M
Marc T. Facciotti
Researcher at University of California, Davis
Publications - 71
Citations - 3953
Marc T. Facciotti is an academic researcher from University of California, Davis. The author has contributed to research in topics: Bacteriorhodopsin & Genome. The author has an hindex of 27, co-authored 70 publications receiving 3646 citations. Previous affiliations of Marc T. Facciotti include University of Washington & Tufts Medical Center.
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Journal ArticleDOI
The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
Richard Bonneau,Richard Bonneau,David J Reiss,Paul Shannon,Marc T. Facciotti,Leroy Hood,Nitin S. Baliga,Vesteinn Thorsson +7 more
TL;DR: The Inferelator uses regression and variable selection to identify transcriptional influences on genes based on the integration of genome annotation and expression data, and successfully predicted Halobacterium's global expression under novel perturbations with predictive power similar to that seen over training data.
Journal ArticleDOI
An integrated pipeline for de novo assembly of microbial genomes.
TL;DR: An assembly pipeline called A5 (Andrew And Aaron's Awesome Assembly pipeline) is presented that simplifies the entire genome assembly process by automating these stages, by integrating several previously published algorithms with new algorithms for quality control and automated assembly parameter selection.
Journal ArticleDOI
Evaluation of algorithm performance in ChIP-seq peak detection.
TL;DR: Eleven different peak calling programs are compared on common empirical, transcription factor datasets and their sensitivity, accuracy and usability are measured to provide an unbiased critical assessment of available technologies and should assist researchers in choosing a suitable tool for handling ChIP-seq data.
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A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell
Richard Bonneau,Richard Bonneau,Marc T. Facciotti,David J Reiss,Amy K. Schmid,Min Pan,Amardeep Kaur,Vesteinn Thorsson,Paul Shannon,Michael H. Johnson,J. Christopher Bare,William J.R. Longabaugh,Madhavi Vuthoori,Kenia Whitehead,Aviv Madar,Lena Suzuki,Tetsuya Mori,Dong Eun Chang,Jocelyne DiRuggiero,Carl Hirschie Johnson,Leroy Hood,Nitin S. Baliga,Nitin S. Baliga +22 more
TL;DR: This study supports the claim that the high degree of connectivity within biological and EF networks will enable the construction of similar models for any organism from relatively modest numbers of experiments.
Journal ArticleDOI
Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea
Nitin S. Baliga,Richard Bonneau,Marc T. Facciotti,Min Pan,Gustavo Glusman,Eric W. Deutsch,Paul Shannon,Yulun Chiu,Rueyhung Sting Weng,Rueichi Richie Gan,Pingliang Hung,Shailesh V. Date,Shailesh V. Date,Edward M. Marcotte,Leroy Hood,Wailap Victor Ng +15 more
TL;DR: In comparing the physiologies of the two halophilic archaea, in addition to the expected extensive similarity, it is discovered several differences in their metabolic strategies and physiological responses such as distinct pathways for arginine breakdown in each halophile.