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Items: 46

1.

Mechanism for microbial population collapse in a fluctuating resource environment.

Turkarslan S, Raman AV, Thompson AW, Arens CE, Gillespie MA, von Netzer F, Hillesland KL, Stolyar S, López García de Lomana A, Reiss DJ, Gorman-Lewis D, Zane GM, Ranish JA, Wall JD, Stahl DA, Baliga NS.

Mol Syst Biol. 2017 Mar 20;13(3):919. doi: 10.15252/msb.20167058.

2.

Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis.

Plaisier CL, O'Brien S, Bernard B, Reynolds S, Simon Z, Toledo CM, Ding Y, Reiss DJ, Paddison PJ, Baliga NS.

Cell Syst. 2016 Aug;3(2):172-186. doi: 10.1016/j.cels.2016.06.006. Epub 2016 Jul 14.

3.

Transcriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii.

López García de Lomana A, Schäuble S, Valenzuela J, Imam S, Carter W, Bilgin DD, Yohn CB, Turkarslan S, Reiss DJ, Orellana MV, Price ND, Baliga NS.

Biotechnol Biofuels. 2015 Dec 2;8:207. doi: 10.1186/s13068-015-0391-z. eCollection 2015.

4.

A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis.

Turkarslan S, Peterson EJ, Rustad TR, Minch KJ, Reiss DJ, Morrison R, Ma S, Price ND, Sherman DR, Baliga NS.

Sci Data. 2015 Mar 31;2:150010. doi: 10.1038/sdata.2015.10. eCollection 2015.

5.

Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions.

Danziger SA, Reiss DJ, Ratushny AV, Smith JJ, Plaisier CL, Aitchison JD, Baliga NS.

BMC Syst Biol. 2015;9 Suppl 2:S1. doi: 10.1186/1752-0509-9-S2-S1. Epub 2015 Apr 15.

6.

cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism.

Reiss DJ, Plaisier CL, Wu WJ, Baliga NS.

Nucleic Acids Res. 2015 Jul 27;43(13):e87. doi: 10.1093/nar/gkv300. Epub 2015 Apr 14.

7.

The DNA-binding network of Mycobacterium tuberculosis.

Minch KJ, Rustad TR, Peterson EJ, Winkler J, Reiss DJ, Ma S, Hickey M, Brabant W, Morrison B, Turkarslan S, Mawhinney C, Galagan JE, Price ND, Baliga NS, Sherman DR.

Nat Commun. 2015 Jan 12;6:5829. doi: 10.1038/ncomms6829.

8.

Evolution of context dependent regulation by expansion of feast/famine regulatory proteins.

Plaisier CL, Lo FY, Ashworth J, Brooks AN, Beer KD, Kaur A, Pan M, Reiss DJ, Facciotti MT, Baliga NS.

BMC Syst Biol. 2014 Nov 14;8:122. doi: 10.1186/s12918-014-0122-2.

9.

Inference of expanded Lrp-like feast/famine transcription factor targets in a non-model organism using protein structure-based prediction.

Ashworth J, Plaisier CL, Lo FY, Reiss DJ, Baliga NS.

PLoS One. 2014 Sep 25;9(9):e107863. doi: 10.1371/journal.pone.0107863. eCollection 2014. Erratum in: PLoS One. 2014;9(11):e114450.

10.

A high-resolution network model for global gene regulation in Mycobacterium tuberculosis.

Peterson EJ, Reiss DJ, Turkarslan S, Minch KJ, Rustad T, Plaisier CL, Longabaugh WJ, Sherman DR, Baliga NS.

Nucleic Acids Res. 2014 Oct;42(18):11291-303. doi: 10.1093/nar/gku777. Epub 2014 Sep 17.

11.

A system-level model for the microbial regulatory genome.

Brooks AN, Reiss DJ, Allard A, Wu WJ, Salvanha DM, Plaisier CL, Chandrasekaran S, Pan M, Kaur A, Baliga NS.

Mol Syst Biol. 2014 Jul 15;10:740. doi: 10.15252/msb.20145160.

12.

Network portal: a database for storage, analysis and visualization of biological networks.

Turkarslan S, Wurtmann EJ, Wu WJ, Jiang N, Bare JC, Foley K, Reiss DJ, Novichkov P, Baliga NS.

Nucleic Acids Res. 2014 Jan;42(Database issue):D184-90. doi: 10.1093/nar/gkt1190. Epub 2013 Nov 23.

13.

Molecular mechanisms of system responses to novel stimuli are predictable from public data.

Danziger SA, Ratushny AV, Smith JJ, Saleem RA, Wan Y, Arens CE, Armstrong AM, Sitko K, Chen WM, Chiang JH, Reiss DJ, Baliga NS, Aitchison JD.

