The Wasserman laboratory focuses on the creation, evaluation and application of computational methods for the analysis of genome sequences, with international strength in the study of cis-regulatory elements regulating gene expression. The lab creates widely used software and databases, performs applied analyses of genome sequences, and partners with diverse research teams on projects at the intersection of the computational and life sciences.

Genome Sequencing has disrupted health research. The lab has been developing computational methods and tools to allow researchers and clinicians to identify functional consequences of genetic variations within cis-regulatory elements such as transcription factor binding sites. Alterations in the TF bound DNA sequences can contribute causally to phenotypes, but much work remains to develop the essential computational methods to study them.

The lab studies gene regulation via multiple lines. First, the lab creates novel algorithms and software to predict interactions between TFs and DNA. Second, the lab collaborates internationally on the analysis of emerging data, such as the international FANTOM project. Third, the lab engages in the applied analysis of genomes for pediatric disorders. Such work is key to translating basic research advances into clinical impacts.


Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer.
Zhang AW, McPherson A, Milne K, Kroeger DR, Hamilton PT, Miranda A, Funnell T, Little N, de Souza CPE, Laan S, LeDoux S, Cochrane DR, Lim JLP, Shah SP
DOI: 10.1016/j.cell.2018.03.073
PubMed: 29754820

Text-based phenotypic profiles incorporating biochemical phenotypes of inborn errors of metabolism improve phenomics-based diagnosis
Journal of Inherited Metabolic Disease
Jessica J. Y. Lee, Michael M. Gottlieb, Jake Lever, Steven J. M. Jones, Nenad Blau, Clara D. M. van Karnebeek, Wyeth W. Wasserman
DOI: 10.1007/s10545-017-0125-4

Integration of genomics and metabolomics for prioritization of rare disease variants: a 2018 literature review.
Journal of inherited metabolic disease
Graham E, Lee J, Price M, Tarailo-Graovac M, Matthews A, Engelke U, Tang J, Kluijtmans LAJ, Wevers RA, Wasserman WW, van Karnebeek CDM, Mostafavi S
DOI: 10.1007/s10545-018-0139-6
PubMed: 29721916

Genome sequencing reveals a novel genetic mechanism underlying dihydropyrimidine dehydrogenase deficiency: A novel missense variant c.1700G>A and a large intragenic inversion in DPYD spanning intron 8 to intron 12.
Human mutation
van Kuilenburg ABP, Tarailo-Graovac M, Meijer J, Drogemoller B, Vockley J, Maurer D, Dobritzsch D, Ross CJ, Wasserman W, Meinsma R, Zoetekouw L, van Karnebeek CDM
DOI: 10.1002/humu.23538
PubMed: 29691939

Bone health and SATB2-associated syndrome.
Clinical genetics
Zarate YA, Steinraths M, Matthews A, Smith WE, Sun A, Wilson LC, Brain C, Allgove J, Jacobs B, Fish JL, Powell CM, Wasserman WW, van Karnebeek CD, Ma NS
DOI: 10.1111/cge.13121
PubMed: 28787087

The genotypic and phenotypic spectrum of MTO1 deficiency.
Molecular genetics and metabolism
O'Byrne JJ, Tarailo-Graovac M, Ghani A, Champion M, Deshpande C, Dursun A, Ozgul RK, Freisinger P, Garber I, Haack TB, Horvath R, Baric I, Husain RA, van Karnebeek CDM
DOI: 10.1016/j.ymgme.2017.11.003
PubMed: 29331171

The SIN3A histone deacetylase complex is required for a complete transcriptional response to hypoxia.
Nucleic acids research
Tiana M, Acosta-Iborra B, Puente-Santamaría L, Hernansanz-Agustin P, Worsley-Hunt R, Masson N, García-Rio F, Mole D, Ratcliffe P, Wasserman WW, Del Peso L
DOI: 10.1093/nar/gkx951
PubMed: 29059365

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.
Nucleic acids research
Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, Bessy A, Chèneby J, Kulkarni SR, Tan G, Baranasic D, Arenillas DJ, Mathelier A
DOI: 10.1093/nar/gkx1126
PubMed: 29140473

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.
Nucleic acids research
Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, Bessy A, Chèneby J, Kulkarni SR, Tan G, Baranasic D, Arenillas DJ, Mathelier A
DOI: 10.1093/nar/gkx1188
PubMed: 29161433

Knowledge base and mini-expert platform for the diagnosis of inborn errors of metabolism.
Genetics in medicine : official journal of the American College of Medical Genetics
Lee JJY, Wasserman WW, Hoffmann GF, van Karnebeek CDM, Blau N
DOI: 10.1038/gim.2017.108
PubMed: 28726811

The role of the clinician in the multi-omics era: are you ready?
Journal of inherited metabolic disease
van Karnebeek CDM, Wortmann SB, Tarailo-Graovac M, Langeveld M, Ferreira CR, van de Kamp JM, Hollak CE, Wasserman WW, Waterham HR, Wevers RA, Boycott KM
DOI: 10.1007/s10545-017-0128-1
PubMed: 29362952

Improvement of Self-Injury With Dopamine and Serotonin Replacement Therapy in a Patient With a Hemizygous PAK3 Mutation: A New Therapeutic Strategy for Neuropsychiatric Features of an Intellectual Disability Syndrome.
Journal of child neurology
Horvath GA, Tarailo-Graovac M, Bartel T, Race S, Van Allen MI, Blydt-Hansen I, Ross CJ, Wasserman WW, Connolly MB, van Karnebeek CDM
DOI: 10.1177/0883073817740443
PubMed: 29246092

Assessment of the ExAC data set for the presence of individuals with pathogenic genotypes implicated in severe Mendelian pediatric disorders.
Genetics in medicine : official journal of the American College of Medical Genetics
Tarailo-Graovac M, Zhu JYA, Matthews A, van Karnebeek CDM, Wasserman WW
DOI: 10.1038/gim.2017.50
PubMed: 28471432

Correction to: FLAGS, frequently mutated genes in public exomes.
BMC medical genomics
Shyr C, Tarailo-Graovac M, Gottlieb M, Lee JJ, van Karnebeek C, Wasserman WW
DOI: 10.1186/s12920-017-0309-7
PubMed: 29187224

