Publications

Found 23 results
Filters: Author is Reiss, D. J.  [Clear All Filters]
2012
Rustad TR, Minch KJ, Brabant W, Winkler JK, Reiss DJ, Baliga NS, Sherman DR.  2012.  Global analysis of mRNA stability in Mycobacterium tuberculosis. Nucleic acids research.
2011
Turkarslan S, Reiss DJ, Gibbins G, Su WL, Pan M, Bare JC, Plaisier CL, Baliga NS.  2011.  Niche adaptation by expansion and reprogramming of general transcription factors. Molecular systems biology. 7:554.
Yoon SH, Reiss DJ, Bare JC, Tenenbaum D, Pan M, Slagel J, Moritz RL, Lim S, Hackett M, Menon AL et al..  2011.  Parallel evolution of transcriptome architecture during genome reorganization. Genome research. 21:1892-904.
2010
Kaur A, Van PT, Busch CR, Robinson CK, Pan M, Pang WL, Reiss DJ, DiRuggiero J, Baliga NS.  2010.  Coordination of frontline defense mechanisms under severe oxidative stress. Mol Syst Biol. 6:393.
Bare JC, Koide T, Reiss DJ, Tenenbaum D, Baliga NS.  2010.  Integration and visualization of systems biology data in context of the genome. BMC Bioinformatics. 11:382.
Facciotti MT, Pang WL, Lo FY, Whitehead K, Koide T, Masumura K, Pan M, Kaur A, Larsen DJ, Reiss DJ et al..  2010.  Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis. BMC Syst Biol. 4:64.
Youn A, Reiss DJ, Stuetzle W.  2010.  Learning transcriptional networks from the integration of ChIP-chip and expression data in a non-parametric model. Bioinformatics. 26:1879-86.
2009
Koide T, Reiss DJ, Bare JC, Pang WL, Facciotti MT, Schmid AK, Pan M, Marzolf B, Van PT, Lo FY et al..  2009.  Prevalence of transcription promoters within archaeal operons and coding sequences. Mol Syst Biol. 5:285.
Schmid AK, Reiss DJ, Pan M, Koide T, Baliga NS.  2009.  A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability. Mol Syst Biol. 5:282.
2008
Rubio ED, Reiss DJ, Welcsh PL, Disteche CM, Filippova GN, Baliga NS, Aebersold R, Ranish JA, Krumm A.  2008.  CTCF physically links cohesin to chromatin. Proc Natl Acad Sci U S A. 105:8309-14.
Van PT, Schmid AK, King NL, Kaur A, Pan M, Whitehead K, Koide T, Facciotti MT, Goo YA, Deutsch EW et al..  2008.  Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage. J Proteome Res. 7:3755-64.
Reiss DJ, Facciotti MT, Baliga NS.  2008.  Model-based deconvolution of genome-wide DNA binding. Bioinformatics. 24:396-403.
2007
Schmid AK, Reiss DJ, Kaur A, Pan M, King N, Van PT, Hohmann L, Martin DB, Baliga NS.  2007.  The anatomy of microbial cell state transitions in response to oxygen. Genome Res. 17:1399-1413.
Avila-Campillo I, Drew K, Lin J, Reiss DJ, Bonneau R.  2007.  BioNetBuilder: automatic integration of biological networks. Bioinformatics. 23:392-3.
Facciotti MT, Reiss DJ, Pan M, Kaur A, Vuthoori M, Bonneau R, Shannon P, Srivastava A, Donohoe SM, Hood LE et al..  2007.  General transcription factor specified global gene regulation in archaea. Proc Natl Acad Sci U S A. 104:4630-5.
Bonneau R, Facciotti MT, Reiss DJ, Schmid AK, Pan M, Kaur A, Thorsson V, Shannon P, Johnson MH, Bare JC et al..  2007.  A predictive model for transcriptional control of physiology in a free living cell. Cell. 131:1354-65.
2006
Shannon P, Reiss DJ, Bonneau R, Baliga NS.  2006.  The Gaggle: an open-source software system for integrating bioinformatics software and data sources. BMC Bioinformatics. 7:176.
Bonneau R, Reiss DJ, Shannon P, Facciotti M, Hood L, Baliga NS, Thorsson V.  2006.  The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol. 7:R36.
Reiss DJ, Baliga NS, Bonneau R.  2006.  Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformatics. 7:280.
Whitehead K, Kish A, Pan M, Kaur A, Reiss DJ, King N, Hohmann L, DiRuggiero J, Baliga NS.  2006.  An integrated systems approach for understanding cellular responses to gamma radiation. Mol Syst Biol. 2:47.
2005
Reiss DJ, Avila-Campillo I, Thorsson V, Schwikowski B, Galitski T.  2005.  Tools enabling the elucidation of molecular pathways active in human disease: application to Hepatitis C virus infection. BMC Bioinformatics. 6:154.
2004
Reiss DJ, Schwikowski B.  2004.  Predicting protein-peptide interactions via a network-based motif sampler. Bioinformatics. 20 Suppl 1:i274-82.
Yan W, Lee H, Yi EC, Reiss D, Shannon P, Kwieciszewski BK, Coito C, Li XJ, Keller A, Eng J et al..  2004.  System-based proteomic analysis of the interferon response in human liver cells. Genome Biol. 5:R54.

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