Nucleic Acids Res. 2014 Feb;42(3):1442-60. doi: 10.1093/nar/gkt938. Epub 2013 Oct 31.

14.

A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen.

Yoon SH, Turkarslan S, Reiss DJ, Pan M, Burn JA, Costa KC, Lie TJ, Slagel J, Moritz RL, Hackett M, Leigh JA, Baliga NS.

Genome Res. 2013 Nov;23(11):1839-51. doi: 10.1101/gr.153916.112. Epub 2013 Oct 2.

15.

Global analysis of mRNA stability in Mycobacterium tuberculosis.

Rustad TR, Minch KJ, Brabant W, Winkler JK, Reiss DJ, Baliga NS, Sherman DR.

Nucleic Acids Res. 2013 Jan 7;41(1):509-17. doi: 10.1093/nar/gks1019. Epub 2012 Nov 3.

16.

A novel approach for transcription factor analysis using SELEX with high-throughput sequencing (TFAST).

Reiss DJ, Howard FM, Mobley HL.

PLoS One. 2012;7(8):e42761. doi: 10.1371/journal.pone.0042761. Epub 2012 Aug 3.

17.

Niche adaptation by expansion and reprogramming of general transcription factors.

Turkarslan S, Reiss DJ, Gibbins G, Su WL, Pan M, Bare JC, Plaisier CL, Baliga NS.

Mol Syst Biol. 2011 Nov 22;7:554. doi: 10.1038/msb.2011.87.

19.

The broadly conserved regulator PhoP links pathogen virulence and membrane potential in Escherichia coli.

Alteri CJ, Lindner JR, Reiss DJ, Smith SN, Mobley HL.

Mol Microbiol. 2011 Oct;82(1):145-63. doi: 10.1111/j.1365-2958.2011.07804.x. Epub 2011 Sep 2.

20.

Parallel evolution of transcriptome architecture during genome reorganization.

Yoon SH, Reiss DJ, Bare JC, Tenenbaum D, Pan M, Slagel J, Moritz RL, Lim S, Hackett M, Menon AL, Adams MW, Barnebey A, Yannone SM, Leigh JA, Baliga NS.

Genome Res. 2011 Nov;21(11):1892-904. doi: 10.1101/gr.122218.111. Epub 2011 Jul 12.

21.

Multi-species integrative biclustering.

Waltman P, Kacmarczyk T, Bate AR, Kearns DB, Reiss DJ, Eichenberger P, Bonneau R.

Genome Biol. 2010;11(9):R96. doi: 10.1186/gb-2010-11-9-r96. Epub 2010 Sep 29.

22.

Coordination of frontline defense mechanisms under severe oxidative stress.

Kaur A, Van PT, Busch CR, Robinson CK, Pan M, Pang WL, Reiss DJ, DiRuggiero J, Baliga NS.

Mol Syst Biol. 2010 Jul;6:393. doi: 10.1038/msb.2010.50.

23.

Integration and visualization of systems biology data in context of the genome.

Bare JC, Koide T, Reiss DJ, Tenenbaum D, Baliga NS.

BMC Bioinformatics. 2010 Jul 19;11:382. doi: 10.1186/1471-2105-11-382.

24.

Learning transcriptional networks from the integration of ChIP-chip and expression data in a non-parametric model.

Youn A, Reiss DJ, Stuetzle W.

Bioinformatics. 2010 Aug 1;26(15):1879-86. doi: 10.1093/bioinformatics/btq289. Epub 2010 Jun 4.

25.

Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis.

Facciotti MT, Pang WL, Lo FY, Whitehead K, Koide T, Masumura K, Pan M, Kaur A, Larsen DJ, Reiss DJ, Hoang L, Kalisiak E, Northen T, Trauger SA, Siuzdak G, Baliga NS.

BMC Syst Biol. 2010 May 14;4:64. doi: 10.1186/1752-0509-4-64.

26.

Prevalence of transcription promoters within archaeal operons and coding sequences.

Koide T, Reiss DJ, Bare JC, Pang WL, Facciotti MT, Schmid AK, Pan M, Marzolf B, Van PT, Lo FY, Pratap A, Deutsch EW, Peterson A, Martin D, Baliga NS.

Mol Syst Biol. 2009;5:285. doi: 10.1038/msb.2009.42. Epub 2009 Jun 16.

27.

A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability.

Schmid AK, Reiss DJ, Pan M, Koide T, Baliga NS.

Mol Syst Biol. 2009;5:282. doi: 10.1038/msb.2009.40. Epub 2009 Jun 16.

28.

Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage.

Van PT, Schmid AK, King NL, Kaur A, Pan M, Whitehead K, Koide T, Facciotti MT, Goo YA, Deutsch EW, Reiss DJ, Mallick P, Baliga NS.

