Wyeth W. Wasserman, PhD
 | Professor Department of Medical Genetics, University of British Columbia Senior Scientist, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute Tel: +1 (604) 875-3812 Fax: +1 (604) 875-3819 Email:  |
Selected Publications:
Fulton DL, Sundararajan S, Badis G, Hughes TR, Wasserman WW, Roach JC, Sladek R. TFCat: the curated catalog of mouse and human transcription factors. Genome Biol. 10(3):R29. (2009) PMID 19284633
Portales-Casamar E, Arenillas D, Lim J, Swanson MI, Jiang S, McCallum A, Kirov S, Wasserman WW. The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences. Nucleic Acids Res. 37(Database issue):D54-60. (2009) PMID 18971253
Saumet A, Vetter G, Bouttier M, Portales-Casamar E, Wasserman WW, Maurin T, Mari B, Barbry P, Vallar L, Friederich E, Arar K, Cassinat B, Chomienne C, Lecellier CH. Transcriptional repression of microRNA genes by PML-RARA increases expression of key cancer proteins in acute promyelocytic leukemia. Blood 113(2):412-21. (2009) PMID 18941112
Brumm J, Conibear E, Wasserman WW, Bryan J. Discovery and expansion of gene modules by seeking isolated groups in a random graph process. PLoS ONE 3(10):e3358. (2008) PMID 18843375
D'Souza CA, Chopra V, Varhol R, Xie YY, Bohacec S, Zhao Y, Lee LL, Bilenky M, Portales-Casamar E, He A, Wasserman WW, Goldowitz D, Marra MA, Holt RA, Simpson EM, Jones SJ. Identification of a set of genes showing regionally enriched expression in the mouse brain. BMC Neuroscience 9:66. (2008) PMID 18625066
Astanehe A, Arenillas D, Wasserman WW, Leung PC, Dunn SE, Davies BR, Mills GB, Auersperg N. Mechanisms underlying p53 regulation of PIK3CA transcription in ovarian surface epithelium and in ovarian cancer. J. Cell. Sci. 121(Pt 5):664-74. (2008) PMID 18270270
Marks VD, Ho Sui SJ, Erasmus D, van der Merwe GK, Brumm J, Wasserman WW, Bryan J, van Vuuren HJ. Dynamics of the yeast transcriptome during wine fermentation reveals a novel fermentation stress response. FEMS Yeast Res. 8(1):35-52. (2008) PMID 18215224
Kemmer D, Podowski RM, Yusuf D, Brumm J, Cheung W, Wahlestedt C, Lenhard B, Wasserman WW. Gene characterization index: assessing the depth of gene annotation. PLoS ONE 3(1):e1440. (2008) PMID 18213364
Andersen MC, Engström PG, Lithwick S, Arenillas D, Eriksson P, Lenhard B, Wasserman WW, Odeberg J. In silico detection of sequence variations modifying transcriptional regulation. PLoS Comput. Biol. 4(1):e5. (2008) PMID 18208319
Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M, Griffith M, Gallo SM, Giardine B, Hooghe B, Van Loo P, Blanco E, Ticoll A, Lithwick S, Portales-Casamar E, Donaldson IJ, Robertson G, Wadelius C, De Bleser P, Vlieghe D, Halfon MS, Wasserman W, Hardison R, Bergman CM, Jones SJ, . ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res. 36(Database issue):D107-13. (2008) PMID 18006570
Portales-Casamar E, Kirov S, Lim J, Lithwick S, Swanson MI, Ticoll A, Snoddy J, Wasserman WW. PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation. Genome Biol. 8(10):R207. (2007) PMID 17916232
Ho Sui SJ, Fulton DL, Arenillas DJ, Kwon AT, Wasserman WW. oPOSSUM: integrated tools for analysis of regulatory motif over-representation. Nucleic Acids Res. 35(Web Server issue):W245-52. (2007) PMID 17576675
Kuo BY, Chen Y, Bohacec S, Johansson O, Wasserman WW, Simpson EM. SAGE2Splice: unmapped SAGE tags reveal novel splice junctions. PLoS Comput. Biol. 2(4):e34. (2006) PMID 16683015
Kemmer D, Podowski RM, Arenillas D, Lim J, Hodges E, Roth P, Sonnhammer EL, Höög C, Wasserman WW. NovelFam3000--uncharacterized human protein domains conserved across model organisms. BMC Genomics 7:48. (2006) PMID 16533400
