gene regulation in mouse macrophages

Ramsey Laboratory @ Oregon State University

Computational Systems Biology


gene icon Our goal: to use the tools of computational systems biology to advance precision medicine. We integrate cellular, molecular, and population genetic information on a variety of scales within network models. By analyzing these network models, we aim to identify new disease mechanisms or therapeutic targets. We use machine learning to study the role of noncoding regulatory elements in pathogenesis. We use cross-species approaches, integrating canine and human datasets in the case of cancer and human and mouse datasets in the case of cardiovascular disease. We gratefully acknowledge support from the NIH, NSF, MRFO, PhRMA, ACF, OHSU KCI, Amazon, and NCATS.


Team members

Stephen Ramsey
Associate Professor
Stephen (originally trained in physics and mathematics, earning an ScB from Brown University and a PhD from the University of Maryland. Building on his computational modeling experience, Stephen trained as a postdoc at the University of Washington Genome Center, where he worked on the Human Genome Project in Maynard Olson's laboratory. Stephen's work on genome mapping algorithms paved the way toward molecular-oriented research projects in the labs of Hamid Bolouri and Ilya Shmulevich at the Institute for Systems Biology. As a senior scientist in Alan Aderem's laboratory at the Center for Infectious Disease Research, Stephen worked on computational methods for mapping gene regulatory networks. At OSU, Stephen holds a dual appointment in the Department of Biomedical Sciences and in the School of Electrical Engineering and Computer Science. Stephen's research has been recognized by multiple awards including an NIH K25 Career Development Award, a PhRMA New Investigator Award, an NSF CAREER award, and the Carlson College of Veterinary Medicine Zoetis Award.
  • Associate Professor, OSU Department of Biomedical Sciences
  • Associate Professor, OSU School of Electrical Engineering and Computer Science
  • Affiliate Member, OHSU Knight Cancer Institute
  • Faculty Affiliate, OSU Center for Genome Research and Biocomputing
Amy Glen
Graduate Assistant
Amy Glen is a graduate student in computer science. She has a BA in biology from the University of Vermont. She is working on the NCATS Translator project.
Erica Wood
Project Assistant
Erica Wood is a student at Crescent Valley High School. They are working on the NCATS Translator Project.
Liliana Acevedo
Analyst Programmer 2
Liliana has a BS CS from Humboldt State University. She is working on the NCATS Translator project.
Lindsey Kvarfordt
Special Project Assistant
Lindsey is an OSU undergraduate student pursuing a B.S. in computer science with a minor in mathematics. She is working on the NCATS Translator project.
Meghamala Sinha
Graduate Assistant
Meghamala Sinha is a graduate student in computer science. She has a BS in information technology from West Bengal University of Technology, an MS in information technology from the National Institute of Technology, Durgapur, and an MS in CS from OSU.
Qi Wei
Graduate Assistant
Qi Wei is a graduate student in computer science. He has a BS in Computer Science from the Luebeck University of Applied Science and an MS in computer science from the University of Washington, where he worked in the lab of Prof. Ka Yee Yeung.
Steven Carrell
Graduate Assistant
Steven Carrell is a graduate student in comparative health sciences. He has a BS in Microbiology from Oregon State University. He is being jointly supervised by Stephen Ramsey and Dr. Dan Rockey.


On various projects, I am collaborating with investigators in five different colleges at OSU (Veterinary Medicine, Engineering, Pharmacy, Science, and Agricultural Sciences). Outside OSU, I am currently collaborating with investigators at NYU, the OHSU Knight Cancer Institute, the Institute for Systems Biology, U. Arizona, and UAB.

Graduate programs that I work with

I am able to serve as an advisor for students in Comparative Health Sciences, Computer Science, Electrical & Computer Engineering, Artificial Intelligence, Biological Data Sciences, and Bioengineering. Email is the preferred way to inquire about openings.


Oregon State University is an Equal Opportunity Employer and the Ramsey Lab is committed to being a respectful, diverse, and inclusive workplace.

Former lab members

[show list...]

(in alphabetical order by last name)

Position in Ramsey Lab:
Now at:
Holly Arnold
postbaccalaureate researcher
OSU CCVM intern
Mudra Choudhury
undergraduate honors student
UCLA (PhD program)
Jun He
graduate student (masters)
Pure Storage
Amita Kashyap
undergraduate honors student
U. Colorado (MD-PhD program)
Ujjval Kumaria
graduate research assistant
Daniel Lin
Dana Farber Cancer Institute
Zheng Liu
graduate student (PhD)
Deqing Qu
graduate research assistant
Kavinda Senewiratne
graduate research assistant
OSU Robotics
Satpreet Singh
graduate research assistant
UW (PhD program)
Finn Womack
graduate student (masters)
Penn State University
Tanjin Xu
graduate student (masters)
Jichen Yang
postdoctoral scholar
Yao Yao
graduate student (PhD)
Alvin Yu
undergraduate honors student


