gene regulation in mouse macrophages

Ramsey Laboratory:  Computational systems biology

gene icon We use the tools of bioinformatics, artificial intelligence, and systems biology to understand the molecular basis of diseases and to advance precision medicine. We are currently working on research projects in the areas of cancer, wound healing, drug repositioning, and genomics. Current and past sponsors include NIH, NSF, PhRMA, ACF, Amazon, MRFO, and the National Center for Advancing Translational Sciences.

Lab members have gone on to jobs at Scripps, Microsoft, Meta, IBM, HP, and the Allen Institute.

 

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 in bioinformatics, first with Maynard Olson at the University of Washington Genome Center and then with 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 with 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 Quantitative Life Sciences
  • Senior Member, International Society for Computational Biology
  • Wayne & Gladys Valley Foundation Fellow in Biohealth
Sydney Bolanos
Graduate Student
 
 
 
Sydney Bolanos is a DVM-MS student in comparative health sciences, co-advised with Dr. Jennifer Johns. She has a bachelors degree in biology from Grand Canyon University. She is working on an immunology project using single-cell transcriptome analysis.
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.
Aravind Kolli
Graduate Student
 
 
 
Aravind Kolli is a graduate student in computer science. He has a BTech in CS from Siddharth Institute of Technology. He is working on the NIBIB wound monitor project.
Liliana Acevedo
Analyst Programmer 2
 
 
 
Liliana has a BS in CS from Humboldt State University. She is working on the NCATS Translator project.
Noël Lefevre
Graduate Assistant
 
 
 
Noël Lefevre is a graduate student in bioengineering. She has a dual degree in CS and neuroscience from Michigan State University. She will be working on the NIDCR saliva bioassay project. She is being co-advised by Dr. Elain Fu.
Sundareswar Pullela
Graduate Assistant
 
 
 
Sundareswar Pullela is a graduate student in computer science. He has a bachelor's in CS from Raghu Engineering College. He is working on the NCATS Translator project.
Thuy Dien
Undergraduate
 
 
 
Thuy Dien is an undergraduate student majoring in BioResource Research and Biology with a minor in Chemistry. She is working on a project to study the role of microRNAs in feline injection-site sarcoma.

Collaborators

We work with researchers across OSU and at Institute for Systems Biology, Penn State, OHSU, and UAB.

Former lab members  

Member
Position in Ramsey Lab
Now at
Jichen Yang
postdoctoral scholar
Microsoft
Yao Yao
graduate student (PhD)
Scripps
Zheng Liu
graduate student (PhD)
Meta
Qi Wei
graduate student (PhD)
Institute for Systems Biology
Meghamala Sinha
graduate student (PhD)
Scripps
Steven Carrell
graduate student (PhD)
OSU CQLS
Tanjin Xu
graduate student (masters)
Salesforce
Jun He
graduate student (masters)
Pure Storage
Finn Womack
graduate student (masters)
Microsoft
Satpreet Singh
graduate research assistant
Meta
Deqing Qu
graduate research assistant
finance industry
Kavinda Senewiratne
graduate research assistant
OSU Robotics
Ujjval Kumaria
graduate research assistant
HP
Carter Peene
Faculty Research Assistant
Allen Institute
Daniel Lin
Faculty Research Assistant
Allen Institute
Holly Arnold
Faculty Research Assistant
OSU CCVM intern
Benjamin Weeder
MPH Biostatistics Intern
OHSU (PhD program)
Mudra Choudhury
undergraduate honors student
UCLA (PhD program)
Alvin Yu
undergraduate honors student
HP
Amita Kashyap
undergraduate honors student
U. Colorado (MD-PhD program)
Lindsey Kvarfordt
undergraduate project assistant
BioFire
Tim Yoon
undergraduate fellow
Harvest Group
E. C. Wood
high school project assistant
Stanford (CS program)
Veronica Flores
high school intern
Santa Clara Univ. (CS program)
Sahana Shah
high school intern
OSU Honors College

