Wyeth W Wasserman

Wyeth W Wasserman

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Wyeth W Wasserman

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TFEA.ChIP: a tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets.

Bioinformatics 2019 Dec;35(24):5339-5340

Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas 'Alberto Sols' (CSIC-UAM), Madrid, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btz573DOI Listing
December 2019

Strabismus in Children With Intellectual Disability: Part of a Broader Motor Control Phenotype?

Pediatr Neurol 2019 11 11;100:87-91. Epub 2019 Apr 11.

Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; BC Children's Hospital and BC Women's Hospital, Vancouver, BC, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.pediatrneurol.2019.04.002DOI Listing
November 2019

Computational Analysis of Transcriptional Regulation Sites at the HTT Gene Locus.

J Huntingtons Dis 2018 ;7(3):223-237

Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada.

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http://www.medra.org/servlet/aliasResolver?alias=iospress&am
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http://dx.doi.org/10.3233/JHD-170272DOI Listing
October 2019

Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis.

BMC Genomics 2019 Sep 18;20(1):718. Epub 2019 Sep 18.

Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.

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http://dx.doi.org/10.1186/s12864-019-6063-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6751898PMC
September 2019

Gene expression models based on transcription factor binding events confer insight into functional cis-regulatory variants.

Bioinformatics 2019 Aug;35(15):2610-2617

Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada.

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http://dx.doi.org/10.1093/bioinformatics/bty992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6662294PMC
August 2019

Introduction to Genomic Analysis Workshop: A catalyst for engaging life-science researchers in high throughput analysis.

F1000Res 2019 30;8:1221. Epub 2019 Jul 30.

Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Vancouver, British Columbia, V5Z 4H4, Canada.

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http://dx.doi.org/10.12688/f1000research.19320.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6774052PMC
July 2019

Curation and bioinformatic analysis of strabismus genes supports functional heterogeneity and proposes candidate genes with connections to RASopathies.

Gene 2019 May 15;697:213-226. Epub 2019 Feb 15.

Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.gene.2019.02.020DOI Listing
May 2019

Glutaminase Deficiency Caused by Short Tandem Repeat Expansion in .

N Engl J Med 2019 04;380(15):1433-1441

From Amsterdam University Medical Centers, University of Amsterdam, Departments of Clinical Chemistry, Pediatrics, and Clinical Genetics, Emma Children's Hospital, Amsterdam Gastroenterology and Metabolism (A.B.P.K., R.L., J.K., J. Meijer, L.A.T., M.T., M.W., R.J.A.W., H.R.W., C.D.M.K.), and United for Metabolic Diseases (A.B.P.K., R.J.A.W., H.R.W., C.D.M.K.), Amsterdam, and the Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht (J.J.F.A.V., J.H.V.), and the Project MinE ALS Sequencing Consortium (J.J.F.A.V., J.H.V.), Utrecht - all in the Netherlands; the Departments of Biochemistry and Molecular Biology and Medical Genetics, Cumming School of Medicine, and Alberta Children's Hospital Research Institute, University of Calgary, Calgary (M.T.-G.), Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute (P.A.R., M.J.J., M.S.K., J. MacIsaac, W.W.W., C.D.M.K.), the Faculty of Pharmaceutical Sciences (B.I.D., G.E.B.W., C.J.R.), and the Departments of Medical Genetics (C.M., I.-S.R.-B., W.W.W.) and Pediatrics (C.D.M.K.), University of British Columbia, Vancouver, the Zebrafish Centre for Advanced Drug Discovery, St. Michael's Hospital and University of Toronto (K.B.-A., F.K., M.L., Y.W., X.-Y.W.), the Centre for Applied Genomics, Genetics and Genome Biology, the Hospital for Sick Children (C.N., S.W.S., B.T., R.K.C.Y.), and the Department of Molecular Genetics (C.N., S.W.S., R.K.C.Y.), the McLaughlin Centre (S.W.S.), and the Departments of Medicine, Physiology, and Laboratory Medicine and Pathobiology, Institute of Medical Science (X.-Y.W.), University of Toronto, Toronto, and the Division of Medical Genetics, Department of Pediatrics, Children's Hospital Eastern Ontario, University of Ottawa, Ottawa (J.S.W., M.T.G.) - all in Canada; the Departments of Medicine and Physiology, National University of Singapore (M.A.P.), and the Translational Laboratory in Genetic Medicine, Agency for Science, Technology, and Research (M.A.P., B.S., X.X., J.Z.) - both in Singapore; Uppsala University, Department of Chemistry-Biomedical Center, Uppsala, Sweden (D.D.); Illumina, San Diego, CA (E.D., M.A.E.); Gene Structure and Disease Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD (B.H., D.K., K.U.); and the Department of Clinical Inherited Metabolic Disorders, Birmingham Children's Hospital, Birmingham, United Kingdom (S.S.).

