gene regulation in mouse macrophages

gene icon We use a computational systems biology approach to study gene regulation in health and disease. We integrate cellular and molecular information on a variety of scales within network models that we analyze in order to uncover molecular mechanisms. Our long-term goal is to use the tools of computational systems biology to advance precision medicine. We use cross-species approaches in our work, integrating canine and human datasets in the case of cancer and human and mouse datasets in the case of cardiovascular disease.

gene icon Our research projects have been supported by funding from the National Institutes of Health, the National Science Foundation (via a 2016 Career award), the Medical Research Foundation of Oregon, the PhRMA Foundation, the Animal Cancer Foundation, and the OHSU Knight Cancer Institute.


Current lab researchers

Stephen Ramsey Assistant Professor email show bio
   [link to portrait]
Stephen earned a PhD in physics from the University of Maryland and an ScB in mathematical physics from Brown University. Building on his computational modeling background from physics, Stephen joined the University of Washington Genome Center as a senior fellow, where he worked on genome mapping algorithms in Maynard Olson's laboratory. Stephen's work on the Human Genome Project paved the way toward more molecular- and network-oriented research projects – primarily in the area of gene regulatory network modeling, analysis, and inference – in the labs of Hamid Bolouri and Ilya Shmulevich at the Institute for Systems Biology. Prior to joining OSU, Stephen held a senior scientist appointment in Alan Aderem's laboratory at the Center for Infectious Disease Research, where his work on computational methods for mapping gene networks earned him a K25 Career Development Award from the National Institutes of Health. At OSU, Stephen holds a dual appointment in the Department of Biomedical Sciences and in the School of Electrical Engineering and Computer Science. Stephen has an NSF CAREER award and he is an affiliate member at the Knight Cancer Institute at OHSU.
Amita Kashyap Undergraduate Student email show bio
  Amita is a University Honors College student majoring in BioResource Research with an option in Bioinformatics/Genomics.
Zheng Liu Graduate Student email show bio
  Zheng is a graduate student in computer science. He has a BS in computer science from Wuhan University of Science and Technology and a MS in computer science from Guizhou University.
Qi Wei Graduate Student email show bio
  Qi 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.
Yao Yao Graduate Student email show bio
  Yao is a graduate student in computer science. He has a BS in computer science from Harbin Institute of Technology and an MS in computer science form Wuhan University. He has also worked at NetEase in China before coming to OSU.
Alvin Yu Undergraduate Student email show bio
  Alvin is a University Honors College student majoring in chemical engineering, who has worked as a summer intern at Genentech.

Current project collaborators

Edward A. Fisher New York University School of Medicine   atherosclerosis
Shay Bracha OSU College of Veterinary Medicine   cancer
Christiane Löhr OSU College of Veterinary Medicine   cancer
Harold Bae OSU School of Biological and Population Health Sciences   genetic epidemiology
Xiaoli Fern OSU School of Electrical Engineering and Computer Science   machine learning
Elain Fu OSU School of Chemical, Biological, and Environmental Engineering   bioengineering for global health applications
Natalia Shulzhenko and Andrey Morgun OSU College of Veterinary Medicine and College of Pharmacy   gene regulation, mouse models
Brett Tyler OSU Department of Botany and Plant Pathology   genome sequencing project
Alan Aderem Center for Infectious Disease Research   epigenetics, innate immunity
Adelaide Rhodes Center for Genome Research and Biocomputing   genome/transcriptome projects

[show lab alumni ...]

Lab Alumni

Trainee (chronological order) Worked in the lab as a Now at
Holly Arnold post-baccalaureate researcher OSU (DVM program)
Jichen Yang postdoctoral scholar Thompson-Reuters
Mudra Choudhury undergraduate honors student UCLA (PhD program)
Tanjin Xu graduate student (masters) IBM
Jun He graduate student (masters) Pure Storage
Satpreet Singh summer graduate student University of Washington (PhD program)

Recent News

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 Steve presents CERENKOV at the ACM-BCB conference in Boston.
Aug. 14, 2017 Steve 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 Steve 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.

[show news archive ...]

