BioInfo bibliography

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2010
Medina I, Carbonell J, Pulido L, et al. "Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling." Nucleic Acids Research. 2010;38:W210-W213. Featured in NAR. Abstract  Download: PDF (78.33 KB)
Nueda M J, Carbonell J, Medina I, Dopazo J, Conesa A. "Serial Expression Analysis: a web tool for the analysis of serial gene expression data." Nucleic acids research. 2010. Abstract
Capriotti E, Marti-Renom MA. "Quantifying the relationship between sequence and three-dimensional structure conservation in RNA." BMC bioinformatics. 2010;11(1):322. Abstract
Shi L, Campbell G, Jones WD, et al. "The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models." Nature biotechnology. 2010. Abstract  Download: PDF (1.12 MB)
Moreno-Manzano V, Rodríguez-Jiménez FJ, Aceña-Bonilla JL, et al. "FM19G11, a new hypoxia-inducible factor (HIF) modulator, affects stem cell differentiation status." J. Biol. Chem.. 2010;285(2):1333-42. Abstract  Download: PDF (2.18 MB)
Prado-Lopez S, Conesa A, Armiñán A, et al. "Hypoxia Promotes Efficient Differentiation of Human Embryonic Stem Cells to Functional Endothelium." Stem cells (Dayton, Ohio). 2010. Abstract  Download: PDF (1014.86 KB)
Huerta-Cepas J, Dopazo J, Gabaldon T. "ETE: a python Environment for Tree Exploration." BMC bioinformatics. 2010;11(1):24. Abstract  Download: PDF (423.89 KB)
Rattei T, Tischler P, Götz S, et al. "SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters." Nucleic Acids Res.. 2010;38(Database issue):D223-6. Abstract  Download: PDF (101.2 KB)
Peña A, Teeling H, Huerta-Cepas J, et al. "Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains." The ISME journal. 2010. Abstract  Download: PDF (990.54 KB)
Javierre BM, Fernandez AF, Richter J, et al. "Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus." Genome Res.. 2010;20(2):170-9. Abstract  Download: PDF (1.01 MB)
Minguez P, Dopazo J. "Functional genomics and networks: new approaches in the extraction of complex gene modules." Expert Rev Proteomics. 2010;7(1):55-63. Abstract  Download: PDF (315.28 KB)
Shi W, Bessarabova M, Dosymbekov D, et al. "Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes." Pharmacogenomics J.. 2010;10(4):310-23. Abstract  Download: PDF (1009.51 KB)
Dopazo J. "Functional profiling methods in cancer." In: Grützmann R, Pilarsky C, eds. Methods in molecular biology (Clifton, N.J.). Vol. 576.; 2010:. Methods Mol. Biol. 576. Abstract  Download: PDF (579.51 KB)
Németh A, Conesa A, Santoyo-Lopez J, et al. "Initial genomics of the human nucleolus." PLoS Genet.. 2010;6(3):e1000889. Abstract  Download: PDF (499.24 KB)
Montaner D, Dopazo J. "Multidimensional gene set analysis of genomic data." PLoS ONE. 2010;5(4):e10348. Abstract  Download: PDF (470.14 KB)
2009
Birmingham A, Selfors LM, Forster T, et al. "Statistical methods for analysis of high-throughput RNA interference screens." Nature Methods. 2009;6(8):569-575. Download: PDF (394.5 KB)
Madhusudhan MS, Webb BM, Marti-Renom MA, Eswar N, Sali A. "Alignment of multiple protein structures based on sequence and structure features." Protein Eng. Des. Sel.. 2009;22(9):569-74. Abstract
Aggarwal M, Sánchez-Beato M, Gómez-López G, et al. "Functional signatures identified in B-cell non-Hodgkin lymphoma profiles." Leuk. Lymphoma. 2009;50(10):1699-708. Abstract  Download: PDF (1.04 MB)
Jantus Lewintre E, Reinoso Martin C, Montaner D, et al. "Analysis of chronic lymphotic leukemia transcriptomic profile: differences between molecular subgroups." Leuk Lymphoma. 2009;50:68-79. Abstract  Download: PDF (2.27 MB)
Dopazo H. "Bioinformática, Genómica y Evolución. Una alianza estratégica para la biología de este siglo." Ciencia Hoy. 2009;19:88-93.
Evolución y Adaptación.150 años después del Origen de las Especies. Dopazo H, Navarro A, eds. Valencia. España: Obrapropia. ; 2009. Abstract
Nobre LS, Al-Shahrour F, Dopazo J, Saraiva LM. "Exploring the antimicrobial action of a carbon monoxide-releasing compound through whole-genome transcription profiling of Escherichia coli." Microbiology. 2009;155:813-24. Abstract  Download: PDF (401.81 KB)
Dopazo J. "Formulating and testing hypotheses in functional genomics." Artif Intell Med. 2009;45:97-107. Abstract  Download: PDF (319.6 KB)
Nueda M J, Sebastián P, Tarazona S, et al. "Functional assessment of time course microarray data." BMC Bioinformatics. 2009;10 Suppl 6:S9.
Montaner D, Minguez P, Al-Shahrour F, Dopazo J. "Gene set internal coherence in the context of functional profiling." BMC Genomics. 2009;10:197.