Publications by authors named "Ron Stewart"

92Publications

Large-Scale Multi-omic Analysis of COVID-19 Severity.

Authors:
Katherine A Overmyer Evgenia Shishkova Ian J Miller Joseph Balnis Matthew N Bernstein Trenton M Peters-Clarke Jesse G Meyer Qiuwen Quan Laura K Muehlbauer Edna A Trujillo Yuchen He Amit Chopra Hau C Chieng Anupama Tiwari Marc A Judson Brett Paulson Dain R Brademan Yunyun Zhu Lia R Serrano Vanessa Linke Lisa A Drake Alejandro P Adam Bradford S Schwartz Harold A Singer Scott Swanson Deane F Mosher Ron Stewart Joshua J Coon Ariel Jaitovich

Cell Syst 2021 01 8;12(1):23-40.e7. Epub 2020 Oct 8.

Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY 12208, USA; Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA. Electronic address:

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January 2021

Reproducibility across single-cell RNA-seq protocols for spatial ordering analysis.

Authors:
Morten Seirup Li-Fang Chu Srikumar Sengupta Ning Leng Hadley Browder Kevin Kapadia Christina M Shafer Bret Duffin Angela L Elwell Jennifer M Bolin Scott Swanson Ron Stewart Christina Kendziorski James A Thomson Rhonda Bacher

PLoS One 2020 28;15(9):e0239711. Epub 2020 Sep 28.

Department of Biostatistics, University of Florida, Gainesville, Florida, United States of America.

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November 2020

Large-scale Multi-omic Analysis of COVID-19 Severity.

Authors:
Katherine A Overmyer Evgenia Shishkova Ian J Miller Joseph Balnis Matthew N Bernstein Trenton M Peters-Clarke Jesse G Meyer Qiuwen Quan Laura K Muehlbauer Edna A Trujillo Yuchen He Amit Chopra Hau C Chieng Anupama Tiwari Marc A Judson Brett Paulson Dain R Brademan Yunyun Zhu Lia R Serrano Vanessa Linke Lisa A Drake Alejandro P Adam Bradford S Schwartz Harold A Singer Scott Swanson Deane F Mosher Ron Stewart Joshua J Coon Ariel Jaitovich

medRxiv 2020 Jul 19. Epub 2020 Jul 19.

Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA.

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July 2020

Machine learning to predict developmental neurotoxicity with high-throughput data from 2D bio-engineered tissues.

Authors:
Finn Kuusisto Vitor Santos Costa Zhonggang Hou James Thomson David Page Ron Stewart

Proc Int Conf Mach Learn Appl 2019 Dec 17;2019:293-298. Epub 2020 Feb 17.

Morgridge Institute for Research, Regenerative Biology, Madison, WI, USA.

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December 2019

TimeMeter assesses temporal gene expression similarity and identifies differentially progressing genes.

Authors:
Peng Jiang Connie S Chamberlain Ray Vanderby James A Thomson Ron Stewart

Nucleic Acids Res 2020 05;48(9):e51

Regenerative Biology Laboratory, Morgridge Institute for Research, Madison, WI 53707, USA.

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May 2020

Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics.

Authors:
Christopher Barry Matthew T Schmitz Cara Argus Jennifer M Bolin Mitchell D Probasco Ning Leng Bret M Duffin John Steill Scott Swanson Brian E McIntosh Ron Stewart Christina Kendziorski James A Thomson Rhonda Bacher

PLoS Comput Biol 2019 12 9;15(12):e1007543. Epub 2019 Dec 9.

Department of Biostatistics, University of Florida, Gainesville, FL, United States of America.

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December 2019

Automated Extraction and Visualization of Protein-Protein Interaction Networks and Beyond: A Text-Mining Protocol.

Authors:
Kalpana Raja Jeyakumar Natarajan Finn Kuusisto John Steill Ian Ross James Thomson Ron Stewart

Methods Mol Biol 2020 ;2074:13-34

Regenerative Biology, Morgridge Institute for Research, Madison, WI, USA.

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January 2021

An In Vitro Human Segmentation Clock Model Derived from Embryonic Stem Cells.

Authors:
Li-Fang Chu Daniel Mamott Zijian Ni Rhonda Bacher Cathy Liu Scott Swanson Christina Kendziorski Ron Stewart James A Thomson

Cell Rep 2019 08;28(9):2247-2255.e5

Morgridge Institute for Research, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Molecular, Cellular, & Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93117, USA. Electronic address:

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August 2019

Data-driven phenotype discovery of premutation carriers in a population-based sample.

Authors:
Arezoo Movaghar David Page Murray Brilliant Mei Wang Baker Jan Greenberg Jinkuk Hong Leann Smith DaWalt Krishanu Saha Finn Kuusisto Ron Stewart Elizabeth Berry-Kravis Marsha R Mailick

Sci Adv 2019 08 21;5(8):eaaw7195. Epub 2019 Aug 21.

Waisman Center, University of Wisconsin-Madison, Madison, WI, USA.

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August 2019

Inferring Regulatory Programs Governing Region Specificity of Neuroepithelial Stem Cells during Early Hindbrain and Spinal Cord Development.