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http://dx.doi.org/10.1056/NEJMoa1806627DOI Listing
April 2019

Development and user evaluation of a rare disease gene prioritization workflow based on cognitive ergonomics.

J Am Med Inform Assoc 2019 02;26(2):124-133

Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.

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https://academic.oup.com/jamia/advance-article/doi/10.1093/j
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http://dx.doi.org/10.1093/jamia/ocy153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6339516PMC
February 2019

Gain-of-function KCNJ6 Mutation in a Severe Hyperkinetic Movement Disorder Phenotype.

Neuroscience 2018 08 29;384:152-164. Epub 2018 May 29.

Division of Biochemical Diseases, Department of Pediatrics, B.C. Children's Hospital, University of British Columbia, Vancouver, Canada; BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada; Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada; Department of Pediatrics and Clinical Genetics, Emma Children's Hospital, Academic Medical Centre, Amsterdam, The Netherlands.

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https://linkinghub.elsevier.com/retrieve/pii/S03064522183038
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http://dx.doi.org/10.1016/j.neuroscience.2018.05.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6679957PMC
August 2018

Human Enhancers Harboring Specific Sequence Composition, Activity, and Genome Organization Are Linked to the Immune Response.

Genetics 2018 08 5;209(4):1055-1071. Epub 2018 Jun 5.

Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, V5Z 4H4, Canada

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http://dx.doi.org/10.1534/genetics.118.301116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6063234PMC
August 2018

c-Myc is a novel virulence factor by proxy that targets the host miRNA system and is essential for survival in human macrophages.

J Biol Chem 2018 08 22;293(33):12805-12819. Epub 2018 Jun 22.

From the Division of Infectious Diseases, Department of Medicine, Vancouver Coastal Health Research Institute, Vancouver, British Columbia V5Z 1M9 and

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http://dx.doi.org/10.1074/jbc.RA118.002462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6102154PMC
August 2018

MANTA2, update of the Mongo database for the analysis of transcription factor binding site alterations.

Sci Data 2018 07 24;5:180141. Epub 2018 Jul 24.

Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway.

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http://dx.doi.org/10.1038/sdata.2018.141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6057437PMC
July 2018

Text-based phenotypic profiles incorporating biochemical phenotypes of inborn errors of metabolism improve phenomics-based diagnosis.

J Inherit Metab Dis 2018 05 16;41(3):555-562. Epub 2018 Jan 16.

Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Room 3109, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.

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http://dx.doi.org/10.1007/s10545-017-0125-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5959948PMC
May 2018

Integration of genomics and metabolomics for prioritization of rare disease variants: a 2018 literature review.

J Inherit Metab Dis 2018 05 2;41(3):435-445. Epub 2018 May 2.

BC Children's Hospital Research Institute, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada.

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http://link.springer.com/10.1007/s10545-018-0139-6
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http://dx.doi.org/10.1007/s10545-018-0139-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5959954PMC
May 2018

Genome-wide prediction of cis-regulatory regions using supervised deep learning methods.

BMC Bioinformatics 2018 05 31;19(1):202. Epub 2018 May 31.

Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Rm 3109, 950 West 28th Avenue, Vancouver, V5Z 4H4, Canada.

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http://dx.doi.org/10.1186/s12859-018-2187-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5984344PMC
May 2018

Knowledge base and mini-expert platform for the diagnosis of inborn errors of metabolism.

Genet Med 2018 01 20;20(1):151-158. Epub 2017 Jul 20.

Division of Metabolism, University Children's Hospital, Zurich, Switzerland.

