Matthew T Weirauch

Matthew T Weirauch

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Matthew T Weirauch

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AP-1 activity induced by co-stimulation is required for chromatin opening during T cell activation.

J Exp Med 2019 Oct 25. Epub 2019 Oct 25.

Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH

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http://dx.doi.org/10.1084/jem.20182009DOI Listing
October 2019

Variants in the fetal genome near pro-inflammatory cytokine genes on 2q13 associate with gestational duration.

Nat Commun 2019 Sep 2;10(1):3927. Epub 2019 Sep 2.

Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.

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http://dx.doi.org/10.1038/s41467-019-11881-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6718389PMC
September 2019

Enrichment of Genomic Pathways Based on Differential DNA Methylation Associated With Chronic Postsurgical Pain and Anxiety in Children: A Prospective, Pilot Study.

J Pain 2019 Jul 9;20(7):771-785. Epub 2019 Jan 9.

Department of Environmental Health, University of Cincinnati; Division of Asthma Research, Cincinnati Children's Hospital, Cincinnati, Ohio.

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http://dx.doi.org/10.1016/j.jpain.2018.12.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6616015PMC
July 2019

Similarity regression predicts evolution of transcription factor sequence specificity.

Nat Genet 2019 06 27;51(6):981-989. Epub 2019 May 27.

Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/s41588-019-0411-1DOI Listing
June 2019

Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome.

Genome Biol 2019 04 2;20(1):64. Epub 2019 Apr 2.

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

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http://dx.doi.org/10.1186/s13059-019-1660-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6444547PMC
April 2019

Defective transcription elongation in a subset of cancers confers immunotherapy resistance.

Nat Commun 2018 10 23;9(1):4410. Epub 2018 Oct 23.

Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, 45229, OH, USA.

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http://www.nature.com/articles/s41467-018-06810-0
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http://dx.doi.org/10.1038/s41467-018-06810-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6199328PMC
October 2018

Genetic variants with gene regulatory effects are associated with diisocyanate-induced asthma.

J Allergy Clin Immunol 2018 09 30;142(3):959-969. Epub 2018 Jun 30.

Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio; Cincinnati VA Medical Center, Cincinnati, Ohio.

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http://dx.doi.org/10.1016/j.jaci.2018.06.022DOI Listing
September 2018

A plausibly causal functional lupus-associated risk variant in the STAT1-STAT4 locus.

Hum Mol Genet 2018 07;27(13):2392-2404

Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.

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http://dx.doi.org/10.1093/hmg/ddy140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6005081PMC
July 2018

Neurospora crassa developmental control mediated by the FLB-3 transcription factor.

Fungal Biol 2018 06 1;122(6):570-582. Epub 2018 Mar 1.

Departamento de Bioquímica e Tecnologia Química, Instituto de Química, UNESP, Universidade Estadual Paulista, 14800-060, Araraquara, SP, Brazil. Electronic address:

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http://dx.doi.org/10.1016/j.funbio.2018.01.004DOI Listing
June 2018

Nasal DNA methylation is associated with childhood asthma.

Epigenomics 2018 05 25;10(5):629-641. Epub 2018 Apr 25.

Pyrosequencing Lab for Genomic & Epigenomic Research, Cincinnati, Children's Hospital Medical Center, Cincinnati, OH 45229, USA.

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https://www.futuremedicine.com/doi/10.2217/epi-2017-0127
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http://dx.doi.org/10.2217/epi-2017-0127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5992571PMC
May 2018

Degenerate Pax2 and Senseless binding motifs improve detection of low-affinity sites required for enhancer specificity.

PLoS Genet 2018 04 4;14(4):e1007289. Epub 2018 Apr 4.

Division of Developmental Biology, Cincinnati Children's Hospital, MLC, Cincinnati, OH, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1007289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5902045PMC
April 2018

The Human Transcription Factors.

Cell 2018 02;172(4):650-665

Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA; Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.01.029DOI Listing
February 2018

The Epstein-Barr Virus B-ZIP Protein Zta Recognizes Specific DNA Sequences Containing 5-Methylcytosine and 5-Hydroxymethylcytosine.