 

Lab News

Oct 18, 2022
I am honored and delighted to have been selected as one of ten Wayne & Gladys Valley Foundation Fellows in Biohealth. Thank you, Valley Foundation and OSU Research Office!
Sep 29, 2022
Our article on RTX-KG2 is now out in BMC Bioinformatics. This project was a great collaborative effort with researchers from Penn State University (David Koslicki and team), Institute for Systems Biology (Eric Deutsch, Jared Roach, and team), and the many members of the NCATS Biomedical Data Translator consortium. Congratulations to first authors E. C. Wood and Amy Glen!
Sep 15, 2022
We welcome two new students to the lab this fall, Sundar Pullela and Noël Lefevre!
Sep 14, 2022
Steven Carrell passed his PhD final exam! Congratulations, Dr. Carrell!
Jun 1, 2022
We welcome Aravind Kolli to the Ramsey Lab team! Aravind will be working on the wound monitor project.
May 20, 2022
Congratulations Steven Carrell for winning the CCVM 2022 Graduate Student Research Award!
Nov 4, 2021
This fall we welcome two new members to the lab, Thuy Dien and Carter Peene!

Lab Publications

Bibliometric data and pre-2004 publications (in physics) are available on Google Scholar.

J Appl Electrochem
2022
Field-use device for the electrochemical quantification of carbamazepine levels in a background of human saliva
Wentland L, Cook J, Minzlaff J, Ramsey SA, Johnston M, Fu E
in press
Infect Immunity
2022
Genomic analysis of MSM-rectal Chlamydia trachomatis isolates identifies predicted tissue-tropic lineages generated by intraspecies lateral-gene-transfer-mediated evolution
Suchland R*, Carrell S*, Ramsey SA, Hybiske K, Debrine A, Sanchez J, Celum C, Rockey DD
 
Frontiers Artif Intellig
2022
The precision medicine process for treating rare disease using the artificial intelligence tool mediKanren
Foksinska A, Crowder CM, Crouse AB, Hennrikson J, Byrd WE, Rosenblatt G, Patton MJ, He K, Tran-Nguyen TK, Zheng M, Ramsey SA, Amin N, Osborne J, Might M, Barnes S, Chen M, Crumbley ME, Eckenrode M, Fargason CA, Fehrmann N, Huls F, Jarrell M, Jenkins L, McCalley M, Osborn T, Pollard E, Ruckra S, Southern NT, Tinglin J, Whitlock JH
 
bioRxiv (preprint)
2022
ARAX: a graph-based modular reasoning tool for translational biomedicine
Glen AK*, Ma C*, Mendoza L, Womack F, Wood EC, Sinha M, Acevedo L, Kvarfordt LG, Peene RC, Liu S, Hoffman AS, Roach JC, Deutsch EW*, Ramsey SA*, Koslicki D*
 
Clin Transl Sci
2022
Biolink Model: a Universal Schema for Knowledge Graphs in Biomedical and Translational Science
Unni D, Moxon S, Bada M, Brush M, Bruskiewich R, Caufield J, Clemons P, DanĨik V, Dumontier M, Fecho K, Glusman G, Harris N, Joshi A, Putman T, Ramsey SA, Shefchek K, Solbrig H, Soman K, Qin G, Hadlock J, Thessen A, Haendel M, Bizon C, Mungall C
 
BMC Bioinform
2022
RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine
Wood EC, Glen AK, Kvarfordt LG, Womack F, Acevedo L, Yoon TS, Ma C, Flores V, Sinha M, Chodpathumwan Y, Termehchy A, Roach JC, Mendoza L, Hoffman AS, Deutsch EW, Koslicki D, Ramsey SA
 
