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Home - Science - Scientist Directory - Wren, Jonathan D.

Jonathan D. Wren, Ph.D.

Associate Member
Genes & Human Disease Research Program

Adjunct Assistant 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 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. Using this method, we’ve been able to predict the function of thousands of the remaining human genes that still have no known function. With collaborators, we have been able to test the predicted functions of dozens of these genes in the lab and discovered that several of these formerly unknown genes play important roles in immune cell movement, coagulation, breast cancer progression, DNA repair and cell division.

We hope to continue to push the boundaries of what we know about human genetics as far as possible with this new algorithm until, hopefully, this “Final Third” of our genome will no longer be a mystery.

Research

My area of research is in Bioinformatics which, briefly defined, is the application of computational methods to solve biomedical problems. I focus on developing methods to enable computers to play a greater role in automatedknowledge discovery. In other words, in addition to using computers to solve specific problems, I am also interested in ways of getting computers to first establish what is known and then be able to condense large amounts of diverse data to infer what is not yet known, but statistically significant and scientifically interesting. As one might suspect, defining what is scientifically interesting turns out to be harder than defining statistical significance, but that’s what makes it fun.

In general, I am interested in both integrating and data-mining large biomedical databases for patterns that can help science accelerate its knowledge regarding the genetic causes that lead to the onset and progression of diseases. Although we’ve known for almost a decade now the physical location of the 25,000 genes we humans have, approximately one-third of them still have no known function. For genes we do know something about, the amount of information per gene is extremely skewed towards those of commercial importance and, for reasons unknown, the rate of new gene discovery has slowed noticably over the past 5 years. Emerging data indicates many, if not most, of these uncharacterized genes are just as important, biologically speaking, as the ones we do know about. These uncharacterized genes are consistently appearing in genome-wide association searches for mutations that cause human disease. Thus, there’s a growing need to accurately predict gene function.

My current research focus is on the refinement and testing of an algorithm I’ve developed to infer gene function by integrating and modeling the information contained both in the massive amount of scientific literature (over 19 million records in MEDLINE, growing at a rate of around 750,000 new scientific papers per year) and in experimental databases such as gene expression and protein-protein interaction databases. With collaborators, mostly local, we are experimentally testing the predicted gene functions and have found that it has performed very accurately so far. We have now discovered approximately 37 new genes involved in important biological processes such as coagulation, immune cell movement, cell division, brain cancer growth, endometriosis and Alzheimer’s Disease, among others. The discovery of these new genes is important because, for many of them, it opens up the possibility that we can create more accurate diagnostics for diseases, prognose disease outcome, and identify new targets for pharmaceutical intervention.

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
Data Processing Management Association Scholarship, 1989
Conoco Scholarship, 1989, 1990
NIH Institutional Training Grant Award in Genomic Science, 1999
Scientific Advisory Board, eTexx Biopharmaceuticals, Inc., 2003-present
Board of Directors, MCBIOS, 2003-present
President, Oklahoma Bioinformatics Society (OKBIOS), 2004-2008
President, MidSouth Bioinformatics Society (MCBIOS), 2007-2008
Who’s Who in Science and Engineering, 2006-2007
Who’s Who in America, 2006-2007
Who’s Who of Emerging Leaders, 2007

Other Activities
Ad hoc reviewer for numerous scientific journals; organizer and judge for annual OKBIOS symposia; senior editor for 2006 and 2007 MCBIOS conference proceedings; scientific review panel for Susan G. Komen Breast Cancer Foundation; selection panel for 2006 Summer Undergraduate Research Program awards (Oklahoma State Regents for Higher Education); grant review panel for Genome Canada 2005 competition III.

Memberships
International Society for Computational Biology, 1998-present
Mid-South Computational Biology and Bioinformatics Society, 2003-present
Oklahoma Bioinformatics Society, 2004-present

Joined OMRF scientific staff in 2007

Publications

View more publications

Recent Publications

Min J, Yang S, Cai Y, Vanderwall DR, Wu Z, Li S, Liu S, Liu B, Wang J, Ding Y, Chen J, Jiang C, Wren JD, Csiszar A, Ungvari Z, Greco C, Kanie T, Peng J, Zhang XA. Tetraspanin Tspan8 restrains interferon signaling to stabilize intestinal epithelium by directing endocytosis of interferon receptor. Cell Mol Life Sci 80:154, 2023 May, PMID: 37204469

Mohammed S, Thadathil N, Ohene-Marfo P, Tran AL, Van Der Veldt M, Georgescu C, Oh S, Nicklas EH, Wang D, Haritha NH, Luo W, Janknecht R, Miller BF, Wren JD, Freeman WM, Deepa SS. Absence of either Ripk3 or Mlkl reduces incidence of hepatocellular carcinoma independent of liver fibrosis. Mol Cancer Res, 2023 May, PMID: 37204757

Longobardi S, Lopez-Davis C, Khatri B, Georgescu C, Pritchett-Frazee C, Lawrence C, Rasmussen A, Radfar L, Scofield RH, Baer AN, Robinson SA, Darrah E, Axtell RC, Pardo G, Wren JD, Koelsch KA, Guthridge JM, James JA, Lessard CJ, Farris AD. Autoantibodies identify primary Sjögren's syndrome in patients lacking serum IgG specific for Ro/SS-A and La/SS-B. Ann Rheum Dis, 2023 May, PMID: 37147113

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.
Post-Doctoral Fellow

Michal Winnicki
Research Trainee

Krish Kumar
Laboratory Technician

Chase Brown
Graduate Student

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

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