Publications

2011

• Perez-Llamas C*, Gundem G* and Lopez-Bigas N. Integrative Cancer Genomics (IntOGen) in Biomart

  Database (201) Sep 7;2011:bar039.

• Pippa R, Espinosa L, Gundem G, García-Escudero R, Dominguez A, Orlando S, Gallastegui E, Saiz C, Besson A, Pujo, l MJ>, López-Bigas N, Paramio JM, Bigas A, Bachs O. p27(Kip1) represses transcription by direct interaction with p130/E2F4 at the promoters of target genes.

  Oncogene (2011) Dec 19. doi: 10.1038/onc.2011.582..

• Rafael-Palou X*, Schroeder MP* and Lopez-Bigas N. SVGMap: configurable image browser for experimental data

  Bioinformatics (2010) Oct 27. s.

• Truscott M, Islam A, Lopez-Bigas N and Frolov MV mir-11 limits the proapoptotic function of its host gene, dE2f1

  Genes and Development (2011) Sep 1;25(17):1820-34. Epub 2011 Aug 19.

• Islam A, Richter WF, Jacobs LA, Lopez-Bigas N and Benevolenskaya EV Coregulation of Histone-modifying Enzymes in Cancer

  PLoS One (2011). 6(8): e24023. doi:10.1371/journal.pone.0024023

• Christian Perez-Llamas and Lopez-Bigas N. Gitools: analysis and visualization of genomic data using interactive heat-maps

  PLoS One, 6(5): e19541 (2011) [ Visit Gitools Webpage ]

• Abel Gonzalez-Perez and Lopez-Bigas N. Improving the assessment of the outcome of non-synonymous SNVs with a Consensus deleteriousness score (Condel)

  Am J Hum Genet, doi:10.1016/j.ajhg.2011.03.004. (2011) [ Visit Condel Webpage ]

• Nicolay BN, Bayarmagnai B, Islam A, Lopez-Bigas N and Frolov MV. Cooperation between dE2F1 and Yki/Sd defines a distinct transcriptional program necessary to bypass cell cycle exit

  Genes & Development, 25(4):323-35. (2011)

• Islam A, Richter W, Lopez-Bigas N, Benevolenskaya, EV. Selective targeting of histone methylation

  Cell Cycle, 10(3):413-24. (2011)

• Guberman JM, Ai J, Arnaiz O, Baran J, Blake A, Baldock R, Chelala C, Croft D, Cros A, Cutts RJ, Di Génova A, Forbes S, Fujisawa T, Gadaleta E, Goodstein DM, Gundem G, Haggarty B, Haider S, Hall M, Harris T, Haw R, Hu S, Hubbard S, Hsu J, Iyer V, Jones P, Katayama T, Kinsella R, Kong L, Lawson D, Liang Y, Lopez-Bigas N, Luo J, Lush M, Mason J, Moreews F, Ndegwa N, Oakley D, Perez-Llamas C, Primig M, Rivkin E, Rosanoff S, Shepherd R, Simon R, Skarnes B, Smedley D, Sperling L, Spooner W, Stevenson P, Stone K, Teague J, Wang J, Wang J, Whitty B, Wong DT, Wong-Erasmus M, Yao L, Youens-Clark K, Yung C, Zhang J, Kasprzyk A. BioMart Central Portal: an open database network for the biological community.

  Database (Oxford). 2011 Sep 18;2011:bar041. Print 2011.

2010

• Richly H, Rocha-Viegas L, Ribeiro JD, Demajo S, Gundem G, Lopez-Bigas N, Nakagawa T, Rospert S, Ito T and Di Croce L. Transcriptional activation of polycomb-repressed genes by ZRF1

  Nature, 468, 1124-1128 (2010)

• International Cancer Genome Consortium (including Lopez-Bigas N). International network of cancer genome projects

  Nature, 464, 993-998 (2010)

• Gundem G, Perez-Llamas C, Jene-Sanz A, Kedzierska A, Islam A, Deu-Pons J, Furney S and Lopez-Bigas N. IntOGen: Integration and data-mining of multidimensional oncogenomic data

  Nature Methods, 7, 92-93 (2010) [ visit IntOGen ].

