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Matthew W. Peterson
Matthew W. Peterson
Paradigm4
Verified email at paradigm4.com
Title
Cited by
Cited by
Year
The Mycobacterium tuberculosis regulatory network and hypoxia
JE Galagan, K Minch, M Peterson, A Lyubetskaya, E Azizi, L Sweet, ...
Nature 499 (7457), 178-183, 2013
4142013
Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis
AM McGuire, B Weiner, ST Park, I Wapinski, S Raman, G Dolganov, ...
BMC genomics 13 (1), 1-27, 2012
922012
Genome-Wide Characterization of Light-Regulated Genes in Neurospora crassa
C Wu, F Yang, KM Smith, M Peterson, R Dekhang, Y Zhang, J Zucker, ...
G3: Genes, Genomes, Genetics 4 (9), 1731-1745, 2014
842014
Comprehensive Definition of the SigH Regulon of Mycobacterium tuberculosis Reveals Transcriptional Control of Diverse Stress Responses
JD Sharp, AK Singh, ST Park, A Lyubetskaya, MW Peterson, ALC Gomes, ...
PLoS One 11 (3), e0152145, 2016
372016
VX hydrolysis by human serum paraoxonase 1: a comparison of experimental and computational results
MW Peterson, SZ Fairchild, TC Otto, M Mohtashemi, DM Cerasoli, ...
PLoS One 6 (5), e20335, 2011
342011
Protein–protein docking: overview and performance analysis
K Wiehe, MW Peterson, B Pierce, J Mintseris, Z Weng
Protein Structure Prediction, 283-314, 2008
342008
Role of intragenic binding of cAMP responsive protein (CRP) in regulation of the succinate dehydrogenase genes Rv0249c-Rv0247c in TB complex mycobacteria
GS Knapp, A Lyubetskaya, MW Peterson, ALC Gomes, Z Ma, JE Galagan, ...
Nucleic acids research 43 (11), 5377-5393, 2015
302015
The Neurospora Transcription Factor ADV-1 Transduces Light Signals and Temporal Information to Control Rhythmic Expression of Genes Involved in Cell Fusion
R Dekhang, C Wu, KM Smith, TM Lamb, M Peterson, EL Bredeweg, ...
G3: Genes, Genomes, Genetics 7 (1), 129-142, 2017
272017
Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction
ALC Gomes, T Abeel, M Peterson, E Azizi, A Lyubetskaya, L Carvalho, ...
Genome research 24 (10), 1686-1697, 2014
262014
Characterization of a cAMP responsive transcription factor, Cmr (Rv1675c), in TB complex mycobacteria reveals overlap with the DosR (DevR) dormancy regulon
S Ranganathan, G Bai, A Lyubetskaya, GS Knapp, MW Peterson, ...
Nucleic acids research 44 (1), 134-151, 2016
252016
Nephele: genotyping via complete composition vectors and MapReduce
ME Colosimo, MW Peterson, S Mardis, L Hirschman
Source code for biology and medicine 6 (1), 1-10, 2011
252011
Computational characterization of how the VX nerve agent binds human serum paraoxonase 1
SZ Fairchild, MW Peterson, A Hamza, CG Zhan, DM Cerasoli, WE Chang
Journal of molecular modeling 17 (1), 97-109, 2011
232011
Transcription factor binding site mapping using ChIP-Seq
S Jaini, A Lyubetskaya, A Gomes, M Peterson, S Tae Park, S Raman, ...
Microbiology Spectrum 2 (2), 2.2. 11, 2014
172014
TreeViewJ: An application for viewing and analyzing phylogenetic trees
MW Peterson, ME Colosimo
Source Code for Biology and Medicine 2 (1), 1-4, 2007
132007
Co-design in synthetic biology: a system-level analysis of the development of an environmental sensing device
DA Ball, MW Lux, RR Graef, MW Peterson, JD Valenti, J Dileo, J Peccoud
Biocomputing 2010, 385-396, 2010
72010
Transcription factor binding site mapping using ChIPSeq. Microbiol Spectr 2: doi: 10.1128/microbiolspec
S Jaini, A Lyubetskaya, A Gomes, M Peterson, ST Park, S Raman, ...
MGM2-0035-2013, 2014
62014
Open-target sparse sensing of biological agents using DNA microarray
M Mohtashemi, DK Walburger, MW Peterson, FN Sutton, HB Skaer, ...
BMC bioinformatics 12 (1), 1-11, 2011
62011
Hallmarks of human-machine collaboration: a framework for assessment in the darpa communicating with computers program
R Kozierok, J Aberdeen, C Clark, C Garay, B Goodman, T Korves, ...
arXiv preprint arXiv:2102.04958, 2021
42021
Pathogen metadata platform: software for accessing and analyzing pathogen strain information
WE Chang, MW Peterson, CD Garay, T Korves
BMC bioinformatics 17 (1), 1-6, 2016
42016
Assessing pathogens for natural versus laboratory origins using genomic data and machine learning
T Korves, C Garay, HA Carleton, A Sabol, E Trees, MW Peterson
BioRxiv, 079541, 2016
22016
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Articles 1–20