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.

Authors:
Merylin Cottagiri Maeva Nyandjo Matthew Stephens Joel J Mantilla Hirohisa Saito Ian R Mackay Noel R Rose Dolores B Njoku

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

Machine learning approach for distinguishing malignant and benign lung nodules utilizing standardized perinodular parenchymal features from CT.

Authors:
Johanna Uthoff Matthew J Stephens John D Newell Eric A Hoffman Jared Larson Nicholas Koehn Frank A De Stefano Chrissy M Lusk Angela S Wenzlaff Donovan Watza Christine Neslund-Dudas Laurie L Carr David A Lynch Ann G Schwartz Jessica C Sieren

Med Phys 2019 Jul 7;46(7):3207-3216. Epub 2019 Jun 7.

Department of Biomedical Engineering, University of Iowa, Iowa City, IA, 52240, USA.

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http://dx.doi.org/10.1002/mp.13592DOI Listing
July 2019

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

Authors:
Siming Zhao Jun Liu Pranav Nanga Yuwen Liu A Ercument Cicek Nicholas Knoblauch Chuan He Matthew Stephens Xin He

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.

Authors:
Alexander E White Kushal K Dey Dhananjai Mohan Matthew Stephens Trevor D Price

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.

Authors:
Matthew Stephens Pierre-Yves von der Weid

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

Identification of Nonaggressive Pulmonary Nodules Using an Optimized Scoring System.

Authors:
Matthew J Stephens Byung H Rho Douglas Curran-Everett Laurie Carr Russell Bowler David Lynch

J Thorac Imaging 2019 May;34(3):170-178

National Jewish Health, Denver, CO.

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http://dx.doi.org/10.1097/RTI.0000000000000405DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6485492PMC
May 2019

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

Authors:
Hussein Al-Asadi Kushal K Dey John Novembre Matthew Stephens

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.

Authors:
Abhishek K Sarkar Po-Yuan Tung John D Blischak Jonathan E Burnett Yang I Li Matthew Stephens Yoav Gilad

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.

Authors:
Luís Felipe Ventorim Ferrão Romário Gava Ferrão Maria Amélia Gava Ferrão Aymbiré Fonseca Peter Carbonetto Matthew Stephens Antonio Augusto Franco Garcia

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

Correction: A Unified Framework for Association Analysis with Multiple Related Phenotypes.

Authors:
Matthew Stephens

PLoS One 2019 19;14(3):e0213951. Epub 2019 Mar 19.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0213951PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6424389PMC
March 2019

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

Authors:
Matthew Stephens Shan Liao Pierre-Yves von der Weid

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.

Authors:
Sarah M Urbut Gao Wang Peter Carbonetto Matthew Stephens

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.

Authors:
Hussein Al-Asadi Desislava Petkova Matthew Stephens John Novembre

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.

Authors:
Kushal K Dey Dongyue Xie Matthew Stephens

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.

Authors:
David Gerard Luis Felipe Ventorim Ferrão Antonio Augusto Franco Garcia Matthew Stephens

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.

Authors:
Xiang Zhu Matthew Stephens

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.

Authors:
David Gerard Matthew Stephens

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.

Authors:
Joel Smith Graham Coop Matthew Stephens John Novembre

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

Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs.

Authors:
Michelle C Ward Siming Zhao Kaixuan Luo Bryan J Pavlovic Mohammad M Karimi Matthew Stephens Yoav Gilad

Elife 2018 04 12;7. Epub 2018 Apr 12.

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

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http://dx.doi.org/10.7554/eLife.33084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5943035PMC
April 2018

Acute small intestinal inflammation results in persistent lymphatic alterations.

Authors:
Sonia Rehal Matthew Stephens Simon Roizes Shan Liao Pierre-Yves von der Weid

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.

Authors:
Matthew Stephens Shan Liao

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

Structure of the Francisella response regulator QseB receiver domain, and characterization of QseB inhibition by antibiofilm 2-aminoimidazole-based compounds.

