gene regulation in mouse macrophages

Ramsey Laboratory at Oregon State University

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 (including 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
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 of the Knight Cancer Institute at OHSU.
Amita Kashyap
Undergraduate Student
 
Amita is a University Honors College student majoring in BioResource Research with an option in Bioinformatics/Genomics.
Zheng Liu
Graduate Student
 
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
 
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
 
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
 
Alvin is a University Honors College student majoring in chemical engineering, who has worked as a summer intern at Genentech.

Current project collaborators

OSU Department of Mathematics
biomedical reasoning engine
Institute for Systems Biology
biomedical reasoning tool
New York University School of Medicine
atherosclerosis
OSU College of Veterinary Medicine
cancer
OSU College of Veterinary Medicine
cancer
OSU School of Biological and Population Health Sciences
genetic epidemiology
OSU School of Electrical Engineering and Computer Science
machine learning
OSU School of Chemical, Biological, and Environmental Engineering
bioengineering for global health applications
OSU College of Veterinary Medicine and College of Pharmacy
gene regulation, mouse models
OSU Department of Botany and Plant Pathology
genome sequencing project
Center for Infectious Disease Research
epigenetics, innate immunity

[show lab alumni ...]

Lab Alumni

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

Nov. 2, 2017
Steve 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
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, 2016
Steve 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
Steve 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
Steve 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
Steve 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
Steve is appointed an affiliate member of the Knight Cancer Institute at OHSU, in the Quantitative Oncology Research Program.
June 1, 2016
Steve 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 College of Veterinary Medicine.
May 18, 2016
Mudra Choudhury successfully defends her University Honors College / BioResource Resesarch thesis. Congratulations, Mudra!
Mar. 29, 2016
Steve 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
Steve gave the OSU Physics Colloquium.
Jan. 26, 2016
Steve gives a presentation on bladder cancer at a joint OHSU-OSU workshop on early cancer detection, at OHSU in Portland.
Jan. 1, 2016
Steve receives a Research Starter Grant award from the PhRMA Foundation (Informatics Program). Thank you, PhRMA Foundation!
Dec. 17, 2015
Steve 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
Steve is designated a Senior Member of the International Society for Computational Biology (ISCB).
Nov. 23, 2015
The Beaver Genome Project is successfully crowdfunded! The project's progress will be documented on the Beaver Genome Project Website.
Nov. 12, 2015
Steve 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 crowdfunding 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 VMB671.
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 lab.saramsey.org.
May 2013
Stephen 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.

Cell Molec Life Sci
2017
Differential gene regulatory networks in development and disease
Singh AJ, Ramsey SA, Filtz TM, Kioussi C.
[accepted]
PLOS ONE
2017
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
2017
CERENKOV: Computational elucidation of the regulatory noncoding variome
Yao Y*, Liu Z*, Singh S, Wei Q, Ramsey SA
J. Clinical Investigation
2017
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
Genes Chromosom Cancer.
2017
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.
2016
Identifying cell type-specific transcription factors by integrating ChIP-seq and eQTL data–application to monocyte gene regulation
Choudhury M, Ramsey SA
Interdiscip Sci Comp Life Sci.
2016
A computational systems biology approach for identifying candidate drugs for repositioning for cardiovascular disease
Yu AZ, Ramsey SA
Bioinform Biol Insights.
2016
An empirical prior improves accuracy for Bayesian estimation of transcription factor binding site frequencies within gene promoters
Ramsey SA
ACM BCB Proceedings
2016
Exploration of regression models for cancer noncoding mutation recurrence
Xu T, Ramsey SA
Analytical Chemistry
2016
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
Bioinformatics
2015
A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites
Yang J, Ramsey SA
Bioinform Biol Insights.
2015
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
2015
An LXR-NCOA5 complex directs inflammatory crosstalk-dependent repression of cholesterol efflux
Gillespie MA, Gold E, Ramsey SA, Podolsky I, Aderem A, Ranish J
Arterioscler Thromb Vasc Biol.
2015
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
2014
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
2014
Multiscale representation of genomic signals
Knijnenburg TA, Ramsey SA, Berman BP, Kennedy KA, Smit AFA, Wessels LFA, Laird PW, Aderem A, Shmulevich I
PLoS ONE
2013
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
2012
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.
2012
Asymmetric positive feedback loops reliably control biological responses
Ratushny AV, Saleem RA, Sitko K, Ramsey SA, Aitchison JD
J. Biol Chem.
2011
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.
2011
Mathematical modeling of biomolecular network dynamics
Ratushny AV, Ramsey SA, Aitchison JD
Microfluidics & Nanofluidics
2011
Transport in two-dimensional paper networks
Fu E, Ramsey SA, Kauffman P, Lutz B, Yager P
Analytical Chemistry
2011
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
2010
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
Bioinformatics
2010
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
2010
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
2010
A systems biology approach to understanding atherosclerosis
Ramsey SA, Gold ES, Aderem A
Analytical Chemistry
2009
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
2009
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.
2009
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
2008
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.
2008
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]
Corrected
Table S17.
Proc Natl Acad Sci U S A.
2008
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
2007
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
2007
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
PLoS ONE
2007
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.
2007
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.
2006
One-dimensional surface plasmon resonance imaging system using wavelength interrogation
Fu E, Ramsey SA, Thariani R, Yager P
Nature Genetics
2006
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
2006
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
Philos Trans R Soc Lond B
2006
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.
2005
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.
2005
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.
2005
Dizzy: Stochastic simulations of large-scale genetic regulatory networks
Ramsey S, Orrell D, Bolouri H
[link]
(Supplement: [link])
Bioinformatics
2005
A method for estimating stochastic noise in large genetic regulatory networks
Orrell D, Ramsey S, de Atauri P, Bolouri H
Biochemical Journal
2005
Is the regulation of galactose-1-phosphate tuned against gene expression noise?
de Atauri P, Orrell D, Ramsey S, Bolouri H
Syst Biol (Stevenage).
2004
Evolution of "design" principles in biochemical networks
de Atauri P, Orrell D, Ramsey S, Bolouri H

