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

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

Mitochondrial Complex III Deficiency with Ketoacidosis and Hyperglycemia Mimicking Neonatal Diabetes.
Anastasio N and Tarailo-Graovac M and Al-Khalifah R and Legault L and Drogemoller B and Ross CJ and Wasserman WW and van Karnebeek C and Buhas D
PubMed: 27074787
04/2016

DeepCAGE Transcriptomics Reveal an Important Role of the Transcription Factor MAFB in the Lymphatic Endothelium.
Dieterich LC and Klein S and Mathelier A and Sliwa-Primorac A and Ma Q and Hong YK and Shin JW and Hamada M and Lizio M and Itoh M and Kawaji H and Lassmann T and Daub CO and Arner E and Carninci P and Hayashizaki Y and Forrest AR and Wasserman WW and Detmar M
DOI: 10.1016/j.celrep.2015.10.002
PubMed: 26549461
11/2015

PAX6 MiniPromoters drive restricted expression from rAAV in the adult mouse retina.
Hickmott JW and Chen CY and Arenillas DJ and Korecki AJ and Lam SL and Molday LL and Bonaguro RJ and Zhou M and Chou AY and Mathelier A and Boye SL and Hauswirth WW and Molday RS and Wasserman WW and Simpson EM
DOI: 10.1038/mtm.2016.51
PubMed: 27556059
2016

CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes.
Hasegawa Y and Tang D and Takahashi N and Hayashizaki Y and Forrest AR and FANTOM Consortium and Suzuki H
DOI: 10.1038/srep05228
PubMed: 24957798
2014

Further Validation of the SIGMAR1 c.151+1G>T Mutation as Cause of Distal Hereditary Motor Neuropathy.
Child neurology open
Lee JJY and van Karnebeek CDM and Drögemoller B and Shyr C and Tarailo-Graovac M and Eydoux P and Ross CJ and Wasserman WW and Björnson B and Wu JK
DOI: 10.1177/2329048x16669912
PubMed: 28503617
2016

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 and Michael M. Gottlieb and Jake Lever and Steven J. M. Jones and Nenad Blau and Clara D. M. van Karnebeek and 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 and Lee J and Price M and Tarailo-Graovac M and Matthews A and Engelke U and Tang J and Kluijtmans LAJ and Wevers RA and Wasserman WW and van Karnebeek CDM and Mostafavi S
DOI: 10.1007/s10545-018-0139-6
PubMed: 29721916
05/2018

Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer.
Cell
Zhang AW and McPherson A and Milne K and Kroeger DR and Hamilton PT and Miranda A and Funnell T and Little N and de Souza CPE and Laan S and LeDoux S and Cochrane DR and Lim JLP and Shah SP
DOI: 10.1016/j.cell.2018.03.073
PubMed: 29754820
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 and Tarailo-Graovac M and Meijer J and Drogemoller B and Vockley J and Maurer D and Dobritzsch D and Ross CJ and Wasserman W and Meinsma R and Zoetekouw L and van Karnebeek CDM
DOI: 10.1002/humu.23538
PubMed: 29691939
04/2018

Bone health and SATB2-associated syndrome.
Clinical genetics
Zarate YA and Steinraths M and Matthews A and Smith WE and Sun A and Wilson LC and Brain C and Allgove J and Jacobs B and Fish JL and Powell CM and Wasserman WW and van Karnebeek CD and Ma NS
DOI: 10.1111/cge.13121
PubMed: 28787087
03/2018

The role of the clinician in the multi-omics era: are you ready?
Journal of inherited metabolic disease
van Karnebeek CDM and Wortmann SB and Tarailo-Graovac M and Langeveld M and Ferreira CR and van de Kamp JM and Hollak CE and Wasserman WW and Waterham HR and Wevers RA and Boycott KM
DOI: 10.1007/s10545-017-0128-1
PubMed: 29362952
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 and Wasserman WW and Hoffmann GF and van Karnebeek CDM and Blau N
DOI: 10.1038/gim.2017.108
PubMed: 28726811
01/2018