Authors:
Morgan E Milton C Leigh Allen Erik A Feldmann Benjamin G Bobay David K Jung Matthew D Stephens Roberta J Melander Kelly E Theisen Daina Zeng Richele J Thompson Christian Melander John Cavanagh

Mol Microbiol 2017 Oct 16;106(2):223-235. Epub 2017 Aug 16.

RTI International, 3040 Cornwallis Rd, RTP, NC 27709, USA.

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http://doi.wiley.com/10.1111/mmi.13759
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http://dx.doi.org/10.1111/mmi.13759DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5630518PMC
October 2017

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

Authors:
Xiang Zhu Matthew Stephens

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

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

Authors:
Kushal K Dey Chiaowen Joyce Hsiao Matthew Stephens

PLoS Genet 2017 May 26;13(5):e1006759. Epub 2017 May 26.

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http://dx.doi.org/10.1371/journal.pgen.1006759DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5446108PMC
May 2017

False discovery rates: a new deal.

Authors:
Matthew Stephens

Biostatistics 2017 04;18(2):275-294

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http://dx.doi.org/10.1093/biostatistics/kxw041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5379932PMC
April 2017

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

Authors:
Ignacio E Schor Jacob F Degner Dermot Harnett Enrico Cannavò Francesco P Casale Heejung Shim David A Garfield Ewan Birney Matthew Stephens Oliver Stegle Eileen E M Furlong

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.

Authors:
Kushal K Dey Chiaowen Joyce Hsiao Matthew Stephens

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

The Impact of Systematic Point-of-Care Ultrasound on Management of Patients in a Resource-Limited Setting.

Authors:
Alastair Stanley Bahati M K Wajanga Hyasinta Jaka Rachael Purcell Lauren Byrne Felicity Williams Candace Rypien Abigail Sharpe Patrick Laws Lucas Faustine Tshepo Leeme Emmanuel Mwabutwa Robert Peck Matthew Stephens Daniel Kaminstein

Am J Trop Med Hyg 2017 Feb 19;96(2):488-492. Epub 2016 Dec 19.

Augusta University, Augusta, Georgia.

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http://dx.doi.org/10.4269/ajtmh.16-0201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5303058PMC
February 2017

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

Authors:
Mairéad Walsh Glennis White Kenneth Romeril Huib Buyck Matthew Stephens Collin Brooks Robert Weinkove

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.

Authors:
Roberta J Melander Hong-Bing Liu Matthew D Stephens Carole A Bewley Christian Melander

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.

Authors:
Mengyin Lu Matthew Stephens

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.

Authors:
Matthew D Stephens Nisakorn Yodsanit Christian Melander

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 .

Authors:
Matthew D Stephens Nisakorn Yodsanit Christian Melander

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.

Authors:
Anil Raj Heejung Shim Yoav Gilad Jonathan K Pritchard Matthew Stephens

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

Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling.

Authors:
Anil Raj Sidney H Wang Heejung Shim Arbel Harpak Yang I Li Brett Engelmann Matthew Stephens Yoav Gilad Jonathan K Pritchard

Elife 2016 05 27;5. Epub 2016 May 27.

Department of Genetics, Stanford University, Stanford, United States.

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https://elifesciences.org/articles/13328
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http://dx.doi.org/10.7554/eLife.13328DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4940163PMC
May 2016

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

Authors:
Heejung Shim Daniel I Chasman Joshua D Smith Samia Mora Paul M Ridker Deborah A Nickerson Ronald M Krauss Matthew Stephens

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.

Authors:
Sandra Sacre Alexandra Lo Bernard Gregory Matthew Stephens Giselle Chamberlain Philip Stott Fionula Brennan

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.

Authors:
Desislava Petkova John Novembre Matthew Stephens

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.

Authors:
Matthew D Stephens Veroncia B Hubble Robert K Ernst Monique L van Hoek Roberta J Melander John Cavanagh Christian Melander

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
Publisher Site
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.

Authors:
Samrat Mondol Ida Moltke John Hart Michael Keigwin Lisa Brown Matthew Stephens Samuel K Wasser

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.