Inform Med Unlocked
2021
An approach for open multivariate analysis of integrated clinical and environmental exposures data
Fecho K, Haaland P, Krishnamurthy A, Lan B, Ramsey SA, Schmitt PL, Sharma P, Sinha M, Xu H
 
BMC Bioinform
2021
Predicting chemotherapy response using a variational autoencoder approach
Wei Q, Ramsey SA
 
Nutrients
2021
Vitamin E deficiency disrupts gene expression networks during zebrafish development
Head B, Ramsey SA, Kioussi C, Tanguay RL, Traber MG
 
ACM SIGMOD
2021
Structural Generalizability: The Case of Similarity Search
Chodpathumwan Y, Termehchy A, Ramsey SA, Shrestha A, Glen A, Liu Z
 
AAAI MAKE
2021
Using a general prior knowledge graph to improve data-driven causal network learning
Sinha M, Ramsey SA
 
eLife
2021
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
 
PLOS ONE
2021
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
 
J Vet Int Med
2020
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
2020
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
2020
CERENKOV3: Clustering and molecular network-derived features improve computational prediction of functional noncoding SNPs
Yao Y, Ramsey SA
 
Methods Mol Biol
2019
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
2019
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
2019
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
2019
Pooling vs. voting: an empirical study of learning causal structures
Sinha M, Tadepalli P, Ramsey SA
 
JCI Insight
2019
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
2019
CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features
Yao Y, Liu Z, Wei Q, Ramsey SA
 
Pac Symp Biocomp
2018
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
2018
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
2018
Toward A Universal Biomedical Data Translator
The Biomedical Data Translator Consortium
 
Clin Transl Sci
2018
The Biomedical Data Translator Consortium: Conception, Culture, and Community
The Biomedical Data Translator Consortium
 
Translat Oncol
2018
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
2018
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
2018
Differential gene regulatory networks in development and disease
Singh AJ, Ramsey SA, Filtz TM, Kioussi C.
 
Methods Mol Biol
2018
A Method for cross-species visualization and analysis of RNA-Sequence data. Chapter in the book Systems Biology (Mariano Bizzarri (ed.)
Ramsey SA
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
2017
CERENKOV: Computational elucidation of the regulatory noncoding variome
Yao Y*, Liu Z*, Singh S, Wei Q, Ramsey SA
 
J Clinical Investigation
2017
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
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
 
Interdis 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
2016
Exploration of regression models for cancer noncoding mutation recurrence
Xu T, Ramsey SA
 
Analyt Chem
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 engineering 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
 
Arteriosc 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 Exp Med
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
Meth 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
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
Proc Natl Acad Sci
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
Analyt Chim 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
Molec Syst Biol
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
 
[model]
[Corrected suppl. note]
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
 
Phil 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
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
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
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

 

Current and future teaching

Spring 2023
Instructor
VMB 652
Cancer systems biology
Winter 2023
Instructor
CS 446/546
Networks in computational biology

Graduate programs that I work with

 

Outreach

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.

Phenotyping activity based on tasting phenylthiocarbamide.
Learn about chromosomes by reconstructing a karyotype.
Learn about genetic conditions by playing Genetic4.
Sequence proteins in fossils using Mass Spectrometry!
What types of protein are in this dinosaur fossil?
Compare dinosaur proteins to modern organisms'
Should we bring back extinct species? An ethics activity.
A Mendelian genetics activity, for elementary school students.
A forensic genomics activity, for middle school students.
A genetics activity, for high school students.
A genetics activity, for elementary school students.

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

Impact

We have hosted four high school summer interns and 17 undergraduate researchers in our lab. We have also hosted science activities at three SMILE teacher training workshops.

Open source

We generally open-source the software that we have developed in our projects; see our lab GitHub page.

 

Contact

 
106 Dryden Hall
Corvallis, OR 97331-4801
 
105 Magruder Hall
Corvallis, OR 97331-4801

 

I am open to both in-person and virtual professional speaking opportunities; reach out via email.