• Aguilar H, Sole X, Bonifaci N, Serra-Musach J, Islam A, Lopez-Bigas N, Méndez-Pertuz M, Beijersbergen RL, Lázaro C, Urruticoechea A, Pujana MA. Biological reprogramming in acquired resistance to endocrine therapy of breast cancer.

  Oncogene. 2010 Aug 16. [Epub ahead of print]

• Beshiri ML, Islam A, DeWaal DC, Richter WF, Love J, Lopez-Bigas N, Benevolenskaya EV. Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets

  JoVE doi: 10.3791/2101

• Isabel Ferreiro, Manel Joaquin, Abul Islam, Gonzalo Gomez, Montserrat Barragan, Luis Lombardia, Orlando Dominguez, David G. Pisano, Nuria Lopez-Bigas, Angel R. Nebreda and Francesc Posas. Whole genome analysis of p38 SAPK-mediated gene expression upon stress.

  BMC Genomics, 1;11(1):144 (2010)

2009

• Furney SJ, Gundem G, and Lopez-Bigas N. Oncogenomics

  Book Chapter in "Genetics of Complex Human Diseases: A Laboratory Manual" CSHL Press 2009.

• Mascarell-Creus A, Canizares J, Vilarrasa-Blassi J, Mora-Garcia S, Blanca J, Gonzalez-Ibeas D, Salalie M, Roig C, Deleu W, Pico-Silvent B, Lopez-Bigas N, Aranda MA, Garcia-Mas J, Nuez F, Puigdomenech P, Cano-Delgado AI. An oligo-based microarray offers novel transcriptomic approaches for the analysis of pathogen resistance and fruit quality traits in melon (Cucumis melo L.).

  BMC Genomics. 10(1):467 (2009).

• Rodilla V, Villanueva V, Obrador-Hevia A, Robert-Moreno A, Fernandez-Majada V, Grilli A, Lopez-Bigas N, Bellora N, Alba MM, Dunach M, Sanjuan X, Gonzalez S, Gridley T, Capella G, Bigas A and Espinosa Ll. Jagged1 is the pathological link between Notch and Wnt pathways in colorectal cancer

  PNAS, 106(15):6315-20 (2009).

• Sole X, Bonifaci N, Lopez-Bigas N, Berenguer A, Hernandez P, Reina O, Maxwell CA, Aguilar H, Urruticoechea A, de Sanjose S, Comellas F, Capella G, Moreno V, Pujana MA. Biological convergence of cancer signatures.

  PLoS ONE 4(2): e4544 (2009).

2008

• Lopez-Bigas N, Kisiel TA, DeWaal D, Holmes KB, Volkert TL, Gupta S, Love J, Murray HL, Young RA, and Benevolenskaya EV. Genome-wide Analysis of the H3K4 Histone Demethylase RBP2 Reveals a Transcriptional Program Controlling Differentiation

  Molecular Cell, 31(0):520-530 (2008).

• Furney SJ, Calvo B, Larranaga P, Lozano JA, Lopez-Bigas N. Prioritization of candidate cancer genes - an aid to oncogenomic studies

  Nucleic Acids Research, (2008).

• Lopez-Bigas N, De S, Teichmann SA. Functional divergence in the evolution of Homo sapiens

  Genome Biology, 9(2):33 (2008).

• Subhajyoti De, Nuria Lopez-Bigas and Sarah A Teichmann. Patterns of evolutionary constraints on genes in humans

  BMC Evolutionary Biology. 8:275, (2008).

• Furney SJ, Madden SF, Kisiel TA, Higgins DG, Lopez-Bigas N. Distinct patterns in the regulation and evolution of human cancer genes.

