• Skip to main content
  • Skip to footer

Oklahoma Medical Research Foundation | OMRF

  • About
    • General Information
    • Disease Research
    • Training & Outreach
    • Events
    • Careers
    • Contact Us
  • Science
    • Scientist Directory
    • Research Programs
    • Research Centers
    • Core Facilities
    • Scientific Publications
    • Scientific Seminars
    • Technology Ventures
  • News
    • Media Resources
    • News Releases
    • Publications
    • On Your Health
    • Bodywork
  • Patients
    • Anti Aging Study
    • Lupus (SLE)
    • MBTPS1 Related Disorders
    • Multiple Sclerosis
    • Rheumatoid Arthritis
    • Sarcoidosis
    • Sjögren’s Disease
    • Osteoarthritis
    • Other Autoimmune Disorders
  • Donate
    • Donate Now
    • Ways to Give
    • Tax Credit
    • Planned Giving
    • Contact Philanthropy
  • My 101
  • Research
  • Brief CV
  • Publications
  • Contact
  • Lab Staff
  • Lab Website
  • News
Home - Science - Scientist Directory - Wren, Jonathan D.

Jonathan D. Wren, Ph.D.

Professor
Genes & Human Disease Research Program

Adjunct Associate Professor, Departments of Biochemistry & Molecular Biology and Geriatric Medicine, University of Oklahoma Health Sciences Center

Associate Member, Stephenson Cancer Center, OUHSC

My 101

In biology and medicine, not only has a lot of data already been generated, but technological advances are enabling us to gather more of it faster every year. Having a lot of data, however, does not necessarily mean we have any greater understanding of how things work.

Discovering how diseases begin and how they might be treated comes from putting the data in a context that it can be understood and then putting the data in the right hands to use it. One example of this is human genetics. Humans have about 25,000 protein-coding genes, and we have data on the location of each gene, but we still don’t know what about one-third of them do.

In my lab, we focus on using computers to make sense of the “data deluge” by finding patterns within large databases and using different sources of information to identify and experimentally verify causal relationships buried within the data. For example, we developed a method to predict what this remaining third of unknown genes do. And, with collaborators, we have been able to validate these predictions experimentally, identifying novel genes that play important roles in immune cell movement and function, blood vessel growth, cancer progression, DNA repair and cell division.

Now, recent technological advances in Artificial Intelligence are helping us accelerate our understanding of the patterns that exist across all experiments. Our goal is to push the boundaries of what we know about human genetics and disease using computational approaches, making inroads into this “Final Third” of our genome and understanding the contribution our genes make to both health and disease.

Research

Many scientific questions can be answered with data that already exists. My lab’s goal is to develop methods to accelerate the pace of scientific discovery.

My area of research is in bioinformatics, which uses computational approaches to solve biomedical problems. Generally, my research interests are in developing computational methods to accelerate our movement from data (observations and measurements) to knowledge (predicting cause and effect). Individual case-control experiments are the backbone of the traditional scientific method, but they lack broader context, such as how unique those changes are to the disease being studied. “What has changed?” is an easier question to answer than “How certain are we these changes are real (i.e., reproducible)?” which, in turn, is easier than “What do these changes mean?”. Modern scientific technologies generate tremendous amounts of data, allowing us to contrast new experiments with prior ones, but this comes with challenges.

One arm of my research is data mining. We are interested in integrating and data mining large biomedical databases, like repositories from the National Center for Biotechnology Information, for patterns that can help science accelerate its knowledge regarding the genetic and epigenetic causes that lead to the onset and progression of diseases. Humans have approximately 25,000 protein-coding genes, and we don’t know the functions of about 33% of them. If we add the 30,000 non-coding RNA to this total, approximately 55% are of unknown function. For genes we know something about, the amount of information per gene is often skewed toward those of commercial importance. Emerging data indicates that many, if not most, of these uncharacterized genes are just as important, biologically speaking, as the ones we do know about. We are working on methods of structuring this data using large language models like ChatGPT in combination with vector databases to store and analyze it with artificial intelligence and machine learning methods.

The second arm of my research is developing methods to automate error-checking, both in the scientific literature and public data. Scientific literature is growing exponentially, both in the number of papers published and the size of the papers. Our current peer-review model is being challenged because literature production is outpacing the number of scientists available to review papers, which is only growing linearly. My studies have shown that certain errors and even ethical breaches are slipping by peer review at a fairly constant rate. Fortunately, we can catch some algorithmically. We have included only a few in a prototype web server to check scientific papers at http://pubqc.omrf.org, which we are working to expand to help increase the quality of published science.

