return to top2012

1   Shah SP, Roth A, Goya R, Oloumi A, Ha G, Zhao Y, Turashvili G, Ding J, Tse K, Haffari G, Bashashati A, Prentice LM, Khattra J, Burleigh A, Yap D, Bernard V, McPherson A, Shumansky K, Crisan A, Giuliany R, Heravi-Moussavi A, Rosner J, Lai D, Birol I, Varhol R, Tam A, Dhalla N, Zeng T, Ma K, Chan SK, Griffith M, Moradian A, Cheng SW, Morin GB, Watson P, Gelmon K, Chia S, Chin SF, Curtis C, Rueda OM, Pharoah PD, Damaraju S, Mackey J, Hoon K, Harkins T, Tadigotla V, Sigaroudinia M, Gascard P, Tlsty T, Costello JF, Meyer IM, Eaves CJ, Wasserman WW, Jones S, Huntsman D, Hirst M, Caldas C, Marra MA, Aparicio S. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. (2012) PMID 22495314

2   Yusuf D, Butland SL, Swanson MI, Bolotin E, Ticoll A, Cheung WA, Zhang XY, Dickman CT, Fulton DL, Lim JS, Schnabl JM, Ramos OH, Vasseur-Cognet M, de Leeuw CN, Simpson EM, Ryffel GU, Lam EW, Kist R, Wilson MS, Marco-Ferreres R, Brosens JJ, Beccari LL, Bovolenta P, Benayoun BA, Monteiro LJ, Schwenen HD, Grontved L, Wederell E, Mandrup S, Veitia RA, Chakravarthy H, Hoodless PA, Mancarelli M, Torbett BE, Banham AH, Reddy SP, Cullum RL, Liedtke M, Tschan MP, Vaz M, Rizzino A, Zannini M, Frietze S, Farnham PJ, Eijkelenboom A, Brown PJ, Laperriere D, Leprince D, de Cristofaro T, Prince KL, Putker M, Del Peso L, Camenisch G, Wenger RH, Mikula M, Rozendaal M, Mader S, Ostrowski J, Rhodes SJ, Van Rechem C, Boulay G, Olechnowicz SW, Breslin MB, Lan MS, Nanan KK, Wegner M, Hou J, Mullen RD, Colvin SC, Noy PJ, Webb CF, Witek ME, Ferrell S, Daniel JM, Park J, Waldman SA, Peet DJ, Taggart M, Jayaraman PS, Karrich JJ, Blom B, Vesuna F, O'Geen H, Sun Y, Gronostajski RM, Woodcroft MW, Hough MR, Chen E, Europe-Finner N, Karolczak-Bayatti M, Bailey J, Hankinson O, Raman V, Lebrun DP, Biswal S, Harvey CJ, Debruyne JP, Hogenesch JB, Hevner RF, Heligon C, Luo XM, Blank MC, Millen KJ, Sharlin DS, Forrest D, Dahlman-Wright K, Zhao C, Mishima Y, Sinha S, Chakrabarti R, Portales-Casamar E, Sladek FM, Bradley PH, Wasserman WW. The Transcription Factor Encyclopedia. 13(3):R24. (2012) PMID 22458515

3   Schmouth JF, Banks KG, Mathelier A, Gregory-Evans CY, Castellarin M, Holt RA, Gregory-Evans K, Wasserman WW, Simpson EM. Retina Restored and Brain Abnormalities Ameliorated by Single-Copy Knock-In of Human NR2E1 in Null Mice. Mol. Cell. Biol. 32(7):1296-311. (2012) PMID 22290436

return to top2011

4   Kwon AT, Chou AY, Arenillas DJ, Wasserman WW. Validation of skeletal muscle cis-regulatory module predictions reveals nucleotide composition bias in functional enhancers. PLoS Comput. Biol. 7(12):e1002256. (2011) PMID 22144875