  In Silico Biol, 8(1):33-46 (2008).

• STAR Consortium (including Lopez-Bigas N, Shikhagaie M). SNP and haplotype mapping for genetic analysis in the rat.

  Nat Genet, 40(5):560-6 (2008).

2007

• The ENCODE Project Consortium (including Lopez-Bigas N). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

  Nature, 447(0):799-816 (2007).

• Calvo B, Lopez-Bigas N, Furney SJ, Larranaga P, Lozano JA. A partially supervised classification approach to dominant and recessive human disease gene prediction.

  Comput Methods Programs Biomed , 85(3):229-37 (2007).

• Marques-Bonet T , Sanchez-Ruiz J, Armengol L, Khaja R , Bertranpetit J, Rocchi M, Gazave E, Lopez-Bigas N, Navarro A. On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees.

  Genome Biology , 8(10) (2007).

2006

• Lopez-Bigas N, Blencowe BJ, Ouzounis CA. Highly consistent patterns for inherited human diseases at the molecular level.

  Bioinformatics, 22(3):269-77 (2006).

• Furney SJ, Higgins DG, Ouzounis CA, Lopez-Bigas N. Structural and functional properties of genes involved in human cancer.

  BMC Genomics, 7(0):3 (2006).

• Tiffin N, Adie E, Turner F, Brunner HG, van Driel MA, Oti M, Lopez-Bigas N, Ouzounis C, Perez-Iratxeta C, Andrade-Navarro MA, Adeyemo A, Patti ME, Semple CA, Hide W. Computational disease gene identification: a concert of methodsprioritizes type 2 diabetes and obesity candidate genes.

  Nucleic Acids Res, 34(10):3067-81 (2006).

• Furney SJ, Alba MM, Lopez-Bigas N. Differences in the evolutionary history of disease genes affected by dominant or recessive mutations.

  BMC Genomics, 7(0):165 (2006).

• Rabionet R, Morales-Peralta E, Lopez-Bigas N, Arbones ML and Estivill X. A novel G21R mutation of the GJB2 gene causes autosomal dominant non-syndromic congenital deafness in a Cuban family

  Genetics and Molecular Biology, 29(3):443-445 (2006).

2005

• Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, Ahren D, Tsoka S, Darzentas N, Kunin V, Lopez-Bigas N. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.

  Nucleic Acids Res, 33(19):6083-9 (2005).

• Goldovsky L, Janssen P, Ahren D, Audit B, Cases I, Darzentas N, Enright AJ, Lopez-Bigas N, Peregrin-Alvarez JM, Smith M, Tsoka S, Kunin V, Ouzounis CA. CoGenT++: an extensive and extensible data environment for computational genomics.

  Bioinformatics, 21(19):3806-10 (2005).

• Lopez-Bigas N, Audit B, Ouzounis C, Parra G, Guigo R. Are splicing mutations the most frequent cause of hereditary disease?

  FEBS Lett, 579(9):1900-3 (2005).

2004

• Lopez-Bigas N, Ouzounis CA. Genome-wide identification of genes likely to be involved in human genetic disease.

  Nucleic Acids Res, 32(10):3108-14 (2004).

2003

• Janssen P, Audit B, Cases I, Darzentas N, Goldovsky L, Kunin V, Lopez-Bigas N, Peregrin-Alvarez JM, Pereira-Leal JB, Tsoka S, Ouzounis CA. Beyond 100 genomes.

  Genome Biol, 4(5):402 (2003).

2002

• Rabionet R, Lopez-Bigas N, Arbones ML, Estivill X. Connexin mutations in hearing loss, dermatological and neurological disorders.

  Trends Mol Med, 8(5):205-12 (2002).

• Lopez-Bigas N, Melchionda S, de Cid R, Grifa A, Zelante L, Govea N, Arbones ML, Gasparini P, Estivill X. Erratum: Identification of five new mutations of PDS/SLC26A4 in Mediterranean families with hearing impairment.

