Matthew Stephens

Matthew Stephens

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Matthew Stephens

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In drug-induced, immune-mediated hepatitis, interleukin-33 reduces hepatitis and improves survival independently and as a consequence of FoxP3+ T-cell activity.

Cell Mol Immunol 2019 Aug 20;16(8):706-717. Epub 2018 Jul 20.

Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University, 1800 Orleans Street, Suite 6349, Baltimore, MD, 21287, USA.

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http://www.nature.com/articles/s41423-018-0087-y
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http://dx.doi.org/10.1038/s41423-018-0087-yDOI Listing
August 2019

Detailed modeling of positive selection improves detection of cancer driver genes.

Nat Commun 2019 Jul 30;10(1):3399. Epub 2019 Jul 30.

Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.

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http://dx.doi.org/10.1038/s41467-019-11284-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6667447PMC
July 2019

Regional influences on community structure across the tropical-temperate divide.

Nat Commun 2019 06 14;10(1):2646. Epub 2019 Jun 14.

Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL, 60637, USA.

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http://dx.doi.org/10.1038/s41467-019-10253-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6570764PMC
June 2019

Lipopolysaccharides modulate intestinal epithelial permeability and inflammation in a species-specific manner.

Gut Microbes 2019 Jun 16:1-12. Epub 2019 Jun 16.

a Snyder Institute for Chronic Diseases, Department of Physiology & Pharmacology, Cumming School of Medicine , University of Calgary , Calgary , Canada.

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http://dx.doi.org/10.1080/19490976.2019.1629235DOI Listing
June 2019

Inference and visualization of DNA damage patterns using a grade of membership model.

Bioinformatics 2019 Apr;35(8):1292-1298

Department of Statistics, University of Chicago, Chicago, IL, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty779DOI Listing
April 2019

Discovery and characterization of variance QTLs in human induced pluripotent stem cells.

PLoS Genet 2019 04 19;15(4):e1008045. Epub 2019 Apr 19.

Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.

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http://dx.plos.org/10.1371/journal.pgen.1008045
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http://dx.doi.org/10.1371/journal.pgen.1008045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6474585PMC
April 2019

Accurate genomic prediction of Coffea canephora in multiple environments using whole-genome statistical models.

Heredity (Edinb) 2019 Mar 25;122(3):261-275. Epub 2018 Jun 25.

Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, 13400-970, Brazil.

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http://dx.doi.org/10.1038/s41437-018-0105-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6460747PMC
March 2019

Mesenteric Lymphatic Alterations Observed During DSS Induced Intestinal Inflammation Are Driven in a TLR4-PAMP/DAMP Discriminative Manner.

Front Immunol 2019 26;10:557. Epub 2019 Mar 26.

Department of Physiology and Pharmacology, Inflammation Research Network, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada.

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https://www.frontiersin.org/article/10.3389/fimmu.2019.00557
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http://dx.doi.org/10.3389/fimmu.2019.00557DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6443629PMC
March 2019

Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions.

Nat Genet 2019 01 26;51(1):187-195. Epub 2018 Nov 26.

Department of Human Genetics, University of Chicago, Chicago, IL, USA.

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http://dx.doi.org/10.1038/s41588-018-0268-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6309609PMC
January 2019

Estimating recent migration and population-size surfaces.

PLoS Genet 2019 01 14;15(1):e1007908. Epub 2019 Jan 14.

Evolutionary Biology, University of Chicago, Chicago, Illinois, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1007908DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6347299PMC
January 2019

A new sequence logo plot to highlight enrichment and depletion.

BMC Bioinformatics 2018 Dec 10;19(1):473. Epub 2018 Dec 10.

Department of Statistics, University of Chicago, Chicago, 60637, USA.

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http://dx.doi.org/10.1186/s12859-018-2489-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6288878PMC
December 2018

Genotyping Polyploids from Messy Sequencing Data.

Genetics 2018 11 5;210(3):789-807. Epub 2018 Sep 5.

Department of Human Genetics, University of Chicago, Illinois 60637.