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http://dx.doi.org/10.1038/gim.2017.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5763153PMC
January 2018

The SIN3A histone deacetylase complex is required for a complete transcriptional response to hypoxia.

Nucleic Acids Res 2018 01;46(1):120-133

Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas 'Alberto Sols' (CSIC-UAM), 28029 Madrid, Spain.

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http://dx.doi.org/10.1093/nar/gkx951DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5758878PMC
January 2018

The genotypic and phenotypic spectrum of MTO1 deficiency.

Mol Genet Metab 2018 01 15;123(1):28-42. Epub 2017 Nov 15.

Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, BC, Canada; BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada; Departments of Pediatrics and Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.ymgme.2017.11.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5780301PMC
January 2018

Correction to: FLAGS, frequently mutated genes in public exomes.

BMC Med Genomics 2017 11 29;10(1):69. Epub 2017 Nov 29.

Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, BC, Canada.

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http://dx.doi.org/10.1186/s12920-017-0309-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5706417PMC
November 2017

A case of splenomegaly in CBL syndrome.

Eur J Med Genet 2017 Jul 13;60(7):374-379. Epub 2017 Apr 13.

British Columbia Children's Hospital Research Institute, Vancouver, Canada; Centre for Molecular Medicine & Therapeutics, University of British Columbia, Vancouver, Canada; Treatable Intellectual Disability Endeavour in British Columbia (TIDE-BC), Vancouver, Canada; Department of Pediatrics, University of British Columbia, Vancouver, Canada; Department of Pediatrics, Emma Children's Hospital, Academic Medical Centre, Amsterdam, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.ejmg.2017.04.009DOI Listing
July 2017

Impact of next-generation sequencing on diagnosis and management of neurometabolic disorders: current advances and future perspectives.

Expert Rev Mol Diagn 2017 04 20;17(4):307-309. Epub 2017 Feb 20.

c BC Children's Hospital Research Institute, Centre for Molecular Medicine and Therapeutics, Department of Pediatrics , University of British Columbia , Vancouver , Canada.

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http://dx.doi.org/10.1080/14737159.2017.1293527DOI Listing
April 2017

A girl with developmental delay, ataxia, cranial nerve palsies, severe respiratory problems in infancy-Expanding NDST1 syndrome.

Am J Med Genet A 2017 Mar;173(3):712-715

BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada.

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http://dx.doi.org/10.1002/ajmg.a.37621DOI Listing
March 2017

Identification of a large intronic transposal insertion in SLC17A5 causing sialic acid storage disease.

Orphanet J Rare Dis 2017 02 10;12(1):28. Epub 2017 Feb 10.

Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.

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http://dx.doi.org/10.1186/s13023-017-0584-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5303239PMC
February 2017

Evaluating the impact of single nucleotide variants on transcription factor binding.

Nucleic Acids Res 2016 12 4;44(21):10106-10116. Epub 2016 Aug 4.

Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child & Family Research Institute, University of British Columbia, 950 28th Ave W, Vancouver, BC V5Z 4H4, Canada

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http://dx.doi.org/10.1093/nar/gkw691DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5137422PMC
December 2016

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs.

Bioinformatics 2016 09 9;32(18):2858-60. Epub 2016 Jun 9.

Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.

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http://dx.doi.org/10.1093/bioinformatics/btw337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5018375PMC
September 2016

DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo.

Cell Syst 2016 09 18;3(3):278-286.e4. Epub 2016 Aug 18.

Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 980 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2016.07.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5042832PMC
September 2016

PAX6 MiniPromoters drive restricted expression from rAAV in the adult mouse retina.

Mol Ther Methods Clin Dev 2016 10;3:16051. Epub 2016 Aug 10.

Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada; Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1038/mtm.2016.51DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4980111PMC
August 2016

Exome Sequencing and the Management of Neurometabolic Disorders.

N Engl J Med 2016 Jun 25;374(23):2246-55. Epub 2016 May 25.