Lab News

Apr. 28, 2021
Steve gave a presentation on genetics for the OSU Science & Math Investigative Learning Experience (SMILE) program.
Apr. 27, 2021
Megha gave a presentation at the Women in Data Science (WiDS) Puget Sound conference, on the topic Usefulness of knowledge graphs for improving data-driven causal network learning.
Apr. 1, 2021
Welcome to our newest team member, Liliana Acevedo!
Mar. 24, 2021
Megha gave a presentation entitled Using a General Prior Knowledge Graph to Improve Data-Driven Causal Network Learning at the 2021 AAAI-MAKE conference.
Mar. 12, 2021
Zheng Liu successfully defended his PhD thesis! Congratulations, Dr. Liu!
Mar. 3, 2021
The Weinstock et al. article on macrophage responses to IL-4 in atherosclerosis regression has been accepted to eLife! Link coming soon.
Feb. 16, 2021
Yao Yao successfully defended his PhD thesis! Congratulations, Dr. Yao!
Jan. 21, 2021
Megha's research article entitled Using a General Prior Knowledge Graph to Improve Data-Driven Causal Network Learning has been accepted into the 2021 AAAI-MAKE conference! Congratulations, Megha!
Jan. 8, 2021
Megha's research article (co-authored with Prasad Tadepalli) entitled Voting-based integration algorithm improves causal network learning from interventional and observational data: an application to cell signaling network inference has been accepted for publication in PLOS ONE! Congratulations, Megha!
Jan. 5, 2021
Steve hosts Chris Plaisier (from ASU) giving the Biomedical Sciences Seminar entitled A quiescent-like state found in neuroepithelial-derived cells and glioma.
Jan. 1, 2021
Kavinda Senewiratne joins the lab. Welcome, Kavi!
Jan. 4, 2021
Stephen gives an OSU CBEE Seminar entitled Computationally analyzing knowledge graphs and using machine-learning for drug repositioning and precision oncology applications.
Nov. 5, 2020
Stephen presents on the Translator project and our ARAX system, at the Oregon Bioengineering Symposium.
Oct. 25, 2020
Zheng Liu and his teammates won the Disparity Prize for their work on improving early detection for Alzheimer's Disease, at the OHSU Invent-a-thon! Congratulations, Zheng!
Oct 20, 2020
Megha Sinha has passed her PhD preliminary exam! Congratulations, Megha!
Sep. 21-24, 2020
Our team—Team Expander Agent—participated in the NCATS Biomedical Data Translator Fall 2020 Relay (hackathon) event, and presented our latest results on a novel subgraph ranking algorithm for biomedical knowledge-based reasoning.
Sep. 16, 2020
Amy Glen has enrolled in the OSU CS PhD program as a Graduate Fellow! Congratulations, Amy!
Sep. 16, 2020
Lindsey Kvarfordt has joined the lab as a special project assistant. Welcome, Lindsey!
Sep. 3, 2020
Finn Womack has passed his MS CS final exam! Congrats, Finn!

[show news archive ...]