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http://dx.doi.org/10.1534/genetics.118.301468DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6218231PMC
November 2018

Large-scale genome-wide enrichment analyses identify new trait-associated genes and pathways across 31 human phenotypes.

Nat Commun 2018 10 19;9(1):4361. Epub 2018 Oct 19.

Department of Statistics, The University of Chicago, Chicago, 60637, IL, USA.

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http://www.nature.com/articles/s41467-018-06805-x
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http://dx.doi.org/10.1038/s41467-018-06805-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6195536PMC
October 2018

Empirical Bayes shrinkage and false discovery rate estimation, allowing for unwanted variation.

Biostatistics 2018 Jul 6. Epub 2018 Jul 6.

Department of Human Genetics, Cummings Life Science Center, University of Chicago, 920 E 58th Street, Chicago, IL 60637, USA and Department of Statistics, George Herbert Jones Laboratory, University of Chicago, 5747 S Ellis Avenue, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1093/biostatistics/kxy029DOI Listing
July 2018

Estimating Time to the Common Ancestor for a Beneficial Allele.

Mol Biol Evol 2018 04;35(4):1003-1017

Department of Ecology and Evolution, University of Chicago, Chicago, IL.

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http://dx.doi.org/10.1093/molbev/msy006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5888984PMC
April 2018

Acute small intestinal inflammation results in persistent lymphatic alterations.

Am J Physiol Gastrointest Liver Physiol 2018 03 14;314(3):G408-G417. Epub 2017 Dec 14.

Inflammation Research Network and Smooth Muscle Research Group, Snyder Institute for Chronic Diseases, Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary , Calgary, Alberta , Canada.

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http://dx.doi.org/10.1152/ajpgi.00340.2017DOI Listing
March 2018

Neutrophil-lymphatic interactions during acute and chronic disease.

Cell Tissue Res 2018 03 8;371(3):599-606. Epub 2018 Feb 8.

Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Room 1647, Health Sciences Centre, 3330 Hospital Drive NW, Calgary, Alberta, AB T2N 4N1, Canada.

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http://dx.doi.org/10.1007/s00441-017-2779-5DOI Listing
March 2018

BAYESIAN LARGE-SCALE MULTIPLE REGRESSION WITH SUMMARY STATISTICS FROM GENOME-WIDE ASSOCIATION STUDIES.

Ann Appl Stat 2017 5;11(3):1561-1592. Epub 2017 Oct 5.

University of Chicago.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5796536PMC
October 2017

Promoter shape varies across populations and affects promoter evolution and expression noise.

Nat Genet 2017 Apr 13;49(4):550-558. Epub 2017 Feb 13.

European Molecular Biology Laboratory (EMBL) Genome Biology Unit, Heidelberg, Germany.

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http://dx.doi.org/10.1038/ng.3791DOI Listing
April 2017

Visualizing the structure of RNA-seq expression data using grade of membership models.

PLoS Genet 2017 Mar 23;13(3):e1006599. Epub 2017 Mar 23.

Department of Statistics, University of Chicago, Chicago, Illinois, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1006599DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5363805PMC
March 2017

Innate-like T cell profile in myeloma: Severe deficiency of Vγ9Vδ2 T cells in aminobisphosphonate-treated patients.

Leuk Lymphoma 2016 9;57(4):977-80. Epub 2015 Oct 9.

b Wellington Blood and Cancer Centre, Capital and Coast District Health Board , Wellington , New Zealand .

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http://dx.doi.org/10.3109/10428194.2015.1088653DOI Listing
December 2016

Marine sponge alkaloids as a source of anti-bacterial adjuvants.

Bioorg Med Chem Lett 2016 12 9;26(24):5863-5866. Epub 2016 Nov 9.

Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8024, United States. Electronic address:

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http://dx.doi.org/10.1016/j.bmcl.2016.11.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5776710PMC
December 2016

Variance adaptive shrinkage (vash): flexible empirical Bayes estimation of variances.

Bioinformatics 2016 11 19;32(22):3428-3434. Epub 2016 Jul 19.