J Proteome Res. 2008 Sep;7(9):3755-64. doi: 10.1021/pr800031f. Epub 2008 Jul 25.

29.

CTCF physically links cohesin to chromatin.

Rubio ED, Reiss DJ, Welcsh PL, Disteche CM, Filippova GN, Baliga NS, Aebersold R, Ranish JA, Krumm A.

Proc Natl Acad Sci U S A. 2008 Jun 17;105(24):8309-14. doi: 10.1073/pnas.0801273105. Epub 2008 Jun 11.

30.

A predictive model for transcriptional control of physiology in a free living cell.

Bonneau R, Facciotti MT, Reiss DJ, Schmid AK, Pan M, Kaur A, Thorsson V, Shannon P, Johnson MH, Bare JC, Longabaugh W, Vuthoori M, Whitehead K, Madar A, Suzuki L, Mori T, Chang DE, Diruggiero J, Johnson CH, Hood L, Baliga NS.

Cell. 2007 Dec 28;131(7):1354-65.

31.

Model-based deconvolution of genome-wide DNA binding.

Reiss DJ, Facciotti MT, Baliga NS.

Bioinformatics. 2008 Feb 1;24(3):396-403. Epub 2007 Dec 1.

PMID:
18056063
32.

The anatomy of microbial cell state transitions in response to oxygen.

Schmid AK, Reiss DJ, Kaur A, Pan M, King N, Van PT, Hohmann L, Martin DB, Baliga NS.

Genome Res. 2007 Oct;17(10):1399-413. Epub 2007 Sep 4.

33.

General transcription factor specified global gene regulation in archaea.

Facciotti MT, Reiss DJ, Pan M, Kaur A, Vuthoori M, Bonneau R, Shannon P, Srivastava A, Donohoe SM, Hood LE, Baliga NS.

Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4630-5. Epub 2007 Mar 7.

34.

BioNetBuilder: automatic integration of biological networks.

Avila-Campillo I, Drew K, Lin J, Reiss DJ, Bonneau R.

Bioinformatics. 2007 Feb 1;23(3):392-3. Epub 2006 Nov 30.

PMID:
17138585
35.

An integrated systems approach for understanding cellular responses to gamma radiation.

Whitehead K, Kish A, Pan M, Kaur A, Reiss DJ, King N, Hohmann L, DiRuggiero J, Baliga NS.

Mol Syst Biol. 2006;2:47. Epub 2006 Sep 12.

36.
37.

The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo.

Bonneau R, Reiss DJ, Shannon P, Facciotti M, Hood L, Baliga NS, Thorsson V.

Genome Biol. 2006;7(5):R36. Epub 2006 May 10.

38.

The Gaggle: an open-source software system for integrating bioinformatics software and data sources.

Shannon PT, Reiss DJ, Bonneau R, Baliga NS.

BMC Bioinformatics. 2006 Mar 28;7:176.

39.

Tools enabling the elucidation of molecular pathways active in human disease: application to Hepatitis C virus infection.

Reiss DJ, Avila-Campillo I, Thorsson V, Schwikowski B, Galitski T.

BMC Bioinformatics. 2005 Jun 20;6:154.

40.

Predicting protein-peptide interactions via a network-based motif sampler.

Reiss DJ, Schwikowski B.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i274-82.

PMID:
15262809
41.

Alterations of Smad signaling in human breast carcinoma are associated with poor outcome: a tissue microarray study.

Xie W, Mertens JC, Reiss DJ, Rimm DL, Camp RL, Haffty BG, Reiss M.

Cancer Res. 2002 Jan 15;62(2):497-505.

43.

Onset and course of tardive dyskinesia.

Munetz MR, Toenniessen L, Scala C, Reiss DJ.

Psychosomatics. 1989 Summer;30(3):346-8. No abstract available.

PMID:
2569752
44.

Family psychoeducation, social skills training, and medication in schizophrenia: the long and short of it.

Hogarty GE, Anderson CM, Reiss DJ.

Psychopharmacol Bull. 1987;23(1):12-3. No abstract available.

PMID:
3602306
45.

Family psychoeducation, social skills training, and maintenance chemotherapy in the aftercare treatment of schizophrenia. I. One-year effects of a controlled study on relapse and expressed emotion.

Hogarty GE, Anderson CM, Reiss DJ, Kornblith SJ, Greenwald DP, Javna CD, Madonia MJ.

Arch Gen Psychiatry. 1986 Jul;43(7):633-42.

PMID:
2872870
46.

Family treatment of adult schizophrenic patients: a psycho-educational approach.

Anderson CM, Hogarty GE, Reiss DJ.

Schizophr Bull. 1980;6(3):490-505.

PMID:
7403810

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