Authors:
Yuichi Shiraishi Georg Tremmel Satoru Miyano Matthew Stephens

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.

Authors:
Yuta Naro Meryl Thomas Matthew D Stephens Colleen M Connelly Alexander Deiters

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

Epigenetic modifications are associated with inter-species gene expression variation in primates.

Authors:
Xiang Zhou Carolyn E Cain Marsha Myrthil Noah Lewellen Katelyn Michelini Emily R Davenport Matthew Stephens Jonathan K Pritchard Yoav Gilad

Genome Biol 2014 ;15(12):547

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http://dx.doi.org/10.1186/s13059-014-0547-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4290387PMC
August 2015

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

Authors:
Ziyue Gao Darrel Waggoner Matthew Stephens Carole Ober Molly Przeworski

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
Web Search
http://www.genetics.org/cgi/doi/10.1534/genetics.114.173351
Publisher Site
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.

Authors:
Jenny Tung Xiang Zhou Susan C Alberts Matthew Stephens Yoav Gilad

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

WAVELET-BASED GENETIC ASSOCIATION ANALYSIS OF FUNCTIONAL PHENOTYPES ARISING FROM HIGH-THROUGHPUT SEQUENCING ASSAYS.

Authors:
Heejung Shim Matthew Stephens

Ann Appl Stat 2015 ;9(2):655-686

University of Chicago.

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http://dx.doi.org/10.1214/14-AOAS776DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5795621PMC
January 2015

Mangravite et al. reply.

Authors:
Lara M Mangravite Barbara E Engelhardt Matthew Stephens Ronald M Krauss

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.

Authors:
Anil Raj Matthew Stephens Jonathan K Pritchard

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.

Authors:
Xiang Zhou Matthew Stephens

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

Interhospital transfer of blunt multiply injured patients to a level 1 trauma center does not adversely affect outcome.

Authors:
Adrian T Billeter Frank B Miller Brian G Harbrecht Wanda Bowen Matthew J Stephens Gregory C Postel Jason W Smith Matthew Penta Royce Coleman Glen A Franklin Donald D Trunkey Hiram C Polk

Am J Surg 2014 Apr;207(4):459-66

Department of Surgery, University of Louisville School of Medicine, Louisville, KY 40292, USA. Electronic address:

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http://dx.doi.org/10.1016/j.amjsurg.2013.04.015DOI Listing
April 2014

Integrated enrichment analysis of variants and pathways in genome-wide association studies indicates central role for IL-2 signaling genes in type 1 diabetes, and cytokine signaling genes in Crohn's disease.

Authors:
Peter Carbonetto Matthew Stephens

PLoS Genet 2013 3;9(10):e1003770. Epub 2013 Oct 3.

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

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March 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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February 2014

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

Authors:
Xiaoquan Wen Matthew Stephens

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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January 2014

Genetic, functional and molecular features of glucocorticoid receptor binding.

Authors:
Francesca Luca Joseph C Maranville Allison L Richards David B Witonsky Matthew Stephens Anna Di Rienzo

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://www.ncbi.nlm.nih.gov/pmc/articles/PMC3640037PMC
November 2013

A statin-dependent QTL for GATM expression is associated with statin-induced myopathy.

Authors:
Lara M Mangravite Barbara E Engelhardt Marisa W Medina Joshua D Smith Christopher D Brown Daniel I Chasman Brigham H Mecham Bryan Howie Heejung Shim Devesh Naidoo QiPing Feng Mark J Rieder Yii-Der I Chen Jerome I Rotter Paul M Ridker Jemma C Hopewell Sarah Parish Jane Armitage Rory Collins Russell A Wilke Deborah A Nickerson Matthew Stephens Ronald M Krauss

Nature 2013 Oct 28;502(7471):377-80. Epub 2013 Aug 28.

Sage Bionetworks, 1100 Fairview Avenue North, Seattle, Washington 98109, USA.

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October 2013

Polygenic modeling with bayesian sparse linear mixed models.