Department of Statistics, University of Chicago, Chicago, 60637, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw483DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5181563PMC
November 2016

Evaluation of ethyl N-(2-phenethyl) carbamate analogues as biofilm inhibitors of methicillin resistant Staphylococcus aureus.

Org Biomol Chem 2016 Jul;14(28):6853-6

Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA.

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http://dx.doi.org/10.1039/c6ob00706fDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4942382PMC
July 2016

Potentiation of the Fosmidomycin analogue FR 900098 with substituted 2-oxazolines against .

Medchemcomm 2016 27;7(10):1952-1956. Epub 2016 Jul 27.

Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695, USA.

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http://dx.doi.org/10.1039/C6MD00365FDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5279706PMC
July 2016

msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding.

PLoS One 2015 25;10(9):e0138030. Epub 2015 Sep 25.

Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America; Department of Statistics, University of Chicago, Chicago, Illinois, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0138030PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4583425PMC
May 2016

A multivariate genome-wide association analysis of 10 LDL subfractions, and their response to statin treatment, in 1868 Caucasians.

PLoS One 2015 21;10(4):e0120758. Epub 2015 Apr 21.

Department of Human Genetics, University of Chicago, Chicago, IL, USA; Department of Statistics, University of Chicago, Chicago, IL, USA.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0120758PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405269PMC
April 2016

Oligodeoxynucleotide inhibition of Toll-like receptors 3, 7, 8, and 9 suppresses cytokine production in a human rheumatoid arthritis model.

Eur J Immunol 2016 Mar 16;46(3):772-81. Epub 2015 Dec 16.

Kennedy Institute of Rheumatology, Faculty of Medicine, Imperial College of Science, Technology and Medicine, Oxford, UK.

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http://dx.doi.org/10.1002/eji.201546123DOI Listing
March 2016

Visualizing spatial population structure with estimated effective migration surfaces.

Nat Genet 2016 Jan 7;48(1):94-100. Epub 2015 Dec 7.

Department of Statistics, The University of Chicago, Chicago, Illinois, USA.

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http://dx.doi.org/10.1038/ng.3464DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4696895PMC
January 2016

Potentiation of Resistance to Conventional Antibiotics through Small Molecule Adjuvants.

Medchemcomm 2016 Jan 30;7(1):128-131. Epub 2015 Sep 30.

Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States.

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http://xlink.rsc.org/?DOI=C5MD00353A
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http://dx.doi.org/10.1039/C5MD00353ADOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4749165PMC
January 2016

New evidence for hybrid zones of forest and savanna elephants in Central and West Africa.

Mol Ecol 2015 12 12;24(24):6134-47. Epub 2015 Dec 12.

Center for Conservation Biology, Department of Biology, University of Washington, Box 351800, Seattle, WA, 98195-1800, USA.

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http://dx.doi.org/10.1111/mec.13472DOI Listing
December 2015

A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures.

PLoS Genet 2015 Dec 2;11(12):e1005657. Epub 2015 Dec 2.

Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005657DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4667891PMC
December 2015

Aryl amide small-molecule inhibitors of microRNA miR-21 function.

Bioorg Med Chem Lett 2015 Nov 17;25(21):4793-4796. Epub 2015 Jul 17.

University of Pittsburgh, Department of Chemistry, 219 Parkman Ave, Pittsburgh, PA 15260, United States. Electronic address:

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http://dx.doi.org/10.1016/j.bmcl.2015.07.016DOI Listing
November 2015

An estimate of the average number of recessive lethal mutations carried by humans.

Genetics 2015 Apr 18;199(4):1243-54. Epub 2015 Feb 18.

Department of Biological Sciences, Columbia University, New York, New York 10027 Department of Systems Biology, Columbia University, New York, New York 10032

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http://www.genetics.org/content/genetics/199/4/1243.full.pdf
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http://www.genetics.org/content/genetics/early/2015/02/18/ge
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http://www.genetics.org/cgi/doi/10.1534/genetics.114.173351
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http://dx.doi.org/10.1534/genetics.114.173351DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4391560PMC
April 2015

The genetic architecture of gene expression levels in wild baboons.