Other Publications or Works

Methods Mol Biol.
2017
A Method for cross-species visualization and analysis of RNA-Sequence data. Chapter in the book Systems Biology (Mariano Bizzarri (ed.)
Ramsey S
U.S. Patent
2009
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
2005
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
 
arXiv.org
1997
Nonequilibrium dynamics of quantum fields in inflationary cosmology (PhD Dissertation, University of Maryland)
Ramsey SA (PhD advisor: Bei-Lok Hu)
arXiv.org
1993
Some statistics for measuring large-scale structure
Brandenberger RH, Kaplan DM, Ramsey SA

[show older publications ...]

 

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

Int J Theo Phys.
2001
Interacting field theories in Robertson-Walker spacetimes: analytic approximations
Molina-Paris C, Anderson PR, Ramsey SA
Physical Review D
2000
One-loop λφ4theory in Robertson-Walker spacetimes: adiabatic regularization and analytic approximation
Molina-Paris C, Anderson PR, Ramsey SA
Physical Review D
2000
Hydrodynamic transport functions from quantum kinetic theory
Calzetta EA, Hu BL, Ramsey SA
Physical Review D
1999
Defect formation and Critical Dynamics in the Early Universe
Stephens GJ, Calzetta EA, Hu BL, Ramsey SA
Int J Theo Phys.
1999
Nonequilibrium dynamics of quantum fields in inflationary cosmology
Ramsey SA
Physical Review D
1998
Nonequilibrium inflaton dynamics and reheating. II. Fermion production, noise, and stochasticity
Ramsey SA, Hu BL, Stylianopoulos AM
Physical Review D
1997
Nonequilibrium inflaton dynamics and reheating: Back reaction of parametric particle creation and curved spacetime effects
Ramsey SA, Hu BL
Physical Review D
1997
O(N) Quantum fields in curved spacetime
Ramsey SA, Hu BL

Current and future teaching and guest lecturing

Fall 2018
Instructor
CS 340
Introduction to databases
Spring 2018
Instructor
VMB 651
Cancer systems biology
Fall 2017
Instructor
Networks in computational biology

Past teaching and guest lecturing

Fall 2017
Guest Lecturer
VMB 671
MCB 671
Molecular Tools
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
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
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
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
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
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

Software and tools

Supplementary material for lab publications

Graduate programs that I work with

I am able to serve as a 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, and Biological Data Sciences. If you have a PhD project idea in the area of computational biology that you wish to discuss, please feel free to contact me (see "contact" tab above).

Diversity

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

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.

Contact

Telephone number:
Laboratory:
U.S. Postal address:

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

UPS/Fedex address:

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

Secure email contact info:
GitHub:
Twitter:
Google Hangout:
ramseyst@oregonstate.edu

 

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