5   Review (Invited)   Worsley-Hunt R, Bernard V, Wasserman WW. Identification of cis-regulatory sequence variations in individual genome sequences. 3(10):65. (2011) PMID 21989199

6   Vilariño-Güell C, Wider C, Ross OA, Dachsel JC, Kachergus JM, Lincoln SJ, Soto-Ortolaza AI, Cobb SA, Wilhoite GJ, Bacon JA, Behrouz B, Melrose HL, Hentati E, Puschmann A, Evans DM, Conibear E, Wasserman WW, Aasly JO, Burkhard PR, Djaldetti R, Ghika J, Hentati F, Krygowska-Wajs A, Lynch T, Melamed E, Rajput A, Rajput AH, Solida A, Wu RM, Uitti RJ, Wszolek ZK, Vingerhoets F, Farrer MJ. VPS35 mutations in Parkinson disease. Am. J. Hum. Genet. 89(1):162-7. (2011) PMID 21763482

7   Fulton DL, Denarier E, Friedman HC, Wasserman WW, Peterson AC. Towards resolving the transcription factor network controlling myelin gene expression. Nucleic Acids Res. 39(18):7974-91. (2011) PMID 21729871

8   Portales-Casamar E, Evans A, Wasserman W, Pavlidis P. The NeuroDevNet Neuroinformatics Core. Semin Pediatr Neurol 18(1):17-20. (2011) PMID 21575836

9   Le Béchec A, Portales-Casamar E, Vetter G, Moes M, Zindy PJ, Saumet A, Arenillas D, Theillet C, Wasserman WW, Lecellier CH, Friederich E. MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model. BMC Bioinformatics 12:67. (2011) PMID 21375730

return to top2010

10   Portales-Casamar E, Swanson DJ, Liu L, de Leeuw CN, Banks KG, Ho Sui SJ, Fulton DL, Ali J, Amirabbasi M, Arenillas DJ, Babyak N, Black SF, Bonaguro RJ, Brauer E, Candido TR, Castellarin M, Chen J, Chen Y, Cheng JC, Chopra V, Docking TR, Dreolini L, D'Souza CA, Flynn EK, Glenn R, Hatakka K, Hearty TG, Imanian B, Jiang S, Khorasan-zadeh S, Komljenovic I, Laprise S, Liao NY, Lim JS, Lithwick S, Liu F, Liu J, Lu M, McConechy M, McLeod AJ, Milisavljevic M, Mis J, O'Connor K, Palma B, Palmquist DL, Schmouth JF, Swanson MI, Tam B, Ticoll A, Turner JL, Varhol R, Vermeulen J, Watkins RF, Wilson G, Wong BK, Wong SH, Wong TY, Yang GS, Ypsilanti AR, Jones SJ, Holt RA, Goldowitz D, Wasserman WW, Simpson EM. A regulatory toolbox of MiniPromoters to drive selective expression in the brain. Proc. Natl. Acad. Sci. U.S.A. 107(38):16589-94. (2010) PMID 20807748

11   Ross CJ, Visscher H, Sistonen J, Brunham LR, Pussegoda K, Loo TT, Rieder MJ, Koren G, Carleton BC, Hayden MR,CPNDS Consortium. The Canadian Pharmacogenomics Network for Drug Safety: a model for safety pharmacology. Thyroid 20(7):681-7. (2010) PMID 20578893

12   Malhotra D, Portales-Casamar E, Singh A, Srivastava S, Arenillas D, Happel C, Shyr C, Wakabayashi N, Kensler TW, Wasserman WW, Biswal S. Global mapping of binding sites for Nrf2 identifies novel targets in cell survival response through ChIP-Seq profiling and network analysis. Nucleic Acids Res. 38(17):5718-34. (2010) PMID 20460467

13   Milisavljevic M, Hearty T, Wong TY, Portales-Casamar E, Simpson EM, Wasserman WW. Laboratory Animal Management Assistant (LAMA): a LIMS for active research colonies. Mamm. Genome 21(5-6):224-30. (2010) PMID 20411264

