michael O.. Dorschner, Mark. Groudine, Michael J.. MacCoss, Patrick. Navas, George. Stamatoyannopoulos, Kathryn. Beal, Alvis. Brazma, Paul. Flicek, Nathan. Johnson, Margus. Lukk, Nicholas M.. Luscombe, Daniel. Sobral, Juan M.. Vaquerizas, Serafim. Batzoglou, Arend. Sidow, Nadine. Hussami, Sofia. Kyriazopoulou-Panagiotopoulou, Max W.. Libbrecht, Marc a.. Schaub, Webb. Miller, Peter J.. Bickel, Balazs. Banfai, Nathan P.. Boley, Haiyan. Huang, Jingyi. Jessica Li, William. Stafford Noble, Jeffrey a.. Bilmes, Orion J.. Buske, Avinash D.. Sahu, Peter V.. Kharchenko, Peter J.. Park, Dannon. Baker, James. Taylor, Lucas. Lochovsky. Nature (2012 Sep). Vol 489, Issue 7414, 57-74 Link
• Sample-level enrichment analysis unravels shared stress phenotypes among multiple cancer types. G. Gundem, N. Lopez-Bigas. Genome Medicine (2012 Mar). Vol 4, Issue 3, Pubmed.
• Functional impact bias reveals cancer drivers. Abel. Gonzalez-Perez, Nuria. Lopez-Bigas. Nucleic acids research (2012 Nov). Vol 40, Issue 21, e169-e169 Link
• Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation. Abel. Gonzalez-Perez, Jordi. Deu-Pons, Nuria. Lopez-Bigas. Genome medicine (2012 Nov). Vol 4, Issue 11, 89-89 Link
• Oncogenomics methods and resources. Simon J. Furney, Gunes. Gundem, Nuria. Lopez-Bigas. Cold Spring Harbor protocols (2012 May). Vol 2012, Issue 5, Link
• Sample-level enrichment analysis unravels shared stress phenotypes among multiple cancer types. Gunes. Gundem, Nuria. Lopez-Bigas. Genome medicine (2012 Jan). Vol 4, Issue 3, 28-28 Link
• SVGMap: configurable image browser for experimental data. Xavier. Rafael-Palou, Michael P. Schroeder, Nuria. Lopez-Bigas. Bioinformatics (Oxford, England) (2012 Jan). Vol 28, Issue 1, 119-20 Link
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• Functional targets of the monogenic diabetes transcription factors HNF-1alpha and HNF-4alpha are highly conserved between mice and humans. S. Boj, J. Servitja, D. Martin, M. Rios, I. Talianidis, R. Guigo, J. Ferrer. Diabetes (2009 May). Vol 58, Issue 5, 1245-1253 Pubmed. Link
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• 2006
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• U12DB: a database of orthologous U12-type spliceosomal introns. TS. Alioto. Nucleic acids research (2006 Nov). Vol 35, Issue Database issue, Pubmed.
• Phylogeography of the human mitochondrial L1c haplogroup: genetic signatures of the prehistory of Central Africa. C. Batini, V. Coia, C. Battaggia, J. Rocha, MM. Pilkington, G. Spedini, D. Comas, G. Destro-Bisol, F. Calafell. Molecular phylogenetics and evolution (2006 Oct). Vol 43, Issue 2, Pubmed.
• Prophet, a web-based tool for class prediction using microarray data. I. Medina, D. Montaner, J. Tárraga, J. Dopazo. Bioinformatics (Oxford, England) (2006 Nov). Vol 23, Issue 3, Pubmed.
• Ligand-induced dynamical regulation of NO conversion in Mycobacterium tuberculosis truncated hemoglobin-N. A. Bidon-Chanal, MA. Martí, A. Crespo, M. Milani, M. Orozco, M. Bolognesi, FJ. Luque, DA. Estrin. Proteins (2006 May). Vol 64, Issue 2, Pubmed.
• The human phylome. J. Huerta-Cepas, H. Dopazo, J. Dopazo, T. Gabaldon. Genome biology (2006 Nov). Vol 8, Issue 6, Pubmed.