News Archive

May 22, 2020
Qi Wei has passed his PhD preliminary exam! Congratulations, Qi!
May 4, 2020
Megha Sinha presented her research at the Women in data science Puget Sound conference. Congratulations, Megha!
Apr. 8, 2020
Zheng Liu has passed his CS PhD preliminary exam! Congratulations, Zheng!
Mar. 18, 2020
Meghamala Sinha has been accepted to give a presentation at the 2020 Women in data science Puget Sound conference. Congratulations, Megha!
Feb. 29, 2020
Qi Wei presents on the smart bandage project at the Data Science and Image Analysis Conference of the Pacific Northwest at Washington State University.
Feb. 20, 2020
Our preprint on the Learn and Vote method for data integration for causal inference is out on bioRxiv! Great work by Meghamala Sinha (co-advised by Stephen Ramsey and Prasad Tadepalli).
Jan. 27, 2020
Qi has been accepted as a speaker at the upcoming Data Science and Image Analysis Conference of the Pacific Northwest conference at WSU in Pullman, WA (2/29-3/1). Congratulations, Qi!
Jan. 24, 2020
Stephen gave a presentation on genetics at the SMILE Winter 2020 Teacher Workshop.
Jan. 16, 2020
Congratulations to Amy Glen on receiving a 2020 RELU Scholarship! Thank you OSU EECS for its support!
Jan. 5, 2020
Yao Yao presented a poster on CERENKOV3 at the Pacific Symposium on Biocomputing.
Dec. 26, 2019
Our study (with Amita Kashyap, Brett Tyler, Clint Epps, Christiane Löhr, Pankaj Jaiswal, Brent Kronmiller, Adelaide Rhodes, Vanessa Petro, Tom Sharpton, David Hendrix, Mitch Finnegan, and the Oregon Zoo) of lncRNAs in the American beaver has been accepted for publication in BMC Genomics.
Nov. 18, 2019
Yao Yao has passed his PhD preliminary exam; congratulations, Yao!
Nov. 7, 2019
Stephen participates as a panelist in the 2019 EECS Portland Connect event.
Sep. 16, 2019
Stephen Ramsey, David Koslicki, Jared Roach, Finn Womack, and Amy Glen represent Team X-ray at the NCATS Biomedical Data Translator Hackathon in Seattle.
Aug. 16, 2019
Veronica Flores and Erica Wood present on their summer internship projects at the Apprenticeships in Science and Engineering Symposium at the University of Portland.
Aug. 5, 2019
Stephen gave presentations on genetics and genetic profiling at the OSU Science & Math Investigative Learning Experiences program's Summer Teacher Workshop.
June 24, 2019
Welcome to our three summer high school interns: Erica Wood, Veronica Flores, and Sahana Shah!
June 12, 2019
Our collaborative work with Dr. Chrissa Kioussi and Dr. Theresa Filtz (College of Pharmacy) on gene regulation in mouse embryo forelimb development is highlighted in an article in the OSU research magazine, Terra.
May. 23, 2019
Stephen receives the 2019 Zoetis Research Excellence Award from the Carlson College of Veterinary Medicine. Thank you, CCVM Awards Committee, CCVM Dean Sue Tornquist, Dr. Bermudez, and Zoetis!
May. 15, 2019
Stephen reports: I have received notification from OSU that I will be promoted to associate professor in Fall 2019. Heartfelt thanks to my lab members (current and former), current & past mentors, OSU colleagues, dossier reviewers, collaborators, and my family.
Apr. 20, 2019
Former student Amita Kashyap will be enrolling in the MD-PhD program at the University of Colorado starting in the fall. Congratulations, Amita!
Apr. 4, 2019
Our paper (in collaboration with Charles Keller, Christiane Löhr, and Bernard Séguin) on the transcriptome of feline injection-site sarcoma is now out in BMC Cancer.
Apr. 3, 2019
Yao Yao presented his work developing improved algorithms for identifying functional noncoding SNPs, at the CGRB Bioinformatics User Group (BUG).
Mar. 27, 2019
Meghamala Sinha presented her work on causal inference at the AAAI Symposium Beyond Curve Fitting in Stanford, CA (the article is available on the symposium website).
Mar. 22, 2019
Meghamala Sinha has passed her MS defense and PhD qualifying exam. Congratulations, Megha!
Mar. 4-8, 2019
Ramsey Lab participates in the NCATS Biomedical Data Translator Hackathon in Chapel Hill, NC, as a part of Team X-ray.
Feb. 20, 2019
NCATS has funded Team X-ray to continue our work on the Biomedical Data Translator in 2019. Thank you, NCATS!
Feb. 11, 2019
Our paper on CERENKOV2 is out in BMC Bioinformatics!
Feb. 8, 2019
Meghamala Sinha and Yao Yao each presented a research poster at the COE Graduate Research Showcase.
Feb. 5, 2019
Megha's article (with Prasad Tadepalli) on causal inference has been accepted into the First AAAI Spring Symposium Beyond Curve Fitting: Causation, Counterfactuals, and Imagination-based AI. Congratulations, Megha!
Jan. 25, 2019
Collaborative paper with Jian-Da Lin, Ed Fisher, and P'ng Loke on single-cell analysis of macrophage heterogeneity in atherosclerosis regression has been accepted to JCI Insight!
Jan. 17, 2019
Our paper on CERENKOV2 (first-authored by student Yao Yao and co-authored by students Zheng Liu and Qi Wei) has been accepted for publication in BMC Bioinformatics. Congratulations, Yao, Zheng, and Qi! You can get the latest code at the CERENKOV2 project site on GitHub.
Jan. 4, 2019
Zheng Liu presents on Res2s2aM, a deep residual network-based method for identifying functional noncoding SNPs, at the Pacific Symposium on Biocomputing.
Nov. 27, 2018
Finn Womack has started the MS CS program (co-advised with David Koslicki). Congratulations, Finn!
Nov. 15, 2018
The Biomedical Data Translator project (on which we are one of ten NCATS-funded teams) is highlighted in two commentaries and an editorial in Clinical and Translational Science.
Oct. 23, 2018
Zheng Liu presents a poster on his work using a deep residual network to identify functional noncoding SNPs, at the OSU150 AI & Robotics Symposium.
Oct. 12, 2018
Qi Wei presents a poster on our work studying feline injection-site sarcoma at the CGRB Fall Conference and Colloquium.
Sep. 21, 2018
Our NSF/NIH Smart and Connected Health (SCH) project with Matt Johnston (Lead PI), Elain Fu, Arun Natarajan, and Milan Milovancev (on technology development for wound monitoring) has been funded!
Sep. 20, 2018
Our team (Team X-ray) attends the NCATS Translator Hackathon in Portland. David Koslicki presents on behalf of Team X-ray.
Sep. 17, 2018
Our article on deep residual networks for identifying functional noncoding variants, on which Zheng Liu is first author, has been accepted into the Pacific Symposium on Biocomputing Conference. Zheng will be presenting on behalf of the lab. Congratulations, Zheng!
Sep. 16, 2018
Steven Carrell joins the lab. Welcome, Steven!
Sep. 11, 2018