A de novo mosaic mutation in SPAST with two novel alternative alleles and chromosomal copy number variant in a boy with spastic paraplegia and autism spectrum disorder
European Journal of Medical Genetics
A.M. Matthews, M. Tarailo-Graovac, E.M. Price, I. Blydt-Hansen, A. Ghani, B.I. Drögemöller, W.P. Robinson, C.J. Ross, W.W. Wasserman, H. Siden, C.D. van Karnebeek
DOI: 10.1016/j.ejmg.2017.07.015

The SIN3A histone deacetylase complex is required for a complete transcriptional response to hypoxia
Maria Tiana Cerrolaza, Barbara Acosta-Iborra, Laura Puente-Santamaria, Pablo Hernansanz, Rebecca Worsley-Hunt, Norma Masson, Francisco Garcia-Rio, David R. Mole, Peter J. Ratcliffe, Wyeth W. Wasserman, Benilde Jimenez Cuenca, Luis del Peso
DOI: 10.1101/182691

A case of splenomegaly in CBL syndrome.
European journal of medical genetics
Coe RR, McKinnon ML, Tarailo-Graovac M, Ross CJ, Wasserman WW, Friedman JM, Rogers PC, van Karnebeek CDM
DOI: 10.1016/j.ejmg.2017.04.009
PubMed: 28414188

Corrigendum: NANS-mediated synthesis of sialic acid is required for brain and skeletal development.
Nature genetics
van Karnebeek CDM, Bonafé L, Wen XY, Tarailo-Graovac M, Balzano S, Royer-Bertrand B, Ashikov A, Garavelli L, Mammi I, Turolla L, Breen C, Donnai D, Superti-Furga A
DOI: 10.1038/ng0617-969a
PubMed: 28546570

Impact of next-generation sequencing on diagnosis and management of neurometabolic disorders: current advances and future perspectives.
Expert review of molecular diagnostics
Tarailo-Graovac M, Wasserman WW, Van Karnebeek CD
DOI: 10.1080/14737159.2017.1293527
PubMed: 28277145

CuboCube: Student creation of a cancer genetics e-textbook using open-access software for social learning.
PLoS biology
Seid-Karbasi P, Ye XC, Zhang AW, Gladish N, Cheng SY, Rothe K, Pilsworth JA, Kang MA, Doolittle N, Jiang X, Stirling PC, Wasserman WW
DOI: 10.1371/journal.pbio.2001192
PubMed: 28267757

A girl with developmental delay, ataxia, cranial nerve palsies, severe respiratory problems in infancy-Expanding NDST1 syndrome.
American journal of medical genetics. Part A
Armstrong L, Tarailo-Graovac M, Sinclair G, Seath KI, Wasserman WW, Ross CJ, van Karnebeek CD
DOI: 10.1002/ajmg.a.37621
PubMed: 28211985

Identification of a large intronic transposal insertion in SLC17A5 causing sialic acid storage disease.
Orphanet journal of rare diseases
Tarailo-Graovac M, Drögemöller BI, Wasserman WW, Ross CJ, van den Ouweland AM, Darin N, Kollberg G, van Karnebeek CD, Blomqvist M
DOI: 10.1186/s13023-017-0584-6
PubMed: 28187749

Optic atrophy, cataracts, lipodystrophy/lipoatrophy, and peripheral neuropathy caused by a de novo OPA3 mutation.
Bourne SC, Townsend KN, Shyr C, Matthews A, Lear SA, Attariwala R, Lehman A, Wasserman WW, van Karnebeek C, Sinclair G, Vallance H, Gibson WT
DOI: 10.1101/mcs.a001156
PubMed: 28050599

Identification of non-coding genetic variants in samples from hypoxemic respiratory disease patients that affect the transcriptional response to hypoxia.
Roche O, Deguiz ML, Tiana M, Galiana-Ribote C, Martinez-Alcazar D, Rey-Serra C, Ranz-Ribeiro B, Casitas R, Galera R, Fernández-Navarro I, Sánchez-Cuéllar S, Bernard V, Ancochea J, Wasserman WW, García-Rio F, Jimenez B, Del Peso L
PubMed: 27625398

YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses.
Chen CY, Shi W, Balaton BP, Matthews AM, Li Y, Arenillas DJ, Mathelier A, Itoh M, Kawaji H, Lassmann T, Hayashizaki Y, Carninci P, Forrest AR, Brown CJ, Wasserman WW
DOI: 10.1038/srep37324
PubMed: 27857184

Human enhancers harboring specific sequence composition, activity, and genome organization are linked to the immune response
Charles-Henri Lecellier, Wyeth W Wasserman, Anthony Mathelier
DOI: 10.1101/078477

DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo.
Mathelier A, Xin B, Chiu TP, Yang L, Rohs R, Wasserman WW
DOI: 10.1016/j.cels.2016.07.001
PubMed: 27546793

Evaluating the impact of single nucleotide variants on transcription factor binding.
Shi W, Fornes O, Mathelier A, Wasserman WW
PubMed: 27492288

NANS-mediated synthesis of sialic acid is required for brain and skeletal development.
van Karnebeek CD, Bonafé L, Wen XY, Tarailo-Graovac M, Balzano S, Royer-Bertrand B, Ashikov A, Garavelli L, Mammi I, Turolla L, Breen C, Donnai D, Cormier V, Heron D, Nishimura G, Uchikawa S, Campos-Xavier B, Rossi A, Hennet T, Brand-Arzamendi K
DOI: 10.1038/ng.3578
PubMed: 27213289

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs.
Arenillas DJ, Forrest AR, Kawaji H, Lassmann T, FANTOM Consortium, Wasserman WW, Mathelier A
PubMed: 27334471

Exome Sequencing and the Management of Neurometabolic Disorders.
Tarailo-Graovac M, Shyr C, Ross CJ, Horvath GA, Salvarinova R, Ye XC, Zhang LH, Bhavsar AP, Lee JJ, Drögemöller BI, Abdelsayed M, Alfadhel M, Armstrong L, Baumgartner MR, Burda P, Connolly MB, Cameron J, Demos M, Dewan T, Dionne J
DOI: 10.1056/NEJMoa1515792
PubMed: 27276562