Brief CV

Education
B.B.A., University of Oklahoma, 1991
B.S., University of Oklahoma, 1996
Ph.D., University of Texas Southwestern Medical Center, 2003

Honors and Awards
NIH Institutional Training Grant Award in Genomic Science, 1999
Scientific Advisory Board, eTexx Biopharmaceuticals, Inc., 2003-present
Board of Directors, MCBIOS, 2003-2014
President, Oklahoma Bioinformatics Society (OKBIOS), 2004-2008
President, MidSouth Bioinformatics Society (MCBIOS), 2007-2008
MCBIOS Outstanding Service Award, 2011, 2019
Associate Editor, Bioinformatics, 2005-2026

Other Activities
Ad hoc reviewer for numerous scientific journals; co-organizer and participant for our campus-wide Data Science Workshop series; grant reviewer NIH & NSF bioinformatics grants

Memberships
International Society for Computational Biology, 1998-present
Mid-South Computational Biology and Bioinformatics Society, 2003-present

Joined OMRF scientific staff in 2007

Publications

View more publications

Recent Publications

Murach KA, Englund DA, Chambers TL, Dungan CM, Porter HL, Wren JD, Freeman WM, Dupont-Versteegden EE, Wen Y. A satellite cell-dependent epigenetic fingerprint in skeletal muscle identity genes after lifelong physical activity. FASEB J 39:e70435, 2025 March, PMID: 40047419, PMCID: PMC11884312

Burge KY, Georgescu C, Zhong H, Wilson AP, Gunasekaran A, Yu Z, Franca A, Eckert JV, Wren JD, Chaaban H. Spatial transcriptomics delineates potential differences in intestinal phenotypes of cardiac and classical necrotizing enterocolitis. iScience 28:112166, 2025 March, PMID: 40201118, PMCID: PMC11978348

Scofield RH, Wren JD, Lewis VM. The toll like receptor 7 pathway and the sex bias of systemic lupus erythematosus. Front Immunol 16:1479814, 2025 February, PMID: 40051623, PMCID: PMC11882868

Selected Publications

Buckley DA, Jennings EM, Burke NN, Roche M, McInerney V, Wren JD, Finn DP, McHugh PC. Erratum to: The Development of Translational Biomarkers as a Tool for Improving the Understanding, Diagnosis and Treatment of Chronic Neuropathic Pain. Mol Neurobiol. 2017 Jul 1. PMID: 28669124 PMCID: PMC4960984

Siefert JC, Georgescu C, Wren JD, Koren A, Sansam CL. DNA replication timing during development anticipates transcriptional programs and parallels enhancer activation. Genome Res. 2017 May 16. pii: gr.218602.116. PMID: 28512193 PMCID: PMC5538556

Unnikrishnan A, Jackson J, Matyi SA, Hadad N, Wronowski B, Georgescu C, Garrett KP, Wren JD, Freeman WM, Richardson A. Role of DNA methylation in the dietary restriction mediated cellular memory. Geroscience. 2017 May 5. PMID: 28477138 PMCID: PMC5505897

Ziegler J, Pody R, Coutinho de Souza P, Evans B, Saunders D, Smith N, Mallory S, Njoku C, Dong Y, Chen H, Dong J, Lerner M, Mian O, Tummala S, Battiste J, Fung KM, Wren JD, Towner RA. ELTD1, an effective anti-angiogenic target for gliomas: preclinical assessment in mouse GL261 and human G55 xenograft glioma models. Neuro Oncol. 2017 Feb 1;19(2):175-185. PMID: 27416955 PMCID: PMC5464087

Kushwaha G, Dozmorov M, Wren JD, Qiu J, Shi H, Xu D. Hypomethylation coordinates antagonistically with hypermethylation in cancer development: a case study of leukemia. Hum Genomics. 2016 Jul 25;10 Suppl 2:18. PMID: 27461342 PMCID: PMC4965721

Hadad N, Masser DR, Logan S, Wronowski B, Mangold CA, Clark N, Otalora L, Unnikrishnan A, Ford MM, Giles CB, Wren JD, Richardson A, Sonntag WE, Stanford DR, Freeman W. Absence of genomic hypomethylation or regulation of cytosine-modifying enzymes with aging in male and female mice. Epigenetics Chromatin. 2016 Jul 13;9:30. eCollection 2016. PMID: 27413395 PMCID: PMC4942942

 

Contact

Genes & Human Disease Research Program, MS 42
Oklahoma Medical Research Foundation
825 N.E. 13th Street
Oklahoma City, OK 73104

Phone: (405) 271-6989
Fax: (405) 271-4110
E-mail: Jonathan-Wren@omrf.org

For media inquiries, please contact OMRF’s Office of Public Affairs at news@omrf.org.