Vlieghe D, Sandelin A, De Bleser PJ, Vleminckx K, Wasserman WW, van Roy F, Lenhard B. A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. Nucleic Acids Res. 34(Database issue):D95-7. (2006) PMID 16381983
Yusuf D, Lim JS, Wasserman WW. The Gene Set Builder: collation, curation, and distribution of sets of genes. BMC Bioinformatics 6:305. (2005) PMID 16371163
Kemmer D, Huang Y, Shah SP, Lim J, Brumm J, Yuen MM, Ling J, Xu T, Wasserman WW, Ouellette BF. Ulysses - an application for the projection of molecular interactions across species. Genome Biol. 6(12):R106. (2005) PMID 16356269
Ho Sui SJ, Mortimer JR, Arenillas DJ, Brumm J, Walsh CJ, Kennedy BP, Wasserman WW. oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes. Nucleic Acids Res. 33(10):3154-64. (2005) PMID 15933209
Coutinho JM, Singaraja RR, Kang M, Arenillas DJ, Bertram LN, Bissada N, Staels B, Fruchart JC, Fievet C, Joseph-George AM, Wasserman WW, Hayden MR. Complete functional rescue of the ABCA1-/- mouse by human BAC transgenesis. J. Lipid Res. 46(6):1113-23. (2005) PMID 15772424
Mottagui-Tabar S, Faghihi MA, Mizuno Y, Engström PG, Lenhard B, Wasserman WW, Wahlestedt C. Identification of functional SNPs in the 5-prime flanking sequences of human genes. BMC Genomics 6(1):18. (2005) PMID 15717931
Sandelin A, Wasserman WW. Prediction of nuclear hormone receptor response elements. Mol. Endocrinol. 19(3):595-606. (2005) PMID 15563547
Kemmer D, Faxén M, Hodges E, Lim J, Herzog E, Ljungström E, Lundmark A, Olsen MK, Podowski R, Sonnhammer EL, Nilsson P, Reimers M, Lenhard B, Roberds SL, Wahlestedt C, Höög C, Agarwal P, Wasserman WW. Exploring the Foundation of Genomics: A Northern Blot Reference set for the Comparative Analysis of Transcript Profiling Technologies. Comp. Funct. Genomics 5(8):584-95. (2004) PMID 18629180
Sandelin A, Bailey P, Bruce S, Engström PG, Klos JM, Wasserman WW, Ericson J, Lenhard B. Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. BMC Genomics 5(1):99. (2004) PMID 15613238
Thompson W, Palumbo MJ, Wasserman WW, Liu JS, Lawrence CE. Decoding human regulatory circuits. Genome Res. 14(10A):1967-74. (2004) PMID 15466295
Alkema WB, Lenhard B, Wasserman WW. Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus. Genome Res. 14(7):1362-73. (2004) PMID 15231752
Sandelin A, Wasserman WW, Lenhard B. ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Res. 32(Web Server issue):W249-52. (2004) PMID 15215389
Alkema WB, Johansson O, Lagergren J, Wasserman WW. MSCAN: identification of functional clusters of transcription factor binding sites. Nucleic Acids Res. 32(Web Server issue):W195-8. (2004) PMID 15215379
Sandelin A, Wasserman WW. Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics. J. Mol. Biol. 338(2):207-15. (2004) PMID 15066426
Sandelin A, Alkema W, Engström P, Wasserman WW, Lenhard B. JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 32(Database issue):D91-4. (2004) PMID 14681366
Johansson O, Alkema W, Wasserman WW, Lagergren J. Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm. Bioinformatics 19 Suppl 1:i169-76. (2003) PMID 12855453
Alkema W, Wasserman WW. Understanding the language of gene regulation. Genome Biol. 4(7):327. (2003) PMID 12844355
Sandelin A, Höglund A, Lenhard B, Wasserman WW. Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes. Funct. Integr. Genomics 3(3):125-34. (2003) PMID 12827523
Lenhard B, Wahlestedt C, Wasserman WW. GeneLynx mouse: integrated portal to the mouse genome. Genome Res. 13(6B):1501-4. (2003) PMID 12819149