DeepCAGE transcriptomics identify HOXD10 as transcription factor regulating lymphatic endothelial responses to VEGF-C.
Klein S, Dieterich LC, Mathelier A, Chong C, Sliwa-Primorac A, Hong YK, Shin JW, Lizio M, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, FANTOM consortium, Carninci P, Hayashizaki Y, Forrest AR, Wasserman WW, Detmar M
PubMed: 27199372

Cytosolic phosphoenolpyruvate carboxykinase deficiency presenting with acute liver failure following gastroenteritis.
Santra S, Cameron JM, Shyr C, Zhang L, Drögemöller B, Ross CJ, Wasserman WW, Wevers RA, Rodenburg RJ, Gupte G, Preece MA, van Karnebeek CD
DOI: 10.1016/j.ymgme.2016.03.001
PubMed: 26971250

Mitochondrial Complex III Deficiency with Ketoacidosis and Hyperglycemia Mimicking Neonatal Diabetes.
Anastasio N, Tarailo-Graovac M, Al-Khalifah R, Legault L, Drogemoller B, Ross CJ, Wasserman WW, van Karnebeek C, Buhas D
PubMed: 27074787

DNA Methylation Profiling in Human Huntington's Disease Brain.
De Souza RA, Islam SA, McEwen LM, Mathelier A, Hill A, Mah SM, Wasserman WW, Kobor MS, Leavitt BR
PubMed: 26953320

Secondary neurotransmitter deficiencies in epilepsy caused by voltage-gated sodium channelopathies: A potential treatment target?
Horvath GA, Demos M, Shyr C, Matthews A, Zhang L, Race S, Stockler-Ipsiroglu S, Van Allen MI, Mancarci O, Toker L, Pavlidis P, Ross CJ, Wasserman WW, Trump N, Heales S, Pope S, Helen Cross J, van Karnebeek CD
DOI: 10.1016/j.ymgme.2015.11.008
PubMed: 26647175

Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters.
Li Y, Chen CY, Wasserman WW
PubMed: 26799292

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles.
Mathelier A, Fornes O, Arenillas DJ, Chen CY, Denay G, Lee J, Shi W, Shyr C, Tan G, Worsley-Hunt R, Zhang AW, Parcy F, Lenhard B, Sandelin A, Wasserman WW
DOI: 10.1093/nar/gkv1176
PubMed: 26531826

Further Validation of the SIGMAR1 c.151+1G>T Mutation as Cause of Distal Hereditary Motor Neuropathy.
Child neurology open
Lee JJY, van Karnebeek CDM, Drögemoller B, Shyr C, Tarailo-Graovac M, Eydoux P, Ross CJ, Wasserman WW, Björnson B, Wu JK
DOI: 10.1177/2329048x16669912
PubMed: 28503617

rAAV-compatible MiniPromoters for restricted expression in the brain and eye.
de Leeuw CN, Korecki AJ, Berry GE, Hickmott JW, Lam SL, Lengyell TC, Bonaguro RJ, Borretta LJ, Chopra V, Chou AY, D'Souza CA, Kaspieva O, Laprise S, McInerny SC, Portales-Casamar E, Swanson-Newman MI, Wong K, Yang GS, Zhou M, Jones SJ
DOI: 10.1186/s13041-016-0232-4
PubMed: 27164903

PAX6 MiniPromoters drive restricted expression from rAAV in the adult mouse retina.
Hickmott JW, Chen CY, Arenillas DJ, Korecki AJ, Lam SL, Molday LL, Bonaguro RJ, Zhou M, Chou AY, Mathelier A, Boye SL, Hauswirth WW, Molday RS, Wasserman WW, Simpson EM
DOI: 10.1038/mtm.2016.51
PubMed: 27556059

The identification of cis-regulatory elements: A review from a machine learning perspective.
Li Y, Chen CY, Kaye AM, Wasserman WW
DOI: 10.1016/j.biosystems.2015.10.002
PubMed: 26499213

DeepCAGE Transcriptomics Reveal an Important Role of the Transcription Factor MAFB in the Lymphatic Endothelium.
Dieterich LC, Klein S, Mathelier A, Sliwa-Primorac A, Ma Q, Hong YK, Shin JW, Hamada M, Lizio M, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, Carninci P, Hayashizaki Y, Forrest AR, Wasserman WW, Detmar M
DOI: 10.1016/j.celrep.2015.10.002
PubMed: 26549461

De novo dominant variants affecting the motor domain of KIF1A are a cause of PEHO syndrome.
Langlois S, Tarailo-Graovac M, Sayson B, Drögemöller B, Swenerton A, Ross CJ, Wasserman WW, van Karnebeek CD
PubMed: 26486474

RMND1 deficiency associated with neonatal lactic acidosis, infantile onset renal failure, deafness, and multiorgan involvement.
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
DOI: 10.1038/ejhg.2014.293
PubMed: 25604853

Cisplatin Nephrotoxicity and Longitudinal Growth in Children With Solid Tumors: A Retrospective Cohort Study.
Jiménez-Triana CA, Castelán-Martínez OD, Rivas-Ruiz R, Jiménez-Méndez R, Medina A, Clark P, Rassekh R, Castañeda-Hernández G, Carleton B, Medeiros M, Canadian Pharmacogenomics Network for Drug Safety Consortium
DOI: 10.1097/MD.0000000000001413
PubMed: 26313789

A SNP in the HTT promoter alters NF-¿B binding and is a bidirectional genetic modifier of Huntington disease.
Becanovic K, Nørremølle A, Neal SJ, Kay C, Collins JA, Arenillas D, Lilja T, Gaudenzi G, Manoharan S, Doty CN, Beck J, Lahiri N, Portales-Casamar E, Warby SC, Connolly C, De Souza RA, REGISTRY Investigators of the European Huntington's Disease Network, Tabrizi SJ, Hermanson O, Langbehn DR
DOI: 10.1038/nn.4014
PubMed: 25938884

Dynamic software design for clinical exome and genome analyses: insights from bioinformaticians, clinical geneticists, and genetic counselors.
Shyr C, Kushniruk A, van Karnebeek CD, Wasserman WW
PubMed: 26117142