Elife 2015 Feb 25;4. Epub 2015 Feb 25.

Department of Human Genetics, University of Chicago, Chicago, United States.

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http://dx.doi.org/10.7554/eLife.04729DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383332PMC
February 2015

Mangravite et al. reply.

Nature 2014 Sep;513(7518):E3

Children's Hospital Research Institute, Oakland, California 94609, USA.

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http://dx.doi.org/10.1038/nature13630DOI Listing
September 2014

fastSTRUCTURE: variational inference of population structure in large SNP data sets.

Genetics 2014 Jun 2;197(2):573-89. Epub 2014 Apr 2.

Department of Genetics, Stanford University, Stanford, California 94305 Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305.

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http://dx.doi.org/10.1534/genetics.114.164350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4063916PMC
June 2014

Efficient multivariate linear mixed model algorithms for genome-wide association studies.

Nat Methods 2014 Apr 16;11(4):407-9. Epub 2014 Feb 16.

1] Department of Human Genetics, University of Chicago, Chicago, Illinois, USA. [2] Department of Statistics, University of Chicago, Chicago, Illinois, USA.

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http://dx.doi.org/10.1038/nmeth.2848DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211878PMC
April 2014

A unified framework for association analysis with multiple related phenotypes.

Authors:
Matthew Stephens

PLoS One 2013 5;8(7):e65245. Epub 2013 Jul 5.

Department of Statistics and Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0065245PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3702528PMC
February 2014

BAYESIAN METHODS FOR GENETIC ASSOCIATION ANALYSIS WITH HETEROGENEOUS SUBGROUPS: FROM META-ANALYSES TO GENE-ENVIRONMENT INTERACTIONS.

Ann Appl Stat 2014;8(1):176-203

Department of Statistics and Department of Human Genetics, University of Chicago, 5734 S. University Avenue, Chicago, IL 60637, USA.

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http://projecteuclid.org/euclid.aoas/1396966283
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http://dx.doi.org/10.1214/13-AOAS695DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4583155PMC
January 2014

Genetic, functional and molecular features of glucocorticoid receptor binding.

PLoS One 2013 30;8(4):e61654. Epub 2013 Apr 30.

Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0061654PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3640037PMC
November 2013

Polygenic modeling with bayesian sparse linear mixed models.

PLoS Genet 2013 7;9(2):e1003264. Epub 2013 Feb 7.

Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.

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http://dx.doi.org/10.1371/journal.pgen.1003264DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3567190PMC
June 2013

A statistical framework for joint eQTL analysis in multiple tissues.

PLoS Genet 2013 May 9;9(5):e1003486. Epub 2013 May 9.

Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1003486DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3649995PMC
May 2013

Variability in drug formularies and implications in decision support.

AMIA Annu Symp Proc 2011 22;2011:1327-36. Epub 2011 Oct 22.

Regenstrief Institute, Indianapolis, IN, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3243218PMC
February 2013

Statistical inference of in vivo properties of human DNA methyltransferases from double-stranded methylation patterns.

PLoS One 2012 19;7(3):e32225. Epub 2012 Mar 19.

Department of Physiology, Development and Neuroscience, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0032225PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3307717PMC
July 2012

Fast and accurate genotype imputation in genome-wide association studies through pre-phasing.

Nat Genet 2012 Jul 22;44(8):955-9. Epub 2012 Jul 22.

Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.

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http://www.nature.com/articles/ng.2354
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http://dx.doi.org/10.1038/ng.2354DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3696580PMC
July 2012

Mapping gene-environment interactions at regulatory polymorphisms: insights into mechanisms of phenotypic variation.

Transcription 2012 Mar-Apr;3(2):56-62. Epub 2012 Mar 1.

Department of Human Genetics, The University of Chicago, Chicago, IL, USA.

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http://dx.doi.org/10.4161/trns.19497DOI Listing
June 2012

Genome-wide efficient mixed-model analysis for association studies.

Nat Genet 2012 Jun 17;44(7):821-4. Epub 2012 Jun 17.

Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.