Authors:
Xiang Zhou Peter Carbonetto Matthew Stephens

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://www.ncbi.nlm.nih.gov/pmc/articles/PMC3567190PMC
June 2013

A statistical framework for joint eQTL analysis in multiple tissues.

Authors:
Timothée Flutre Xiaoquan Wen Jonathan Pritchard Matthew Stephens

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://www.ncbi.nlm.nih.gov/pmc/articles/PMC3649995PMC
May 2013

The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels.

Authors:
Athma A Pai Carolyn E Cain Orna Mizrahi-Man Sherryl De Leon Noah Lewellen Jean-Baptiste Veyrieras Jacob F Degner Daniel J Gaffney Joseph K Pickrell Matthew Stephens Jonathan K Pritchard Yoav Gilad

PLoS Genet 2012 11;8(10):e1003000. Epub 2012 Oct 11.

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

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March 2013

Variability in drug formularies and implications in decision support.

Authors:
Matthew J Stephens John T Finnell Linas Simonaitis J Marc Overhage

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

Regenstrief Institute, Indianapolis, IN, USA.

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February 2013

Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13).

Authors:
Amy B Hart Barbara E Engelhardt Margaret C Wardle Greta Sokoloff Matthew Stephens Harriet de Wit Abraham A Palmer

PLoS One 2012 28;7(8):e42646. Epub 2012 Aug 28.

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

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3429486PMC
February 2013

Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data.

Authors:
Jean-Baptiste Veyrieras Daniel J Gaffney Joseph K Pickrell Yoav Gilad Matthew Stephens Jonathan K Pritchard

PLoS One 2012 16;7(2):e30629. Epub 2012 Feb 16.

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

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3281037PMC
August 2012

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

Authors:
Audrey Q Fu Diane P Genereux Reinhard Stöger Alice F Burden Charles D Laird Matthew Stephens

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://www.ncbi.nlm.nih.gov/pmc/articles/PMC3307717PMC
July 2012

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

Authors:
Bryan Howie Christian Fuchsberger Matthew Stephens Jonathan Marchini Gonçalo R Abecasis

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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July 2012

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

Authors:
Joseph C Maranville Francesca Luca Matthew Stephens Anna Di Rienzo

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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June 2012

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

Authors:
Xiang Zhou Matthew Stephens

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://www.ncbi.nlm.nih.gov/pmc/articles/PMC3386377PMC
June 2012

Comparative RNA sequencing reveals substantial genetic variation in endangered primates.

Authors:
George H Perry Páll Melsted John C Marioni Ying Wang Russell Bainer Joseph K Pickrell Katelyn Michelini Sarah Zehr Anne D Yoder Matthew Stephens Jonathan K Pritchard Yoav Gilad

Genome Res 2012 Apr 29;22(4):602-10. Epub 2011 Dec 29.

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

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http://dx.doi.org/10.1101/gr.130468.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3317143PMC
April 2012

DNase I sensitivity QTLs are a major determinant of human expression variation.

Authors:
Jacob F Degner Athma A Pai Roger Pique-Regi Jean-Baptiste Veyrieras Daniel J Gaffney Joseph K Pickrell Sherryl De Leon Katelyn Michelini Noah Lewellen Gregory E Crawford Matthew Stephens Yoav Gilad Jonathan K Pritchard

Nature 2012 Feb 5;482(7385):390-4. Epub 2012 Feb 5.

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

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http://dx.doi.org/10.1038/nature10808DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3501342PMC
February 2012

Next generation analytic tools for large scale genetic epidemiology studies of complex diseases.

Authors:
Leah E Mechanic Huann-Sheng Chen Christopher I Amos Nilanjan Chatterjee Nancy J Cox Rao L Divi Ruzong Fan Emily L Harris Kevin Jacobs Peter Kraft Suzanne M Leal Kimberly McAllister Jason H Moore Dina N Paltoo Michael A Province Erin M Ramos Marylyn D Ritchie Kathryn Roeder Daniel J Schaid Matthew Stephens Duncan C Thomas Clarice R Weinberg John S Witte Shunpu Zhang Sebastian Zöllner Eric J Feuer Elizabeth M Gillanders

Genet Epidemiol 2012 Jan 6;36(1):22-35. Epub 2011 Dec 6.