From the Centre for Molecular Medicine and Therapeutics (M.T.-G., C. Shyr, X.C.Y., L.-H.Z., J.J.Y.L., B.I.D., I.G., W.W.W., C.D.K.), the Departments of Medical Genetics (M.T.-G., C. Shyr, C.J.R., X.C.Y., J.J.Y.L., L.A., J.M.F., S.L., M.M., M.I.V.A., A.M.L., W.W.W.), Pediatrics (C.J.R., G.A.H., R.S., L.-H.Z., A.P.B., B.I.D., M.B.C., M.D., T.D., J.D., A. Michoulas, D.M., J.R., K.R.S., K.S., S.E.T., John Wu, S.S.-I., C.D.K.), and Pathology and Laboratory Medicine (B.R., P.E., H.V., G.S.), the Child and Family Research Institute (M.T.-G., C. Shyr, C.J.R., G.A.H., X.C.Y., A.P.B., J.J.Y.L., B.I.D., L.A., M.B.C., M.D., J.D., J.M.F., I.G., S.L., M.M., D.M., J.R., K.R.S., K.S., S.E.T., M.I.V.A., John Wu, P.E., A.M.L., H.V., S.S.-I., G.S., W.W.W., C.D.K.), and the Division of Endocrinology, Adult Metabolic Diseases Clinic (A. Mattman, S. Sirrs), University of British Columbia, and the Divisions of Biochemical Diseases (G.A.H., R.S., B.S., S.S.-I., C.D.K.), Pediatric Neurology (M.B.C., M.D., A. Michoulas, K.S.), Pediatric Nephrology (J.D.), Pediatric Endocrinology (D.M.), and Immunology (S.E.T.) and the Division of Hematology, Oncology and Transplantation, Michael Cuccione Childhood Cancer Research Program (J.R., K.R.S., John Wu), BC Children's Hospital, Vancouver, the Department of Pathology and Laboratory Medicine, Hospital for Sick Children, University of Toronto, Toronto (J.C.), the Department of Biological and Computing Sciences, University of Alberta (R.M., D.W.), and the National Institute for Nanotechnology (D.W.), Edmonton, AB, and the Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC (M. Abdelsayed, P.R.) - all in Canada; the Division of Genetics, Department of Pediatrics, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia (M. Alfadhel); the Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zurich (M.R.B., P.B.), and the Departmen

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http://dx.doi.org/10.1056/NEJMoa1515792DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4983272PMC
June 2016

Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters.

J Comput Biol 2016 05 22;23(5):322-36. Epub 2016 Jan 22.

2 Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, BC Children's Hospital, University of British Columbia , Vancouver, British Columbia, Canada .

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http://dx.doi.org/10.1089/cmb.2015.0189DOI Listing
May 2016

DNA methylation profiling in human Huntington's disease brain.

Hum Mol Genet 2016 05 6;25(10):2013-2030. Epub 2016 Mar 6.

Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4.

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http://dx.doi.org/10.1093/hmg/ddw076DOI Listing
May 2016

Cytosolic phosphoenolpyruvate carboxykinase deficiency presenting with acute liver failure following gastroenteritis.

Mol Genet Metab 2016 May 4;118(1):21-7. Epub 2016 Mar 4.

Centre for Molecular Medicine, Child & Family Research Institute, Vancouver, Canada; Department of Pediatrics, University of British Columbia, Canada. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10967192163002
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http://dx.doi.org/10.1016/j.ymgme.2016.03.001DOI Listing
May 2016

Dynamic software design for clinical exome and genome analyses: insights from bioinformaticians, clinical geneticists, and genetic counselors.

J Am Med Inform Assoc 2016 Mar 27;23(2):257-68. Epub 2015 Jun 27.

Centre for Molecular Medicine and Therapeutics; Child and Family Research Institute, Vancouver BC, Canada Treatable Intellectual Disability Endeavour in British Columbia (www.tidebc.org), Vancouver, Canada Department of Medical Genetics, University of British Columbia, Vancouver BC, Canada

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http://dx.doi.org/10.1093/jamia/ocv053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4784553PMC
March 2016

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles.

Nucleic Acids Res 2016 Jan 3;44(D1):D110-5. Epub 2015 Nov 3.

Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, V5Z 4H4, BC, Canada

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http://dx.doi.org/10.1093/nar/gkv1176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702842PMC
January 2016

Secondary neurotransmitter deficiencies in epilepsy caused by voltage-gated sodium channelopathies: A potential treatment target?

Mol Genet Metab 2016 Jan 17;117(1):42-8. Epub 2015 Nov 17.

