1   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

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

1   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

2   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

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

4   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

5   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

6   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

7   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

8   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

9   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

10   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

11   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

12   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

13   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

14   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

15   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

16   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

17   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

18   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

19   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

20   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

21   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

22   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

23   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

24   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

25   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

26   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)

27   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

28   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

29   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

30   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

31   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

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

33   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

34   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

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

36   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

37   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

38   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

39   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

40   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

41   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

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

43   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

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

45   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

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

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

48   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

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

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

51   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

52   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

53   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

54   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

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

56   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)

57   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

58   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

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

60   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

61   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

62   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

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