Authors:
Deborah Chasman Nisha Iyer Alireza Fotuhi Siahpirani Maria Estevez Silva Ethan Lippmann Brian McIntosh Mitchell D Probasco Peng Jiang Ron Stewart James A Thomson Randolph S Ashton Sushmita Roy

Cell Syst 2019 08 10;9(2):167-186.e12. Epub 2019 Jul 10.

Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53792, USA. Electronic address:

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August 2019

Machine Learning Assisted Discovery of Novel Predictive Lab Tests Using Electronic Health Record Data.

Authors:
Ross Kleiman Finn Kuusisto Ian Ross Peggy L Peissig Ron Stewart C David Page Jeremy Weiss

AMIA Jt Summits Transl Sci Proc 2019 6;2019:572-581. Epub 2019 May 6.

Carnegie Mellon University, Pittsburgh, PA.

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May 2019

AP-1/miR-200a regulate the pro-regenerative glial cell response during axolotl spinal cord regeneration.

Authors:
Keith Z Sabin Peng Jiang Micah D Gearhart Ron Stewart Karen Echeverri

Commun Biol 2019 6;2:91. Epub 2019 Mar 6.

Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA.

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April 2020

Time-dependent Pax3-mediated chromatin remodeling and cooperation with Six4 and Tead2 specify the skeletal myogenic lineage in developing mesoderm.

Authors:
Alessandro Magli June Baik Lauren J Mills Il-Youp Kwak Bridget S Dillon Ricardo Mondragon Gonzalez David A Stafford Scott A Swanson Ron Stewart James A Thomson Daniel J Garry Brian D Dynlacht Rita C R Perlingeiro

PLoS Biol 2019 02 26;17(2):e3000153. Epub 2019 Feb 26.

Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, Minnesota, United States of America.

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February 2019

Pluripotent stem cell-derived myogenic progenitors remodel their molecular signature upon in vivo engraftment.

Authors:
Tania Incitti Alessandro Magli Radbod Darabi Ce Yuan Karena Lin Robert W Arpke Karim Azzag Ami Yamamoto Ron Stewart James A Thomson Michael Kyba Rita C R Perlingeiro

Proc Natl Acad Sci U S A 2019 03 13;116(10):4346-4351. Epub 2019 Feb 13.

Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN 55455;

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March 2019

A Machine-Learning-Based Drug Repurposing Approach Using Baseline Regularization.

Authors:
Zhaobin Kuang Yujia Bao James Thomson Michael Caldwell Peggy Peissig Ron Stewart Rebecca Willett David Page

Methods Mol Biol 2019 ;1903:255-267

The University of Wisconsin, Madison, WI, USA.

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June 2019

Trendy: segmented regression analysis of expression dynamics in high-throughput ordered profiling experiments.

Authors:
Rhonda Bacher Ning Leng Li-Fang Chu Zijian Ni James A Thomson Christina Kendziorski Ron Stewart

BMC Bioinformatics 2018 Oct 16;19(1):380. Epub 2018 Oct 16.

Morgridge Institute for Research, Madison, WI, USA.

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October 2018

Spatial patterns of gene expression are unveiled in the chick primitive streak by ordering single-cell transcriptomes.

Authors:
Katie L Vermillion Rhonda Bacher Alex P Tannenbaum Scott Swanson Peng Jiang Li-Fang Chu Ron Stewart James A Thomson David T Vereide

Dev Biol 2018 07 17;439(1):30-41. Epub 2018 Apr 17.

Morgridge Institute for Research, Madison, WI 53715, USA. Electronic address:

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July 2018

A Novel Approach to Single Cell RNA-Sequence Analysis Facilitates In Silico Gene Reporting of Human Pluripotent Stem Cell-Derived Retinal Cell Types.

Authors:
M Joseph Phillips Peng Jiang Sara Howden Patrick Barney Jee Min Nathaniel W York Li-Fang Chu Elizabeth E Capowski Abigail Cash Shivani Jain Katherine Barlow Tasnia Tabassum Ron Stewart Bikash R Pattnaik James A Thomson David M Gamm

Stem Cells 2018 03 25;36(3):313-324. Epub 2017 Dec 25.

Waisman Center.

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March 2018

RNA-Seq of Human Neural Progenitor Cells Exposed to Lead (Pb) Reveals Transcriptome Dynamics, Splicing Alterations and Disease Risk Associations.

Authors:
Peng Jiang Zhonggang Hou Jennifer M Bolin James A Thomson Ron Stewart

Toxicol Sci 2017 09;159(1):251-265

Regenerative Biology Laboratory, Morgridge Institute for Research, Madison, Wisconsin 53707.

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September 2017

A Simple Text Mining Approach for Ranking Pairwise Associations in Biomedical Applications.

Authors:
Finn Kuusisto John Steill Zhaobin Kuang James Thomson David Page Ron Stewart

AMIA Jt Summits Transl Sci Proc 2017 26;2017:166-174. Epub 2017 Jul 26.

Morgridge Institute for Research, Madison, USA.

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July 2017