Publications by authors named "Chad A Shaw"

100Publications

Bayesian modelling of high-throughput sequencing assays with malacoda.

PLoS Comput Biol 2020 07 21;16(7):e1007504. Epub 2020 Jul 21.

Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1007504DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7394446PMC
July 2020

Validation Studies for Single Circulating Trophoblast Genetic Testing as a Form of Noninvasive Prenatal Diagnosis.

Am J Hum Genet 2019 12 27;105(6):1262-1273. Epub 2019 Nov 27.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2019.11.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6904821PMC
December 2019

Functionalization of CD36 cardiovascular disease and expression associated variants by interdisciplinary high throughput analysis.

PLoS Genet 2019 07 25;15(7):e1008287. Epub 2019 Jul 25.

Cardeza Foundation for Hematologic Research/Department of Medicine, Sidney Kimmel Medical School, Thomas Jefferson University, Philadelphia, PA, United States of America.

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http://dx.plos.org/10.1371/journal.pgen.1008287
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http://dx.doi.org/10.1371/journal.pgen.1008287DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6684090PMC
July 2019

Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2.

Cell 2019 03 28;176(6):1310-1324.e10. Epub 2019 Feb 28.

Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Human Genome Sequencing Center, BCM, Houston, TX 77030, USA; Department of Pediatrics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, BCM, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.01.045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6438178PMC
March 2019

Identification of the Regulatory Elements and Target Genes of Megakaryopoietic Transcription Factor MEF2C.

Thromb Haemost 2019 May 7;119(5):716-725. Epub 2019 Feb 7.

Department of Medicine, Cardeza Foundation for Hematologic Research, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, Pennsylvania, United States.

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http://dx.doi.org/10.1055/s-0039-1678694DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6932631PMC
May 2019

Design tools for MPRA experiments.

Bioinformatics 2018 08;34(15):2682-2683

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6454564PMC
August 2018

Predicting human genes susceptible to genomic instability associated with /-mediated rearrangements.

Genome Res 2018 08 15;28(8):1228-1242. Epub 2018 Jun 15.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1101/gr.229401.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6071635PMC
August 2018

Sustained endocrine profiles of a girl with WAGR syndrome.

BMC Med Genet 2017 10 23;18(1):117. Epub 2017 Oct 23.

Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan.

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http://dx.doi.org/10.1186/s12881-017-0477-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5654094PMC
October 2017

EMT cells increase breast cancer metastasis via paracrine GLI activation in neighbouring tumour cells.

Nat Commun 2017 06 12;8:15773. Epub 2017 Jun 12.

Department of Pharmacology, University of Colorado-Denver, 12800 East 19th Avenue, Room P18-6115, Aurora, Colorado 80045, USA.

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http://dx.doi.org/10.1038/ncomms15773DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5472791PMC
June 2017

Identification of a functional genetic variant driving racially dimorphic platelet gene expression of the thrombin receptor regulator, PCTP.

Thromb Haemost 2017 05 2;117(5):962-970. Epub 2017 Mar 2.

Leonard C. Edelstein, Department of Medicine Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Suite 394, Philadelphia, PA 19107, USA, Tel.: +1 215 955 1797, Fax: +1 215 955 9170,

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http://dx.doi.org/10.1160/TH16-09-0692DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5512274PMC
May 2017

An Organismal CNV Mutator Phenotype Restricted to Early Human Development.

Cell 2017 02;168(5):830-842.e7

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2017.01.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5407901PMC
February 2017

Resolution of Disease Phenotypes Resulting from Multilocus Genomic Variation.

N Engl J Med 2017 01 7;376(1):21-31. Epub 2016 Dec 7.

From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston.

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http://dx.doi.org/10.1056/NEJMoa1516767DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5335876PMC
January 2017

Clinical bioinformatics: emergence of a new laboratory discipline.

Expert Rev Mol Diagn 2016 11 20;16(11):1139-1141. Epub 2016 Oct 20.

b Department of Molecular and Human Genetics, Director of Bioinformatics, Baylor Genetics Laboratories , Baylor College of Medicine , Houston , TX , USA.

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http://dx.doi.org/10.1080/14737159.2016.1246184DOI Listing
November 2016

De Novo Truncating Mutation of TRIM8 Causes Early-Onset Epileptic Encephalopathy.

Ann Hum Genet 2016 Jul;80(4):235-40

Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan.

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http://dx.doi.org/10.1111/ahg.12157DOI Listing
July 2016

Integrative Multi-omic Analysis of Human Platelet eQTLs Reveals Alternative Start Site in Mitofusin 2.