The genotypic and phenotypic spectrum of MTO1 deficiency.
Molecular genetics and metabolism
O'Byrne JJ and Tarailo-Graovac M and Ghani A and Champion M and Deshpande C and Dursun A and Ozgul RK and Freisinger P and Garber I and Haack TB and Horvath R and Baric I and Husain RA and 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 and Acosta-Iborra B and Puente-Santamaría L and Hernansanz-Agustin P and Worsley-Hunt R and Masson N and García-Rio F and Mole D and Ratcliffe P and Wasserman WW and 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 and Fornes O and Stigliani A and Gheorghe M and Castro-Mondragon JA and van der Lee R and Bessy A and Chèneby J and Kulkarni SR and Tan G and Baranasic D and Arenillas DJ and 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 and Fornes O and Stigliani A and Gheorghe M and Castro-Mondragon JA and van der Lee R and Bessy A and Chèneby J and Kulkarni SR and Tan G and Baranasic D and Arenillas DJ and Mathelier A
DOI: 10.1093/nar/gkx1188
PubMed: 29161433
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 and Tarailo-Graovac M and Bartel T and Race S and Van Allen MI and Blydt-Hansen I and Ross CJ and Wasserman WW and Connolly MB and 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 and Zhu JYA and Matthews A and van Karnebeek CDM and 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 and Tarailo-Graovac M and Gottlieb M and Lee JJ and van Karnebeek C and 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 and M. Tarailo-Graovac and E.M. Price and I. Blydt-Hansen and A. Ghani and B.I. Drögemöller and W.P. Robinson and C.J. Ross and W.W. Wasserman and H. Siden and 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 and Barbara Acosta-Iborra and Laura Puente-Santamaría and Pablo Hernansanz-Agustin and Rebecca Worsley-Hunt and Norma Masson and Francisco García-Rio and David Mole and Peter Ratcliffe and Wyeth W. Wasserman and Benilde Jimenez and Luis del Peso
DOI: 10.1101/182691
09/2017

A case of splenomegaly in CBL syndrome.
European journal of medical genetics
Coe RR and McKinnon ML and Tarailo-Graovac M and Ross CJ and Wasserman WW and Friedman JM and Rogers PC and 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 and Bonafé L and Wen XY and Tarailo-Graovac M and Balzano S and Royer-Bertrand B and Ashikov A and Garavelli L and Mammi I and Turolla L and Breen C and Donnai D and 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 and Wasserman WW and 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 and Ye XC and Zhang AW and Gladish N and Cheng SY and Rothe K and Pilsworth JA and Kang MA and Doolittle N and Jiang X and Stirling PC and 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 and Tarailo-Graovac M and Sinclair G and Seath KI and Wasserman WW and Ross CJ and 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 and Drögemöller BI and Wasserman WW and Ross CJ and van den Ouweland AM and Darin N and Kollberg G and van Karnebeek CD and 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 and Townsend KN and Shyr C and Matthews A and Lear SA and Attariwala R and Lehman A and Wasserman WW and van Karnebeek C and Sinclair G and Vallance H and Gibson WT
DOI: 10.1101/mcs.a001156
PubMed: 28050599
01/2017

YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses.
Chen CY and Shi W and Balaton BP and Matthews AM and Li Y and Arenillas DJ and Mathelier A and Itoh M and Kawaji H and Lassmann T and Hayashizaki Y and Carninci P and Forrest AR and Brown CJ and Wasserman WW
DOI: 10.1038/srep37324
PubMed: 27857184
11/2016

Identification of non-coding genetic variants in samples from hypoxemic respiratory disease patients that affect the transcriptional response to hypoxia.
Roche O and Deguiz ML and Tiana M and Galiana-Ribote C and Martinez-Alcazar D and Rey-Serra C and Ranz-Ribeiro B and Casitas R and Galera R and Fernández-Navarro I and Sánchez-Cuéllar S and Bernard V and Ancochea J and Wasserman WW and García-Rio F and Jimenez B and Del Peso L
PubMed: 27625398
11/2016

Human enhancers harboring specific sequence composition, activity, and genome organization are linked to the immune response
Charles-Henri Lecellier and Wyeth W. Wasserman and Anthony Mathelier
DOI: 10.1101/078477
09/2016

DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo.
Mathelier A and Xin B and Chiu TP and Yang L and Rohs R and 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 and Fornes O and Mathelier A and Wasserman WW
PubMed: 27492288
08/2016

NANS-mediated synthesis of sialic acid is required for brain and skeletal development.
van Karnebeek CD and Bonafé L and Wen XY and Tarailo-Graovac M and Balzano S and Royer-Bertrand B and Ashikov A and Garavelli L and Mammi I and Turolla L and Breen C and Donnai D and Cormier V and Heron D and Nishimura G and Uchikawa S and Campos-Xavier B and Rossi A and Hennet T and Brand-Arzamendi K
DOI: 10.1038/ng.3578
PubMed: 27213289
07/2016

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs.
Arenillas DJ and Forrest AR and Kawaji H and Lassmann T and FANTOM Consortium and Wasserman WW and Mathelier A
PubMed: 27334471
06/2016

Exome Sequencing and the Management of Neurometabolic Disorders.
Tarailo-Graovac M and Shyr C and Ross CJ and Horvath GA and Salvarinova R and Ye XC and Zhang LH and Bhavsar AP and Lee JJ and Drögemöller BI and Abdelsayed M and Alfadhel M and Armstrong L and Baumgartner MR and Burda P and Connolly MB and Cameron J and Demos M and Dewan T and 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 and Dieterich LC and Mathelier A and Chong C and Sliwa-Primorac A and Hong YK and Shin JW and Lizio M and Itoh M and Kawaji H and Lassmann T and Daub CO and Arner E and FANTOM consortium and Carninci P and Hayashizaki Y and Forrest AR and Wasserman WW and Detmar M
PubMed: 27199372
05/2016

