Professor, Department of Medical Genetics, UBC
Senior Scientist, Centre for Molecular Medicine and Therapeutics, Research Institute, BC Children’s Hospital
Executive Director, Research Institute, BC Children’s Hospital
Associate Dean, Research, CFRI, Faculty of Medicine, UBC
phone: 6048753812
fax: 6048753819

Research Interests: Computational analysis of human genome sequence for the study of gene regulation and rare pediatric disorders.

Selected Publications:

  1. Janer A, van Karnebeek CD, Sasarman F, Antonicka H, Al Ghamdi M, Shyr C, Dunbar M, Stockler-Ispiroglu S, Ross CJ, Vallance H, Dionne J, Wasserman WW, Shoubridge EA. RMND1 deficiency associated with neonatal lactic acidosis, infantile onset renal failure, deafness, and multiorgan involvement. Eur. J. Hum. Genet. (2015) PMID 25604853
  2. Shyr C, Tarailo-Graovac M, Gottlieb M, Lee J, van Karnebeek C, Wasserman WW.FLAGS, frequently mutated genes in public exomes. BMC Med Genomics 7(1):64. (2014) PMID 25466818
  3. Salvarinova R, Ye CX, Rossi A, Biancheri R, Roland EH, Pavlidis P, Ross CJ, Tarailo-Graovac M, Wasserman WW, van Karnebeek CD. Expansion of the QARS deficiency phenotype with report of a family with isolated supratentorial brain abnormalities.Neurogenetics (2014) PMID 25432320
  4. Stockler S, Corvera S, Lambright D, Fogarty K, Nosova E, Leonard D, Steinfeld R, Ackerley C, Shyr C, Au N, Selby K, van Allen M, Vallance H, Wevers R, Watkins D, Rosenblatt D, Ross CJ, Conibear E, Wasserman W, van Karnebeek C. Single point mutation in Rabenosyn-5 in a female with intractable seizures and evidence of defective endocytotic trafficking. Orphanet J Rare Dis 9(1):141. (2014) PMID 25233840
  5. Worsley Hunt R, Wasserman WW. Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets. Genome Biol. 15(7):412. (2014) PMID 25070602
  6. Armstrong L, Biancheri R, Shyr C, Rossi A, Sinclair G, Ross CJ, Tarailo-Graovac M, Wasserman WW, van Karnebeek CD. AIMP1 deficiency presents as a cortical neurodegenerative disease with infantile onset. Neurogenetics 15(3):157-9. (2014)PMID 24958424
  7. Worsley Hunt R, Mathelier A, Del Peso L, Wasserman WW. Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment. BMC Genomics 15:472. (2014) PMID 24927817
  8. Chen CY, Chang IS, Hsiung CA, Wasserman WW. On the identification of potential regulatory variants within genome wide association candidate SNP sets. BMC Med Genomics 7:34. (2014) PMID 24920305
  9. Shyr C, Kushniruk A, Wasserman WW. Usability study of clinical exome analysis software: top lessons learned and recommendations. J Biomed Inform 51:129-36. (2014) PMID 24860971
  10. de Leeuw CN, Dyka FM, Boye SL, Laprise S, Zhou M, Chou AY, Borretta L, McInerny SC, Banks KG, Portales-Casamar E, Swanson MI, D’Souza CA, Boye SE, Jones SJ, Holt RA, Goldowitz D, Hauswirth WW, Wasserman WW, Simpson EM. Targeted CNS Delivery Using Human MiniPromoters and Demonstrated Compatibility with Adeno-Associated Viral Vectors. Mol Ther Methods Clin Dev 1:5. (2014) PMID 24761428
  11. FANTOM Consortium and the RIKEN PMI and CLST (DGT). (Mathelier/Wasserman are authors and members of the FANTOM Consortium). A promoter-level mammalian expression atlas. Nature 507(7493):462-70. (2014) PMID 24670764
  12. Review   Ye XC, Pegado V, Patel MS, Wasserman WW. Strabismus genetics across a spectrum of eye misalignment disorders. Clin. Genet. (2014) PMID 24579652
  13. van Karnebeek CD, Sly WS, Ross CJ, Salvarinova R, Yaplito-Lee J, Santra S, Shyr C, Horvath GA, Eydoux P, Lehman AM, Bernard V, Newlove T, Ukpeh H, Chakrapani A, Preece MA, Ball S, Pitt J, Vallance HD, Coulter-Mackie M, Nguyen H, Zhang LH, Bhavsar AP, Sinclair G, Waheed A, Wasserman WW, Stockler-Ipsiroglu S. Mitochondrial carbonic anhydrase VA deficiency resulting from CA5A alterations presents with hyperammonemia in early childhood. Am. J. Hum. Genet. 94(3):453-61. (2014) PMID 24530203
  14. Vilariño-Güell C, Rajput A, Milnerwood AJ, Shah B, Szu-Tu C, Trinh J, Yu I, Encarnacion M, Munsie LN, Tapia L, Gustavsson EK, Chou P, Tatarnikov I, Evans DM, Pishotta FT, Volta M, Beccano-Kelly D, Thompson C, Lin MK, Sherman HE, Han HJ, Guenther BL, Wasserman WW, Bernard V, Ross CJ, Appel-Cresswell S, Stoessl AJ, Robinson CA, Dickson DW, Ross OA, Wszolek ZK, Aasly JO, Wu RM, Hentati F, Gibson RA, McPherson PS, Girard M, Rajput M, Rajput AH, Farrer MJ. DNAJC13 mutations in Parkinson disease. Hum. Mol. Genet. 23(7):1794-801. (2014) PMID 24218364