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• Essential Dynamics: A Tool for Efficient Trajectory Compression and Management. T. Meyer, C. Ferrer-Costa, A. Pérez, M. Rueda, A. Bidon-Chanal, F.J. Luque, C.A. Laughton. Journal of Chemical Theory and Computation (2006 Feb). Vol 2, Issue 2, 251-258 Link
• On the origin of the stereoselectivity in the alkylation of oxazolopiperidone enolates. I. Soteras, O. Lozano, A. Gómez-Esqué, C. Escolano, M. Orozco, M. Amat, J. Bosch, FJ. Luque. Journal of the American Chemical Society (2006 May). Vol 128, Issue 20, Pubmed.
• A hydrophobic similarity analysis of solvation effects on nucleic acid bases. J. Muñoz-Muriedas, X. Barril, JM. López, M. Orozco, FJ. Luque. Journal of molecular modeling (2006 Sep). Vol 13, Issue 2, Pubmed.
• Local aromaticity in natural nucleobases and their size-expanded benzo-fused derivatives. O. Huertas, J. Poater, M. Fuentes-Cabrera, M. Orozco, M. Solà, FJ. Luque. The journal of physical chemistry. A (2006 Nov). Vol 110, Issue 44, Pubmed.
• Structural and functional properties of genes involved in human cancer. SJ. Furney, DG. Higgins, CA. Ouzounis, N. López-Bigas. BMC genomics (2006 Jan). Vol 7, Issue , Pubmed.
• Structural and functional properties of genes involved in human cancer. SJ. Furney, DG. Higgins, CA. Ouzounis, N. López-Bigas. BMC genomics (2006 Jan). Vol 7, Issue , Pubmed.
• Treatment effects of combined radio-frequency current and a 900 nm diode laser on leg blood vessels. MA. Trelles, M. Martín-Vázquez, OR. Trelles, SR. Mordon. Lasers in surgery and medicine (2006 Feb). Vol 38, Issue 3, Pubmed.
• Patterns and rates of intron divergence between humans and chimpanzees. E. Gazave, T. Marqués-Bonet, O. Fernando, B. Charlesworth, A. Navarro. Genome biology (2006 Aug). Vol 8, Issue 2, Pubmed.
• On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees. T. Marques-Bonet, J. Sànchez-Ruiz, L. Armengol, R. Khaja, J. Bertranpetit, N. Lopez-Bigas, M. Rocchi, E. Gazave, A. Navarro. Genome biology (2006 Aug). Vol 8, Issue 10, Pubmed.
• Microarray-based analysis of spinal versus intracranial meningiomas: different clinical, biological, and genetic characteristics associated with distinct patterns of gene expression. JM. Sayagués, MD. Tabernero, A. Maíllo, O. Trelles, AB. Espinosa, ME. Sarasquete, M. Merino, A. Rasillo, JF. Vera, A. Santos-Briz, E. de Alava, MC. Garcia-Macias, A. Orfao. Journal of neuropathology and experimental neurology (2006 Jun). Vol 65, Issue 5, Pubmed.
• A fast method for the determination of fractional contributions to solvation in proteins. D. Talavera, A. Morreale, T. Meyer, A. Hospital, C. Ferrer-Costa, JL. Gelpi, X. de la Cruz, R. Soliva, FJ. Luque, M. Orozco. Protein science : a publication of the Protein Society (2006 Sep). Vol 15, Issue 11, Pubmed.
• A fast method for the determination of fractional contributions to solvation in proteins. D. Talavera, A. Morreale, T. Meyer, A. Hospital, C. Ferrer-Costa, JL. Gelpi, X. de la Cruz, R. Soliva, FJ. Luque, M. Orozco. Protein science : a publication of the Protein Society (2006 Sep). Vol 15, Issue 11, Pubmed.
• Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions. JR. Goñi, JM. Vaquerizas, J. Dopazo, M. Orozco. BMC genomics (2006 Mar). Vol 7, Issue , Pubmed.
• Exploring the dynamics of calix[4]pyrrole: effect of solvent and fluorine substitution. JR. Blas, JM. López-Bes, M. Márquez, JL. Sessler, FJ. Luque, M. Orozco. Chemistry (Weinheim an der Bergstrasse, Germany) (2006 Nov). Vol 13, Issue 4, Pubmed.
• Integrated analysis of gene expression by Association Rules Discovery. P. Carmona-Saez, M. Chagoyen, A. Rodriguez, O. Trelles, JM. Carazo, A. Pascual-Montano. BMC bioinformatics (2006 Feb). Vol 7, Issue , Pubmed.
• PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease. A. Schlüter, S. Fourcade, E. Domènech-Estévez, T. Gabaldón, J. Huerta-Cepas, G. Berthommier, R. Ripp, RJ. Wanders, O. Poch, A. Pujol. Nucleic acids research (2006 Nov). Vol 35, Issue Database issue, Pubmed.
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• Dispersion and repulsion contributions to the solvation free energy: comparison of quantum mechanical and classical approaches in the polarizable continuum model. C. Curutchet, M. Orozco, FJ. Luque, B. Mennucci, J. Tomasi. Journal of computational chemistry (2006 Aug). Vol 27, Issue 15, Pubmed.
• A new user-friendly software platform for systematic classification of skin lesions to aid in their diagnosis and prognosis. MJ. Martín-Vázquez, MA. Trelles, A. Sola, RG. Calderhead, O. Trelles. Lasers in medical science (2006 Mar). Vol 21, Issue 1, Pubmed.
• Bio-Broker: a tool for integration of biological data sources and data analysis tools. J.F. Aldana, MINavas. Roldán-Castro, M.M.. Roldán-Garcí­a, M. Hidalgo-Conde, O. Trelles. Software, Practice and Experience (2006 ). Vol 36, Issue 14, 1585-1604 Link
• FireDB--a database of functionally important residues from proteins of known structure. G. Lopez, A. Valencia, M. Tress. Nucleic acids research (2006 Nov). Vol 35, Issue Database issue, Pubmed.
• An analysis of the Sargasso Sea resource and the consequences for database composition. ML. Tress, D. Cozzetto, A. Tramontano, A. Valencia. BMC bioinformatics (2006 Apr). Vol 7, Issue , Pubmed.
• BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. F. Al-Shahrour, P. Minguez, J. Tárraga, D. Montaner, E. Alloza, JM. Vaquerizas, L. Conde, C. Blaschke, J. Vera. Nucleic Acids Research (2006 Jul). Vol 34, Issue Web server issue, W472-W476 Pubmed.
• Aromaticity-induced changes in electronic properties of size-expanded DNA bases: Case of xC. M. Fuentes-Cabrera, P. Lipkowski, O. Huertas, B.G.. Sumpter, M. Orozco, F.J. Luque, J.C. Wells. International Journal of Quantum Chemistry (2006 ). Vol 106, Issue 11, 2339-2346 Link
• Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. JM. Aury, O. Jaillon, L. Duret, B. Noel, C. Jubin, BM. Porcel, B. Ségurens, V. Daubin, V. Anthouard, N. Aiach, O. Arnaiz, A. Billaut, J. Beisson, I. Blanc, K. Bouhouche, F. Câmara, S. Duharcourt, R. Guigo, D. Gogendeau, M. Katinka, AM. Keller, R. Kissmehl, C. Klotz, F. Koll, A. Le Mouël, G. Lepère, S. Malinsky, M. Nowacki, JK. Nowak, H. Plattner, J. Poulain, F. Ruiz, V. Serrano, M. Zagulski, P. Dessen, M. Bétermier, J. Weissenbach, C. Scarpelli, V. Schächter, L. Sperling, E. Meyer, J. Cohen, P. Wincker. Nature (2006 Nov). Vol 444, Issue 7116, Pubmed.
• Characterization of compensated mutations in terms of structural and physico-chemical properties. C. Ferrer-Costa, M. Orozco, X. delaCruz. Journal of molecular biology (2006 Sep). Vol 365, Issue 1, Pubmed.
• The (in)dependence of alternative splicing and gene duplication. D. Talavera, C. Vogel, M. Orozco, SA. Teichmann, X. delaCruz. PLoS computational biology (2006 Jun). Vol 3, Issue 3, Pubmed.
• 2005
• Gene finding in the chicken genome. E. Eyras, A. Reymond, R. Castelo, JM. Bye, F. Camara, P. Flicek, EJ. Huckle, G. Parra, DD. Shteynberg, C. Wyss, J. Rogers, SE. Antonarakis, E. Birney, R. Guigo, MR. Brent. BMC bioinformatics (2005 May). Vol 6, Issue , Pubmed.
• BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments. F. Al-Shahrour, P. Minguez, JM. Vaquerizas, L. Conde. Nucleic Acids Research (2005 Jul). Vol 33, Issue Web Server Issue, W460-W464 Pubmed.