Cytosolic phosphoenolpyruvate carboxykinase deficiency presenting with acute liver failure following gastroenteritis.
Santra S and Cameron JM and Shyr C and Zhang L and Drögemöller B and Ross CJ and Wasserman WW and Wevers RA and Rodenburg RJ and Gupte G and Preece MA and van Karnebeek CD
DOI: 10.1016/j.ymgme.2016.03.001
PubMed: 26971250
05/2016

DNA Methylation Profiling in Human Huntington's Disease Brain.
De Souza RA and Islam SA and McEwen LM and Mathelier A and Hill A and Mah SM and Wasserman WW and Kobor MS and Leavitt BR
PubMed: 26953320
03/2016

Secondary neurotransmitter deficiencies in epilepsy caused by voltage-gated sodium channelopathies: A potential treatment target?
Horvath GA and Demos M and Shyr C and Matthews A and Zhang L and Race S and Stockler-Ipsiroglu S and Van Allen MI and Mancarci O and Toker L and Pavlidis P and Ross CJ and Wasserman WW and Trump N and Heales S and Pope S and Helen Cross J and van Karnebeek CD
DOI: 10.1016/j.ymgme.2015.11.008
PubMed: 26647175
01/2016

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles.
Mathelier A and Fornes O and Arenillas DJ and Chen CY and Denay G and Lee J and Shi W and Shyr C and Tan G and Worsley-Hunt R and Zhang AW and Parcy F and Lenhard B and Sandelin A and Wasserman WW
DOI: 10.1093/nar/gkv1176
PubMed: 26531826
01/2016

rAAV-compatible MiniPromoters for restricted expression in the brain and eye.
de Leeuw CN and Korecki AJ and Berry GE and Hickmott JW and Lam SL and Lengyell TC and Bonaguro RJ and Borretta LJ and Chopra V and Chou AY and D'Souza CA and Kaspieva O and Laprise S and McInerny SC and Portales-Casamar E and Swanson-Newman MI and Wong K and Yang GS and Zhou M and Jones SJ
DOI: 10.1186/s13041-016-0232-4
PubMed: 27164903
2016

The identification of cis-regulatory elements: A review from a machine learning perspective.
Li Y and Chen CY and Kaye AM and Wasserman WW
DOI: 10.1016/j.biosystems.2015.10.002
PubMed: 26499213
12/2015

De novo dominant variants affecting the motor domain of KIF1A are a cause of PEHO syndrome.
Langlois S and Tarailo-Graovac M and Sayson B and Drögemöller B and Swenerton A and Ross CJ and Wasserman WW and van Karnebeek CD
PubMed: 26486474
10/2015

RMND1 deficiency associated with neonatal lactic acidosis, infantile onset renal failure, deafness, and multiorgan involvement.
Janer A and van Karnebeek CD and Sasarman F and Antonicka H and Al Ghamdi M and Shyr C and Dunbar M and Stockler-Ispiroglu S and Ross CJ and Vallance H and Dionne J and Wasserman WW and 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 and Castelán-Martínez OD and Rivas-Ruiz R and Jiménez-Méndez R and Medina A and Clark P and Rassekh R and Castañeda-Hernández G and Carleton B and Medeiros M and Canadian Pharmacogenomics Network for Drug Safety Consortium
DOI: 10.1097/MD.0000000000001413
PubMed: 26313789
08/2015

Dynamic software design for clinical exome and genome analyses: insights from bioinformaticians, clinical geneticists, and genetic counselors.
Shyr C and Kushniruk A and van Karnebeek CD and Wasserman WW
PubMed: 26117142
06/2015

A SNP in the HTT promoter alters NF-¿B binding and is a bidirectional genetic modifier of Huntington disease.
Becanovic K and Nørremølle A and Neal SJ and Kay C and Collins JA and Arenillas D and Lilja T and Gaudenzi G and Manoharan S and Doty CN and Beck J and Lahiri N and Portales-Casamar E and Warby SC and Connolly C and De Souza RA and REGISTRY Investigators of the European Huntington's Disease Network and Tabrizi SJ and Hermanson O and Langbehn DR
DOI: 10.1038/nn.4014
PubMed: 25938884
06/2015

GeneYenta: a phenotype-based rare disease case matching tool based on online dating algorithms for the acceleration of exome interpretation.
Gottlieb MM and Arenillas DJ and Maithripala S and Maurer ZD and Tarailo Graovac M and Armstrong L and Patel M and van Karnebeek C and 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 and Ye CX and Rossi A and Biancheri R and Roland EH and Pavlidis P and Ross CJ and Tarailo-Graovac M and Wasserman WW and 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 and Shi W and Wasserman WW
DOI: 10.1016/j.tig.2014.12.003
PubMed: 25637093
02/2015