Biochemistry 2017 11 10;56(47):6200-6210. Epub 2017 Nov 10.

Center for Autoimmune Genomics and Etiology and Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, and Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, Ohio 45229, United States.

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http://dx.doi.org/10.1021/acs.biochem.7b00741DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5907473PMC
November 2017

Analysis of chromatin accessibility in human epidermis identifies putative barrier dysfunction-sensing enhancers.

PLoS One 2017 27;12(9):e0184500. Epub 2017 Sep 27.

Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0184500PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617145PMC
October 2017

Nasal DNA methylation differentiates corticosteroid treatment response in pediatric asthma: A pilot study.

PLoS One 2017 13;12(10):e0186150. Epub 2017 Oct 13.

Pyrosequencing lab for genomic and epigenomic research, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0186150PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5640236PMC
October 2017

A FOXO1-induced oncogenic network defines the AML1-ETO preleukemic program.

Blood 2017 09 14;130(10):1213-1222. Epub 2017 Jul 14.

Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.

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http://dx.doi.org/10.1182/blood-2016-11-750976DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5606002PMC
September 2017

Genetic Associations with Gestational Duration and Spontaneous Preterm Birth.

N Engl J Med 2017 09 6;377(12):1156-1167. Epub 2017 Sep 6.

From the Division of Human Genetics (G.Z., L.J.M.), Center for Autoimmune Genomics and Etiology (M.T.W., D.E.M., X.C., C.R.F., L.C.K.) and the Divisions of Biomedical Informatics and Developmental Biology (M.T.W.), Cincinnati Children's Hospital Medical Center, and the Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center and March of Dimes Prematurity Research Center Ohio Collaborative (G.Z., L.M.M., M.P., J.M.H., L.J.M.), Cincinnati; the Department of Epidemiology Research, Statens Serum Institut (B.F., X.L., F.G., H.A.B., M.M.), and the Department of Clinical Medicine, University of Copenhagen (M.M.), Copenhagen, and the Research Unit of Gynecology and Obstetrics, Institute of Clinical Research, University of Southern Denmark, Odense (E.A.N.) - all in Denmark; the Department of Obstetrics and Gynecology, Sahlgrenska University Hospital Östra (J.B., V.S.), the Department of Obstetrics and Gynecology, Institute of Clinical Sciences (J.J.), and the Department of Obstetrics and Gynecology (B.J.), Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; 23andMe, Mountain View (N.L., P.-P.J., L.R., D.A.H., Y.H.), and the Department of Medicine, Stanford University School of Medicine, Stanford (M.M.) - both in California; the Department of Ecology and Evolutionary Biology, Yale University (A.R.C., G.P.W., M.C.N., J.M.), and the Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale Medical School (G.P.W.), New Haven, and the Yale Systems Biology Institute, West Haven (A.R.C., G.P.W., M.C.N., J.M.) - all in Connecticut; the Department of Obstetrics and Gynecology, Wayne State University, Detroit (G.P.W.); the PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu, and the Department of Children and Adolescents, Oulu University Hospital, Oulu (M.K.K., M.R., J.M.H., M.H.), and the Institute for Molecular Medicine Finland, University of Helsinki (A.P.), and Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital (K.T.), Helsinki - all in Finland; the Analytic and Translational Genetics Unit, Department of Medicine, the Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, and the Department of Neurology, Massachusetts General Hospital, Boston (A.P.), and the Program in Medical and Population Genetics and the Stanley Center for Psychiatric Research, Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge (A.P.) - both in Massachusetts; the Departments of Pediatrics (A.M., B.B.) and Epidemiology (K.K.R.), College of Public Health, and the Department of Pediatrics (K.K.R.), Carver College of Medicine, University of Iowa, Iowa City; the Medical Research Council Integrative Epidemiology Unit at the University of Bristol, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom (G.D.S.); and the Department of Genetics and Bioinformatics, Area of Health Data and Digitalization, Norwegian Institute of Public Health, Oslo (B.J.).