Epidemiology and Genetics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA.

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http://dx.doi.org/10.1002/gepi.20652DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3368075PMC
January 2012

Dissecting the regulatory architecture of gene expression QTLs.

Authors:
Daniel J Gaffney Jean-Baptiste Veyrieras Jacob F Degner Roger Pique-Regi Athma A Pai Gregory E Crawford Matthew Stephens Yoav Gilad Jonathan K Pritchard

Genome Biol 2012 Jan 31;13(1):R7. Epub 2012 Jan 31.

Department of Human Genetics, University of Chicago, 920 E58th Street, Chicago, IL 60637, USA.

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January 2012

Variation in human recombination rates and its genetic determinants.

Authors:
Adi Fledel-Alon Ellen Miranda Leffler Yongtao Guan Matthew Stephens Graham Coop Molly Przeworski

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://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117798PMC
November 2011

Genotype imputation with thousands of genomes.

Authors:
Bryan Howie Jonathan Marchini Matthew Stephens

G3 (Bethesda) 2011 Nov 1;1(6):457-70. Epub 2011 Nov 1.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3276165PMC
November 2011

Interactions between glucocorticoid treatment and cis-regulatory polymorphisms contribute to cellular response phenotypes.

Authors:
Joseph C Maranville Francesca Luca Allison L Richards Xiaoquan Wen David B Witonsky Shaneen Baxter Matthew Stephens Anna Di Rienzo

PLoS Genet 2011 Jul 7;7(7):e1002162. Epub 2011 Jul 7.

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

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July 2011

Functional comparison of innate immune signaling pathways in primates.

Authors:
Luis B Barreiro John C Marioni Ran Blekhman Matthew Stephens Yoav Gilad

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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December 2010

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

Authors:
Barbara E Engelhardt Matthew Stephens

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://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940725PMC
September 2010

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

Authors:
Xiaoquan Wen Matthew Stephens

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

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

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September 2010

Response to Cavalli-Sforza interview [Human Biology 82(3):245-266 (June 2010)].

Authors:
John Novembre Matthew Stephens

Hum Biol 2010 Aug;82(4):469-70

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August 2010

Understanding mechanisms underlying human gene expression variation with RNA sequencing.

Authors:
Joseph K Pickrell John C Marioni Athma A Pai Jacob F Degner Barbara E Engelhardt Everlyne Nkadori Jean-Baptiste Veyrieras Matthew Stephens Yoav Gilad Jonathan K Pritchard

Nature 2010 Apr 10;464(7289):768-72. Epub 2010 Mar 10.

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

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http://dx.doi.org/10.1038/nature08872DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3089435PMC
April 2010

Genome-wide association of lipid-lowering response to statins in combined study populations.

Authors:
Mathew J Barber Lara M Mangravite Craig L Hyde Daniel I Chasman Joshua D Smith Catherine A McCarty Xiaohui Li Russell A Wilke Mark J Rieder Paul T Williams Paul M Ridker Aurobindo Chatterjee Jerome I Rotter Deborah A Nickerson Matthew Stephens Ronald M Krauss

PLoS One 2010 Mar 22;5(3):e9763. Epub 2010 Mar 22.

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

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842298PMC
March 2010

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

Authors:
Matthew D Stephens Guangwei Yuan Kevin L Lear David S Dandy

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://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860394PMC
March 2010

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

Authors:
Ran Blekhman John C Marioni Paul Zumbo Matthew Stephens Yoav Gilad

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

STATISTICAL INFERENCE OF TRANSMISSION FIDELITY OF DNA METHYLATION PATTERNS OVER SOMATIC CELL DIVISIONS IN MAMMALS.

Authors:
Audrey Qiuyan Fu Diane P Genereux Reinhard Stöger Charles D Laird Matthew Stephens

Ann Appl Stat 2010 ;4(2):871-892

University of Washington.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3103139PMC
January 2010

Bayesian statistical methods for genetic association studies.