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http://dx.doi.org/10.1038/ng.2310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3386377PMC
June 2012

Variation in human recombination rates and its genetic determinants.

PLoS One 2011 17;6(6):e20321. Epub 2011 Jun 17.

Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0020321PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117798PMC
November 2011

Functional comparison of innate immune signaling pathways in primates.

PLoS Genet 2010 Dec 16;6(12):e1001249. Epub 2010 Dec 16.

Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.

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https://dx.plos.org/10.1371/journal.pgen.1001249
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http://dx.doi.org/10.1371/journal.pgen.1001249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3002988PMC
December 2010

Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis.

PLoS Genet 2010 Sep 16;6(9):e1001117. Epub 2010 Sep 16.

Computer Science Department, University of Chicago, Chicago, Illinois, USA.

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http://dx.doi.org/10.1371/journal.pgen.1001117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940725PMC
September 2010

USING LINEAR PREDICTORS TO IMPUTE ALLELE FREQUENCIES FROM SUMMARY OR POOLED GENOTYPE DATA.

Ann Appl Stat 2010 Sep;4(3):1158-1182

Department of Statistics, University of Chicago, Chicago, IL 60637, USA,

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072818PMC
September 2010

Optical and physical characterization of a local evanescent array coupled biosensor: Use of evanescent field perturbations for multianalyte sensing.

Sens Actuators B Chem 2010 Mar;145(2):769-774

Dept. of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado, USA.

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http://dx.doi.org/10.1016/j.snb.2010.01.046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860394PMC
March 2010

Sex-specific and lineage-specific alternative splicing in primates.

Genome Res 2010 Feb 15;20(2):180-9. Epub 2009 Dec 15.

Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1101/gr.099226.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2813474PMC
February 2010

Bayesian statistical methods for genetic association studies.

Nat Rev Genet 2009 Oct;10(10):681-90

Departments of Statistics and Human Genetics, University of Chicago, Chicago, IL 60637, USA.

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http://www.nature.com/articles/nrg2615
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http://dx.doi.org/10.1038/nrg2615DOI Listing
October 2009

Development of electronic learning courses for surgical training of animal research personnel.

Lab Anim (NY) 2009 Sep;38(9):295-304

Veterinary Bioscience Institute, Harleysville, PA, USA.

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http://dx.doi.org/10.1038/laban0909-295DOI Listing
September 2009

Inferring weak population structure with the assistance of sample group information.

Mol Ecol Resour 2009 Sep 1;9(5):1322-32. Epub 2009 Apr 1.

Department of Human Genetics, Department of Statistics, and Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA, Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA, Environmental Research Institute, Department of Microbiology, University College Cork, Cork, Ireland.

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http://dx.doi.org/10.1111/j.1755-0998.2009.02591.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518025PMC
September 2009

Practical issues in imputation-based association mapping.

PLoS Genet 2008 Dec 5;4(12):e1000279. Epub 2008 Dec 5.

Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2585794PMC
December 2008

Genes mirror geography within Europe.

Nature 2008 Nov 31;456(7218):98-101. Epub 2008 Aug 31.

Department of Ecology and Evolutionary Biology, Interdepartmental Program in Bioinformatics, University of California-Los Angeles, Los Angeles, California 90095, USA.

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http://dx.doi.org/10.1038/nature07331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735096PMC
November 2008

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays.

Genome Res 2008 Sep 11;18(9):1509-17. Epub 2008 Jun 11.

Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1101/gr.079558.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527709PMC
September 2008

Linkage disequilibrium-based quality control for large-scale genetic studies.

PLoS Genet 2008 Aug 1;4(8):e1000147. Epub 2008 Aug 1.

Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2475504PMC
August 2008

Combating the illegal trade in African elephant ivory with DNA forensics.

Conserv Biol 2008 Aug;22(4):1065-71

Center for Conservation Biology, Department of Biology, University of Washington, Seattle, WA 98195-1800, USA.

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http://dx.doi.org/10.1111/j.1523-1739.2008.01012.xDOI Listing
August 2008

Interpreting principal component analyses of spatial population genetic variation.