Am J Hum Genet 2016 05 28;98(5):883-897. Epub 2016 Apr 28.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Statistics, Rice University, Houston, TX 77251, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2016.03.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4863560PMC
May 2016

Respiratory syncytial virus and rhinovirus severe bronchiolitis are associated with distinct nasopharyngeal microbiota.

J Allergy Clin Immunol 2016 06 6;137(6):1909-1913.e4. Epub 2016 Apr 6.

Department of Emergency Medicine, Massachusetts General Hospital, Boston, Mass; Division of Rheumatology, Allergy and Immunology, Department of Medicine, Massachusetts General Hospital, Boston, Mass.

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http://dx.doi.org/10.1016/j.jaci.2016.01.036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4899255PMC
June 2016

Erratum to: Somatic Mosaicism: Implications for Disease and Transmission Genetics.

Trends Genet 2016 02 22;32(2):138. Epub 2015 Dec 22.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1016/j.tig.2015.07.004DOI Listing
February 2016

Multiallelic Positions in the Human Genome: Challenges for Genetic Analyses.

Hum Mutat 2016 Mar 31;37(3):231-234. Epub 2015 Dec 31.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1002/humu.22944DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4752396PMC
March 2016

An essential role for Gα(i2) in Smoothened-stimulated epithelial cell proliferation in the mammary gland.

Sci Signal 2015 Sep 15;8(394):ra92. Epub 2015 Sep 15.

Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA. Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA. Department of Radiology, Baylor College of Medicine, Houston, TX 77030, USA.

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http://stke.sciencemag.org/lookup/doi/10.1126/scisignal.aaa7
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http://dx.doi.org/10.1126/scisignal.aaa7355DOI Listing
September 2015

DNA REPAIR. Mus81 and converging forks limit the mutagenicity of replication fork breakage.

Science 2015 Aug;349(6249):742-7

Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.

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http://dx.doi.org/10.1126/science.aaa8391DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4782627PMC
August 2015

Somatic mosaicism: implications for disease and transmission genetics.

Trends Genet 2015 Jul 21;31(7):382-92. Epub 2015 Apr 21.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tig.2015.03.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4490042PMC
July 2015

Alu-mediated diverse and complex pathogenic copy-number variants within human chromosome 17 at p13.3.

Hum Mol Genet 2015 Jul 23;24(14):4061-77. Epub 2015 Apr 23.

Department of Molecular & Human Genetics, Department of Pediatrics and Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA, Texas Children's Hospital, Houston, TX 77030, USA and

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http://dx.doi.org/10.1093/hmg/ddv146DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4476451PMC
July 2015

MeCP2 binds to non-CG methylated DNA as neurons mature, influencing transcription and the timing of onset for Rett syndrome.

Proc Natl Acad Sci U S A 2015 Apr 13;112(17):5509-14. Epub 2015 Apr 13.

Department of Molecular and Human Genetics, Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030 Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030; and

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http://dx.doi.org/10.1073/pnas.1505909112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4418849PMC
April 2015

Absence of heterozygosity due to template switching during replicative rearrangements.

Am J Hum Genet 2015 Apr 19;96(4):555-64. Epub 2015 Mar 19.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2015.01.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4385179PMC
April 2015

Variant interpretation through Bayesian fusion of frequency and genomic knowledge.

Genome Med 2015 28;7(1). Epub 2015 Jan 28.

Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA.

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http://dx.doi.org/10.1186/s13073-015-0129-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4308929PMC
January 2015

Genome-wide analyses of LINE-LINE-mediated nonallelic homologous recombination.

Nucleic Acids Res 2015 Feb 22;43(4):2188-98. Epub 2015 Jan 22.

Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 2 Banacha street, 02-097 Warsaw, Poland Mossakowski Medical Research Centre, Polish Academy of Sciences, 5 Pawińskiego street, 02-106 Warsaw, Poland

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http://dx.doi.org/10.1093/nar/gku1394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344489PMC
February 2015

The oncogenic STP axis promotes triple-negative breast cancer via degradation of the REST tumor suppressor.

Cell Rep 2014 Nov 6;9(4):1318-32. Epub 2014 Nov 6.

Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Integrative Molecular and Biomedical Sciences Program, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA. Electronic address:

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http://www.cell.com/cms/attachment/2020816778/2040986338/mmc
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http://linkinghub.elsevier.com/retrieve/pii/S221112471400865
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http://dx.doi.org/10.1016/j.celrep.2014.10.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4427000PMC
November 2014

Human endogenous retroviral elements promote genome instability via non-allelic homologous recombination.

BMC Biol 2014 Sep 23;12:74. Epub 2014 Sep 23.

Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm ABBR-R809, Houston, TX, USA.