• Domain definition and target classification for CASP6. M. Tress, CH. Tai, G. Wang, I. Ezkurdia, G. López, A. Valencia, B. Lee, RL. Dunbrack. Proteins (2005 Sep). Vol 61 Suppl 7, Issue , Pubmed.
• ABS: a database of Annotated regulatory Binding Sites from orthologous promoters. E. Blanco, D. Farré, MM. Albà, X. Messeguer, R. Guigó. Nucleic acids research (2005 Dec). Vol 34, Issue Database issue, Pubmed.
• Data mining of molecular dynamics trajectories of nucleic acids. A. Noy, T. Meyer, M. Rueda, C. Ferrer, A. Valencia, A. Pérez, X. de la Cruz, JM. López-Bes, R. Pouplana, J. Fernandez-Recio, FJ. Luque, M. Orozco. Journal of biomolecular structure & dynamics (2005 Dec). Vol 23, Issue 4, Pubmed.
• Intelligent client for integrating bioinformatics services. I. Navas-Delgado, Mdel M. Rojano-Muñoz, S. Ramírez, AJ. Pérez, E. Andrés León, JF. Aldana-Montes, O. Trelles. Bioinformatics (Oxford, England) (2005 Oct). Vol 22, Issue 1, Pubmed.
• CASP6 assessment of contact prediction. O. Graña, D. Baker, RM. MacCallum, J. Meiler, M. Punta, B. Rost, ML. Tress, A. Valencia. Proteins (2005 Sep). Vol 61 Suppl 7, Issue , Pubmed.
• Assessment of predictions submitted for the CASP6 comparative modeling category. M. Tress, I. Ezkurdia, O. Graña, G. López, A. Valencia. Proteins (2005 Sep). Vol 61 Suppl 7, Issue , Pubmed.
• Scoring docking models with evolutionary information. M. Tress, D. de Juan, O. Graña, MJ. Gómez, P. Gómez-Puertas, JM. González, G. López, A. Valencia. Proteins (2005 Jun). Vol 60, Issue 2, Pubmed.
• 2004
• Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. . International Chicken Genome Sequencing Consortium, EE. Eichler. Nature (2004 Jul). Vol 432, Issue 7018, Pubmed.
• SQUARE--determining reliable regions in sequence alignments. ML. Tress, O. Graña. Bioinformatics (2004 Apr). Vol 20, Issue , 974-975 Pubmed.
• The 800-nm diode laser in the treatment of leg veins: assessment at 6 months. MA. Trelles, I. Allones, J. Alvarez, M. Vélez, M. Martín-Vázquez, OR. Trelles, R. Luna, C. Buil, SR. Mordon. Journal of the American Academy of Dermatology (2004 Aug). Vol 54, Issue 2, Pubmed.
• Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. O. Jaillon, JM. Aury, F. Brunet, JL. Petit, N. Stange-Thomann, E. Mauceli, L. Bouneau, C. Fischer, C. Ozouf-Costaz, A. Bernot, S. Nicaud, D. Jaffe, S. Fisher, G. Lutfalla, C. Dossat, B. Segurens, C. Dasilva, M. Salanoubat, M. Levy, N. Boudet, S. Castellano, V. Anthouard, C. Jubin, V. Castelli, M. Katinka, B. Vacherie, C. Biémont, Z. Skalli, L. Cattolico, J. Poulain, V. De Berardinis, C. Cruaud, S. Duprat, P. Brottier, JP. Coutanceau, J. Gouzy, G. Parra, G. Lardier, C. Chapple, KJ. McKernan, P. McEwan, S. Bosak, M. Kellis, JN. Volff, R. Guigó, MC. Zody, J. Mesirov, K. Lindblad-Toh, B. Birren, C. Nusbaum, D. Kahn, M. Robinson-Rechavi, V. Laudet, V. Schachter, F. Quétier, W. Saurin, C. Scarpelli, P. Wincker, ES. Lander, J. Weissenbach, H. RoestCrollius. Nature (2004 Jul). Vol 431, Issue 7011, Pubmed.
• Empirical limits for template-based protein structure prediction: the CASP5 example. B. Contreras-Moreira, I. Ezkurdia, ML. Tress, A. Valencia. FEBS letters (2004 Nov). Vol 579, Issue 5, Pubmed.
• 2003
• Predicting reliable regions in protein alignments from sequence profiles. ML. Tress, D. Jones, A. Valencia. Journal of molecular biology (2003 Jul). Vol 330, Issue 4, Pubmed.