Genetic variants in SLC22A17 and SLC22A7 are associated with anthracycline-induced cardiotoxicity in children.
Visscher H and Rassekh SR and Sandor GS and Caron HN and van Dalen EC and Kremer LC and van der Pal HJ and Rogers PC and Rieder MJ and Carleton BC and Hayden MR and Ross CJ and CPNDS consortium
DOI: 10.2217/pgs.15.61
PubMed: 26230641
2015

The statistical geometry of transcriptome divergence in cell-type evolution and cancer.
Liang C and FANTOM Consortium and Forrest AR and Wagner GP
DOI: 10.1038/ncomms7066
PubMed: 25585899
2015

The genotypic and phenotypic spectrum of PIGA deficiency.
Tarailo-Graovac M and Sinclair G and Stockler-Ipsiroglu S and Van Allen M and Rozmus J and Shyr C and Biancheri R and Oh T and Sayson B and Lafek M and Ross CJ and Robinson WP and Wasserman WW and Rossi A and 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 and Ohmiya H and Hara S and Kawasaki S and FANTOM consortium and Hayashizaki Y and Itoh M and Kawaji H and Tsujikawa M and 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 and van Karnebeek CD and Peng X and Shyr C and Tarailo-Graovac M and Mandal R and Testa D and Dubin D and Carbonetti G and Glynn SE and Sayson B and Robinson WP and Han B and Wishart D and Ross CJ and Wasserman WW and Hurwitz TA and Sinclair G and Kaczocha M
DOI: 10.1186/s13023-015-0248-3
PubMed: 25885783
2015

Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas.
Mathelier A and Lefebvre C and Zhang AW and Arenillas DJ and Ding J and Wasserman WW and Shah SP
DOI: 10.1186/s13059-015-0648-7
PubMed: 25903198
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 and Arenillas D and Corso-Díaz X and Xie YY and Bohacec S and Banks KG and Bonaguro RJ and Wong SH and Jones SJ and Marra MA and Simpson EM and Wasserman WW
DOI: 10.1186/s12864-015-1770-3
PubMed: 26204903
2015

Usability study of clinical exome analysis software: Top lessons learned and recommendations
Journal of Biomedical Informatics
Casper Shyr and Andre Kushniruk and 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 and Nosova E and Bruder E and Tercanli S and Townsend K and Gibson WT and Röthlisberger B and Heinimann K and Hall JG and Gregory-Evans CY and Wasserman WW and Miny P and Friedman JM
DOI: 10.1111/cge.12301
PubMed: 24128419
09/2014

AIMP1 deficiency presents as a cortical neurodegenerative disease with infantile onset.
Armstrong L and Biancheri R and Shyr C and Rossi A and Sinclair G and Ross CJ and Tarailo-Graovac M and Wasserman WW and 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 and Pegado V and Patel MS and Wasserman WW
DOI: 10.1111/cge.12367
PubMed: 24579652
08/2014

Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation.
Morikawa H and Ohkura N and Vandenbon A and Itoh M and Nagao-Sato S and Kawaji H and Lassmann T and Carninci P and Hayashizaki Y and Forrest AR and Standley DM and Date H and Sakaguchi S and 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 and Ross CJ and Rassekh SR and Brunham LR and Sistonen J and Dube MP and Ibrahim M and Nyambo TB and Omar SA and Froment A and Bodo JM and Tishkoff S and Carleton BC and Hayden MR and Canadian Pharmacogenomics Network for Drug Safety Consortium
DOI: 10.1038/tpj.2013.13
PubMed: 23588107
04/2014

DNAJC13 mutations in Parkinson disease.
Vilariño-Güell C and Rajput A and Milnerwood AJ and Shah B and Szu-Tu C and Trinh J and Yu I and Encarnacion M and Munsie LN and Tapia L and Gustavsson EK and Chou P and Tatarnikov I and Evans DM and Pishotta FT and Volta M and Beccano-Kelly D and Thompson C and Lin MK and Sherman HE
DOI: 10.1093/hmg/ddt570
PubMed: 24218364
04/2014

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 and William S. Sly and Colin J. Ross and Ramona Salvarinova and Joy Yaplito-Lee and Saikat Santra and Casper Shyr and Gabriella A. Horvath and Patrice Eydoux and Anna M. Lehman and Virginie Bernard and Theresa Newlove and Henry Ukpeh and Anupam Chakrapani and Mary Anne Preece and Sarah Ball and James Pitt and Hilary D. Vallance and Marion Coulter-Mackie and Hien Nguyen and Lin-Hua Zhang and Amit P. Bhavsar and Graham Sinclair and Abdul Waheed and Wyeth W. Wasserman and Sylvia Stockler-Ipsiroglu
DOI: 10.1016/j.ajhg.2014.01.006
03/2014