News Archive

Apr. 12, 2017 Amita's work (with Adelaide Rhodes) on identifying beaver lncRNAs has been highlighted on the OSU Foundation website.
Feb. 9, 2017 Steve 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, 2016Steve is featured in an OSU College of Engineering podcast in the series Engineering Out Loud, entitled Hearts & Phantoms.
Dec. 12, 2016Jun He has successfully completed his MS final exam. Congratulations and best wishes, Jun!
Dec. 7, 2016Steve gave a research seminar at the Systems Biology Interest Group (SBIG) meeting at OSU.
Nov. 9, 2016Zheng Liu and Yao Yao have passed their PhD qualifying examinations. Congratulations!
Nov. 7, 2016Our manuscript on combined eQTL and ChIP-seq analysis has been accepted for publication. Congratulations, Mudra!
Oct. 13, 2016Two 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, 2016Steve gives a research presentation at the BigLS 2016 conference in Seattle.
Sep. 7, 2016Amita presents her research project (with Adelaide Rhodes and Jackson Wells) on the beaver transcriptome at the CVM Undergraduate Research Day. Congratulations Amita!
Aug. 30, 2016Amita presents her research project (with Adelaide Rhodes and Jackson Wells) on the beaver transcriptome at the OSU Undergraduate Research Symposium. Congratulations Amita!
Aug. 22, 2016Ada Weinstock and Karishma Rahman visit from Dr. Edward Fisher's lab at NYU. Welcome to OSU, Ada and Karishma!
June 21, 2016Steve is recognized with a PhRMA Foundation Research Starter Grant Award at the 2016 Intelligent Systems in Molecular Biology conference in Orlando.
June 21, 2016Steve's NSF Career award is highlighted in the Vet Gazette.
June 20, 2016Summer students Lexi, Demi, Morgan, and Emma have joined the lab. Welcome!
June 13, 2016Steve is appointed an affiliate member of the Knight Cancer Institute at OHSU, in the Quantitative Oncology Research Program.
June 1, 2016Steve gives the Mathbio seminar over in the Department of Mathematics.
May 31, 2016Qi Wei has joined the lab. Welcome, Qi!
May 31, 2016Tanjin Xu successfully defends his MS CS thesis. Congratulations, Tanjin!
May 29, 2016Mudra'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, 2016Steve's research is recognized with the New Investigator Award from the OSU College of Veterinary Medicine.
May 18, 2016Mudra Choudhury successfully defends her University Honors College / BioResource Resesarch thesis. Congratulations, Mudra!
Mar. 29, 2016Steve 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, 2016Amita's CVM summer research project on lncRNAs has been funded. Congratulations, Amita!
Mar. 4, 2016The Beaver Genome Project is covered in the Wall Street Journal.
Feb. 29, 2016Steve gave the OSU Physics Colloquium.
Jan. 26, 2016Steve gives a presentation on bladder cancer at a joint OHSU-OSU workshop on early cancer detection, at OHSU in Portland.
Jan. 1, 2016Steve receives a Research Starter Grant award from the PhRMA Foundation (Informatics Program). Thank you, PhRMA Foundation!
Dec. 17, 2015Steve gives the Biomedical Engineering seminar at OHSU.
Dec. 16, 2015The lab's research is featured in an article on personalized medicine in Momentum!, the OSU College of Engineering magazine.
Dec. 14, 2015Steve is designated a Senior Member of the International Society for Computational Biology (ISCB).
Nov. 23, 2015The Beaver Genome Project is successfully crowdfunded! The project's progress will be documented on the Beaver Genome Project Website.
Nov. 12, 2015Steve 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, 2015The Beaver Genome Project is featured in the This week in science column in the journal Nature.
Sep. 16, 2015Together with the CGRB and with help from the Oregon Zoo, we are launching a crowdfunding campaign for the Beaver Genome Project.
Aug. 14, 2015Yao Yao and Zheng Liu have joined the lab. Welcome, Yao and Zheng!
Jun. 24, 2015Our 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, 2015Satpreet Singh has joined the lab as a summer graduate assistant. Welcome, Satpreet!
Jun. 2, 2015Stephen gave a seminar for the students in the OSU Aging Sciences IGERT program.
Jun. 1, 2015Jun He has joined the lab. Welcome, Jun!
May. 21, 2015Stephen gave the OSU Department of Pharmaceutical Sciences Research Seminar.
Apr. 10, 2015Stephen represented OSU at the NSF/USENIX Big Data Regional Innovation Hub meeting in Salt Lake City, Utah.
Mar. 6, 2015Stephen gave a guest lecture on genetic variation in BB485/585.
Mar. 4, 2015Ilya Shmulevich visited from the Institute for Systems Biology.
Feb. 26, 2015Our 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, 2015Dan Zak visits from the Center for Infectious Disease Research.
Jan. 15, 2015Stephen gave a research presentation at the Institute for Systems Biology in Seattle.
Dec. 24, 2014Our 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, 2014Mudra'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, 2014Stephen gave a seminar on systems biology in the course Z507, What is systems biology?
Dec. 4, 2014Our 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, 2014Stephen gave a lecture on systems biology in the BRR100 seminar series.
Sep. 16, 2014Stephen served on a panel discussion for the MCB 525 course "Quantitative Biology".
Nov. 20, 2014Both 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, 2014Stephen gave a presentation on bioinformatics and genomics in VMB671.
Oct. 21, 2014Tanjin 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, 2014Stephen gave a research seminar at the University of Tampere in Finland.
Jun. 17-19, 2014Stephen 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, 2014Stephen was a guest instructor in the course Molecular Host-Microbe Interactions, MCB 637.
May 4, 2014Stephen gave an invited talk on systems biology at the Pediatrics Academic Societies meeting in Vancouver, British Columbia.
Apr. 28, 2014Mudra Choudhury has joined the lab. Welcome, Mudra!
Apr. 14, 2014Manuscript "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, 2014Stephen 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, 2014Alvin Yu has joined the lab. Welcome, Alvin!
Dec. 2013The Molecular and Cellular Biology Program has approved Stephen's appointment to their graduate faculty.
Dec. 2013Laboratory 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. 2013The Center for Genome Research and Biocomputing has designated Stephen as a CGRB faculty affiliate.
Sep. 2013The lab website is up and running, at
May 2013Stephen gives an invited talk at the McGill Systems Biology Atherosclerosis Symposium in Montréal, Québec.