Lenhard B, Sandelin A, Mendoza L, Engström P, Jareborg N, Wasserman WW. Identification of conserved regulatory elements by comparative genome analysis. J. Biol. 2(2):13. (2003) PMID 12760745
Wasserman WW, Krivan W. In silico identification of metazoan transcriptional regulatory regions. Naturwissenschaften 90(4):156-66. (2003) PMID 12712249
Lenhard B, Wasserman WW. TFBS: Computational framework for transcription factor binding site analysis. Bioinformatics 18(8):1135-6. (2002) PMID 12176838
Kutsenko AS, Gizatullin RZ, Al-Amin AN, Wang F, Kvasha SM, Podowski RM, Matushkin YG, Gyanchandani A, Muravenko OV, Levitsky VG, Kolchanov NA, Protopopov AI, Kashuba VI, Kisselev LL, Wasserman W, Wahlestedt C, Zabarovsky ER. NotI flanking sequences: a tool for gene discovery and verification of the human genome. Nucleic Acids Res. 30(14):3163-70. (2002) PMID 12136098
Lenhard B, Hayes WS, Wasserman WW. GeneLynx: a gene-centric portal to the human genome. Genome Res. 11(12):2151-7. (2001) PMID 11731507
Krivan W, Wasserman WW. A predictive model for regulatory sequences directing liver-specific transcription. Genome Res. 11(9):1559-66. (2001) PMID 11544200
Kashuba VI, Kvasha SM, Protopopov AI, Gizatullin RZ, Rynditch AV, Wahlestedt C, Wasserman WW, Zabarovsky ER. Initial isolation and analysis of the human Kv1.7 (KCNA7) gene, a member of the voltage-gated potassium channel gene family. Gene 268(1-2):115-22. (2001) PMID 11368907
Zhu M, Chapman WG, Oberley MJ, Wasserman WW, Fahl WE. Polymorphic electrophile response elements in the mouse glutathione S-transferase GSTa1 gene that confer increased induction. Cancer Lett. 164(2):113-8. (2001) PMID 11179824
Fredholm BB, Arslan G, Halldner L, Kull B, Schulte G, Wasserman W. Structure and function of adenosine receptors and their genes. Naunyn Schmiedebergs Arch. Pharmacol. 362(4-5):364-74. (2000) PMID 11111830
Wasserman WW, Palumbo M, Thompson W, Fickett JW, Lawrence CE. Human-mouse genome comparisons to locate regulatory sites. Nat. Genet. 26(2):225-8. (2000) PMID 11017083
Fickett JW, Wasserman WW. Discovery and modeling of transcriptional regulatory regions. Curr. Opin. Biotechnol. 11(1):19-24. (2000) PMID 10679343
Mao NC, Steingrimsson E, DuHadaway J, Wasserman W, Ruiz JC, Copeland NG, Jenkins NA, Prendergast GC. The murine Bin1 gene functions early in myogenesis and defines a new region of synteny between mouse chromosome 18 and human chromosome 2. Genomics 56(1):51-8. (1999) PMID 10036185
Allikmets R, Wasserman WW, Hutchinson A, Smallwood P, Nathans J, Rogan PK, Schneider TD, Dean M. Organization of the ABCR gene: analysis of promoter and splice junction sequences. Gene 215(1):111-22. (1998) PMID 9666097
Wasserman WW, Fickett JW. Identification of regulatory regions which confer muscle-specific gene expression. J. Mol. Biol. 278(1):167-81. (1998) PMID 9571041
Geisler JG, Stubbs LJ, Wasserman WW, Mucenski ML. Molecular cloning of a novel mouse gene with predominant muscle and neural expression. Mamm. Genome 9(4):274-82. (1998) PMID 9530622
Krämer A, Carstens CP, Wasserman WW, Fahl WE. CBP/cycA, a CCAAT-binding protein necessary for adhesion-dependent cyclin A transcription, consists of NF-Y and a novel Mr 115,000 subunit. Cancer Res. 57(22):5117-21. (1997) PMID 9371512
Wasserman WW, Fahl WE. Comprehensive analysis of proteins which interact with the antioxidant responsive element: correlation of ARE-BP-1 with the chemoprotective induction response. Arch. Biochem. Biophys. 344(2):387-96. (1997) PMID 9264553
Wasserman WW, Fahl WE. Functional antioxidant responsive elements. Proc. Natl. Acad. Sci. U.S.A. 94(10):5361-6. (1997) PMID 9144242