Dr. Christiane Löhr will be presenting our collaborative work on feline injection-site sarcoma at the Annual Meeting of the American College of Veterinary Pathologists on Nov. 7 in Washington, DC.
Aug. 16, 2018
Our NCATS Translator reasoning tool project is featured in a news article on the EECS website.
Jul. 6, 2018
Our article with Shay Bracha, Jaqueline Bracy, Ryan Troyer, Carl Ruby, Cheri Goodall, Oleh Taratula, and Claudia Maier on circulating exosomes as biomarkers for canine osteosarcoma has been accepted to Translational Oncology.
Jun. 18, 2018
Sahana Shah (a Saturday Academy summer high school intern) and Ashley LaBarre (an undergraduate student) join the lab to work on the canine osteosarcoma project. Welcome!
Jun. 6, 2018
Our NCATS Translator reasoning tool project is featured in a news article on the EECS website.
May. 25, 2018
Our team (Team X-ray) attends the NCATS Translator Hackathon in Bethesda, MD.
May. 14, 2018
Our work on the NCATS Translator project is highlighed in an article on NCATS Features and Briefs.
Apr. 27, 2018
Stephen gives a presentation on CERENKOV at the OSU CGRB Spring Conference and Colloquium.
Apr. 2, 2018
Deqing Qu joins the lab to work on the NCATS Translator Reasoning Tool project. Welcome, Deqing!
Mar. 14, 2018
Stephen gave the Bioinformatics Users' Group (BUG) seminar on the NCATS Translator project.
Mar. 12, 2018
Our work on the NCATS Translator project is highlighted in an article in the Vet Gazette.
Mar. 7, 2018
The National Center for Advancing Translational Sciences (NCATS) has funded a project, with Steve, David Koslicki (Math), Eric Deutsch (ISB), and Arnab Nandi (Ohio State Univ.) as PIs, to develop a biomedical translator software reasoning tool. In the NCATS Translator project ecosystem, our team has been designated Team X-ray. We will be presenting our prototype reasoning tool at the NCATS Hackathon in DC in May 2018.
Mar. 5, 2018
Finn Womack joins the lab to work on the NCATS Translator Reasoning tool project. Welcome, Finn!
Jan. 25, 2018
Stephen gave the Pathogen Research In Progress Seminar (PRIPS) in the Department of Biomedical Sciences, on the subject of feline injection-site sarcoma.
Jan. 19, 2018
Benjamin Weeder joins the lab for a 10-week MPH biostatistics internship. Welcome, Ben!
Jan. 15, 2018
The COE podcast about our human regulome project is featured on the NSF Science 360 website.
Jan. 8-10, 2018
Stephen (and Co-PIs David Koslicki and Eric Deutsch) attend the NCATS Translator Hackathon in San Diego, CA, under the banner of Team X-Ray.
Nov. 29, 2017
Amita Kashyap successfully defends her BRR/UHC thesis. Congratulations, Amita!
Nov. 2, 2017
Stephen gives a presentation on machine learning in biomedical research, for the OSU Machine Learning Club.
Sep. 1, 2017
Our article on macrophage epigenetics (with Peter Askovich, Alan Aderem, and Dr. Aderem's lab) has been accepted by PLOS ONE.
Aug. 21, 2017
Stephen presents CERENKOV at the ACM-BCB conference in Boston.
Aug. 14, 2017
Stephen presents CERENKOV at UW Tacoma.
Aug. 7, 2017
Summer NSF trainees Baylee Goodwin and Dane Besser give three presentations on bioinformatics, at the 2017 SMILE Teacher Workshop.
June 26, 2017
Atherosclerosis macrophage polarization article with Ed Fisher, Karishma Rahman, P'ng Loke, and Kathryn Moore has been featured in an AAAS EurekaAlert.
June 7, 2017
Our paper on a machine-learning approach for identifying regulatory SNPs (CERENKOV) has just been accepted to the 2017 ACM-BCB conference. See you in Boston!
May. 4, 2017
Atherosclerosis macrophage polarization article with Ed Fisher, Karishma Rahman, P'ng Loke, and Kathryn Moore has been accepted by JCI!
Apr. 28, 2017
Amita's work (with Adelaide Rhodes) on identifying beaver lncRNAs has been highlighted in the Spring 2017 edition of the Oregon Stater magazine.
Apr. 19, 2017
Stephen gave the Pathogen Research In Progress Seminar (PRIPS) in the Department of Biomedical Sciences, on the subject of feline injection-site sarcoma.
Apr. 18, 2017
Dr. Nathan Price (Associate Director, Institute for Systems Biology) visits the lab.
Apr. 12, 2017
Amita's work (with Adelaide Rhodes) on identifying beaver lncRNAs has been highlighted on the OSU Foundation website.
Feb. 9, 2017
Stephen gives a public outreach science presentation on the Beaver Genome Project at an OSU SPARK event, Beaver Tales.
Dec. 28, 2016
Our manuscript (co-authored with Shay Bracha) on bladder cancer has been accepted for publication in Genes, Chromosomes and Cancer.
Dec. 21, 2016
Stephen is featured in an OSU College of Engineering podcast in the series Engineering Out Loud, entitled Hearts & Phantoms.
Dec. 12, 2016
Jun He has successfully completed his MS final exam. Congratulations and best wishes, Jun!
Dec. 7, 2016
Stephen gave a research seminar at the Systems Biology Interest Group (SBIG) meeting at OSU.
Nov. 9, 2016
Zheng Liu and Yao Yao have passed their PhD qualifying examinations. Congratulations!
Nov. 7, 2016
Our manuscript on combined eQTL and ChIP-seq analysis has been accepted for publication. Congratulations, Mudra!
Oct. 13, 2016
Two new manuscripts accepted for publication -- one article describes a new method for transcription factor binding site enrichment analysis, and the other article describes a systems biology approach for drug repositioning.
Oct. 2, 2016
Stephen gives a research presentation at the BigLS 2016 conference in Seattle.
Sep. 7, 2016
Amita presents her research project (with Adelaide Rhodes and Jackson Wells) on the beaver transcriptome at the CVM Undergraduate Research Day. Congratulations Amita!
Aug. 30, 2016
Amita presents her research project (with Adelaide Rhodes and Jackson Wells) on the beaver transcriptome at the OSU Undergraduate Research Symposium. Congratulations Amita!
Aug. 22, 2016
Ada Weinstock and Karishma Rahman visit from Dr. Edward Fisher's lab at NYU. Welcome to OSU, Ada and Karishma!
June 21, 2016
Stephen is recognized with a PhRMA Foundation Research Starter Grant Award at the 2016 Intelligent Systems in Molecular Biology conference in Orlando.
June 21, 2016
Steve's NSF Career award is highlighted in the Vet Gazette.
June 20, 2016
Summer students Lexi, Demi, Morgan, and Emma have joined the lab. Welcome!
June 13, 2016
Stephen is appointed an affiliate member of the Knight Cancer Institute at OHSU, in the Quantitative Oncology Research Program.
June 1, 2016
Stephen gives the Mathbio seminar over in the Department of Mathematics.
May 31, 2016
Qi Wei has joined the lab. Welcome, Qi!
May 31, 2016
Tanjin Xu successfully defends his MS CS thesis. Congratulations, Tanjin!
May 29, 2016