Division of Biochemical Diseases, Dept of Pediatrics, B.C. Children's Hospital, University of British Columbia, Vancouver, Canada; Center for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.ymgme.2015.11.008DOI Listing
January 2016

The identification of cis-regulatory elements: A review from a machine learning perspective.

Biosystems 2015 Dec 21;138:6-17. Epub 2015 Oct 21.

Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia Vancouver, British Columbia V5Z 4H4, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.biosystems.2015.10.002DOI Listing
December 2015

Expansion of the QARS deficiency phenotype with report of a family with isolated supratentorial brain abnormalities.

Neurogenetics 2015 Apr 30;16(2):145-9. Epub 2014 Nov 30.

Division of Biochemical Diseases, Rm K3-201, Department of Pediatrics, B.C. Children's & Women's Hospital, 4480 Oak Street, Vancouver, BC, V6H 3 V4, Canada.

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http://link.springer.com/content/pdf/10.1007/s10048-014-0432
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http://link.springer.com/10.1007/s10048-014-0432-y
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http://dx.doi.org/10.1007/s10048-014-0432-yDOI Listing
April 2015

Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas.

Genome Biol 2015 Apr 23;16:84. Epub 2015 Apr 23.

Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, V5Z 1L3, BC, Canada.

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http://dx.doi.org/10.1186/s13059-015-0648-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4467049PMC
April 2015

Identification of altered cis-regulatory elements in human disease.

Trends Genet 2015 Feb 27;31(2):67-76. Epub 2015 Jan 27.

Centre for Molecular Medicine and Therapeutics, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.tig.2014.12.003DOI Listing
February 2015

FLAGS, frequently mutated genes in public exomes.

BMC Med Genomics 2014 Dec 3;7:64. Epub 2014 Dec 3.

Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, BC, Canada.

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http://dx.doi.org/10.1186/s12920-014-0064-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4267152PMC
December 2014

Usability study of clinical exome analysis software: top lessons learned and recommendations.

J Biomed Inform 2014 Oct 24;51:129-36. Epub 2014 May 24.

Centre for Molecular Medicine and Therapeutics, Child & Family Research Institute, 950 28th Ave W, Vancouver, BC V5Z 4H4, Canada; Department of Medical Genetics, University of British Columbia, 2329 West Mall, Vancouver, BC V6T 1Z4, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.jbi.2014.05.004DOI Listing
October 2014

On the identification of potential regulatory variants within genome wide association candidate SNP sets.

BMC Med Genomics 2014 Jun 11;7:34. Epub 2014 Jun 11.

Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1186/1755-8794-7-34DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4066296PMC
June 2014

Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment.

BMC Genomics 2014 Jun 13;15:472. Epub 2014 Jun 13.

Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.

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http://dx.doi.org/10.1186/1471-2164-15-472DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4082612PMC
June 2014

Inferring novel gene-disease associations using Medical Subject Heading Over-representation Profiles.

Genome Med 2012 28;4(9):75. Epub 2012 Sep 28.

Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, 980 W. 28th Ave, Vancouver, V5Z 4H4, Canada.

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http://dx.doi.org/10.1186/gm376DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3580445PMC
May 2014

The next generation of transcription factor binding site prediction.

PLoS Comput Biol 2013 5;9(9):e1003214. Epub 2013 Sep 5.

Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1371/journal.pcbi.1003214DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3764009PMC
April 2014

Mitochondrial carbonic anhydrase VA deficiency resulting from CA5A alterations presents with hyperammonemia in early childhood.

Am J Hum Genet 2014 Mar 13;94(3):453-61. Epub 2014 Feb 13.

Division of Biochemical Diseases, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3V4, Canada; Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3V4, Canada; Treatable Intellectual Disability Endeavour in British Columbia, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada.

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http://dx.doi.org/10.1016/j.ajhg.2014.01.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951944PMC
March 2014

A promoter-level mammalian expression atlas.