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http://www.nejm.org/doi/10.1056/NEJMoa1612665
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http://dx.doi.org/10.1056/NEJMoa1612665DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5561422PMC
September 2017

Non-base-contacting residues enable kaleidoscopic evolution of metazoan C2H2 zinc finger DNA binding.

Genome Biol 2017 09 6;18(1):167. Epub 2017 Sep 6.

Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.

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http://dx.doi.org/10.1186/s13059-017-1287-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5588721PMC
September 2017

Paternally Inherited DLK1 Deletion Associated With Familial Central Precocious Puberty.

J Clin Endocrinol Metab 2017 05;102(5):1557-1567

Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular/LIM42, Hospital das Clínicas, Disciplina de Endocrinologia, Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-093, Brazil.

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http://dx.doi.org/10.1210/jc.2016-3677DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5443333PMC
May 2017

Temporal, spatial, and phenotypical changes of PDGFRα expressing fibroblasts during late lung development.

Dev Biol 2017 05 11;425(2):161-175. Epub 2017 Apr 11.

Perinatal Institute, Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ydbio.2017.03.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5492510PMC
May 2017

Requirement for Dicer in Maintenance of Monosynaptic Sensory-Motor Circuits in the Spinal Cord.

Cell Rep 2016 11;17(9):2163-2172

Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.10.083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5152923PMC
November 2016

5-Hydroxymethylcytosine in E-box motifs ACAT|GTG and ACAC|GTG increases DNA-binding of the B-HLH transcription factor TCF4.

Integr Biol (Camb) 2016 09 3;8(9):936-45. Epub 2016 Aug 3.

Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Room 3128, Building 37, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1039/c6ib00079gDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6289052PMC
September 2016

Multiple layers of transcriptional regulation by PLZF in NKT-cell development.

Proc Natl Acad Sci U S A 2016 07 20;113(27):7602-7. Epub 2016 Jun 20.

Committee on Immunology, University of Chicago, Chicago, IL 60637; Department of Pathology, University of Chicago, Chicago, IL 60637;

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http://dx.doi.org/10.1073/pnas.1601504113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4941452PMC
July 2016

DREAMTools: a Python package for scoring collaborative challenges.

F1000Res 2015 9;4:1030. Epub 2015 Oct 9.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI),Wellcome Trust Genome Campus, Cambridge, UK; RWTH Aachen University Medical Hospital, Joint Research Centre for Computational Biomedicine (JRCCOMBINE), Aachen, Germany.

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http://dx.doi.org/10.12688/f1000research.7118.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4837986PMC
May 2016

A catalogue of eukaryotic transcription factor types, their evolutionary origin, and species distribution.

Subcell Biochem 2011 ;52:25-73

Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada,

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http://dx.doi.org/10.1007/978-90-481-9069-0_3DOI Listing
April 2016

Meta-analysis of differential gene co-expression: application to lupus.

Pac Symp Biocomput 2015 :443-54

Lindner College of Business, University of Cincinnati, 2925 Campus Green Dr., Cincinnati, OH 45221, USA.

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April 2016

Unique features of a global human ectoparasite identified through sequencing of the bed bug genome.

Nat Commun 2016 Feb 2;7:10165. Epub 2016 Feb 2.

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

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http://dx.doi.org/10.1038/ncomms10165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4740739PMC
February 2016

: a user-friendly web resource for genome-scale exploration of gene regulation in .

Curr Plant Biol 2015 Sep-Dec;3-4:48-55

Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229; Division of Biomedical Informatics and Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229.

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http://dx.doi.org/10.1016/j.cpb.2015.09.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4740912PMC
February 2016

Affinity regression predicts the recognition code of nucleic acid-binding proteins.

Nat Biotechnol 2015 Dec 16;33(12):1242-1249. Epub 2015 Nov 16.

Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.

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http://dx.doi.org/10.1038/nbt.3343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4871164PMC
December 2015

Transcription Factor Repertoire of Homeostatic Eosinophilopoiesis.

J Immunol 2015 Sep 12;195(6):2683-95. Epub 2015 Aug 12.

Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229;

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http://dx.doi.org/10.4049/jimmunol.1500510DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4561201PMC
September 2015

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning.

Nat Biotechnol 2015 Aug 27;33(8):831-8. Epub 2015 Jul 27.

1] Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario, Canada. [2] Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada. [3] Canadian Institute for Advanced Research, Programs on Genetic Networks and Neural Computation, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/nbt.3300DOI Listing
August 2015

GABPα Binding to Overlapping ETS and CRE DNA Motifs Is Enhanced by CREB1: Custom DNA Microarrays.

G3 (Bethesda) 2015 Jul 16;5(9):1909-18. Epub 2015 Jul 16.

Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892

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http://g3journal.org/lookup/doi/10.1534/g3.115.020248
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http://dx.doi.org/10.1534/g3.115.020248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4555227PMC
July 2015

C2H2 zinc finger proteins greatly expand the human regulatory lexicon.

Nat Biotechnol 2015 May 18;33(5):555-62. Epub 2015 Feb 18.

1] Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada. [2] Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. [3] Canadian Institutes for Advanced Research, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/nbt.3128DOI Listing
May 2015

MiR-125a targets effector programs to stabilize Treg-mediated immune homeostasis.

Nat Commun 2015 May 12;6:7096. Epub 2015 May 12.

1] State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200032, China [2] Joint Molecular Rheumatology Laboratory of the Institute of Health Sciences and Shanghai Renji Hospital, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Jiaotong University School of Medicine, Shanghai 200025, China [3] Center for Autoimmune Genomics and Etiology (CAGE) and Divisions of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati Ohio 45229, USA [4] Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiaotong University, Shanghai 200240, China.

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http://dx.doi.org/10.1038/ncomms8096DOI Listing
May 2015

Divergence of transcriptional landscape occurs early in B cell activation.

Epigenetics Chromatin 2015 14;8:20. Epub 2015 May 14.

Department of Developmental, Chemical and Molecular Biology, Sackler School of Biomedical Science, Tufts University School of Medicine, 150 Harrison Avenue, Boston, MA 02111 USA.

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http://www.epigeneticsandchromatin.com/content/8/1/20
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http://dx.doi.org/10.1186/s13072-015-0012-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4434543PMC
May 2015

Quantifying inter-laboratory variability in stable isotope analysis of ancient skeletal remains.

PLoS One 2014 25;9(7):e102844. Epub 2014 Jul 25.

Center for Autoimmune Genomics and Etiology, and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0102844PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4111498PMC
April 2015

The IRF5-TNPO3 association with systemic lupus erythematosus has two components that other autoimmune disorders variably share.

Hum Mol Genet 2015 Jan 8;24(2):582-96. Epub 2014 Sep 8.

Division of Rheumatology, Center for Autoimmune Genomics and Etiology and US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA.

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http://dx.doi.org/10.1093/hmg/ddu455DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4275071PMC
January 2015

Making it big in allergy.

J Allergy Clin Immunol 2015 Jan;135(1):43-5

Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio. Electronic address:

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http://dx.doi.org/10.1016/j.jaci.2014.10.041DOI Listing
January 2015

Whole exome sequencing for familial bicuspid aortic valve identifies putative variants.

Circ Cardiovasc Genet 2014 Oct 1;7(5):677-83. Epub 2014 Aug 1.

From the Department of Pediatrics, Cincinnati Children's Hospital Medical Center, OH (L.J.M., V.P., K.M.K., L.C.K., M.K., P.D., M.T.W.); Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati OH (L.J.M., K.M.K., M.K., M.T.W.); Department of Pediatrics, Nationwide Children's Hospital, The Ohio State University, Columbus (L.C.); Herma Heart Center, Children's Hospital of Wisconsin, Milwaukee (D.W.B.); and Department of Pediatrics, Medical College of Wisconsin, Milwaukee (D.W.B.).

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http://dx.doi.org/10.1161/CIRCGENETICS.114.000526DOI Listing
October 2014

Myeloid malignancies with chromosome 5q deletions acquire a dependency on an intrachromosomal NF-κB gene network.