Nat Genet 2008 May 20;40(5):646-9. Epub 2008 Apr 20.

Department of Human Genetics, University of Chicago, 920 E. 58th Street, CLSC 5th floor, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1038/ng.139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3989108PMC
May 2008

A second generation human haplotype map of over 3.1 million SNPs.

Authors:
Kelly A Frazer Dennis G Ballinger David R Cox David A Hinds Laura L Stuve Richard A Gibbs John W Belmont Andrew Boudreau Paul Hardenbol Suzanne M Leal Shiran Pasternak David A Wheeler Thomas D Willis Fuli Yu Huanming Yang Changqing Zeng Yang Gao Haoran Hu Weitao Hu Chaohua Li Wei Lin Siqi Liu Hao Pan Xiaoli Tang Jian Wang Wei Wang Jun Yu Bo Zhang Qingrun Zhang Hongbin Zhao Hui Zhao Jun Zhou Stacey B Gabriel Rachel Barry Brendan Blumenstiel Amy Camargo Matthew Defelice Maura Faggart Mary Goyette Supriya Gupta Jamie Moore Huy Nguyen Robert C Onofrio Melissa Parkin Jessica Roy Erich Stahl Ellen Winchester Liuda Ziaugra David Altshuler Yan Shen Zhijian Yao Wei Huang Xun Chu Yungang He Li Jin Yangfan Liu Yayun Shen Weiwei Sun Haifeng Wang Yi Wang Ying Wang Xiaoyan Xiong Liang Xu Mary M Y Waye Stephen K W Tsui Hong Xue J Tze-Fei Wong Luana M Galver Jian-Bing Fan Kevin Gunderson Sarah S Murray Arnold R Oliphant Mark S Chee Alexandre Montpetit Fanny Chagnon Vincent Ferretti Martin Leboeuf Jean-François Olivier Michael S Phillips Stéphanie Roumy Clémentine Sallée Andrei Verner Thomas J Hudson Pui-Yan Kwok Dongmei Cai Daniel C Koboldt Raymond D Miller Ludmila Pawlikowska Patricia Taillon-Miller Ming Xiao Lap-Chee Tsui William Mak You Qiang Song Paul K H Tam Yusuke Nakamura Takahisa Kawaguchi Takuya Kitamoto Takashi Morizono Atsushi Nagashima Yozo Ohnishi Akihiro Sekine Toshihiro Tanaka Tatsuhiko Tsunoda Panos Deloukas Christine P Bird Marcos Delgado Emmanouil T Dermitzakis Rhian Gwilliam Sarah Hunt Jonathan Morrison Don Powell Barbara E Stranger Pamela Whittaker David R Bentley Mark J Daly Paul I W de Bakker Jeff Barrett Yves R Chretien Julian Maller Steve McCarroll Nick Patterson Itsik Pe'er Alkes Price Shaun Purcell Daniel J Richter Pardis Sabeti Richa Saxena Stephen F Schaffner Pak C Sham Patrick Varilly David Altshuler Lincoln D Stein Lalitha Krishnan Albert Vernon Smith Marcela K Tello-Ruiz Gudmundur A Thorisson Aravinda Chakravarti Peter E Chen David J Cutler Carl S Kashuk Shin Lin Gonçalo R Abecasis Weihua Guan Yun Li Heather M Munro Zhaohui Steve Qin Daryl J Thomas Gilean McVean Adam Auton Leonardo Bottolo Niall Cardin Susana Eyheramendy Colin Freeman Jonathan Marchini Simon Myers Chris Spencer Matthew Stephens Peter Donnelly Lon R Cardon Geraldine Clarke David M Evans Andrew P Morris Bruce S Weir Tatsuhiko Tsunoda James C Mullikin Stephen T Sherry Michael Feolo Andrew Skol Houcan Zhang Changqing Zeng Hui Zhao Ichiro Matsuda Yoshimitsu Fukushima Darryl R Macer Eiko Suda Charles N Rotimi Clement A Adebamowo Ike Ajayi Toyin Aniagwu Patricia A Marshall Chibuzor Nkwodimmah Charmaine D M Royal Mark F Leppert Missy Dixon Andy Peiffer Renzong Qiu Alastair Kent Kazuto Kato Norio Niikawa Isaac F Adewole Bartha M Knoppers Morris W Foster Ellen Wright Clayton Jessica Watkin Richard A Gibbs John W Belmont Donna Muzny Lynne Nazareth Erica Sodergren George M Weinstock David A Wheeler Imtaz Yakub Stacey B Gabriel Robert C Onofrio Daniel J Richter Liuda Ziaugra Bruce W Birren Mark J Daly David Altshuler Richard K Wilson Lucinda L Fulton Jane Rogers John Burton Nigel P Carter Christopher M Clee Mark Griffiths Matthew C Jones Kirsten McLay Robert W Plumb Mark T Ross Sarah K Sims David L Willey Zhu Chen Hua Han Le Kang Martin Godbout John C Wallenburg Paul L'Archevêque Guy Bellemare Koji Saeki Hongguang Wang Daochang An Hongbo Fu Qing Li Zhen Wang Renwu Wang Arthur L Holden Lisa D Brooks Jean E McEwen Mark S Guyer Vivian Ota Wang Jane L Peterson Michael Shi Jack Spiegel Lawrence M Sung Lynn F Zacharia Francis S Collins Karen Kennedy Ruth Jamieson John Stewart