Lab Staff

Constantin Georgescu, Ph.D.
Associate Staff Scientist

Cory Giles, Ph.D.
Bioinformatics Scientist

Hunter Porter, Ph.D.
Postdoctoral Scientist

Susan "Suzy" Collins
Project Coordinator II

News from the Wren lab

Dr. Wren in the Media

News from the Wren lab

Discovery casts light on workings of the immune system
May 23, 2019

The discovery could lead to new therapeutic approaches to a wide range of illnesses, including asthma, inflammatory bowel disease and psoriasis.

OMRF launches new genetics research program
April 1, 2019

The new Genes and Human Disease Research Program will broaden OMRF’s investigation into genetic mechanisms in various diseases.

OMRF researcher develops tool to catch errors in scientific literature
February 5, 2018

OMRF scientist Jonathan Wren has developed a computer program to sniff out a wide range of mistakes that commonly appear in scientific studies.

OMRF researchers identify genes that may cause cancer to recur after treatment
December 20, 2017

Cancer often returns after successful therapy, but why?

OMRF researchers identify protein critical to healthy cell division
September 8, 2017

OMRF researchers discovered a protein critical to ensuring mitosis functions properly.

OMRF scientists find clues to MS-induced vision loss
July 14, 2016

For nearly 20 percent of MS patients, vision loss is the first symptom.

Researchers discover 10 new lupus genes in Asian population study
January 25, 2016

The findings were published in the Jan. 25 issue of Nature Genetics.

Joint $3.8 million grant to create aging research center
October 13, 2015

OMRF, OU and VA collaborate to combat diseases associated with aging.

Scientists identify origins of process that is key to diabetes
June 1, 2015

OMRF’s Lorin Olson has pinpointed a cell that starts scarring in fatty tissue.

Controlling a protein may help prevent cancer from spreading
November 5, 2014

New OMRF research could improve cancer, diabetes treatments.

OMRF scientists look ahead to research in 2014
January 2, 2014

A new year brings new challenges for medical researchers.

International coalition finds six new Sjögren’s syndrome genes
October 7, 2013

Researchers have exponentially increased their understanding of Sjögren’s genetics.

Biomarkers help doctors decide how to treat brain cancers
September 10, 2013

OMRF’s biomarker discoveries could bring new therapies for beating gliomas.

$7.8 million grant will invest in junior researchers
March 12, 2013

A new COBRE grant is jump-starting innovative research projects at OMRF.

OMRF discovery could change brain cancer surgeries
November 12, 2012

A biomarker will help doctors better see and treat gliomas.

OMRF’s “cyber-sleuth” hunts new genes
August 11, 2011

Scientist Jonathan Wren uses computers to predict gene functions.

OMRF receives $26 million for two federal research grants
September 3, 2009

The National Institutes of Health has awarded two grants worth a total of $26.3 million to OMRF for research into anthrax and to help train new scientists. Each grant will allow scientists to continue research started in 2004 and 2005 and keep them working through 2014 on several interconnected projects. In the first project, a $14.5 […]

Stealing Science: OMRF scientist helps craft anti-plagiarism tool
February 18, 2008

Much like the world of college essays, scientific journals are often plagued with authors trying to publish someone else’s work as their own. For Oklahoma Medical Research Foundation scientist Jonathan Wren, Ph.D., the issue hit home as part of his duties as an editor for the journal Bioinformatics, when a reviewer recognized a paper as […]

Lost in the middle: Author order matters, OMRF paper says
November 5, 2007

Rare is the scientific paper today written by a single author. With research being conducted by teams of scientists, most studies now boast a half-dozen or so authors. According to a new study led by a scientist at the Oklahoma Medical Research Foundation, credit for those papers is far from evenly distributed, and the order […]

OMRF adds four faculty members
June 14, 2007

The Oklahoma Medical Research Foundation today announced the addition of four scientists to the faculty of its Arthritis & Immunology Research Program. The four new faculty members are Patrick Gaffney, M.D., Kathy Moser, Ph.D., Jonathan Wren, Ph.D., and Igor Dozmorov, Ph.D. “Their recruitment gives us a depth of scientific commitment and expertise that is unparalleled […]

Dr. Wren in the Media

Before Footer

Equal Opportunity Employer

Footer

  • Jobs
  • Directory
  • Donor Privacy Statement
  • Ethics Point
  • Intranet
Facebook Twitter Instagram Linkedin

Subscribe to OMRF News
  • Contact
  • Careers
  • Donor Privacy
  • Ethics Point
  • Intranet
OMRF Logo
OKLAHOMA MEDICAL RESEARCH FOUNDATION
825 NE 13th St.
Oklahoma City, OK 73104
(405) 271-6673
Charity navigatorUnited WayTop Workplace