A promoter-level mammalian expression atlas.
FANTOM Consortium and the RIKEN PMI and CLST (DGT) and Forrest AR and Kawaji H and Rehli M and Baillie JK and de Hoon MJ and Haberle V and Lassmann T and Kulakovskiy IV and Lizio M and Itoh M and Andersson R and Mungall CJ and Meehan TF and Schmeier S and Bertin N and Jørgensen M and Dimont E and Arner E and Schmidl C
DOI: 10.1038/nature13182
PubMed: 24670764
03/2014

An atlas of active enhancers across human cell types and tissues.
Andersson R and Gebhard C and Miguel-Escalada I and Hoof I and Bornholdt J and Boyd M and Chen Y and Zhao X and Schmidl C and Suzuki T and Ntini E and Arner E and Valen E and Li K and Schwarzfischer L and Glatz D and Raithel J and Lilje B and Rapin N and Bagger FO
DOI: 10.1038/nature12787
PubMed: 24670763
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 and Frank M Dyka and Sanford L Boye and Stéphanie Laprise and Michelle Zhou and Alice Y Chou and Lisa Borretta and Simone C McInerny and Kathleen G Banks and Elodie Portales-Casamar and Magdalena I Swanson and Cletus A D’Souza and Shannon E Boye and Steven JM Jones and Robert A Holt and Daniel Goldowitz and William W Hauswirth and Wyeth W Wasserman and Elizabeth M Simpson
DOI: 10.1038/mtm.2013.5
01/2014

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles.
Mathelier A and Zhao X and Zhang AW and Parcy F and Worsley-Hunt R and Arenillas DJ and Buchman S and Chen CY and Chou A and Ienasescu H and Lim J and Shyr C and Tan G and Zhou M and Lenhard B and Sandelin A and Wasserman WW
DOI: 10.1093/nar/gkt997
PubMed: 24194598
01/2014

TFBSshape: a motif database for DNA shape features of transcription factor binding sites.
Yang L and Zhou T and Dror I and Mathelier A and Wasserman WW and Gordân R and Rohs R
DOI: 10.1093/nar/gkt1087
PubMed: 24214955
01/2014

Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets
Genome Biology
Rebecca Worsley Hunt and Wyeth W Wasserman
DOI: 10.1186/s13059-014-0412-4
2014

Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells.
Arner E and Forrest AR and Ehrlund A and Mejhert N and Itoh M and Kawaji H and Lassmann T and Laurencikiene J and Rydén M and Arner P and FANTOM Consortium
DOI: 10.1371/journal.pone.0080274
PubMed: 24676332
2014

Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets.
Worsley Hunt R and Wasserman WW
DOI: 10.1186/PREACCEPT-1454983695127944
PubMed: 25070602
2014

FLAGS, frequently mutated genes in public exomes.
Shyr C and Tarailo-Graovac M and Gottlieb M and Lee JJ and van Karnebeek C and Wasserman WW
DOI: 10.1186/s12920-014-0064-y
PubMed: 25466818
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 and Silvia Corvera and David Lambright and Kevin Fogarty and Ekaterina Nosova and Deborah Leonard and Robert Steinfeld and Cameron Ackerley and Casper Shyr and Nicolas Au and Kathrin Selby and Margot van Allen and Hilary Vallance and Ron Wevers and David Watkins and David Rosenblatt and Colin J Ross and Elizabeth Conibear and Wyeth Wasserman and Clara van Karnebeek
DOI: 10.1186/s13023-014-0141-5
2014

Exome sequencing pilot study in children with carbamazepine-induced serious skin reactions
Clinical and Translational Allergy
Ursula Amstutz and Casper Shyr and Neil H Shear and Michael J Rieder and Wyeth W Wasserman and Colin J Ross and Bruce C Carleton
DOI: 10.1186/2045-7022-4-s3-p119
2014

On the identification of potential regulatory variants within genome wide association candidate SNP sets
BMC Medical Genomics
Chih-yu Chen and I-Shou Chang and Chao A Hsiung and Wyeth W Wasserman
DOI: 10.1186/1755-8794-7-34
2014

Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment
BMC Genomics
Rebecca Worsley Hunt and Anthony Mathelier and Luis del Peso and Wyeth W Wasserman
DOI: 10.1186/1471-2164-15-472
2014

Validation of variants in SLC28A3 and UGT1A6 as genetic markers predictive of anthracycline-induced cardiotoxicity in children.
Visscher H and Ross CJ and Rassekh SR and Sandor GS and Caron HN and van Dalen EC and Kremer LC and van der Pal HJ and Rogers PC and Rieder MJ and Carleton BC and Hayden MR and CPNDS Consortium
DOI: 10.1002/pbc.24505
PubMed: 23441093
08/2013

Non-coding-regulatory regions of human brain genes delineated by bacterial artificial chromosome knock-in mice.
Schmouth JF and Castellarin M and Laprise S and Banks KG and Bonaguro RJ and McInerny SC and Borretta L and Amirabbasi M and Korecki AJ and Portales-Casamar E and Wilson G and Dreolini L and Jones SJ and Wasserman WW and Goldowitz D and Holt RA and Simpson EM
DOI: 10.1186/1741-7007-11-106
PubMed: 24124870
2013