GeneYenta: a phenotype-based rare disease case matching tool based on online dating algorithms for the acceleration of exome interpretation.
Gottlieb MM, Arenillas DJ, Maithripala S, Maurer ZD, Tarailo Graovac M, Armstrong L, Patel M, van Karnebeek C, Wasserman WW
DOI: 10.1002/humu.22772
PubMed: 25703386

Expansion of the QARS deficiency phenotype with report of a family with isolated supratentorial brain abnormalities.
Salvarinova R, Ye CX, Rossi A, Biancheri R, Roland EH, Pavlidis P, Ross CJ, Tarailo-Graovac M, Wasserman WW, van Karnebeek CD
DOI: 10.1007/s10048-014-0432-y
PubMed: 25432320

Identification of altered cis-regulatory elements in human disease.
Mathelier A, Shi W, Wasserman WW
DOI: 10.1016/j.tig.2014.12.003
PubMed: 25637093

The statistical geometry of transcriptome divergence in cell-type evolution and cancer.
Liang C, FANTOM Consortium, Forrest AR, Wagner GP
DOI: 10.1038/ncomms7066
PubMed: 25585899

The genotypic and phenotypic spectrum of PIGA deficiency.
Tarailo-Graovac M, Sinclair G, Stockler-Ipsiroglu S, Van Allen M, Rozmus J, Shyr C, Biancheri R, Oh T, Sayson B, Lafek M, Ross CJ, Robinson WP, Wasserman WW, Rossi A, van Karnebeek CD
DOI: 10.1186/s13023-015-0243-8
PubMed: 25885527

Discovery of molecular markers to discriminate corneal endothelial cells in the human body.
Yoshihara M, Ohmiya H, Hara S, Kawasaki S, FANTOM consortium, Hayashizaki Y, Itoh M, Kawaji H, Tsujikawa M, Nishida K
DOI: 10.1371/journal.pone.0117581
PubMed: 25807145

Defects in fatty acid amide hydrolase 2 in a male with neurologic and psychiatric symptoms.
Sirrs S, van Karnebeek CD, Peng X, Shyr C, Tarailo-Graovac M, Mandal R, Testa D, Dubin D, Carbonetti G, Glynn SE, Sayson B, Robinson WP, Han B, Wishart D, Ross CJ, Wasserman WW, Hurwitz TA, Sinclair G, Kaczocha M
DOI: 10.1186/s13023-015-0248-3
PubMed: 25885783

Combined serial analysis of gene expression and transcription factor binding site prediction identifies novel-candidate-target genes of Nr2e1 in neocortex development.
Schmouth JF, Arenillas D, Corso-Díaz X, Xie YY, Bohacec S, Banks KG, Bonaguro RJ, Wong SH, Jones SJ, Marra MA, Simpson EM, Wasserman WW
DOI: 10.1186/s12864-015-1770-3
PubMed: 26204903

Genetic variants in SLC22A17 and SLC22A7 are associated with anthracycline-induced cardiotoxicity in children.
Visscher H, Rassekh SR, Sandor GS, Caron HN, van Dalen EC, Kremer LC, van der Pal HJ, Rogers PC, Rieder MJ, Carleton BC, Hayden MR, Ross CJ, CPNDS consortium
DOI: 10.2217/pgs.15.61
PubMed: 26230641

Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas.
Mathelier A, Lefebvre C, Zhang AW, Arenillas DJ, Ding J, Wasserman WW, Shah SP
DOI: 10.1186/s13059-015-0648-7
PubMed: 25903198

Usability study of clinical exome analysis software: Top lessons learned and recommendations
Journal of Biomedical Informatics
Casper Shyr, Andre Kushniruk, Wyeth W. Wasserman
DOI: 10.1016/j.jbi.2014.05.004

Exome sequencing identifies mutations in KIF14 as a novel cause of an autosomal recessive lethal fetal ciliopathy phenotype.
Filges I, Nosova E, Bruder E, Tercanli S, Townsend K, Gibson WT, Röthlisberger B, Heinimann K, Hall JG, Gregory-Evans CY, Wasserman WW, Miny P, Friedman JM
DOI: 10.1111/cge.12301
PubMed: 24128419

AIMP1 deficiency presents as a cortical neurodegenerative disease with infantile onset.
Armstrong L, Biancheri R, Shyr C, Rossi A, Sinclair G, Ross CJ, Tarailo-Graovac M, Wasserman WW, van Karnebeek CD
DOI: 10.1007/s10048-014-0411-3
PubMed: 24958424

Strabismus genetics across a spectrum of eye misalignment disorders.
Ye XC, Pegado V, Patel MS, Wasserman WW
DOI: 10.1111/cge.12367
PubMed: 24579652

DNAJC13 mutations in Parkinson disease.
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
DOI: 10.1093/hmg/ddt570
PubMed: 24218364

Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation.
Morikawa H, Ohkura N, Vandenbon A, Itoh M, Nagao-Sato S, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR, Standley DM, Date H, Sakaguchi S, FANTOM Consortium
DOI: 10.1073/pnas.1312717110
PubMed: 24706905

Higher frequency of genetic variants conferring increased risk for ADRs for commonly used drugs treating cancer, AIDS and tuberculosis in persons of African descent.
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, Canadian Pharmacogenomics Network for Drug Safety Consortium
DOI: 10.1038/tpj.2013.13
PubMed: 23588107

A promoter-level mammalian expression atlas.
FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmidl C
DOI: 10.1038/nature13182
PubMed: 24670764

An atlas of active enhancers across human cell types and tissues.
Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO
DOI: 10.1038/nature12787
PubMed: 24670763

Mitochondrial Carbonic Anhydrase VA Deficiency Resulting from CA5A Alterations Presents with Hyperammonemia in Early Childhood
The American Journal of Human Genetics
Clara D. van Karnebeek, William S. Sly, Colin J. Ross, Ramona Salvarinova, Joy Yaplito-Lee, Saikat Santra, Casper Shyr, Gabriella A. Horvath, Patrice Eydoux, Anna M. Lehman, Virginie Bernard, Theresa Newlove, Henry Ukpeh, Anupam Chakrapani, Mary Anne Preece, Sarah Ball, James Pitt, Hilary D. Vallance, Marion Coulter-Mackie, Hien Nguyen, Lin-Hua Zhang, Amit P. Bhavsar, Graham Sinclair, Abdul Waheed, Wyeth W. Wasserman, Sylvia Stockler-Ipsiroglu
DOI: 10.1016/j.ajhg.2014.01.006