  15. Yang L, Zhou T, Dror I, Mathelier A, Wasserman WW, Gordân R, Rohs R.TFBSshape: a motif database for DNA shape features of transcription factor binding sites. Nucleic Acids Res. 42(Database issue):D148-55. (2014) PMID 24214955
  16. Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, Buchman S, Chen CY, Chou A, Ienasescu H, Lim J, Shyr C, Tan G, Zhou M, Lenhard B, Sandelin A, Wasserman WW. JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 42(Database issue):D142-7. (2014) PMID 24194598
  17. Cotton AM, Chen CY, Lam LL, Wasserman WW, Kobor MS, Brown CJ. Spread of X-chromosome inactivation into autosomal sequences: role for DNA elements, chromatin features and chromosomal domains. Hum. Mol. Genet. 23(5):1211-23. (2014) PMID 24158853
  18. Filges I, Nosova E, Bruder E, Tercanli S, Townsend K, Gibson W, Röthlisberger B, Heinimann K, Hall J, Gregory-Evans C, Wasserman W, Miny P, Friedman J. Exome sequencing identifies mutations in KIF14 as a novel cause of an autosomal recessive lethal fetal ciliopathy phenotype. Clin. Genet. 86(3):220-228. (2014) PMID 24128419
  19. Aminkeng F, Ross CJ, Rassekh SR, Brunham LR, Sistonen J, Dube MP, Ibrahim M, Nyambo TB, Omar SA, Froment A, Bodo JM, Tishkoff S, Carleton BC, Hayden MR, .Higher frequency of genetic variants conferring increased risk for ADRs for commonly used drugs treating cancer, AIDS and tuberculosis in persons of African descent. Pharmacogenomics J. 14(2):160-70. (2014) PMID 23588107
  20. Schmouth JF, Castellarin M, Laprise S, Banks KG, Bonaguro RJ, McInerny SC, Borretta L, Amirabbasi M, Korecki AJ, Portales-Casamar E, Wilson G, Dreolini L, Jones SJ, Wasserman WW, Goldowitz D, Holt RA, Simpson EM. Non-coding-regulatory regions of human brain genes delineated by bacterial artificial chromosome knock-in mice. BMC Biol. 11:106. (2013) PMID 24124870
  21. Mathelier A, Wasserman WW. The next generation of transcription factor binding site prediction. PLoS Comput. Biol. 9(9):e1003214. (2013) PMID 24039567
  22. Ye XC, Ng I, Seid-Karbasi P, Imam T, Lee CE, Chen SY, Herman A, Sharma B, Johal G, Gu B, Wasserman WW. Portal for Families Overcoming Neurodevelopmental Disorders (PFOND): Implementation of a Software Framework for Facilitated Community Website Creation by Nontechnical Volunteers. JMIR Res Protoc 2(2):e25. (2013) PMID 23920006
  23. Cheung WA, Ouellette BF, Wasserman WW. Compensating for literature annotation bias when predicting novel drug-disease relationships through Medical Subject Heading Over-representation Profile (MeSHOP) similarity. BMC Med Genomics 6 Suppl 2:S3. (2013) PMID 23819887
  24. Robillard JM, Whiteley L, Johnson TW, Lim J, Wasserman WW, Illes J. Utilizing social media to study information-seeking and ethical issues in gene therapy. J. Med. Internet Res. 15(3):e44. (2013) PMID 23470490
  25. Visscher H, Ross CJ, Rassekh SR, Sandor GS, Caron HN, van Dalen EC, Kremer LC, van der Pal HJ, Rogers PC, Rieder MJ, Carleton BC, Hayden MR, . Validation of variants in SLC28A3 and UGT1A6 as genetic markers predictive of anthracycline-induced cardiotoxicity in children. Pediatr Blood Cancer 60(8):1375-81. (2013) PMID 23441093
  26. Cheung WA, Francis Ouellette B, Wasserman WW. Inferring novel gene-disease associations using Medical Subject Heading Over-representation Profiles. Genome Med 4(9):75. (2012) PMID 23021552
  27. Cheung WA, Ouellette BF, Wasserman WW. Quantitative biomedical annotation using medical subject heading over-representation profiles (MeSHOPs). BMC Bioinformatics 13:249. (2012) PMID 23017167
  28. Kwon AT, Arenillas DJ, Worsley Hunt R, Wasserman WW. oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets. G3 (Bethesda) 2(9):987-1002. (2012) PMID 22973536
  29. 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. Nature 486(7403):395-9. (2012) PMID 22495314
  30. 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 MM, 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, Laperrière 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 GN, Karolczak-Bayatti M, Bailey J, Hankinson O, Raman V, LeBrun DP, Biswal S, Harvey CJ, DeBruyne JP, Hogenesch JB, Hevner RF, Héligon 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. Genome Biol.13(3):R24. (2012) PMID 22458515
  31. 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
  32. 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