Stephen Ramsey's Peer-Reviewed Publications

Bibliometric data are available at: Google Scholar.

Reference Title Author(s) Link
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. [accepted]
ACM BCB Proceedings
CERENKOV: Computational elucidation of the regulatory noncoding variome Yao Y*, Liu Z*, Singh S, Wei Q, Ramsey SA [accepted]
J. Clinical Investigation
Recruitment of Ly6Chigh monocytes and their conversion to M2 macrophages are required for regression of atherosclerosis in mice 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 [in press]
Genes Chromosom 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. [link]
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 [link]
Interdiscip Sci Comp Life Sci.
A computational systems biology approach for identifying candidate drugs for repositioning for cardiovascular disease Yu AZ, Ramsey SA [link]
Bioinform Biol Insights.
An empirical prior improves accuracy for Bayesian estimation of transcription factor binding site frequencies within gene promoters Ramsey SA [link]
ACM BCB Proceedings
Exploration of regression models for cancer noncoding mutation recurrence Xu T, Ramsey SA [link]
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 [link]
A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites Yang J, Ramsey SA [link]
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 [link]
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 [link]
Arterioscler 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 [link]
Featured in editorial
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 [link]
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 [link]
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 [link]
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 [link]
Molec Syst Biol.
Asymmetric positive feedback loops reliably control biological responses Ratushny AV, Saleem RA, Sitko K, Ramsey SA, Aitchison JD [link]
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 [link]
Methods Molec. Biol.
Mathematical modeling of biomolecular network dynamics Ratushny AV, Ramsey SA, Aitchison JD [link]
Microfluidics & Nanofluidics
Transport in two-dimensional paper networks Fu E, Ramsey SA, Kauffman P, Lutz B, Yager P [link]
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 [link]
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 [link]
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 [link]
Corrected supplement. doc.
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 [link]
EMBO Molecular Medicine
A systems biology approach to understanding atherosclerosis Ramsey SA, Gold ES, Aderem A [link]
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 [link]
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 [link]
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 [link]
Biophysical Journal
Control of transcriptional variability by overlapping feed-forward regulatory motifs Ratushny AV*, Ramsey SA*, Roda O, Wan Y, Smith JJ, Aitchison JD [link]
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 [link]
Table S17.
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 [link]
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 [link]
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 [link]
Control of signaling in a MAP-kinase pathway by an RNA-binding protein Prinz S, Aldridge C, Ramsey SA, Taylor RJ, Galitski T [link]
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 [link]
Rev Sci Inst.
One-dimensional surface plasmon resonance imaging system using wavelength interrogation Fu E, Ramsey SA, Thariani R, Yager P [link]
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 [link]
Corrected supplementary note.
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 [link]
Philos 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 [link]
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 [link]
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 [link]
J Bioinform Comp Biol.
Dizzy: Stochastic simulations of large-scale genetic regulatory networks Ramsey S, Orrell D, Bolouri H [link]
(Supplement: [link])
A method for estimating stochastic noise in large genetic regulatory networks Orrell D, Ramsey S, de Atauri P, Bolouri H [link]
Biochemical Journal
Is the regulation of galactose-1-phosphate tuned against gene expression noise? de Atauri P, Orrell D, Ramsey S, Bolouri H [link]
Syst Biol (Stevenage).
Evolution of "design" principles in biochemical networks de Atauri P, Orrell D, Ramsey S, Bolouri H [link]

* indicates equal co-author contributions to the publication.