Mudra's senior thesis has been nominated by the BioResource Research degree program for the Writing Intensive Curriculum programs's Culture of Writing Award. Congratulations, Mudra!
May 26, 2016
Steve's research is recognized with the New Investigator Award from the OSU Carlson College of Veterinary Medicine.
May 18, 2016
Mudra Choudhury successfully defends her University Honors College / BioResource Resesarch thesis. Congratulations, Mudra!
Mar. 29, 2016
Stephen receives an NSF Career Award for his project to investigate the effects of genetic variants in the noncoding genome. Thank you, NSF Division of Biological Infrastructure!
Mar. 23, 2016
Amita's CVM summer research project on lncRNAs has been funded. Congratulations, Amita!
Mar. 4, 2016
The Beaver Genome Project is covered in the Wall Street Journal.
Feb. 29, 2016
Stephen gave the OSU Physics Colloquium.
Jan. 26, 2016
Stephen gives a presentation on bladder cancer at a joint OHSU-OSU workshop on early cancer detection, at OHSU in Portland.
Jan. 1, 2016
Stephen receives a Research Starter Grant award from the PhRMA Foundation (Informatics Program). Thank you, PhRMA Foundation!
Dec. 17, 2015
Stephen gives the Biomedical Engineering seminar at OHSU.
Dec. 16, 2015
The lab's research is featured in an article on personalized medicine in Momentum!, the OSU College of Engineering magazine.
Dec. 14, 2015
Stephen is designated a Senior Member of the International Society for Computational Biology (ISCB).
Nov. 23, 2015
The Beaver Genome Project is successfully crow mb-2dfunded! The project's progress will be documented on the Beaver Genome Project Website.
Nov. 12, 2015
Stephen presents research (in collaboration with Shay Bracha) on bladder cancer at the NIH Big Data to Knowledge (BD2K) All-Hands Meeting in Bethesda, MD.
Sep. 23, 2015
The Beaver Genome Project is featured in the This week in science column in the journal Nature.
Sep. 16, 2015
Together with the CGRB and with help from the Oregon Zoo, we are launching a crow mb-2dfunding campaign for the Beaver Genome Project.
Aug. 14, 2015
Yao Yao and Zheng Liu have joined the lab. Welcome, Yao and Zheng!
Jun. 24, 2015
Our article on DNA shape has been accepted for publication in Bioinformatics. The regshape software package is available on the Ramsey Lab GitHub page.
Jun. 16, 2015
Satpreet Singh has joined the lab as a summer graduate assistant. Welcome, Satpreet!
Jun. 2, 2015
Stephen gave a seminar for the students in the OSU Aging Sciences IGERT program.
Jun. 1, 2015
Jun He has joined the lab. Welcome, Jun!
May. 21, 2015
Stephen gave the OSU Department of Pharmaceutical Sciences Research Seminar.
Apr. 10, 2015
Stephen represented OSU at the NSF/USENIX Big Data Regional Innovation Hub meeting in Salt Lake City, Utah.
Mar. 6, 2015
Stephen gave a guest lecture on genetic variation in BB485/585.
Mar. 4, 2015
Ilya Shmulevich visited from the Institute for Systems Biology.
Feb. 26, 2015
Our collaboration's' article on smooth muscle foam cells is the online "Editor's Pick" for March 2015 and it is highlighted in an editorial in the March edition of ATVB!
Jan. 20, 2015
Dan Zak visits from the Center for Infectious Disease Research.
Jan. 15, 2015
Stephen gave a research presentation at the Institute for Systems Biology in Seattle.
Dec. 24, 2014
Our jointly authored paper on smooth muscle foam cells (with Ed Fisher's lab at NYU, Joe Miano's lab at U. Rochester, Xiaochun Long's lab at Albany Medical College, Fernando Martinez's lab at Oxford, and Kathryn Moore's lab at NYU) has been accepted for publication by Arteriosclerosis, Thrombosis, and Vascular Biology.
Dec. 23, 2014
Mudra's research grant proposal has been funded under the URISC program (one of only nine awards made, university-wide). Congratulations, Mudra, and thank you for your support, OSU Research Office!
Dec. 5, 2014
Stephen gave a seminar on systems biology in the course Z507, What is systems biology?
Dec. 4, 2014
Our manuscript (with co-authors at CIDR and NYU) on a systems biology approach to studying gene regulation in atherosclerosis regression has been published in PLOS Genetics.
Dec. 1, 2014
Stephen gave a lecture on systems biology in the BRR100 seminar series.
Sep. 16, 2014
Stephen served on a panel discussion for the MCB 525 course "Quantitative Biology".
Nov. 20, 2014
Both Alvin Yu and Mudra Choudhury have been awarded DeLoach Work Scholarships from the University Honors College. Congratulations! And thank you, for your support, UHC!
Nov. 19, 2014
Stephen gave a presentation on bioinformatics and genomics in VMB 671.
Oct. 21, 2014
Tanjin Xu has joined the lab. Welcome, Tanjin!
Sep. 12, 2014
Alvin Yu's poster on his drug repurposing project was the winner of the Poster Award for the undergraduate student category, at the OSU CGRB Fall Conference. Congratulations, Alvin!
Aug. 28, 2014
Stephen gave a research presentation at the summer workshop "Genetic, epigenetic, and functional aspects of complex diseases IV" at the University of Eastern Finland.
Aug. 27, 2014
Stephen gave a research seminar at the University of Tampere in Finland.
Jun. 17, 2014
Stephen presented a poster on Holly Arnold's work on machine learning for biological network analysis, at the conference Systems Biology of Human Disease 2014 in Boston.
May 28, 2014
Stephen was a guest instructor in the course Molecular Host-Microbe Interactions, MCB 637.
May 4, 2014
Stephen gave an invited talk on systems biology at the Pediatrics Academic Societies meeting in Vancouver, British Columbia.
Apr. 28, 2014
Mudra Choudhury has joined the lab. Welcome, Mudra!
Apr. 14, 2014
Manuscript "Multiscale representation of genomic signals" has been published online in Nature Methods (with Theo Knijnenburg, Ilya Shmulevich, and colleagues at Institute for Systems Biology and collaborators at TU-Delft, NKI, USC, and UCLA).
Apr. 7, 2014
Stephen gave a presentation entitled "An integrative computational systems biology approach to mapping gene regulatory networks" at the 2014 CGRB Spring Conference at OSU.
Mar. 16, 2014
Alvin Yu has joined the lab. Welcome, Alvin!
Dec. 2013
The Molecular and Cellular Biology Program has approved Stephen's appointment to their graduate faculty.
Dec. 2013
Laboratory renovations of the first floor in Dryden Hall are complete, and as a result, we now have our lab space on the third floor of Dryden Hall.
Oct. 2013
The Center for Genome Research and Biocomputing has designated Stephen as a CGRB faculty affiliate.
Sep. 2013
The lab website is up and running, at
May 2013
Stephen gives an invited talk at the McGill Systems Biology Atherosclerosis Symposium in Montréal, Québec.