Utilizing social media to study information-seeking and ethical issues in gene therapy.
Robillard JM and Whiteley L and Johnson TW and Lim J and Wasserman WW and Illes J
DOI: 10.2196/jmir.2313
PubMed: 23470490
2013

Compensating for literature annotation bias when predicting novel drug-disease relationships through Medical Subject Heading Over-representation Profile (MeSHOP) similarity.
Cheung WA and Ouellette BF and Wasserman WW
DOI: 10.1186/1755-8794-6-S3-S3
PubMed: 23819887
2013

Portal for Families Overcoming Neurodevelopmental Disorders (PFOND): Implementation of a Software Framework for Facilitated Community Website Creation by Nontechnical Volunteers.
Ye XC and Ng I and Seid-Karbasi P and Imam T and Lee CE and Chen SY and Herman A and Sharma B and Johal G and Gu B and Wasserman WW
DOI: 10.2196/resprot.2675
PubMed: 23920006
2013

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

oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets.
Kwon AT and Arenillas DJ and Worsley Hunt R and 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 and Roth A and Goya R and Oloumi A and Ha G and Zhao Y and Turashvili G and Ding J and Tse K and Haffari G and Bashashati A and Prentice LM and Khattra J and Burleigh A and Yap D and Bernard V and McPherson A and Shumansky K and Crisan A and 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 and Banks KG and Mathelier A and Gregory-Evans CY and Castellarin M and Holt RA and Gregory-Evans K and Wasserman WW and Simpson EM
DOI: 10.1128/MCB.06016-11
PubMed: 22290436
04/2012

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

The transcription factor encyclopedia.
Yusuf D and Butland SL and Swanson MI and Bolotin E and Ticoll A and Cheung WA and Zhang XY and Dickman CT and Fulton DL and Lim JS and Schnabl JM and Ramos OH and Vasseur-Cognet M and de Leeuw CN and Simpson EM and Ryffel GU and Lam EW and Kist R and Wilson MS and Marco-Ferreres R
DOI: 10.1186/gb-2012-13-3-r24
PubMed: 22458515
2012

Quantitative biomedical annotation using medical subject heading over-representation profiles (MeSHOPs).
Cheung WA and Ouellette BF and Wasserman WW
DOI: 10.1186/1471-2105-13-249
PubMed: 23017167
2012

Validation of skeletal muscle cis-regulatory module predictions reveals nucleotide composition bias in functional enhancers.
Kwon AT and Chou AY and Arenillas DJ and Wasserman WW
DOI: 10.1371/journal.pcbi.1002256
PubMed: 22144875
12/2011

Towards resolving the transcription factor network controlling myelin gene expression.
Fulton DL and Denarier E and Friedman HC and Wasserman WW and Peterson AC
DOI: 10.1093/nar/gkr326
PubMed: 21729871
10/2011

VPS35 Mutations in Parkinson Disease.
Vilari?o-G?ell C and Wider C and Ross O and Dachsel J and Kachergus J and Lincoln S and Soto-Ortolaza A and Cobb S and Wilhoite G and Bacon J and Behrouz B and Melrose H and Hentati E and Puschmann A and Evans D and Conibear E and Wasserman W and Aasly J and Burkhard P and Djaldetti R
DOI: 10.1016/j.ajhg.2011.07.018
08/2011

VPS35 mutations in Parkinson disease.
Vilariño-Güell C and Wider C and Ross OA and Dachsel JC and Kachergus JM and Lincoln SJ and Soto-Ortolaza AI and Cobb SA and Wilhoite GJ and Bacon JA and Behrouz B and Melrose HL and Hentati E and Puschmann A and Evans DM and Conibear E and Wasserman WW and Aasly JO and Burkhard PR and Djaldetti R
DOI: 10.1016/j.ajhg.2011.06.001
PubMed: 21763482
07/2011

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

Identification of cis-regulatory sequence variations in individual genome sequences.
Worsley-Hunt R and Bernard V and Wasserman WW
DOI: 10.1186/gm281
PubMed: 21989199
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 and Portales-Casamar E and Vetter G and Moes M and Zindy PJ and Saumet A and Arenillas D and Theillet C and Wasserman WW and Lecellier CH and Friederich E
DOI: 10.1186/1471-2105-12-67
PubMed: 21375730
2011

