Matthew Stephens

Ultra-purification of Lipopolysaccharides reveals species-specific signalling bias of TLR4: importance in macrophage function.

Authors:

Matthew Stephens Shan Liao Pierre-Yves von der Weid

Sci Rep 2021 Jan 14;11(1):1335. Epub 2021 Jan 14.

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

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January 2021

Disinfection of from N95 respirators with ozone: a pilot study.

Authors:

Edward P Manning Matthew D Stephens Sylvie Dufresne Bruce Silver Patricia Gerbarg Zach Gerbarg Charles S Dela Cruz Lokesh Sharma

BMJ Open Respir Res 2021 Jan;8(1)

Section of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA

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January 2021

Cell type-specific genetic regulation of gene expression across human tissues.

Science 2020 09;369(6509)

New York Genome Center, New York, NY, USA.

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September 2020

The impact of sex on gene expression across human tissues.

Science 2020 09;369(6509)

Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.

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September 2020

Genetic analyses support the contribution of mRNA N-methyladenosine (mA) modification to human disease heritability.

Authors:

Zijie Zhang Kaixuan Luo Zhongyu Zou Maguanyun Qiu Jiakun Tian Laura Sieh Hailing Shi Yuxin Zou Gao Wang Jean Morrison Allen C Zhu Min Qiao Zhongshan Li Matthew Stephens Xin He Chuan He

Nat Genet 2020 09 29;52(9):939-949. Epub 2020 Jun 29.

Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.

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September 2020

Publisher Correction: Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics.

Authors:

Jean Morrison Nicholas Knoblauch Joseph H Marcus Matthew Stephens Xin He

Nat Genet 2020 Jul;52(7):750

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

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July 2020

Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics.

Authors:

Jean Morrison Nicholas Knoblauch Joseph H Marcus Matthew Stephens Xin He

Nat Genet 2020 07 25;52(7):740-747. Epub 2020 May 25.

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

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July 2020

Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis.

Authors:

Chiaowen Joyce Hsiao PoYuan Tung John D Blischak Jonathan E Burnett Kenneth A Barr Kushal K Dey Matthew Stephens Yoav Gilad

Genome Res 2020 04 20;30(4):611-621. Epub 2020 Apr 20.

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

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April 2020

Creating and sharing reproducible research code the workflowr way.

Authors:

John D Blischak Peter Carbonetto Matthew Stephens

F1000Res 2019 14;8:1749. Epub 2019 Oct 14.

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

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June 2020

Bayesian multivariate reanalysis of large genetic studies identifies many new associations.

Authors:

Michael C Turchin Matthew Stephens

PLoS Genet 2019 10 9;15(10):e1008431. Epub 2019 Oct 9.

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

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October 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 07 30;10(1):3399. Epub 2019 Jul 30.

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

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July 2019

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

Authors:

Matthew Stephens Pierre-Yves von der Weid

Gut Microbes 2020 05 16;11(3):421-432. Epub 2019 Jun 16.

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

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May 2020

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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June 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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July 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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April 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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September 2020