Lab Publications

Bibliometric data are available on my Google Scholar page.

Structural Generalizability: The Case of Similarity Search
Chodpathumwan Y, Glen A, Ramsey SA, Termehchy A
[in press]
Using a general prior knowledge graph to improve data-driven causal network learning
Sinha M, Ramsey SA
Wnt signaling enhances macrophage responses to IL-4 and promotes resolution of atherosclerosis
Weinstock A, Rahman K, Or Y, Nishi H, Menon P, Brown E, Ruggles KV, Ramsey SA, Nikain CA, Garabedian ML, Pena S, Heffron SP, Liu J, Marecki G, Fernandez D, Giannarelli C, Sansbury BE, Spite M, Loke P, Fisher EA
Voting-based integration algorithm improves causal network learning from interventional and observational data: An application to cell signaling network inference
Sinha M, Tadepalli P, Ramsey SA
Predicting chemotherapy response using a variational autoencoder approach
Wei Q, Ramsey SA
J Vet Int Med
Prospective evaluation of the lymph node proteome in dogs with multicentric lymphoma supplemented with sulforaphane
Parachini-Winter C, Bracha S, Ramsey SA, Yang L, Ho E, Leeper H, Curran KL
BMC Genomics
Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis
Kashyap A, Rhodes A, Kronmiller B, Berger J, Champagne A, Davis EW, Finnegan MV, Geniza M, Hendrix DA, Löhr CV, Petro VM, Sharpton TJ, Wells J, Epps CW, Jaiswal P, Tyler BM, Ramsey SA
Pac Symp Biocomp.
CERENKOV3: Clustering and molecular network-derived features improve computational prediction of functional noncoding SNPs
Yao Y, Ramsey SA
Methods Mol Biol.
Combining eQTL and SNP Annotation Data to Identify Functional Noncoding SNPs in GWAS Trait-Associated Regions
Ramsey SA, Liu Z, Yao Y, Weeder B
Comp Immunol Microbiol Infect Dis.
Analysis of staphylococcus infections in a veterinary teaching hospital from 2012 to 2015
Shoen HRC, Rose SJ, Ramsey SA, de Morais H, Bermudez L
BMC Cancer
Elucidating the transcriptional program of feline injection-site sarcoma using a cross-species mRNA-sequencing approach
Wei Q*, Ramsey SA*, Larson MK, Berlow NE, Ochola D, Shiprack C, Kashyap A, Séguin B, Keller C, Löhr CV
AAAI Symposium
Pooling vs. voting: an empirical study of learning causal structures
Sinha M, Tadepalli P, Ramsey SA
JCI Insight
Single-cell analysis of fate-mapped macrophages reveals heterogeneity, including stem-like properties, during atherosclerosis progression and regression
Lin JD, Nishi H, Poles J, Niu X, McCauley CS, Rahman K, Brown EJ, Yeung ST, Vozhilla N, Weinstock A, Ramsey SA, Fisher EA, Loke P
BMC Bioinform.
CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features
Yao Y, Liu Z, Wei Q, Ramsey SA
Pac Symp Biocomp.
Res2s2aM: Deep residual network-based model for identifying functional noncoding SNPs in trait-associated regions
Liu Z, Yao Y, Wei Q, Weeder B, Ramsey SA
Arteriosc Thromb Vasc Biol.
Loss of two Akt (Protein Kinase B) isoforms in hematopoietic cells diminished monocyte and macrophage survival and reduces atherosclerosis in Ldl-receptor null mice
Babaev VR, Ding L, Zhang Y, May JM, Ramsey SA, Vickers KC, Linton MF
Clin Transl Sci
Toward A Universal Biomedical Data Translator
The Biomedical Data Translator Consortium
Clin Transl Sci
The Biomedical Data Translator Consortium: Conception, Culture, and Community
The Biomedical Data Translator Consortium
Translat Oncol
A preliminary proteomic investigation of circulating exosomes and discovery of biomarkers associated with the progression of osteosarcoma in a clinical model of spontaneous disease
Brady JV, Troyer RM, Ramsey SA, Leeper H, Yang L, Maier CS, Goodall CP, Ruby CE, Albarqi HA, Taratula O, Bracha S
Sci Rep
FACS-Seq analysis of Pax3+ cells identifies non-myogenic lineages in the embryonic forelimb
Singh AJ, Chang CN, Ma HY, Ramsey SA, Filtz TM, Kioussi C.
Cell Molec Life Sci
Differential gene regulatory networks in development and disease
Singh AJ, Ramsey SA, Filtz TM, Kioussi C.
Methods Mol Biol.
A Method for cross-species visualization and analysis of RNA-Sequence data. Chapter in the book Systems Biology (Mariano Bizzarri (ed.)
Ramsey SA
Identifying novel transcription factors involved in the inflammatory response by using binding site motif scanning in genomic regions defined by histone acetylation
Askovich P, Ramsey SA, Diercks AH, Kennedy KA, Knijnenburg T, Aderem A.
ACM BCB Proceedings
CERENKOV: Computational elucidation of the regulatory noncoding variome
Yao Y*, Liu Z*, Singh S, Wei Q, Ramsey SA
J. Clinical Investigation
Inflammatory Ly6Chigh monocytes and their conversion to M2 macrophages drive atherosclerosis regression
Rahman K, Vengrenyuk Y, Ramsey SA, Rotllan Vila N, Girgis NM, Liu J, Gusarova V, Gromada J, Weinstock A, Moore KJ, Loke P, Fisher EA
Genes Chrom Cancer.
Cross-species analysis of the canine and human bladder cancer transcriptome and exome
Ramsey SA, Xu T, Goodall C, Rhodes AC, Kashyap A, He J, Bracha S.
Gene Regul Syst Biol.
Identifying cell type-specific transcription factors by integrating ChIP-seq and eQTL data–application to monocyte gene regulation
Choudhury M, Ramsey SA
Interdis Sci Comp Life Sci.
A computational systems biology approach for identifying candidate drugs for repositioning for cardiovascular disease
Yu AZ, Ramsey SA
Bioinform Biol Insights.
An empirical prior improves accuracy for Bayesian estimation of transcription factor binding site frequencies within gene promoters
Ramsey SA
ACM BCB Proceedings
Exploration of regression models for cancer noncoding mutation recurrence
Xu T, Ramsey SA
Analytical Chemistry
Investigation of reagent delivery formats in a multivalent malaria sandwich immunoassay and implications for assay performance
Liang T, Robinson R, Houghtaling J, Fridley G, Ramsey SA, Fu E
A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites
Yang J, Ramsey SA
Bioinform Biol Insights.
Reverse enGENEering of regulatory networks from Big Data: a roadmap for biologists
Dong X, Yambartsev A, Ramsey SA, Thomas L, Shulzhenko N, Morgun A
EMBO Journal
An LXR-NCOA5 complex directs inflammatory crosstalk-dependent repression of cholesterol efflux
Gillespie MA, Gold E, Ramsey SA, Podolsky I, Aderem A, Ranish J
Arteriosc Thromb Vasc Biol.