[show older publications ...]

Stephen Ramsey's Peer-Reviewed Publications – Pre-2001

Reference Title Author(s) Link
Int J Theo Phys.
Interacting field theories in Robertson-Walker spacetimes: analytic approximations Molina-Paris C, Anderson PR, Ramsey SA [link]
Physical Review D
One-loop λφ4theory in Robertson-Walker spacetimes: adiabatic regularization and analytic approximation Molina-Paris C, Anderson PR, Ramsey SA [link]
Physical Review D
Hydrodynamic transport functions from quantum kinetic theory Calzetta EA, Hu BL, Ramsey SA [link]
Physical Review D
Defect formation and Critical Dynamics in the Early Universe Stephens GJ, Calzetta EA, Hu BL, Ramsey SA [link]
Int J Theo Phys.
Nonequilibrium dynamics of quantum fields in inflationary cosmology Ramsey SA [link]
Physical Review D
Nonequilibrium inflaton dynamics and reheating. II. Fermion production, noise, and stochasticity Ramsey SA, Hu BL, Stylianopoulos AM [link]
Physical Review D
Nonequilibrium inflaton dynamics and reheating: Back reaction of parametric particle creation and curved spacetime effects Ramsey SA, Hu BL [link]
Physical Review D
O(N) Quantum fields in curved spacetime Ramsey SA, Hu BL [link]

Other Publications or Works

Reference Title Author(s) Link
U.S. Patent
Method and system for directing requests for content to a content server based on network performance. (U.S. patent number 7555542) Ayers M, Black BJ, Brown C, Carlson J, Cohn D, Laird S, Miller J, Ronen O, Schachter P, Stiffelman O, Ramsey S  
U.S. Patent
Method and system for optimizing routing through multiple available Internet route providers. (U.S. patent number 6981055) Ahuja A, Ayers M, Black B, Brown C, Cohn DT, Ramsey S, Ronen O, Schachter PJ, Stiffelman OB, Wheeler CD
Nonequilibrium dynamics of quantum fields in inflationary cosmology (PhD Dissertation, University of Maryland) Ramsey SA (PhD advisor: Bei-Lok Hu) [link]
Some statistics for measuring large-scale structure Brandenberger RH, Kaplan DM, Ramsey SA [link]


Current and future teaching and guest lecturing

Fall 2018 Instructor CS 340 Introduction to databases
Spring 2018 TBD TBD TBD
Fall 2017 Instructor CS 446/546 Networks in computational biology

Past teaching and guest lecturing

Spring 2017 Instructor 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 Instructor CS 446/519 Networks in computational biology
Fall 2016 Guest Lecturer VMB 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 Co-Instructor VMB 670 Introduction to Systems Biology
Winter 2016 Discussion Leader VMB 741 Veterinary Integrated Problem Solving
Fall 2015 Instructor CS 446 Biological Networks
Fall 2015 Gest Lecturer VMB 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 Co-Instructor MCB 555 Genome Expression
Winter 2015 Guest lecturer BB 485/585 Applied Bioinformatics
Fall 2014 Guest Speaker MCB 525 Quantitative biology
Fall 2014 Instructor CS 419/519 Selected Topics in Computer ScienceNetwork Methods in Bioinformatics
Fall 2014 Guest Lecturer VMB 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

Software and tools

  • Code for our 2008 article on using the time-lagged correlation to analyze time-course gene expression data.

Supplementary material for lab publications

Graduate programs that I work with

I am approved to serve as major professor (i.e., thesis advisor) for graduate students in any of six graduate programs: Computer Science, Electrical and Computer Engineering, Molecular and Cellular Biology, Comparative Health Sciences, Bioengineering, or Biological Data Sciences. If you have a PhD project idea you wish to discuss, please feel free to contact me (see "contact" tab above).

We value diversity

Oregon State University is an Equal Opportunity Employer and the Ramsey Lab group members respect, value, and support diversity in the workplace and in the broader OSU community.



Office (Biomedical Sciences)


U.S. Post

Stephen Ramsey
Oregon State University
Department of Biomedical Sciences
106 Dryden Hall
Corvallis, OR 97331-4801


Stephen Ramsey
Oregon State University
Department of Biomedical Sciences
105 Magruder Hall
Corvallis, OR 97331-4801

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© 2013–2017 Stephen Ramsey.    The orange OSU logo is a trademark of Oregon State University and is used with permission.