  Hum Mutat, 20(1):77-8 (2002).

• Lopez-Bigas N, Melchionda S, Gasparini P, Borragan A, Arbones ML, Estivill X. A common frameshift mutation and other variants in GJB4 (connexin 30.3): Analysis of hearing impairment families.

  Hum Mutat, 19(4):458 (2002).

• Lopez-Bigas N, Arbones ML, Estivill X, Simonneau L. Expression profiles of the connexin genes, Gjb1 and Gjb3, in thedeveloping mouse cochlea.

  Gene Expr Patterns, 2(1):113-7 (2002).

2001

• Lopez-Bigas N, Olive M, Rabionet R, Ben-David O, Martinez-Matos JA, Bravo O, Banchs I, Volpini V, Gasparini P, Avraham KB, Ferrer I, Arbones ML, Estivill X. Connexin 31 (GJB3) is expressed in the peripheral and auditory nerves andcauses neuropathy and hearing impairment.

  Hum Mol Genet, 10(9):947-52 (2001).

• Lopez-Bigas N, Melchionda S, de Cid R, Grifa A, Zelante L, Govea N, Arbones ML, Gasparini P, Estivill X. Identification of five new mutations of PDS/SLC26A4 in Mediterraneanfamilies with hearing impairment.

  Hum Mutat, 18(6):548 (2001).

• Lopez-Bigas N, Rabionet R, Arbones ML, Estivill X. R32W variant in Connexin 31: mutation or polymorphism for deafness andskin disease?

  Eur J Hum Genet, 9(1):1 (2001).

2000

• Lopez-Bigas N, Rabionet R, Martinez E, Banchs I, Volpini V, Vance JM, Arbones ML, Estivill X. Identification of seven novel SNPS (five nucleotide and two amino acidsubstitutions) in the connexin31 (GJB3) gene.

  Hum Mutat, 15(5):481-2 (2000).

• Rabionet R, Zelante L, Lopez-Bigas N, DAgruma L, Melchionda S, Restagno G, Arbones ML, Gasparini P, Estivill X. Molecular basis of childhood deafness resulting from mutations in the GJB2 (connexin 26) gene.

  Hum Genet, 106(1):40-4 (2000).

• Lopez-Bigas N, Rabionet R, Martinez E, Bravo O, Girons J, Borragan A, Pellicer M, Arbones ML, Estivill X. Mutations in the mitochondrial tRNA Ser(UCN) and in the GJB2 (connexin 26) gene are not modifiers of the age at onset or severity of hearing loss in Spanish patients with the 12S rRNA A1555G mutation.

  Am J Hum Genet, 66(4):4 (2000).

1999

• Grifa A, Wagner CA, DAmbrosio L, Melchionda S, Bernardi F, Lopez-Bigas N, Rabionet R, Arbones M, Monica MD, Estivill X, Zelante L, Lang F, Gasparini P. Mutations in GJB6 cause nonsyndromic autosomal dominant deafness at DFNA3 locus.

  Nat Genet, 23(1):16-8 (1999).

• Lopez-Bigas N, Rabionet R, de Cid R, Govea N, Gasparini P, Zelante L, Arbones ML, Estivill X. Splice-site mutation in the PDS gene may result in intrafamilial variability for deafness in Pendred syndrome.

  Hum Mutat, 14(6):520-6 (1999).

• Torroni A, Cruciani F, Rengo C, Sellitto D, Lopez-Bigas N, Rabionet R, Govea N, Lopez De Munain A, Sarduy M, Romero L, Villamar M, del Castillo I, Moreno F, Estivill X, Scozzari R. The A1555G mutation in the 12S rRNA gene of human mtDNA: recurrent origins and founder events in families affected by sensorineural deafness.

  Am J Hum Genet, 65(5):1349-58 (1999).