14   Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, Valen E, Yusuf D, Lenhard B, Wasserman WW, Sandelin A. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res. 38 (Database issue):D105-10. (2010) PMID 19906716

return to top2009

15   Ross CJ, Katzov-Eckert H, Dubé MP, Brooks B, Rassekh SR, Barhdadi A, Feroz-Zada Y, Visscher H, Brown AM, Rieder MJ, Rogers PC, Phillips MS, Carleton BC, Hayden MR, CPNDS Consortium. Genetic variants in TPMT and COMT are associated with hearing loss in children receiving cisplatin chemotherapy. Nat. Genet. 41(12):1345-9. (2009) PMID 19898482

16   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

17   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

18   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

return to top2008

19   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

20   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 Neurosci 9:66. (2008) PMID 18625066

21   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

22   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

23   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

24   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

25   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

return to top2007

26   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

27   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

return to top2006

28   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

29   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

30   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

31   Podowski RM, Miller B, Wasserman WW. Visualization of complementary systems biology data with parallel heatmaps IBM Journal of Research and Development 50(6):575-581. (2006)

return to top2005

32   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

33   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

34   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

35   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

36   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

37   Sandelin A, Wasserman WW. Prediction of nuclear hormone receptor response elements. Mol. Endocrinol. 19(3):595-606. (2005) PMID 15563547

return to top2004

38   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

39   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

40   Thompson W, Palumbo MJ, Wasserman WW, Liu JS, Lawrence CE. Decoding human regulatory circuits. Genome Res. 14(10A):1967-74. (2004) PMID 15466295

41   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

42   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

43   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

44   Review   Wasserman WW, Sandelin A. Applied bioinformatics for the identification of regulatory elements. Nat. Rev. Genet. 5(4):276-87. (2004) PMID 15131651

45   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

46   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

return to top2003

47   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

48   Alkema W, Wasserman WW. Understanding the language of gene regulation. Genome Biol. 4(7):327. (2003) PMID 12844355

49   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

50   Lenhard B, Wahlestedt C, Wasserman WW. GeneLynx mouse: integrated portal to the mouse genome. Genome Res. 13(6B):1501-4. (2003) PMID 12819149

51   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

52   Wasserman WW, Krivan W. In silico identification of metazoan transcriptional regulatory regions. Naturwissenschaften 90(4):156-66. (2003) PMID 12712249

return to top2002

53   Lenhard B, Wasserman WW. TFBS: Computational framework for transcription factor binding site analysis. Bioinformatics 18(8):1135-6. (2002) PMID 12176838

54   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

return to top2001

55   Lenhard B, Hayes WS, Wasserman WW. GeneLynx: a gene-centric portal to the human genome. Genome Res. 11(12):2151-7. (2001) PMID 11731507

56   Krivan W, Wasserman WW. A predictive model for regulatory sequences directing liver-specific transcription. Genome Res. 11(9):1559-66. (2001) PMID 11544200

57   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

58   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

return to top2000

59   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

60   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

61   Fickett JW, Wasserman WW. Discovery and modeling of transcriptional regulatory regions. Curr. Opin. Biotechnol. 11(1):19-24. (2000) PMID 10679343

62   Zhu M, Oberley MJ, Chapman WG, Wasserman WW, Fahl WE. Chemoprotection Conferred by Electrophile Responsive Element-regulated Expression of Endogenous Glutathione S-transferase Genes Clinical Chemistry and Enzymology Communications 8:303-313. (2000)

return to top1999

63   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

return to top1998

64   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

65   Wasserman WW, Fickett JW. Identification of regulatory regions which confer muscle-specific gene expression. J. Mol. Biol. 278(1):167-81. (1998) PMID 9571041

66   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

return to top1997

67   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

68   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

69   Wasserman WW, Fahl WE. Functional antioxidant responsive elements. Proc. Natl. Acad. Sci. U.S.A. 94(10):5361-6. (1997) PMID 9144242