Cholesterol loading re-programs the miR-143/145-myocardin axis to convert aortic smooth muscle cells to a dysfunctional macrophage-like phenotype
Vengrenyuk Y, Nishi H, Long X, Ouimet M, Savji N, Martinez FO, Cassella C, Moore KJ, Ramsey SA, Miano JM, Fisher EA
PLOS Genetics
Epigenome-guided analysis of the transcriptome of plaque macrophages during atherosclerosis regression reveals activation of the Wnt signaling pathway
Ramsey SA*, Vengrenyuk Y*, Menon P, Podolsky I, Feig JE, Aderem A, Fisher EA, Gold ES
Nature Methods
Multiscale representation of genomic signals
Knijnenburg TA, Ramsey SA, Berman BP, Kennedy KA, Smit AFA, Wessels LFA, Laird PW, Aderem A, Shmulevich I
Urokinase plasminogen activator induces pro-fibrotic/M2 phenotype in murine cardiac macrophages
Meznarich J, Malchodi L, Helterline D, Ramsey SA, Bertko K, Plummer T, Plawman A, Gold E, Stempien-Otero A
J. Experimental Medicine
ATF3 protects against atherosclerosis by suppressing 25-hydroxycholesterol-induced lipid body formation
Gold ES*, Ramsey SA*, Sartain MJ, Selinummi J, Podolsky I, Rodriguez DJ, Moritz RL, Aderem A
Molec Syst Biol.
Asymmetric positive feedback loops reliably control biological responses
Ratushny AV, Saleem RA, Sitko K, Ramsey SA, Aitchison JD
J. Biol Chem.
Mechanisms of urokinase plasminogen activator (uPA)-mediated atherosclerosis: Role of the uPA receptor and S100A8/A9 proteins
Farris SD, Hu JH, Krishnan R, Emery I, Chu T, Du L, Kremen M, Dichek HL, Gold E, Ramsey SA, Dichek DA
Methods Molec. Biol.
Mathematical modeling of biomolecular network dynamics
Ratushny AV, Ramsey SA, Aitchison JD
Microfluidics & Nanofluidics
Transport in two-dimensional paper networks
Fu E, Ramsey SA, Kauffman P, Lutz B, Yager P
Analytical Chemistry
Enhanced sensitivity of lateral flow tests using a two-dimensional paper network format
Fu E, Liang T, Houghtaling J, Ramachandran S, Ramsey SA, Lutz B, Yager P
J. Cell Science
ATF3, an adaptive-response gene, enhances TGFβ signaling and cancer-initiating cell features in breast cancer cells
Yin X, Wolford CC, Chang YS, McConoughey SJ, Ramsey SA, Aderem A, Hai T
Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites
Ramsey SA, Knijnenburg TA, Kennedy KA, Zak DE, Gilchrist M, Gold ES, Johnson CD, Lampano AE, Litvak V, Navarro G, Stolyar T, Aderem A, Shmulevich I
BMC Bioinformatics
SeqAdapt: an adaptable system for the tracking, storage, and analysis of high-throughput sequencing experiments
Burdick DB, Cavnor CC, Handcock J, Killcoyne S, Lin J, Marzolf B, Ramsey SA, Rovira H, Bressler R, Shmulevich I, Boyle J
EMBO Molecular Medicine
A systems biology approach to understanding atherosclerosis
Ramsey SA, Gold ES, Aderem A
Analytical Chemistry
Modeling of a competitive microfluidic heterogeneous immunoassay: sensitivity of the assay response to varying system parameters
Fu E, Nelson KE, Ramsey SA, Foley JO, Helton K, Yager P
Nature Immunology
Function of C/EBPδ in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals
Litvak V, Ramsey SA, Rust AG, Zak DE, Kennedy KA, Lampano AE, Nykter M, Shmulevich I, Aderem A
Proc Natl Acad Sci U S A.
Dynamic analysis of MAPK signaling using a high-throughput microfluidic single-cell imaging platform
Taylor RJ, Falconnet D, Niemistö A, Ramsey SA, Prinz S, Shmulevich I, Galitski T, Hansen CL
Biophysical Journal
Control of transcriptional variability by overlapping feed-forward regulatory motifs
Ratushny AV*, Ramsey SA*, Roda O, Wan Y, Smith JJ, Aitchison JD
PLOS Comput Biol.
Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics
Ramsey SA, Klemm SL, Zak DE, Kennedy KA, Thorsson V, Li B, Gilchrist M, Gold ES, Johnson CD, Litvak V, Navarro G, Roach JC, Rosenberger CM, Rust AG, Yudkovsky N, Aderem A, Shmulevich I
Proc Natl Acad Sci U S A.
Gene expression dynamics in the macrophage exhibit criticality
Nykter M, Price ND, Aldana M, Ramsey SA, Kauffman SA, Hood L, Yli-Harja O, Shmulevich I
Analytical Chimica Acta
Dependence of the signal amplification potential of colloidal gold nanoparticles on resonance wavelength in surface plasmon resonance-based detection
Fu ES, Ramsey SA, Yager P
Molecular Systems Biology
Transcriptional responses to fatty acid are coordinated by combinatorial control
Smith JJ, Ramsey SA, Marelli M, Marzolf B, Hwang D, Saleem RA, Rachubinski RA, Aitchison JD
Control of signaling in a MAP-kinase pathway by an RNA-binding protein
Prinz S, Aldridge C, Ramsey SA, Taylor RJ, Galitski T
Sens Act B Chem.
Resonance wavelength-dependent signal of absorptive particles in surface plasmon resonance-based detection
Fu E, Ramsey SA, Chen J, Chinowsky TM, Wiley B, Xia Y, Yager P
Rev Sci Inst.
One-dimensional surface plasmon resonance imaging system using wavelength interrogation
Fu E, Ramsey SA, Thariani R, Yager P
Nature Genetics
Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast
Ramsey SA, Smith JJ, Orrell D, Marelli M, Petersen TW, de Atauri P, Bolouri H, Aitchison JD
Physica D
Feedback control of stochastic noise in the yeast galactose utilization pathway
Orrell D, Ramsey S, Marelli M, Smith JJ, Petersen TW, de Atauri P, Aitchison JD, Bolouri H
Phil Trans R Soc Lond B
Transcriptional noise and cellular heterogeneity in mammalian macrophages
Ramsey S, Ozinsky A, Clark A, Smith KD, de Atauri P, Thorsson V, Orrell D, Bolouri H
Proc Natl Acad Sci U S A.
A data integration methodology for systems biology
Hwang D, Rust AG, Ramsey S, Smith JJ, Leslie DM, Weston AD, de Atauri P, Aitchison JD, Hood L, Siegel AF, Bolouri H
Proc Natl Acad Sci U S A.
A data integration methodology for systems biology: experimental validation
Hwang D, Smith JJ, Leslie DM, Weston AD, Rust AG, Ramsey S, de Atauri P, Siegel AF, Bolouri H, Aitchison JD, Hood L
J Bioinform Comp Biol.
Dizzy: Stochastic simulations of large-scale genetic regulatory networks
Ramsey S, Orrell D, Bolouri H
A method for estimating stochastic noise in large genetic regulatory networks
Orrell D, Ramsey S, de Atauri P, Bolouri H
Biochemical Journal
Is the regulation of galactose-1-phosphate tuned against gene expression noise?
de Atauri P, Orrell D, Ramsey S, Bolouri H
Syst Biol (Stevenage).
Evolution of "design" principles in biochemical networks
de Atauri P, Orrell D, Ramsey S, Bolouri H