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http://dx.doi.org/10.1186/s12915-014-0074-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4195946PMC
September 2014

Parent of origin, mosaicism, and recurrence risk: probabilistic modeling explains the broken symmetry of transmission genetics.

Am J Hum Genet 2014 Oct 18;95(4):345-59. Epub 2014 Sep 18.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Statistics, Rice University, Houston, TX 77005, USA; Department of Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2014.08.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4185125PMC
October 2014

NetComm: a network analysis tool based on communicability.

Bioinformatics 2014 Dec 13;30(23):3387-9. Epub 2014 Aug 13.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77054, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu536DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4274347PMC
December 2014

MicroRNA expression differences in human hematopoietic cell lineages enable regulated transgene expression.

PLoS One 2014 16;9(7):e102259. Epub 2014 Jul 16.

Cardeza Foundation for Hematologic Research and Department of Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0102259PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4100820PMC
March 2015

Testicular sex cord-stromal tumor in a boy with 2q37 deletion syndrome.

BMC Med Genomics 2014 Apr 22;7:19. Epub 2014 Apr 22.

Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.

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http://dx.doi.org/10.1186/1755-8794-7-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4021669PMC
April 2014

Gene sequence variability of the three surface proteins of human respiratory syncytial virus (HRSV) in Texas.

PLoS One 2014 13;9(3):e90786. Epub 2014 Mar 13.

Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America; Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0090786PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3953119PMC
January 2016

An efficient algorithm for accurate computation of the Dirichlet-multinomial log-likelihood function.

Authors:
Peng Yu Chad A Shaw

Bioinformatics 2014 Jun 11;30(11):1547-54. Epub 2014 Feb 11.

Department of Electrical and Computer Engineering & TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering (CBGSE), Texas A&M University, College Station, TX 77843, USA and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4081639PMC
June 2014

Integrative genomic analysis of the human immune response to influenza vaccination.

Elife 2013 Jul 16;2:e00299. Epub 2013 Jul 16.

Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , United States ; Department of Medicine , Baylor College of Medicine , Houston , United States.

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http://dx.doi.org/10.7554/eLife.00299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3713456PMC
July 2013

Neuroendocrine phenotypes in a boy with 5q14 deletion syndrome implicate the regulatory roles of myocyte-specific enhancer factor 2C in the postnatal hypothalamus.

Eur J Med Genet 2013 Sep 5;56(9):475-83. Epub 2013 Jul 5.

Department of Pediatrics, Kyushu University Hospital, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.ejmg.2013.06.009DOI Listing
September 2013

Ataxin1L is a regulator of HSC function highlighting the utility of cross-tissue comparisons for gene discovery.

PLoS Genet 2013 Mar 28;9(3):e1003359. Epub 2013 Mar 28.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1003359DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3610904PMC
March 2013

The Hematopoietic Expression Viewer: expanding mobile apps as a scientific tool.

Bioinformatics 2012 Jul 9;28(14):1941-2. Epub 2012 May 9.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491999PMC
July 2012

Crh and Oprm1 mediate anxiety-related behavior and social approach in a mouse model of MECP2 duplication syndrome.

Nat Genet 2012 Jan 8;44(2):206-11. Epub 2012 Jan 8.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.

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http://dx.doi.org/10.1038/ng.1066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3267865PMC
January 2012

High frequency of known copy number abnormalities and maternal duplication 15q11-q13 in patients with combined schizophrenia and epilepsy.

BMC Med Genet 2011 Nov 25;12:154. Epub 2011 Nov 25.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA.

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http://dx.doi.org/10.1186/1471-2350-12-154DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3239290PMC
November 2011

Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.

Neuron 2011 Jun;70(5):863-85

Program on Neurogenetics, Yale University School of Medicine, 230 South Frontage Road, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1016/j.neuron.2011.05.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3939065PMC
June 2011

Protein interactome reveals converging molecular pathways among autism disorders.

Sci Transl Med 2011 Jun;3(86):86ra49

Howard Hughes Medical Institute, Department of Molecular and Human Genetics, Baylor College of Medicine, and Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA.

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http://dx.doi.org/10.1126/scitranslmed.3002166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169432PMC
June 2011

Early patterns of gene expression correlate with the humoral immune response to influenza vaccination in humans.

J Infect Dis 2011 Apr 28;203(7):921-9. Epub 2011 Feb 28.

Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030-2504, USA.

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http://dx.doi.org/10.1093/infdis/jiq156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3068032PMC
April 2011

Comparison of an expanded ataxia interactome with patient medical records reveals a relationship between macular degeneration and ataxia.

Hum Mol Genet 2011 Feb 15;20(3):510-27. Epub 2010 Nov 15.

Department of Cellular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/hmg/ddq496DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3016911PMC
February 2011