Nature 2007 Oct;449(7164):851-61

The Scripps Research Institute, 10550 North Torrey Pines Road MEM275, La Jolla, California 92037, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689609PMC
October 2007

Genome-wide detection and characterization of positive selection in human populations.

Authors:
Pardis C Sabeti Patrick Varilly Ben Fry Jason Lohmueller Elizabeth Hostetter Chris Cotsapas Xiaohui Xie Elizabeth H Byrne Steven A McCarroll Rachelle Gaudet Stephen F Schaffner Eric S Lander Kelly A Frazer Dennis G Ballinger David R Cox David A Hinds Laura L Stuve Richard A Gibbs John W Belmont Andrew Boudreau Paul Hardenbol Suzanne M Leal Shiran Pasternak David A Wheeler Thomas D Willis Fuli Yu Huanming Yang Changqing Zeng Yang Gao Haoran Hu Weitao Hu Chaohua Li Wei Lin Siqi Liu Hao Pan Xiaoli Tang Jian Wang Wei Wang Jun Yu Bo Zhang Qingrun Zhang Hongbin Zhao Hui Zhao Jun Zhou Stacey B Gabriel Rachel Barry Brendan Blumenstiel Amy Camargo Matthew Defelice Maura Faggart Mary Goyette Supriya Gupta Jamie Moore Huy Nguyen Robert C Onofrio Melissa Parkin Jessica Roy Erich Stahl Ellen Winchester Liuda Ziaugra David Altshuler Yan Shen Zhijian Yao Wei Huang Xun Chu Yungang He Li Jin Yangfan Liu Yayun Shen Weiwei Sun Haifeng Wang Yi Wang Ying Wang Xiaoyan Xiong Liang Xu Mary M Y Waye Stephen K W Tsui Hong Xue J Tze-Fei Wong Luana M Galver Jian-Bing Fan Kevin Gunderson Sarah S Murray Arnold R Oliphant Mark S Chee Alexandre Montpetit Fanny Chagnon Vincent Ferretti Martin Leboeuf Jean-François Olivier Michael S Phillips Stéphanie Roumy Clémentine Sallée Andrei Verner Thomas J Hudson Pui-Yan Kwok Dongmei Cai Daniel C Koboldt Raymond D Miller Ludmila Pawlikowska Patricia Taillon-Miller Ming Xiao Lap-Chee Tsui William Mak You Qiang Song Paul K H Tam Yusuke Nakamura Takahisa Kawaguchi Takuya Kitamoto Takashi Morizono Atsushi Nagashima Yozo Ohnishi Akihiro Sekine Toshihiro Tanaka Tatsuhiko Tsunoda Panos Deloukas Christine P Bird Marcos Delgado Emmanouil T Dermitzakis Rhian Gwilliam Sarah Hunt Jonathan Morrison Don Powell Barbara E Stranger Pamela Whittaker David R Bentley Mark J Daly Paul I W de Bakker Jeff Barrett Yves R Chretien Julian Maller Steve McCarroll Nick Patterson Itsik Pe'er Alkes Price Shaun Purcell Daniel J Richter Pardis Sabeti Richa Saxena Stephen F Schaffner Pak C Sham Patrick Varilly David Altshuler Lincoln D Stein Lalitha Krishnan Albert Vernon Smith Marcela K Tello-Ruiz Gudmundur A Thorisson Aravinda Chakravarti Peter E Chen David J Cutler Carl S Kashuk Shin Lin Gonçalo R Abecasis Weihua Guan Yun Li Heather M Munro Zhaohui Steve Qin Daryl J Thomas Gilean McVean Adam Auton Leonardo Bottolo Niall Cardin Susana Eyheramendy Colin Freeman Jonathan Marchini Simon Myers Chris Spencer Matthew Stephens Peter Donnelly