Targeted CNS delivery using human MiniPromoters and demonstrated compatibility with adeno-associated viral vectors
Mol Ther Methods Clin Dev
Charles N de Leeuw, Frank M Dyka, Sanford L Boye, Stéphanie Laprise, Michelle Zhou, Alice Y Chou, Lisa Borretta, Simone C McInerny, Kathleen G Banks, Elodie Portales-Casamar, Magdalena I Swanson, Cletus A D’Souza, Shannon E Boye, Steven JM Jones, Robert A Holt, Daniel Goldowitz, William W Hauswirth, Wyeth W Wasserman, Elizabeth M Simpson
DOI: 10.1038/mtm.2013.5

TFBSshape: a motif database for DNA shape features of transcription factor binding sites.
Yang L, Zhou T, Dror I, Mathelier A, Wasserman WW, Gordân R, Rohs R
DOI: 10.1093/nar/gkt1087
PubMed: 24214955

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles.
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
DOI: 10.1093/nar/gkt997
PubMed: 24194598

Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells.
Arner E, Forrest AR, Ehrlund A, Mejhert N, Itoh M, Kawaji H, Lassmann T, Laurencikiene J, Rydén M, Arner P, FANTOM Consortium
DOI: 10.1371/journal.pone.0080274
PubMed: 24676332

On the identification of potential regulatory variants within genome wide association candidate SNP sets
BMC Medical Genomics
Chih-yu Chen, I-Shou Chang, Chao A Hsiung, Wyeth W Wasserman
DOI: 10.1186/1755-8794-7-34

Single point mutation in Rabenosyn-5 in a female with intractable seizures and evidence of defective endocytotic trafficking
Orphanet Journal of Rare Diseases
Sylvia Stockler, Silvia Corvera, David Lambright, Kevin Fogarty, Ekaterina Nosova, Deborah Leonard, Robert Steinfeld, Cameron Ackerley, Casper Shyr, Nicolas Au, Kathrin Selby, Margot van Allen, Hilary Vallance, Ron Wevers, David Watkins, David Rosenblatt, Colin J Ross, Elizabeth Conibear, Wyeth Wasserman, Clara van Karnebeek
DOI: 10.1186/s13023-014-0141-5

Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment
BMC Genomics
Rebecca Worsley Hunt, Anthony Mathelier, Luis del Peso, Wyeth W Wasserman
DOI: 10.1186/1471-2164-15-472

Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets.
Worsley Hunt R, Wasserman WW
DOI: 10.1186/PREACCEPT-1454983695127944
PubMed: 25070602

Exome sequencing pilot study in children with carbamazepine-induced serious skin reactions
Clinical and Translational Allergy
Ursula Amstutz, Casper Shyr, Neil H Shear, Michael J Rieder, Wyeth W Wasserman, Colin J Ross, Bruce C Carleton
DOI: 10.1186/2045-7022-4-s3-p119

FLAGS, frequently mutated genes in public exomes.
Shyr C, Tarailo-Graovac M, Gottlieb M, Lee JJ, van Karnebeek C, Wasserman WW
DOI: 10.1186/s12920-014-0064-y
PubMed: 25466818

CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes.
Hasegawa Y, Tang D, Takahashi N, Hayashizaki Y, Forrest AR, FANTOM Consortium, Suzuki H
DOI: 10.1038/srep05228
PubMed: 24957798

Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets
Genome Biology
Rebecca Worsley Hunt, Wyeth W Wasserman
DOI: 10.1186/s13059-014-0412-4

Validation of variants in SLC28A3 and UGT1A6 as genetic markers predictive of anthracycline-induced cardiotoxicity in children.
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, CPNDS Consortium
DOI: 10.1002/pbc.24505
PubMed: 23441093

The next generation of transcription factor binding site prediction.
Mathelier A, Wasserman WW
DOI: 10.1371/journal.pcbi.1003214
PubMed: 24039567

Compensating for literature annotation bias when predicting novel drug-disease relationships through Medical Subject Heading Over-representation Profile (MeSHOP) similarity.
Cheung WA, Ouellette BF, Wasserman WW
DOI: 10.1186/1755-8794-6-S3-S3
PubMed: 23819887

Utilizing social media to study information-seeking and ethical issues in gene therapy.
Robillard JM, Whiteley L, Johnson TW, Lim J, Wasserman WW, Illes J
DOI: 10.2196/jmir.2313
PubMed: 23470490

Non-coding-regulatory regions of human brain genes delineated by bacterial artificial chromosome knock-in mice.
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
DOI: 10.1186/1741-7007-11-106
PubMed: 24124870

Portal for Families Overcoming Neurodevelopmental Disorders (PFOND): Implementation of a Software Framework for Facilitated Community Website Creation by Nontechnical Volunteers.
Ye XC, Ng I, Seid-Karbasi P, Imam T, Lee CE, Chen SY, Herman A, Sharma B, Johal G, Gu B, Wasserman WW
DOI: 10.2196/resprot.2675
PubMed: 23920006

oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets.
Kwon AT, Arenillas DJ, Worsley Hunt R, Wasserman WW
DOI: 10.1534/g3.112.003202
PubMed: 22973536

The clonal and mutational evolution spectrum of primary triple-negative breast cancers.
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
DOI: 10.1038/nature10933
PubMed: 22495314

Retina restored and brain abnormalities ameliorated by single-copy knock-in of human NR2E1 in null mice.
Schmouth JF, Banks KG, Mathelier A, Gregory-Evans CY, Castellarin M, Holt RA, Gregory-Evans K, Wasserman WW, Simpson EM
DOI: 10.1128/MCB.06016-11
PubMed: 22290436

Quantitative biomedical annotation using medical subject heading over-representation profiles (MeSHOPs).
Cheung WA, Ouellette BF, Wasserman WW
DOI: 10.1186/1471-2105-13-249
PubMed: 23017167