Authors:
Alistair R R Forrest Hideya Kawaji Michael Rehli J Kenneth Baillie Michiel J L de Hoon Vanja Haberle Timo Lassmann Ivan V Kulakovskiy Marina Lizio Masayoshi Itoh Robin Andersson Christopher J Mungall Terrence F Meehan Sebastian Schmeier Nicolas Bertin Mette Jørgensen Emmanuel Dimont Erik Arner Christian Schmidl Ulf Schaefer Yulia A Medvedeva Charles Plessy Morana Vitezic Jessica Severin Colin A Semple Yuri Ishizu Robert S Young Margherita Francescatto Intikhab Alam Davide Albanese Gabriel M Altschuler Takahiro Arakawa John A C Archer Peter Arner Magda Babina Sarah Rennie Piotr J Balwierz Anthony G Beckhouse Swati Pradhan-Bhatt Judith A Blake Antje Blumenthal Beatrice Bodega Alessandro Bonetti James Briggs Frank Brombacher A Maxwell Burroughs Andrea Califano Carlo V Cannistraci Daniel Carbajo Yun Chen Marco Chierici Yari Ciani Hans C Clevers Emiliano Dalla Carrie A Davis Michael Detmar Alexander D Diehl Taeko Dohi Finn Drabløs Albert S B Edge Matthias Edinger Karl Ekwall Mitsuhiro Endoh Hideki Enomoto Michela Fagiolini Lynsey Fairbairn Hai Fang Mary C Farach-Carson Geoffrey J Faulkner Alexander V Favorov Malcolm E Fisher Martin C Frith Rie Fujita Shiro Fukuda Cesare Furlanello Masaaki Furino Jun-ichi Furusawa Teunis B Geijtenbeek Andrew P Gibson Thomas Gingeras Daniel Goldowitz Julian Gough Sven Guhl Reto Guler Stefano Gustincich Thomas J Ha Masahide Hamaguchi Mitsuko Hara Matthias Harbers Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Takehiro Hashimoto Meenhard Herlyn Kelly J Hitchens Shannan J Ho Sui Oliver M Hofmann Ilka Hoof Furni Hori Lukasz Huminiecki Kei Iida Tomokatsu Ikawa Boris R Jankovic Hui Jia Anagha Joshi Giuseppe Jurman Bogumil Kaczkowski Chieko Kai Kaoru Kaida Ai Kaiho Kazuhiro Kajiyama Mutsumi Kanamori-Katayama Artem S Kasianov Takeya Kasukawa Shintaro Katayama Sachi Kato Shuji Kawaguchi Hiroshi Kawamoto Yuki I Kawamura Tsugumi Kawashima Judith S Kempfle Tony J Kenna Juha Kere Levon M Khachigian Toshio Kitamura S Peter Klinken Alan J Knox Miki Kojima Soichi Kojima Naoto Kondo Haruhiko Koseki Shigeo Koyasu Sarah Krampitz Atsutaka Kubosaki Andrew T Kwon Jeroen F J Laros Weonju Lee Andreas Lennartsson Kang Li Berit Lilje Leonard Lipovich Alan Mackay-Sim Ri-ichiroh Manabe Jessica C Mar Benoit Marchand Anthony Mathelier Niklas Mejhert Alison Meynert Yosuke Mizuno David A de Lima Morais Hiromasa Morikawa Mitsuru Morimoto Kazuyo Moro Efthymios Motakis Hozumi Motohashi Christine L Mummery Mitsuyoshi Murata Sayaka Nagao-Sato Yutaka Nakachi Fumio Nakahara Toshiyuki Nakamura Yukio Nakamura Kenichi Nakazato Erik van Nimwegen Noriko Ninomiya Hiromi Nishiyori Shohei Noma Shohei Noma Tadasuke Noazaki Soichi Ogishima Naganari Ohkura Hiroko Ohimiya Hiroshi Ohno Mitsuhiro Ohshima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry A Ovchinnikov Arnab Pain Robert Passier Margaret Patrikakis Helena Persson Silvano Piazza James G D Prendergast Owen J L Rackham Jordan A Ramilowski Mamoon Rashid Timothy Ravasi Patrizia Rizzu Marco Roncador Sugata Roy Morten B Rye Eri Saijyo Antti Sajantila Akiko Saka Shimon Sakaguchi Mizuho Sakai Hiroki Sato Suzana Savvi Alka Saxena Claudio Schneider Erik A Schultes Gundula G Schulze-Tanzil Anita Schwegmann Thierry Sengstag Guojun Sheng Hisashi Shimoji Yishai Shimoni Jay W Shin Christophe Simon Daisuke Sugiyama Takaai Sugiyama Masanori Suzuki Naoko Suzuki Rolf K Swoboda Peter A C 't Hoen Michihira Tagami Naoko Takahashi Jun Takai Hiroshi Tanaka Hideki Tatsukawa Zuotian Tatum Mark Thompson Hiroo Toyodo Tetsuro Toyoda Elvind Valen Marc van de Wetering Linda M van den Berg Roberto Verado Dipti Vijayan Ilya E Vorontsov Wyeth W Wasserman Shoko Watanabe Christine A Wells Louise N Winteringham Ernst Wolvetang Emily J Wood Yoko Yamaguchi Masayuki Yamamoto Misako Yoneda Yohei Yonekura Shigehiro Yoshida Susan E Zabierowski Peter G Zhang Xiaobei Zhao Silvia Zucchelli Kim M Summers Harukazu Suzuki Carsten O Daub Jun Kawai Peter Heutink Winston Hide Tom C Freeman Boris Lenhard Vladimir B Bajic Martin S Taylor Vsevolod J Makeev Albin Sandelin David A Hume Piero Carninci Yoshihide Hayashizaki