Lon R Cardon Geraldine Clarke David M Evans Andrew P Morris Bruce S Weir Tatsuhiko Tsunoda Todd A Johnson James C Mullikin Stephen T Sherry Michael Feolo Andrew Skol Houcan Zhang Changqing Zeng Hui Zhao Ichiro Matsuda Yoshimitsu Fukushima Darryl R Macer Eiko Suda Charles N Rotimi Clement A Adebamowo Ike Ajayi Toyin Aniagwu Patricia A Marshall Chibuzor Nkwodimmah Charmaine D M Royal Mark F Leppert Missy Dixon Andy Peiffer Renzong Qiu Alastair Kent Kazuto Kato Norio Niikawa Isaac F Adewole Bartha M Knoppers Morris W Foster Ellen Wright Clayton Jessica Watkin Richard A Gibbs John W Belmont Donna Muzny Lynne Nazareth Erica Sodergren George M Weinstock David A Wheeler Imtaz Yakub Stacey B Gabriel Robert C Onofrio Daniel J Richter Liuda Ziaugra Bruce W Birren Mark J Daly David Altshuler Richard K Wilson Lucinda L Fulton Jane Rogers John Burton Nigel P Carter Christopher M Clee Mark Griffiths Matthew C Jones Kirsten McLay Robert W Plumb Mark T Ross Sarah K Sims David L Willey Zhu Chen Hua Han Le Kang Martin Godbout John C Wallenburg Paul L'Archevêque Guy Bellemare Koji Saeki Hongguang Wang Daochang An Hongbo Fu Qing Li Zhen Wang Renwu Wang Arthur L Holden Lisa D Brooks Jean E McEwen Mark S Guyer Vivian Ota Wang Jane L Peterson Michael Shi Jack Spiegel Lawrence M Sung Lynn F Zacharia Francis S Collins Karen Kennedy Ruth Jamieson John Stewart

Nature 2007 Oct;449(7164):913-8

Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA.

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http://www.nature.com/doifinder/10.1038/nature06250
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687721PMC
October 2007

Imputation-based analysis of association studies: candidate regions and quantitative traits.

PLoS Genet 2007 Jul 30;3(7):e114. Epub 2007 May 30.

Department of Statistics, University of Washington, Seattle, Washington, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.0030114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1934390PMC
July 2007

Fast and accurate estimation of the population-scaled mutation rate, theta, from microsatellite genotype data.

Genetics 2007 Jun;176(2):1363-6

Department of Statistics, University of Washington, Seattle, Washington 98195-4322, USA.

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http://dx.doi.org/10.1534/genetics.105.049080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1894599PMC
June 2007

Using DNA to track the origin of the largest ivory seizure since the 1989 trade ban.

Proc Natl Acad Sci U S A 2007 Mar 26;104(10):4228-33. Epub 2007 Feb 26.

Center for Conservation Biology, Department of Biology, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1073/pnas.0609714104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1805457PMC
March 2007