Cell Rep 2014 Sep 4;8(5):1328-38. Epub 2014 Sep 4.

Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S22111247140066
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http://dx.doi.org/10.1016/j.celrep.2014.07.062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4237069PMC
September 2014

DNA methylation dynamics during ex vivo differentiation and maturation of human dendritic cells.

Epigenetics Chromatin 2014 20;7:21. Epub 2014 Aug 20.

Division of Asthma Research, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH 45229, USA.

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http://dx.doi.org/10.1186/1756-8935-7-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4144987PMC
August 2014

The 253-kb inversion and deep intronic mutations in UNC13D are present in North American patients with familial hemophagocytic lymphohistiocytosis 3.

Pediatr Blood Cancer 2014 Jun 28;61(6):1034-40. Epub 2014 Jan 28.

Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio.

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http://dx.doi.org/10.1002/pbc.24955DOI Listing
June 2014

Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters.

Nucleic Acids Res 2014 Jan 24;42(1):153-62. Epub 2013 Sep 24.

Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA, Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA and Divisions of Rheumatology and Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.

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http://dx.doi.org/10.1093/nar/gkt858DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874175PMC
January 2014

Early evolution of the T-box transcription factor family.

Proc Natl Acad Sci U S A 2013 Oct 16;110(40):16050-5. Epub 2013 Sep 16.

Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), 08003 Barcelona, Spain.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791752PMC
http://dx.doi.org/10.1073/pnas.1309748110DOI Listing
October 2013

Structural basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins.

Proc Natl Acad Sci U S A 2011 Jun 14;108(26):10690-5. Epub 2011 Jun 14.

Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8.

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http://dx.doi.org/10.1073/pnas.1102544108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3127928PMC
June 2011

Dramatic changes in transcription factor binding over evolutionary time.

Genome Biol 2010 1;11(6):122. Epub 2010 Jun 1.

Banting and Best Department of Medical Research and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.

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http://dx.doi.org/10.1186/gb-2010-11-6-122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911098PMC
November 2010

A global analysis of genetic interactions in Caenorhabditis elegans.

J Biol 2007 26;6(3). Epub 2007 Sep 26.

Department of Medical Genetics and Microbiology, The Terrence Donnelly Centre for Cellular and Biomolecular Research, 160 College St, University of Toronto, Toronto, ON, M5S 3E1, Canada.

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http://jbiol.biomedcentral.com/articles/10.1186/jbiol58
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http://dx.doi.org/10.1186/jbiol58DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2373897PMC
March 2010

Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same.

Trends Genet 2010 Feb 18;26(2):66-74. Epub 2010 Jan 18.

Banting and Best Department of Medical Research and Donnelly Centre for Cellular and Biomolecular Research, Ontario, Canada.

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http://dx.doi.org/10.1016/j.tig.2009.12.002DOI Listing
February 2010

Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum.

J Bacteriol 2009 Feb 1;191(3):782-94. Epub 2008 Dec 1.

Department of Ocean Sciences, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA.

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http://jb.asm.org/lookup/doi/10.1128/JB.00965-08
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http://dx.doi.org/10.1128/JB.00965-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632070PMC
February 2009

Identification of conserved regulatory elements in mammalian promoter regions: a case study using the PCK1 promoter.

Genomics Proteomics Bioinformatics 2008 Dec;6(3-4):129-43

Bovine Functional Genomics Laboratory, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA.

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http://dx.doi.org/10.1016/S1672-0229(09)60001-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054123PMC
December 2008

Information-based methods for predicting gene function from systematic gene knock-downs.

BMC Bioinformatics 2008 Oct 29;9:463. Epub 2008 Oct 29.

Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1186/1471-2105-9-463DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2596148PMC
October 2008

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

A search engine to identify pathway genes from expression data on multiple organisms.

BMC Syst Biol 2007 May 4;1:20. Epub 2007 May 4.

Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1186/1752-0509-1-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1878502PMC
May 2007

Rapid knot detection and application to protein structure prediction.

Bioinformatics 2006 Jul;22(14):e252-9

Department of Biomolecular Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl236DOI Listing
July 2006