The transcription factor encyclopedia.
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
DOI: 10.1186/gb-2012-13-3-r24
PubMed: 22458515

Inferring novel gene-disease associations using Medical Subject Heading Over-representation Profiles.
Cheung WA, Ouellette BF, Wasserman WW
DOI: 10.1186/gm376
PubMed: 23021552

Validation of skeletal muscle cis-regulatory module predictions reveals nucleotide composition bias in functional enhancers.
Kwon AT, Chou AY, Arenillas DJ, Wasserman WW
DOI: 10.1371/journal.pcbi.1002256
PubMed: 22144875

Towards resolving the transcription factor network controlling myelin gene expression.
Fulton DL, Denarier E, Friedman HC, Wasserman WW, Peterson AC
DOI: 10.1093/nar/gkr326
PubMed: 21729871

VPS35 Mutations in Parkinson Disease.
Vilari?o-G?ell C, Wider C, Ross O, Dachsel J, Kachergus J, Lincoln S, Soto-Ortolaza A, Cobb S, Wilhoite G, Bacon J, Behrouz B, Melrose H, Hentati E, Puschmann A, Evans D, Conibear E, Wasserman W, Aasly J, Burkhard P, Djaldetti R
DOI: 10.1016/j.ajhg.2011.07.018

VPS35 mutations in Parkinson disease.
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
DOI: 10.1016/j.ajhg.2011.06.001
PubMed: 21763482

The NeuroDevNet Neuroinformatics Core.
Portales-Casamar E, Evans A, Wasserman W, Pavlidis P
DOI: 10.1016/j.spen.2011.02.001
PubMed: 21575836

MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model.
Le Béchec A, Portales-Casamar E, Vetter G, Moes M, Zindy PJ, Saumet A, Arenillas D, Theillet C, Wasserman WW, Lecellier CH, Friederich E
DOI: 10.1186/1471-2105-12-67
PubMed: 21375730

Identification of cis-regulatory sequence variations in individual genome sequences.
Worsley-Hunt R, Bernard V, Wasserman WW
DOI: 10.1186/gm281
PubMed: 21989199

A regulatory toolbox of MiniPromoters to drive selective expression in the brain.
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
DOI: 10.1073/pnas.1009158107
PubMed: 20807748

Global mapping of binding sites for Nrf2 identifies novel targets in cell survival response through ChIP-Seq profiling and network analysis.
Malhotra D, Portales-Casamar E, Singh A, Srivastava S, Arenillas D, Happel C, Shyr C, Wakabayashi N, Kensler TW, Wasserman WW, Biswal S
DOI: 10.1093/nar/gkq212
PubMed: 20460467

The Canadian Pharmacogenomics Network for Drug Safety: a model for safety pharmacology.
Ross CJ, Visscher H, Sistonen J, Brunham LR, Pussegoda K, Loo TT, Rieder MJ, Koren G, Carleton BC, Hayden MR, CPNDS Consortium
DOI: 10.1089/thy.2010.1642
PubMed: 20578893

Laboratory Animal Management Assistant (LAMA): a LIMS for active research colonies.
Milisavljevic M, Hearty T, Wong TY, Portales-Casamar E, Simpson EM, Wasserman WW
DOI: 10.1007/s00335-010-9258-6
PubMed: 20411264

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles.
Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, Valen E, Yusuf D, Lenhard B, Wasserman WW, Sandelin A
DOI: 10.1093/nar/gkp950
PubMed: 19906716

Genetic variants in TPMT and COMT are associated with hearing loss in children receiving cisplatin chemotherapy.
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
DOI: 10.1038/ng.478
PubMed: 19898482

The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences.
Portales-Casamar E, Arenillas D, Lim J, Swanson MI, Jiang S, McCallum A, Kirov S, Wasserman WW
DOI: 10.1093/nar/gkn783
PubMed: 18971253

Transcriptional repression of microRNA genes by PML-RARA increases expression of key cancer proteins in acute promyelocytic leukemia.
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
DOI: 10.1182/blood-2008-05-158139
PubMed: 18941112

TFCat: the curated catalog of mouse and human transcription factors.
Fulton DL, Sundararajan S, Badis G, Hughes TR, Wasserman WW, Roach JC, Sladek R
DOI: 10.1186/gb-2009-10-3-r29
PubMed: 19284633

Mechanisms underlying p53 regulation of PIK3CA transcription in ovarian surface epithelium and in ovarian cancer.
Astanehe A, Arenillas D, Wasserman WW, Leung PC, Dunn SE, Davies BR, Mills GB, Auersperg N
DOI: 10.1242/jcs.013029
PubMed: 18270270

Dynamics of the yeast transcriptome during wine fermentation reveals a novel fermentation stress response.
Marks VD, Ho Sui SJ, Erasmus D, van der Merwe GK, Brumm J, Wasserman WW, Bryan J, van Vuuren HJ
DOI: 10.1111/j.1567-1364.2007.00338.x
PubMed: 18215224

In silico detection of sequence variations modifying transcriptional regulation.
Andersen MC, Engström PG, Lithwick S, Arenillas D, Eriksson P, Lenhard B, Wasserman WW, Odeberg J
DOI: 10.1371/journal.pcbi.0040005
PubMed: 18208319

ORegAnno: an open-access community-driven resource for regulatory annotation.
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
DOI: 10.1093/nar/gkm967
PubMed: 18006570

Gene characterization index: assessing the depth of gene annotation.
Kemmer D, Podowski RM, Yusuf D, Brumm J, Cheung W, Wahlestedt C, Lenhard B, Wasserman WW
DOI: 10.1371/journal.pone.0001440
PubMed: 18213364

Identification of a set of genes showing regionally enriched expression in the mouse brain.
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
DOI: 10.1186/1471-2202-9-66
PubMed: 18625066

Discovery and expansion of gene modules by seeking isolated groups in a random graph process.
Brumm J, Conibear E, Wasserman WW, Bryan J
DOI: 10.1371/journal.pone.0003358
PubMed: 18843375

oPOSSUM: integrated tools for analysis of regulatory motif over-representation.
Ho Sui SJ, Fulton DL, Arenillas DJ, Kwon AT, Wasserman WW
DOI: 10.1093/nar/gkm427
PubMed: 17576675

PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation.
Portales-Casamar E, Kirov S, Lim J, Lithwick S, Swanson MI, Ticoll A, Snoddy J, Wasserman WW
DOI: 10.1186/gb-2007-8-10-r207
PubMed: 17916232

SAGE2Splice: unmapped SAGE tags reveal novel splice junctions.
Kuo BY, Chen Y, Bohacec S, Johansson O, Wasserman WW, Simpson EM
DOI: 10.1371/journal.pcbi.0020034
PubMed: 16683015

A new generation of JASPAR, the open-access repository for transcription factor binding site profiles.
Vlieghe D, Sandelin A, De Bleser PJ, Vleminckx K, Wasserman WW, van Roy F, Lenhard B
DOI: 10.1093/nar/gkj115
PubMed: 16381983

NovelFam3000--uncharacterized human protein domains conserved across model organisms.
Kemmer D, Podowski RM, Arenillas D, Lim J, Hodges E, Roth P, Sonnhammer EL, Höög C, Wasserman WW
DOI: 10.1186/1471-2164-7-48
PubMed: 16533400

Complete functional rescue of the ABCA1-/- mouse by human BAC transgenesis.
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
DOI: 10.1194/jlr.M400506-JLR200
PubMed: 15772424

Prediction of nuclear hormone receptor response elements.
Sandelin A, Wasserman WW
DOI: 10.1210/me.2004-0101
PubMed: 15563547

Ulysses - an application for the projection of molecular interactions across species.
Kemmer D, Huang Y, Shah SP, Lim J, Brumm J, Yuen MM, Ling J, Xu T, Wasserman WW, Ouellette BF
DOI: 10.1186/gb-2005-6-12-r106
PubMed: 16356269

oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes.
Ho Sui SJ, Mortimer JR, Arenillas DJ, Brumm J, Walsh CJ, Kennedy BP, Wasserman WW
DOI: 10.1093/nar/gki624
PubMed: 15933209

Identification of functional SNPs in the 5-prime flanking sequences of human genes.
Mottagui-Tabar S, Faghihi MA, Mizuno Y, Engström PG, Lenhard B, Wasserman WW, Wahlestedt C
DOI: 10.1186/1471-2164-6-18
PubMed: 15717931

The Gene Set Builder: collation, curation, and distribution of sets of genes.
Yusuf D, Lim JS, Wasserman WW
DOI: 10.1186/1471-2105-6-305
PubMed: 16371163

Transcriptional promoters
Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics
Wyeth W. Wasserman
DOI: 10.1002/047001153x.g203309

Decoding human regulatory circuits.
Thompson W, Palumbo MJ, Wasserman WW, Liu JS, Lawrence CE
DOI: 10.1101/gr.2589004
PubMed: 15466295

ConSite: web-based prediction of regulatory elements using cross-species comparison.
Sandelin A, Wasserman WW, Lenhard B
DOI: 10.1093/nar/gkh372
PubMed: 15215389

Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus.
Alkema WB, Lenhard B, Wasserman WW
DOI: 10.1101/gr.2242604
PubMed: 15231752

MSCAN: identification of functional clusters of transcription factor binding sites.
Alkema WB, Johansson O, Lagergren J, Wasserman WW
DOI: 10.1093/nar/gkh387
PubMed: 15215379

Applied bioinformatics for the identification of regulatory elements.
Wasserman WW, Sandelin A
DOI: 10.1038/nrg1315
PubMed: 15131651

Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics.
Sandelin A, Wasserman WW
DOI: 10.1016/j.jmb.2004.02.048
PubMed: 15066426

JASPAR: an open-access database for eukaryotic transcription factor binding profiles.
Sandelin A, Alkema W, Engström P, Wasserman WW, Lenhard B
DOI: 10.1093/nar/gkh012
PubMed: 14681366

Exploring the foundation of genomics: a northern blot reference set for the comparative analysis of transcript profiling technologies.
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
DOI: 10.1002/cfg.443
PubMed: 18629180

Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes.
Sandelin A, Bailey P, Bruce S, Engström PG, Klos JM, Wasserman WW, Ericson J, Lenhard B
DOI: 10.1186/1471-2164-5-99
PubMed: 15613238

Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes.
Sandelin A, Höglund A, Lenhard B, Wasserman WW
DOI: 10.1007/s10142-003-0086-6
PubMed: 12827523

GeneLynx mouse: integrated portal to the mouse genome.
Lenhard B, Wahlestedt C, Wasserman WW
DOI: 10.1101/gr.951403
PubMed: 12819149

In silico identification of metazoan transcriptional regulatory regions.
Wasserman WW, Krivan W
PubMed: 12712249

Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm.
Johansson O, Alkema W, Wasserman WW, Lagergren J
DOI: 10.1093/bioinformatics/btg1021
PubMed: 12855453

Identification of conserved regulatory elements by comparative genome analysis.
Lenhard B, Sandelin A, Mendoza L, Engström P, Jareborg N, Wasserman WW
DOI: 10.1186/1475-4924-2-13
PubMed: 12760745

Understanding the language of gene regulation.
Alkema W, Wasserman WW
DOI: 10.1186/gb-2003-4-7-327
PubMed: 12844355

TFBS: Computational framework for transcription factor binding site analysis.
Lenhard B, Wasserman WW
DOI: 10.1093/bioinformatics/18.8.1135
PubMed: 12176838

NotI flanking sequences: a tool for gene discovery and verification of the human genome.
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
DOI: 10.1093/nar/gkf428
PubMed: 12136098

GeneLynx: a gene-centric portal to the human genome.
Lenhard B, Hayes WS, Wasserman WW
DOI: 10.1101/gr.199801
PubMed: 11731507

A predictive model for regulatory sequences directing liver-specific transcription.
Krivan W, Wasserman WW
DOI: 10.1101/gr.180601
PubMed: 11544200

Phylogenetic Footprinting
Encyclopedia of Life Sciences
Wyeth W Wasserman, Wynand Alkema
DOI: 10.1002/9780470015902.a0005091.pub2