[show older publications ...]


Publications – Pre-2001

Int J Theo Phys.
Interacting field theories in Robertson-Walker spacetimes: analytic approximations
Molina-Paris C, Anderson PR, Ramsey SA
Physical Review D
One-loop λφ4theory in Robertson-Walker spacetimes: adiabatic regularization and analytic approximation
Molina-Paris C, Anderson PR, Ramsey SA
Physical Review D
Hydrodynamic transport functions from quantum kinetic theory
Calzetta EA, Hu BL, Ramsey SA
Physical Review D
Defect formation and Critical Dynamics in the Early Universe
Stephens GJ, Calzetta EA, Hu BL, Ramsey SA
Int J Theo Phys.
Nonequilibrium dynamics of quantum fields in inflationary cosmology
Ramsey SA
Physical Review D
Nonequilibrium inflaton dynamics and reheating. II. Fermion production, noise, and stochasticity
Ramsey SA, Hu BL, Stylianopoulos AM
Nonequilibrium dynamics of quantum fields in inflationary cosmology (PhD Dissertation, University of Maryland)
Ramsey SA (PhD advisor: Bei-Lok Hu)
Physical Review D
Nonequilibrium inflaton dynamics and reheating: Back reaction of parametric particle creation and curved spacetime effects
Ramsey SA, Hu BL
Physical Review D
O(N) Quantum fields in curved spacetime
Ramsey SA, Hu BL
Some statistics for measuring large-scale structure
Brandenberger RH, Kaplan DM, Ramsey SA


Current & future teaching

Spring 2021
(course development)
Developing an online course, Cancer Systems Biology (aiming to offer during the 2021-2022 academic year).

Past teaching

Fall 2020
Networks in computational biology
Spring 2020
VMB 651
Bioinformatics workshop
Winter 2020
CS 446/546
Networks in computational biology
Fall 2019
Guest instructor
VMB 671
Molecular Tools
Spring 2019
VMB 651
Cancer Systems Biology
Winter 2019
Discussion Leader
VMB 741
Veterinary Integrated Problem Solving
Fall 2018
CS 340
Introduction to databases
Spring 2018
VMB 651
Cancer systems biology
Spring 2018
VMB 722
Research Reading and Skills
Spring 2018
Guest instructor
VMB 631
Mathematical modeling of biological systems
Winter 2018
Discussion Leader
VMB 741
Veterinary Integrated Problem Solving
Fall 2017
CS 446/546
Networks in computational biology
Fall 2017
Guest Lecturer
VMB 671/
MCB 671
Molecular Tools
Spring 2017
VMB 651
Cancer systems biology
Spring 2017
Discussion Leader
VMB 742
Veterinary Integrated Problem Solving
Winter 2017
Discussion Leader
VMB 741
Veterinary Integrated Problem Solving
Fall 2016
CS 446/519
Networks in computational biology
Fall 2016
Guest Lecturer
VMB 671/
MCB 671
Molecular Tools
Spring 2016
Guest Instructor
MCB 637
Molecular host-microbe interactions
Spring 2016
Guest Instructor
MTH 607
Mathematical Biology
Spring 2016
Discussion Leader
VMB 742
Veterinary Integrated Problem Solving
Winter 2016
VMB 670
Introduction to Systems Biology
Winter 2016
Discussion Leader
VMB 741
Veterinary Integrated Problem Solving
Fall 2015
CS 446
Biological Networks
Fall 2015
Gest Lecturer
VMB 671/
MCB 671
Molecular Tools
Fall 2015
Gest Lecturer
BIOE 459
Cell Engineering
Spring 2015
Lead Instructor
VMB 670
Systems Biology and Bioinformatics
(Instructors: Stephen Ramsey, Natalia Shulzhenko, Jan Medlock, and Andrey Morgun)
Spring 2015
Discussion Leader
VMB 742
Veterinary Integrated Problem Solving
Winter 2015
MCB 555
Genome Expression
Winter 2015
Guest lecturer
BB 485/585
Applied Bioinformatics
Fall 2014
Guest Speaker
MCB 525
Quantitative biology
Fall 2014
CS 419/519
Selected Topics in Computer ScienceNetwork Methods in Bioinformatics
Fall 2014
Guest Lecturer
VMB 671/
MCB 671
Molecular Tools
Fall 2014
Seminar Speaker
Z 507
What is Systems Biology?
Fall 2014
Guest Speaker
BRR 100
Great experiments
Spring 2014
Guest Lecturer
MCB 637
Molecular host-microbe interactions
Winter 2014
Guest Instructor
VMB 631
Mathematical modeling of biological systems
Winter 2014
Guest Lecturer
BB 499
Applied Bioinformatics



In partnership with the Science & Math Investigative Learning Experiences (SMILE) organization, we have developed a series of one-hour science activities for high school students. The student guides and teacher guides for these activities are freely distributed here under the Creative Commons (CC-BY) license.

PTC Taste Test
See if you can taste PTC or not. It's all in your genes!
Paper Karyotypes
Learn about chromosomes by reconstructing a karyotype.
Learn about genetic conditions by playing Genetic4.
Dinosaur Mass Spec!
Sequence proteins in fossils using Mass Spectrometry!
What types of protein are in this dinosaur fossil?
Phylogenetic Trees
Compare dinosaur proteins to modern organisms'
Ethics of De-Extinction
Should we bring back extinct species? An ethics activity.
Build an alien
A Mendelian genetics activity, for elementary school students.
Solve a murder mystery
A forensic genomics activity, for middle school students.
Build an alien
A genetics activity, for high school students.

Credits: Jay Well, Dominique Brooks, Morgan McCarthy, Demi Butler, Emma Cushing, Lexi Wilson, Dane Besser, Baylee Goodwin, and Stephen Ramsey.


We have hosted four high school summer interns in our lab and six undergraduate summer researchers in our lab. We have also hosted science activities at three SMILE teacher training workshops.

Open source policy

We are committeed to open science and to providing to the scientific community the software code that we have developed in our research projects; see our GitHub page.

Note: I am working from home, due to COVID-19.


U.S. Post:

106 Dryden Hall
Corvallis, OR 97331-4801


105 Magruder Hall
Corvallis, OR 97331-4801

Encrypted email:
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