Bibliometric data and pre-2004 publications (in physics) are available on Google Scholar.
Vet Comparat Oncol
2024
Comparative transcriptomes of canine and human prostate cancers identify mediators of castration resistance
Riveros Angel M,
Séguin B,
Löhr CV,
Beer TM,
Feliciano J,
Ramsey SA,
Thomas G
J Appl Electrochem
2024
Electrochemical signal quantification in saliva: Investigation of signal analysis methods
Lefevre N,
Khederlou K,
Ramsey SA,
Fu E
Computation
2024
Predicting time-to-healing from a digital wound image: a hybrid neural network and decision tree approach improves performance
Kolli A,
Wei Q,
Ramsey SA
Chemosensors
2023
Progress on Electrochemical Sensing of Pharmaceutical Drugs in Complex Biofluids
Fu E,
Khederlou K,
Lefevre N,
Ramsey SA,
Johnston ML,
Wentland L
Clin Transl Sci
2023
An Approach for Collaborative Development of
a Federated Biomedical Knowledge Graph–Based Question-Answering
System: Question-of-the-Month Challenges
Fecho K, Bizon C, Issabekova T, Moxon S,
Thessen A, Abdollahi S, Baranzini S, Belhu B,
Chung L, Crouse A, Duby M, Ferguson S,
Friedman J, Forero L, Foksinska A, Gardner V,
Glusman G, Hadlock J, Hanspers K, Hinderer E,
Hobbs C, Hyde G, Huang S, Koslicki D,
Mease P, Ramsey SA, Rubin I, Shalev A,
Schurman S, Smith B, Soman K, Stemann S,
Su A, Ta C, Watkins P, Williams M, Wu C,
Xu C
Bioinformatics
2023
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*
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
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
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,
Dančik 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
Cancer Cell Int
2021
Exosomal proteomic signatures correlate with drug resistance and carboplatin treatment outcome in a spontaneous model of canine osteosarcoma
Weinman MA,
Ramsey SA,
Leeper HJ,
Brady JV,
Schlueter A,
Stanisheuski S,
Maier CS,
Miller T,
Ruby CE,
Bracha S
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
2020
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
2019
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
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
IET Systems Biology
2004
Evolution of "design" principles in biochemical networks
de Atauri P, Orrell D, Ramsey S, Bolouri H
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.
We sincerely thank our current and past research sponsors, which
include NIH (NHLBI, NIBIB, NIDCR, NIAID, NIGMS, and NCATS), NSF,
PhRMA, Amazon.com, the Medical Research Foundation, the Animal Cancer
Foundation, the Valley Foundation, and the Research to the People
Foundation.
![[studio photo]](sramsey_studio.jpg){kind=link}