Phylogenetic Footprinting
Encyclopedia of Life Sciences
Wyeth W Wasserman, Wynand Alkema
DOI: 10.1038/npg.els.0005091

Initial isolation and analysis of the human Kv1.7 (KCNA7) gene, a member of the voltage-gated potassium channel gene family.
Kashuba VI, Kvasha SM, Protopopov AI, Gizatullin RZ, Rynditch AV, Wahlestedt C, Wasserman WW, Zabarovsky ER
DOI: 10.1016/S0378-1119(01)00423-1
PubMed: 11368907

Polymorphic electrophile response elements in the mouse glutathione S-transferase GSTa1 gene that confer increased induction.
Zhu M, Chapman WG, Oberley MJ, Wasserman WW, Fahl WE
DOI: 10.1016/S0304-3835(00)00664-9
PubMed: 11179824

Structure and function of adenosine receptors and their genes.
Fredholm BB, Arslan G, Halldner L, Kull B, Schulte G, Wasserman W
DOI: 10.1007/s002100000313
PubMed: 11111830

Human-mouse genome comparisons to locate regulatory sites.
Wasserman WW, Palumbo M, Thompson W, Fickett JW, Lawrence CE
DOI: 10.1038/79965
PubMed: 11017083

Discovery and modeling of transcriptional regulatory regions.
Fickett JW, Wasserman WW
DOI: 10.1016/S0958-1669(99)00049-X
PubMed: 10679343

The murine Bin1 gene functions early in myogenesis and defines a new region of synteny between mouse chromosome 18 and human chromosome 2.
Mao NC, Steingrimsson E, DuHadaway J, Wasserman W, Ruiz JC, Copeland NG, Jenkins NA, Prendergast GC
DOI: 10.1006/geno.1998.5709
PubMed: 10036185

Organization of the ABCR gene: analysis of promoter and splice junction sequences.
Allikmets R, Wasserman WW, Hutchinson A, Smallwood P, Nathans J, Rogan PK, Schneider TD, Dean M
DOI: 10.1016/S0378-1119(98)00269-8
PubMed: 9666097

Molecular cloning of a novel mouse gene with predominant muscle and neural expression.
Geisler JG, Stubbs LJ, Wasserman WW, Mucenski ML
DOI: 10.1007/s003359900748
PubMed: 9530622

Identification of regulatory regions which confer muscle-specific gene expression.
Wasserman WW, Fickett JW
DOI: 10.1006/jmbi.1998.1700
PubMed: 9571041

CBP/cycA, a CCAAT-binding protein necessary for adhesion-dependent cyclin A transcription, consists of NF-Y and a novel Mr 115,000 subunit.
Krämer A, Carstens CP, Wasserman WW, Fahl WE
PubMed: 9371512

Comprehensive analysis of proteins which interact with the antioxidant responsive element: correlation of ARE-BP-1 with the chemoprotective induction response.
Wasserman WW, Fahl WE
DOI: 10.1006/abbi.1997.0215
PubMed: 9264553

Functional antioxidant responsive elements.
Wasserman WW, Fahl WE
DOI: 10.1073/pnas.94.10.5361
PubMed: 9144242

Analysis of R59022 actions in Xenopus laevis oocytes.
Sadler SE, Frith T, Wasserman WJ
DOI: 10.1002/(SICI)1097-010X(19960401)274:53.3.CO;2-O
PubMed: 8618105

Spread of X-chromosome inactivation
PubMed: 24158853


Applied Bioinformatics
At the CMMT we maintain a strong link between research and application. We work closely with our collaborators to impact human health. At present we are engineering regulatory sequences to direct gene expression selectively to target cells and tissues in the CanEuCre/Pleiades Promoter Project. With partners at BC Children’s Hospital, we are developing methods for efficient analysis of exome and genome sequences for children with genetic disorders.

Identification and Analysis of Sequences Regulating Transcription
Regulatory sequence analysis is complicated by a signal-to-noise problem. Transcription is regulated at one level by proteins that bind to short segments of DNA. These transcription factors activate or suppress gene activity by modulating the recruitment of RNA polymerase enzymes to the beginning of genes. As the target sequences for transcription factors are short, and transcription factors are tolerant of considerable variation in the sequences to which they bind, it is extremely difficult to distinguish functional binding sites in the vastness of the human genome.

Using high-throughput ChIP-Seq and chromatin property data, we are developing a new generation of bioinformatics methods for the identification of regulatory sequences. Our work is increasingly focused on coupling the regulatory region discrimination with the interpretation of mutations detected by whole genome sequencing.


Genome Canada Disruptive Innovations Grant

NSERC Discovery Grant

Genome Canada Silent Genomes Project

Honours & Awards

Career Investigator Award, Michael Smith Foundation for Health Research (MSFHR), 2004-2009.

National Merit Scholar, National Merit Program, 1987-1988.

Valedictorian, James A. Garfield High School, Seattle, Washington, 1987.

UBC Killam Teaching Prize, 2013.

Cremer Scholar, University of Wisconsin School of Medicine, 1992-1996.

New Investigator Award, Canadian Institutes of Health Research (CIHR), 2004-2009.

Seattle 's Young Achiever of the Year / American Academy of Achievement Honoree, 1987.

Washington Scholar, Washington State Legislature, 1987-1991.

Basic Science Teaching Award, Department of Medical Genetics, University of British Columbia, 2011.

Wisconsin Alumni Research Foundation Fellow, 1991-1992.

Paul Fowler Scholar, Washington State Legislature, 1987-1991.

Robert Byrd Scholar, United States Senate, 1987-1988.

Research Group Members

Alice Kaye
Wenqiang Shi
Jessica Lee
Allen Zhang
Xin (Cynthia) Ye
Phillip Richmond, PhD Candidate
Rachelle Farkas
Ahmad Shikib Mehri, Student
Coulter Beeson, Student
Oriol Fornés Crespo
Eric Lee, Undergraduate Student
Tamar Av-Shalom, Undergraduate Student
Robin van der Lee
William Qi, Student
German Novakovskiy
Kevin Zhang
Edwin Zhou
Owen Tsai
Lap-Tak Chu
Jessica Zhang
Danique van Vliet, Graduate Student
Taylor Lundy