  33. Worsley-Hunt R, Bernard V, Wasserman WW. Identification of cis-regulatory sequence variations in individual genome sequences. Genome Med 3(10):65. (2011)PMID 21989199
  34. 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
  35. 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
  36. Portales-Casamar E, Evans A, Wasserman W, Pavlidis P. The NeuroDevNet Neuroinformatics Core. Semin Pediatr Neurol 18(1):17-20. (2011) PMID 21575836
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. 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
  48. 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
  49. 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
  50. 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
  51. 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
  52. 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
  53. 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
  54. 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
  55. 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
  56. 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
  57. 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
  58. 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
  59. 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
  60. 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
  61. 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
  62. 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
  63. 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
  64. Sandelin A, Wasserman WW. Prediction of nuclear hormone receptor response elements. Mol. Endocrinol. 19(3):595-606. (2005) PMID 15563547
  65. 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
  66. 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
  67. Thompson W, Palumbo MJ, Wasserman WW, Liu JS, Lawrence CE. Decoding human regulatory circuits. Genome Res. 14(10A):1967-74. (2004) PMID 15466295
  68. 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
  69. 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
  70. 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
  71. 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
  72. 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
  73. 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
  74. Alkema W, Wasserman WW. Understanding the language of gene regulation. Genome Biol. 4(7):327. (2003) PMID 12844355
  75. 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
  76. Lenhard B, Wahlestedt C, Wasserman WW. GeneLynx mouse: integrated portal to the mouse genome. Genome Res. 13(6B):1501-4. (2003) PMID 12819149
  77. 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
  78. Wasserman WW, Krivan W. In silico identification of metazoan transcriptional regulatory regions. Naturwissenschaften 90(4):156-66. (2003) PMID 12712249
  79. Lenhard B, Wasserman WW. TFBS: Computational framework for transcription factor binding site analysis. Bioinformatics 18(8):1135-6. (2002) PMID 12176838
  80. 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
  81. Lenhard B, Hayes WS, Wasserman WW. GeneLynx: a gene-centric portal to the human genome. Genome Res. 11(12):2151-7. (2001) PMID 11731507
  82. Krivan W, Wasserman WW. A predictive model for regulatory sequences directing liver-specific transcription. Genome Res. 11(9):1559-66. (2001) PMID 11544200
  83. 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
  84. 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
  85. 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
  86. 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
  87. Fickett JW, Wasserman WW. Discovery and modeling of transcriptional regulatory regions. Curr. Opin. Biotechnol. 11(1):19-24. (2000) PMID 10679343
  88. 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
  89. 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
  90. Wasserman WW, Fickett JW. Identification of regulatory regions which confer muscle-specific gene expression. J. Mol. Biol. 278(1):167-81. (1998) PMID 9571041
  91. 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
  92. 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
  93. 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
  94. Wasserman WW, Fahl WE. Functional antioxidant responsive elements. Proc. Natl. Acad. Sci. U.S.A. 94(10):5361-6. (1997) PMID 9144242