Overview

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.

Publications

Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer.
Cell
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
05/2018

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
05/2018

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
05/2018

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
04/2018

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
03/2018

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
01/2018

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
01/2018

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
01/2018

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
01/2018

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
01/2018

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
01/2018

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
01/2018

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
12/2017

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
11/2017

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
10/2017

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
09/2017

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
07/2017

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
05/2017

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
04/2017

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
03/2017

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
03/2017

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
02/2017

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
01/2017

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
11/2016

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
11/2016

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
09/2016

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
09/2016

Evaluating the impact of single nucleotide variants on transcription factor binding.
Shi W, Fornes O, Mathelier A, Wasserman WW
PubMed: 27492288
08/2016

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
07/2016

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
06/2016

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
06/2016

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
05/2016

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
05/2016

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
04/2016

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
03/2016

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
01/2016

Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters.
Li Y, Chen CY, Wasserman WW
PubMed: 26799292
01/2016

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
01/2016

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
2016

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
2016

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
2016

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
12/2015

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
11/2015

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
10/2015

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
10/2015

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
08/2015

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
06/2015

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
06/2015

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
04/2015

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
04/2015

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
02/2015

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
2015

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
2015

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
2015

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
2015

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
2015

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
2015

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
2015

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
10/2014

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
09/2014

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
08/2014

Strabismus genetics across a spectrum of eye misalignment disorders.
Ye XC, Pegado V, Patel MS, Wasserman WW
DOI: 10.1111/cge.12367
PubMed: 24579652
08/2014

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
04/2014

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
04/2014

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
04/2014

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
03/2014

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
03/2014

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
03/2014

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
01/2014

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
01/2014

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
01/2014

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
2014

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
2014

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
2014

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
2014

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
2014

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
2014

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
2014

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
2014

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
2014

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
08/2013

The next generation of transcription factor binding site prediction.
Mathelier A, Wasserman WW
DOI: 10.1371/journal.pcbi.1003214
PubMed: 24039567
2013

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
2013

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
2013

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
2013

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
2013

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
09/2012

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
06/2012

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
04/2012

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
2012

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
2012

Inferring novel gene-disease associations using Medical Subject Heading Over-representation Profiles.
Cheung WA, Ouellette BF, Wasserman WW
DOI: 10.1186/gm376
PubMed: 23021552
2012

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
12/2011

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
10/2011

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
08/2011

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
07/2011

The NeuroDevNet Neuroinformatics Core.
Portales-Casamar E, Evans A, Wasserman W, Pavlidis P
DOI: 10.1016/j.spen.2011.02.001
PubMed: 21575836
03/2011

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
2011

Identification of cis-regulatory sequence variations in individual genome sequences.
Worsley-Hunt R, Bernard V, Wasserman WW
DOI: 10.1186/gm281
PubMed: 21989199
2011

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
09/2010

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
09/2010

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
07/2010

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
06/2010

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
01/2010

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
12/2009

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
01/2009

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
01/2009

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
2009

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
03/2008

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
02/2008

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
01/2008

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
01/2008

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
2008

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
2008

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
2008

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
07/2007

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
2007

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
04/2006

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
01/2006

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
2006

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
06/2005

Prediction of nuclear hormone receptor response elements.
Sandelin A, Wasserman WW
DOI: 10.1210/me.2004-0101
PubMed: 15563547
03/2005

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
2005

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
2005

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
2005

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
2005

Transcriptional promoters
Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics
Wyeth W. Wasserman
DOI: 10.1002/047001153x.g203309
10/2004

Decoding human regulatory circuits.
Thompson W, Palumbo MJ, Wasserman WW, Liu JS, Lawrence CE
DOI: 10.1101/gr.2589004
PubMed: 15466295
10/2004

ConSite: web-based prediction of regulatory elements using cross-species comparison.
Sandelin A, Wasserman WW, Lenhard B
DOI: 10.1093/nar/gkh372
PubMed: 15215389
07/2004

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
07/2004

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
07/2004

Applied bioinformatics for the identification of regulatory elements.
Wasserman WW, Sandelin A
DOI: 10.1038/nrg1315
PubMed: 15131651
04/2004

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
04/2004

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
01/2004

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
2004

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
2004

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
07/2003

GeneLynx mouse: integrated portal to the mouse genome.
Lenhard B, Wahlestedt C, Wasserman WW
DOI: 10.1101/gr.951403
PubMed: 12819149
06/2003

In silico identification of metazoan transcriptional regulatory regions.
Wasserman WW, Krivan W
PubMed: 12712249
04/2003

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
2003

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
2003

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

TFBS: Computational framework for transcription factor binding site analysis.
Lenhard B, Wasserman WW
DOI: 10.1093/bioinformatics/18.8.1135
PubMed: 12176838
08/2002

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
07/2002

GeneLynx: a gene-centric portal to the human genome.
Lenhard B, Hayes WS, Wasserman WW
DOI: 10.1101/gr.199801
PubMed: 11731507
12/2001

A predictive model for regulatory sequences directing liver-specific transcription.
Krivan W, Wasserman WW
DOI: 10.1101/gr.180601
PubMed: 11544200
09/2001

Phylogenetic Footprinting
Encyclopedia of Life Sciences
Wyeth W Wasserman, Wynand Alkema
DOI: 10.1002/9780470015902.a0005091.pub2
05/2001

Phylogenetic Footprinting
Encyclopedia of Life Sciences
Wyeth W Wasserman, Wynand Alkema
DOI: 10.1038/npg.els.0005091
05/2001

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
05/2001

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
03/2001

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
11/2000

Human-mouse genome comparisons to locate regulatory sites.
Wasserman WW, Palumbo M, Thompson W, Fickett JW, Lawrence CE
DOI: 10.1038/79965
PubMed: 11017083
10/2000

Discovery and modeling of transcriptional regulatory regions.
Fickett JW, Wasserman WW
DOI: 10.1016/S0958-1669(99)00049-X
PubMed: 10679343
02/2000

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
02/1999

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
07/1998

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
04/1998

Identification of regulatory regions which confer muscle-specific gene expression.
Wasserman WW, Fickett JW
DOI: 10.1006/jmbi.1998.1700
PubMed: 9571041
04/1998

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
11/1997

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
08/1997

Functional antioxidant responsive elements.
Wasserman WW, Fahl WE
DOI: 10.1073/pnas.94.10.5361
PubMed: 9144242
05/1997

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
04/1996

Spread of X-chromosome inactivation
PubMed: 24158853

Research

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.

Grants

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