A regulatory toolbox of MiniPromoters to drive selective expression in the brain.
Portales-Casamar E and Swanson DJ and Liu L and de Leeuw CN and Banks KG and Ho Sui SJ and Fulton DL and Ali J and Amirabbasi M and Arenillas DJ and Babyak N and Black SF and Bonaguro RJ and Brauer E and Candido TR and Castellarin M and Chen J and Chen Y and Cheng JC and 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 and Portales-Casamar E and Singh A and Srivastava S and Arenillas D and Happel C and Shyr C and Wakabayashi N and Kensler TW and Wasserman WW and 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 and Visscher H and Sistonen J and Brunham LR and Pussegoda K and Loo TT and Rieder MJ and Koren G and Carleton BC and Hayden MR and 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 and Hearty T and Wong TY and Portales-Casamar E and Simpson EM and 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 and Thongjuea S and Kwon AT and Arenillas D and Zhao X and Valen E and Yusuf D and Lenhard B and Wasserman WW and 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 and Katzov-Eckert H and Dubé MP and Brooks B and Rassekh SR and Barhdadi A and Feroz-Zada Y and Visscher H and Brown AM and Rieder MJ and Rogers PC and Phillips MS and Carleton BC and Hayden MR and 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 and Arenillas D and Lim J and Swanson MI and Jiang S and McCallum A and Kirov S and 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 and Vetter G and Bouttier M and Portales-Casamar E and Wasserman WW and Maurin T and Mari B and Barbry P and Vallar L and Friederich E and Arar K and Cassinat B and Chomienne C and 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 and Sundararajan S and Badis G and Hughes TR and Wasserman WW and Roach JC and 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 and Arenillas D and Wasserman WW and Leung PC and Dunn SE and Davies BR and Mills GB and 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 and Ho Sui SJ and Erasmus D and van der Merwe GK and Brumm J and Wasserman WW and Bryan J and 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 and Engström PG and Lithwick S and Arenillas D and Eriksson P and Lenhard B and Wasserman WW and Odeberg J
DOI: 10.1371/journal.pcbi.0040005
PubMed: 18208319
01/2008

ORegAnno: an open-access community-driven resource for regulatory annotation.
Griffith OL and Montgomery SB and Bernier B and Chu B and Kasaian K and Aerts S and Mahony S and Sleumer MC and Bilenky M and Haeussler M and Griffith M and Gallo SM and Giardine B and Hooghe B and Van Loo P and Blanco E and Ticoll A and Lithwick S and Portales-Casamar E and Donaldson IJ
DOI: 10.1093/nar/gkm967
PubMed: 18006570
01/2008

Discovery and expansion of gene modules by seeking isolated groups in a random graph process.
Brumm J and Conibear E and Wasserman WW and Bryan J
DOI: 10.1371/journal.pone.0003358
PubMed: 18843375
2008

Gene characterization index: assessing the depth of gene annotation.
Kemmer D and Podowski RM and Yusuf D and Brumm J and Cheung W and Wahlestedt C and Lenhard B and 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 and Chopra V and Varhol R and Xie YY and Bohacec S and Zhao Y and Lee LL and Bilenky M and Portales-Casamar E and He A and Wasserman WW and Goldowitz D and Marra MA and Holt RA and Simpson EM and Jones SJ
DOI: 10.1186/1471-2202-9-66
PubMed: 18625066
2008

oPOSSUM: integrated tools for analysis of regulatory motif over-representation.
Ho Sui SJ and Fulton DL and Arenillas DJ and Kwon AT and 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 and Kirov S and Lim J and Lithwick S and Swanson MI and Ticoll A and Snoddy J and Wasserman WW
DOI: 10.1186/gb-2007-8-10-r207
PubMed: 17916232
2007

SAGE2Splice: unmapped SAGE tags reveal novel splice junctions.
Kuo BY and Chen Y and Bohacec S and Johansson O and Wasserman WW and 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 and Sandelin A and De Bleser PJ and Vleminckx K and Wasserman WW and van Roy F and Lenhard B
DOI: 10.1093/nar/gkj115
PubMed: 16381983
01/2006

NovelFam3000--uncharacterized human protein domains conserved across model organisms.
Kemmer D and Podowski RM and Arenillas D and Lim J and Hodges E and Roth P and Sonnhammer EL and Höög C and 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 and Singaraja RR and Kang M and Arenillas DJ and Bertram LN and Bissada N and Staels B and Fruchart JC and Fievet C and Joseph-George AM and Wasserman WW and Hayden MR
DOI: 10.1194/jlr.M400506-JLR200
PubMed: 15772424
06/2005

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

The Gene Set Builder: collation, curation, and distribution of sets of genes.
Yusuf D and Lim JS and Wasserman WW
DOI: 10.1186/1471-2105-6-305
PubMed: 16371163
2005

Identification of functional SNPs in the 5-prime flanking sequences of human genes.
Mottagui-Tabar S and Faghihi MA and Mizuno Y and Engström PG and Lenhard B and Wasserman WW and Wahlestedt C
DOI: 10.1186/1471-2164-6-18
PubMed: 15717931
2005

oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes.
Ho Sui SJ and Mortimer JR and Arenillas DJ and Brumm J and Walsh CJ and Kennedy BP and Wasserman WW
DOI: 10.1093/nar/gki624
PubMed: 15933209
2005