Nature 2014 Mar;507(7493):462-70

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http://dx.doi.org/10.1038/nature13182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529748PMC
March 2014

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles.

Nucleic Acids Res 2014 Jan 4;42(Database issue):D142-7. Epub 2013 Nov 4.

Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada, Department of Biology and Biotech Research and Innovation Centre, The Bioinformatics Centre, Copenhagen University, Ole Maaloes Vej 5, DK-2200, Denmark, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA, Laboratoire Physiologie Cellulaire & Végétale, Université Grenoble Alpes, CNRS, CEA, iRTSV, INRA, 38054 Grenoble, France, Computational Regulatory Genomics, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK, and Department of Informatics, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway.

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http://dx.doi.org/10.1093/nar/gkt997DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965086PMC
January 2014

TFBSshape: a motif database for DNA shape features of transcription factor binding sites.

Nucleic Acids Res 2014 Jan 7;42(Database issue):D148-55. Epub 2013 Nov 7.

Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA, Department of Biology, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada and Institute for Genome Sciences & Policy, Duke University, Durham, NC 27708, USA.

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http://dx.doi.org/10.1093/nar/gkt1087DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964943PMC
January 2014

Targeted CNS Delivery Using Human MiniPromoters and Demonstrated Compatibility with Adeno-Associated Viral Vectors.

Mol Ther Methods Clin Dev 2014 Jan;1

Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4 ; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V5Z 4H4 ; Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada V6T 2A1.

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http://dx.doi.org/10.1038/mtm.2013.5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3992516PMC
January 2014

Compensating for literature annotation bias when predicting novel drug-disease relationships through Medical Subject Heading Over-representation Profile (MeSHOP) similarity.

BMC Med Genomics 2013 7;6 Suppl 2:S3. Epub 2013 May 7.

Centre for Molecular Medicine and Therapeutics at Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada.

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http://dx.doi.org/10.1186/1755-8794-6-S2-S3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654871PMC
October 2013

Portal for Families Overcoming Neurodevelopmental Disorders (PFOND): Implementation of a Software Framework for Facilitated Community Website Creation by Nontechnical Volunteers.

JMIR Res Protoc 2013 Aug 6;2(2):e25. Epub 2013 Aug 6.

Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.

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http://dx.doi.org/10.2196/resprot.2675DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3742411PMC
August 2013

Utilizing social media to study information-seeking and ethical issues in gene therapy.

J Med Internet Res 2013 Mar 4;15(3):e44. Epub 2013 Mar 4.

National Core for Neuroethics, Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.

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http://dx.doi.org/10.2196/jmir.2313DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3636301PMC
March 2013

The transcription factor encyclopedia.

