J
James M. McCollum
Researcher at Virginia Commonwealth University
Publications - 19
Citations - 1379
James M. McCollum is an academic researcher from Virginia Commonwealth University. The author has contributed to research in topics: Noise & Stochastic simulation. The author has an hindex of 12, co-authored 19 publications receiving 1272 citations. Previous affiliations of James M. McCollum include University of Tennessee & Oak Ridge National Laboratory.
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Journal ArticleDOI
Transcriptional burst frequency and burst size are equally modulated across the human genome
Roy D. Dar,Brandon S. Razooky,Brandon S. Razooky,Brandon S. Razooky,Abhyudai Singh,Thomas V. Trimeloni,James M. McCollum,Christopher Cox,Michael L. Simpson,Michael L. Simpson,Leor S. Weinberger,Leor S. Weinberger,Leor S. Weinberger +12 more
TL;DR: Time-lapse fluorescence microscopy is used to analyze 8,000 individual human genomic loci and finds that at virtually all loci, episodic bursting—as opposed to constitutive expression—is the predominant mode of expression.
Journal ArticleDOI
Gene network shaping of inherent noise spectra
Derek W. Austin,Derek W. Austin,Michael S. Allen,James M. McCollum,Roy D. Dar,Gary S. Sayler,Nagiza F. Samatova,Christopher Cox,Michael L. Simpson,Michael L. Simpson +9 more
TL;DR: Noise spectral measurements provide mechanistic insights into gene regulation, as perturbations of gene circuit parameters are discernible in the measured noise frequency ranges, and suggest that noise spectral measurements could facilitate the discovery of novel regulatory relationships.
Journal ArticleDOI
The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior
TL;DR: This work examines the performance of different versions of Gillespie's stochastic simulation algorithm when applied to several biochemical models and proposes a new algorithm called the sorting direct method that maintains a loosely sorted order of the reactions as the simulation executes.
Proceedings ArticleDOI
Gene network shaping of inherent noise spectra
Derek W. Austin,Michael S. Allen,James M. McCollum,Roy D. Dar,Gary S. Sayler,Nagiza F. Samatova,Christopher Cox,Michael L. Simpson,Michael L. Simpson +8 more
TL;DR: Noise spectral measurements provide mechanistic insights into gene regulation as perturbations of gene circuit parameters are discernible in the measured noise frequency ranges, and suggest that noise spectral measurements could facilitate the discovery of novel regulatory relationships.
Journal ArticleDOI
Using noise to probe and characterize gene circuits
Christopher Cox,James M. McCollum,Michael S. Allen,Roy D. Dar,Roy D. Dar,Michael L. Simpson,Michael L. Simpson +6 more
TL;DR: The noise regulatory vector is introduced as a generalized framework for making inferences concerning the structure and biokinetic rates of a gene circuit from its noise autocorrelation function.