Authors:
Matthew Stephens David J Balding

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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October 2009

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

Authors:
Szczepan W Baran Elizabeth J Johnson Matthew A Stephens James Kehler

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

Veterinary Bioscience Institute, Harleysville, PA, USA.

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September 2009

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

Authors:
Melissa J Hubisz Daniel Falush Matthew Stephens Jonathan K Pritchard

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.

Authors:
Yongtao Guan Matthew Stephens

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.

Authors:
John Novembre Toby Johnson Katarzyna Bryc Zoltán Kutalik Adam R Boyko Adam Auton Amit Indap Karen S King Sven Bergmann Matthew R Nelson Matthew Stephens Carlos D Bustamante

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

High-resolution mapping of expression-QTLs yields insight into human gene regulation.

Authors:
Jean-Baptiste Veyrieras Sridhar Kudaravalli Su Yeon Kim Emmanouil T Dermitzakis Yoav Gilad Matthew Stephens Jonathan K Pritchard

PLoS Genet 2008 Oct 10;4(10):e1000214. Epub 2008 Oct 10.

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

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2556086PMC
October 2008

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

Authors:
John C Marioni Christopher E Mason Shrikant M Mane Matthew Stephens Yoav Gilad

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

Evanescent field response to immunoassay layer thickness on planar waveguides.

Authors:
Rongjin Yan Guangwei Yuan Matthew D Stephens Xinya He Charles S Henry David S Dandy Kevin L Lear

Appl Phys Lett 2008 Sep 11;93(10):101110. Epub 2008 Sep 11.

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http://dx.doi.org/10.1063/1.2981212DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2682747PMC
September 2008

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

Authors:
Paul Scheet Matthew Stephens

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.

Authors:
Samuel K Wasser William Joseph Clark Ofir Drori Emily Stephen Kisamo Celia Mailand Benezeth Mutayoba Matthew Stephens

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.

Authors:
John Novembre Matthew Stephens

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

Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are associated with C-reactive protein.

Authors:
Alexander P Reiner Mathew J Barber Yongtao Guan Paul M Ridker Leslie A Lange Daniel I Chasman Jeremy D Walston Gregory M Cooper Nancy S Jenny Mark J Rieder J Peter Durda Joshua D Smith John Novembre Russell P Tracy Jerome I Rotter Matthew Stephens Deborah A Nickerson Ronald M Krauss

Am J Hum Genet 2008 May 24;82(5):1193-201. Epub 2008 Apr 24.

University of Washington, Department of Epidemiology, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1016/j.ajhg.2008.03.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2427318PMC
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.ncbi.nlm.nih.gov/pmc/articles/PMC2687721PMC
October 2007

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

Authors:
Bertrand Servin Matthew Stephens

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

Inference of population structure using multilocus genotype data: dominant markers and null alleles.

Authors:
Daniel Falush Matthew Stephens Jonathan K Pritchard

Mol Ecol Notes 2007 Jul;7(4):574-578

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http://dx.doi.org/10.1111/j.1471-8286.2007.01758.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1974779PMC
July 2007

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

Authors:
Arindam Roychoudhury Matthew Stephens

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

Changes in gene expression during pegylated interferon and ribavirin therapy of chronic hepatitis C virus distinguish responders from nonresponders to antiviral therapy.

Authors:
Milton W Taylor Takuma Tsukahara Leonid Brodsky Joel Schaley Corneliu Sanda Matthew J Stephens Jeanette N McClintick Howard J Edenberg Lang Li John E Tavis Charles Howell Steven H Belle

J Virol 2007 Apr 31;81(7):3391-401. Epub 2007 Jan 31.

Department of Biology, Indiana University, Bloomington, IN 47401, USA.

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http://dx.doi.org/10.1128/JVI.02640-06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1866036PMC
April 2007

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

Authors:
Samuel K Wasser Celia Mailand Rebecca Booth Benezeth Mutayoba Emily Kisamo Bill Clark Matthew Stephens

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://www.ncbi.nlm.nih.gov/pmc/articles/PMC1805457PMC
March 2007