Authors:
Dimas Yusuf Stefanie L Butland Magdalena I Swanson Eugene Bolotin Amy Ticoll Warren A Cheung Xiao Yu Cindy Zhang Christopher T D Dickman Debra L Fulton Jonathan S Lim Jake M Schnabl Oscar H P Ramos Mireille Vasseur-Cognet Charles N de Leeuw Elizabeth M Simpson Gerhart U Ryffel Eric W-F Lam Ralf Kist Miranda S C Wilson Raquel Marco-Ferreres Jan J Brosens Leonardo L Beccari Paola Bovolenta Bérénice A Benayoun Lara J Monteiro Helma D C Schwenen Lars Grontved Elizabeth Wederell Susanne Mandrup Reiner A Veitia Harini Chakravarthy Pamela A Hoodless M Michela Mancarelli Bruce E Torbett Alison H Banham Sekhar P Reddy Rebecca L Cullum Michaela Liedtke Mario P Tschan Michelle Vaz Angie Rizzino Mariastella Zannini Seth Frietze Peggy J Farnham Astrid Eijkelenboom Philip J Brown David Laperrière Dominique Leprince Tiziana de Cristofaro Kelly L Prince Marrit Putker Luis del Peso Gieri Camenisch Roland H Wenger Michal Mikula Marieke Rozendaal Sylvie Mader Jerzy Ostrowski Simon J Rhodes Capucine Van Rechem Gaylor Boulay Sam W Z Olechnowicz Mary B Breslin Michael S Lan Kyster K Nanan Michael Wegner Juan Hou Rachel D Mullen Stephanie C Colvin Peter John Noy Carol F Webb Matthew E Witek Scott Ferrell Juliet M Daniel Jason Park Scott A Waldman Daniel J Peet Michael Taggart Padma-Sheela Jayaraman Julien J Karrich Bianca Blom Farhad Vesuna Henriette O'Geen Yunfu Sun Richard M Gronostajski Mark W Woodcroft Margaret R Hough Edwin Chen G Nicholas Europe-Finner Magdalena Karolczak-Bayatti Jarrod Bailey Oliver Hankinson Venu Raman David P LeBrun Shyam Biswal Christopher J Harvey Jason P DeBruyne John B Hogenesch Robert F Hevner Christophe Héligon Xin M Luo Marissa Cathleen Blank Kathleen Joyce Millen David S Sharlin Douglas Forrest Karin Dahlman-Wright Chunyan Zhao Yuriko Mishima Satrajit Sinha Rumela Chakrabarti Elodie Portales-Casamar Frances M Sladek Philip H Bradley Wyeth W Wasserman

Genome Biol 2012 ;13(3):R24

Department of Medical Genetics, Faculty of Medicine, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, Canada.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439975PMC
September 2012

oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets.

G3 (Bethesda) 2012 Sep 1;2(9):987-1002. Epub 2012 Sep 1.

Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, V5Z 4H4, Canada.

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http://g3journal.org/lookup/doi/10.1534/g3.112.003202
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http://dx.doi.org/10.1534/g3.112.003202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3429929PMC
September 2012

Quantitative biomedical annotation using medical subject heading over-representation profiles (MeSHOPs).

BMC Bioinformatics 2012 Sep 27;13:249. Epub 2012 Sep 27.

Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.

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http://dx.doi.org/10.1186/1471-2105-13-249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3564935PMC
September 2012

Validation of skeletal muscle cis-regulatory module predictions reveals nucleotide composition bias in functional enhancers.

PLoS Comput Biol 2011 Dec 1;7(12):e1002256. Epub 2011 Dec 1.

Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Genetics Graduate Program, and Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1371/journal.pcbi.1002256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228787PMC
December 2011

Towards resolving the transcription factor network controlling myelin gene expression.

Nucleic Acids Res 2011 Oct 5;39(18):7974-91. Epub 2011 Jul 5.

Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, V5Z 4H4, Canada.

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http://dx.doi.org/10.1093/nar/gkr326DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3185407PMC
October 2011

Identification of cis-regulatory sequence variations in individual genome sequences.

Genome Med 2011 Oct 10;3(10):65. Epub 2011 Oct 10.

Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada.

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http://dx.doi.org/10.1186/gm281DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3239227PMC
October 2011

Laboratory Animal Management Assistant (LAMA): a LIMS for active research colonies.

Mamm Genome 2010 Jun 22;21(5-6):224-30. Epub 2010 Apr 22.

Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, Vancouver, BC, Canada.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047758PMC
http://dx.doi.org/10.1007/s00335-010-9258-6DOI Listing
June 2010