Ulysses - an application for the projection of molecular interactions across species.
Kemmer D and Huang Y and Shah SP and Lim J and Brumm J and Yuen MM and Ling J and Xu T and Wasserman WW and Ouellette BF
DOI: 10.1186/gb-2005-6-12-r106
PubMed: 16356269
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 and Palumbo MJ and Wasserman WW and Liu JS and Lawrence CE
DOI: 10.1101/gr.2589004
PubMed: 15466295
10/2004

Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus.
Alkema WB and Lenhard B and Wasserman WW
DOI: 10.1101/gr.2242604
PubMed: 15231752
07/2004

MSCAN: identification of functional clusters of transcription factor binding sites.
Alkema WB and Johansson O and Lagergren J and Wasserman WW
DOI: 10.1093/nar/gkh387
PubMed: 15215379
07/2004

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

Applied bioinformatics for the identification of regulatory elements.
Wasserman WW and 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 and 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 and Alkema W and Engström P and Wasserman WW and Lenhard B
DOI: 10.1093/nar/gkh012
PubMed: 14681366
01/2004

Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes.
Sandelin A and Bailey P and Bruce S and Engström PG and Klos JM and Wasserman WW and Ericson J and Lenhard B
DOI: 10.1186/1471-2164-5-99
PubMed: 15613238
2004

Exploring the foundation of genomics: a northern blot reference set for the comparative analysis of transcript profiling technologies.
Kemmer D and Faxén M and Hodges E and Lim J and Herzog E and Ljungström E and Lundmark A and Olsen MK and Podowski R and Sonnhammer EL and Nilsson P and Reimers M and Lenhard B and Roberds SL and Wahlestedt C and Höög C and Agarwal P and Wasserman WW
DOI: 10.1002/cfg.443
PubMed: 18629180
2004

Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes.
Sandelin A and Höglund A and Lenhard B and Wasserman WW
DOI: 10.1007/s10142-003-0086-6
PubMed: 12827523
07/2003

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

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

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

Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm.
Johansson O and Alkema W and Wasserman WW and Lagergren J
DOI: 10.1093/bioinformatics/btg1021
PubMed: 12855453
2003

Identification of conserved regulatory elements by comparative genome analysis.
Lenhard B and Sandelin A and Mendoza L and Engström P and Jareborg N and Wasserman WW
DOI: 10.1186/1475-4924-2-13
PubMed: 12760745
2003

TFBS: Computational framework for transcription factor binding site analysis.
Lenhard B and 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 and Gizatullin RZ and Al-Amin AN and Wang F and Kvasha SM and Podowski RM and Matushkin YG and Gyanchandani A and Muravenko OV and Levitsky VG and Kolchanov NA and Protopopov AI and Kashuba VI and Kisselev LL and Wasserman W and Wahlestedt C and Zabarovsky ER
DOI: 10.1093/nar/gkf428
PubMed: 12136098
07/2002

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

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

Phylogenetic Footprinting
Encyclopedia of Life Sciences
Wyeth W Wasserman and 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 and Kvasha SM and Protopopov AI and Gizatullin RZ and Rynditch AV and Wahlestedt C and Wasserman WW and Zabarovsky ER
DOI: 10.1016/S0378-1119(01)00423-1
PubMed: 11368907
05/2001

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

Polymorphic electrophile response elements in the mouse glutathione S-transferase GSTa1 gene that confer increased induction.
Zhu M and Chapman WG and Oberley MJ and Wasserman WW and 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 and Arslan G and Halldner L and Kull B and Schulte G and Wasserman W
DOI: 10.1007/s002100000313
PubMed: 11111830
11/2000

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

Discovery and modeling of transcriptional regulatory regions.
Fickett JW and 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 and Steingrimsson E and DuHadaway J and Wasserman W and Ruiz JC and Copeland NG and Jenkins NA and 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 and Wasserman WW and Hutchinson A and Smallwood P and Nathans J and Rogan PK and Schneider TD and 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 and Stubbs LJ and Wasserman WW and Mucenski ML
DOI: 10.1007/s003359900748
PubMed: 9530622
04/1998

Identification of regulatory regions which confer muscle-specific gene expression.
Wasserman WW and 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 and Carstens CP and Wasserman WW and 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 and Fahl WE
DOI: 10.1006/abbi.1997.0215
PubMed: 9264553
08/1997

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

Analysis of R59022 actions in Xenopus laevis oocytes.
Sadler SE and Frith T and 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

Tamar Av-Shalom, Undergraduate Student
Chloe Bessiere, Visiting Scientist
Solenne Correard, Postdoctoral Fellow
Oriol Fornés Crespo
Michelle Kang
Alice Kaye
Bhavi Pinesh Modi, Postdoctoral Fellow
German Novakovskiy
Bianca Oricchio Kirsh, Work Learn Student
Dora Pak, Research Manager
Phillip Richmond, PhD Candidate
Manu Saraswat, Software Developer
Xin (Cynthia) Ye
Nicole Zhang, Graduate Student
Allen Zhang
Jessica Zhang
Tibor van Rooij, Universal Health Records Research Scientist
Robin van der Lee