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Baliga Lab Publications

2010

Nils Gehlenborg, Seán I O'Donoghue, Nitin S Baliga, Alexander Goesmann, Matthew A Hibbs, Hiroaki Kitano, Oliver Kohlbacher, Heiko Neuweger, Reinhard Schneider, Dan Tenenbaum & Anne-Claude Gavin. Visualization of omics data for systems biology. Nature Methods 7, S56 - S68 (2010)

 

2009

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. Prevalence of transcription promoters within archaeal operons and coding sequences. Mol Syst Biol. 2009;5:285. Epub 2009 Jun 16.

 

Schmid AK, Reiss DJ, Pan M, Koide T, Baliga NS. A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability. Mol Syst Biol. 2009;5:282. Epub 2009 Jun 16.

 

Whitehead K, Pan M, Masumura K, Bonneau R, Baliga NS. Diurnally entrained anticipatory behavior in archaea. PLoS One. 2009;4(5):e5485. Epub 2009 May 8.

 

Koide T, Pang WL, Baliga NS. The role of predictive modelling in rationally re-engineering biological systems. Nature Reviews Microbiology. 2009 Apr;7(4):297-305.

2008

Rubio ED, Reiss DJ, Disteche CM, Filippova GN, Baliga NS, Aebersold R, Ranish J, Krumm A
CTCF Physically Links Chesin to Chromatin.
Proc Natl Acad Sci U S A. 2008 Jun 17;105(24):8309-14.
 

Van P, Schmid AK, King N, Kaur A, Pan M, Whitehead K, Koide T, Facciotti M, Goo YA, Deutsch E, Reiss DJ, Mallick P, Baliga NS
Halobacterium salinarium NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage.
Journal of Proteome Research. 2008 Sep;7(9):3755-64

Baliga NS

Science. 2008 June 6: 320(5880): 1297-1298.

 

Reiss DJ, Facciotti MT, Baliga NS
Model-based deconvolution of genome-wide DNA binding.
Bioinformatics. 2008 Feb1: 24(3):396-403. PMID: 18056063 [PubMed - as supplied by publisher]

2007

Bare JC, Shannon P, Schmid A, Baliga NS
The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications.
BMC Bioinformatics. 2007 Nov 19; 8(1), 456.
PMID: 18021453 [PubMed - as supplied by publisher]

 

Bonneau R, Facciotti MT, Reiss DJ, Schmid AK, Pan M, Kaur A, Thorsson T, Shannon P, Johnson MH, Bare CJ, Longabaugh W, Vuthoori M, Whitehead K, Madar A, Suzuki L, Mori T, Chang DE, DiRuggiero J, Johnson CH, Hood L, Baliga NS
A predictive model for transcriptional control of physiology in a free living cell.
Cell. 2007 Dec 28; 131 (7): 1354-65.
PMID: 18160043 [PubMed - in process]

 

Schmid AK, Reiss DJ, Kaur A, Pan M, King N, Van PT, Hohmann L, Martin DB, Baliga NS
The anatomy of microbial cell state transitions in response to oxygen.
Genome Research. 2007 Oct; 17(10): 1399-413. Epub 2007 Sep 4.
PMID: 17785531 [PubMed- indexed for MEDLINE]

 

Facciotti MT, Reiss DJ, Pan M, Kaur A, Vuthoori M, Bonneau R, Shannon P, Srivastava A, Donohoe SM, Hood LE, Baliga NS
General transcription factor specified global gene regulation in archaea.
Proc Natl Acad Sci U S A. 2007; 104(11): 4630-4635.
PMID: 17360575

 

Amy K. Schmid and Nitin S. Baliga
Prokaryotic Systems Biology.
Cell Engineering 2007, Vol. 5: Systems Biology. p395-423; M. Al-Rubeai and M. Fussenegger (ed.), Springer Press, New York, NY.

2006

Kenia Whitehead, Adrienne Kish, Min Pan, Amardeep Kaur, David J Reiss, Nichole King, Laura Hohmann, Jocelyne DiRuggiero, Nitin S Baliga
An integrated systems approach for understanding cellular responses to gamma radiation.
Molecular Systems Biology, 2006; 2:47. PMID: 16969339

 

Kaur A, Pan M, Meislin M, Facciotti MT, El-Geweley R, Baliga NS.
 A systems view of haloarchaeal strategies to withstand stress from transition metals.
Genome Research, 2006 July;16:841-854. PMID: 16751342

 

Reiss DJ, Baliga NS, Bonneau R.
 Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks.
BMC Bioinformatics, 2006 Jun 2;7:280. PMID: 16749936

 

Shannon P, Reiss D, Bonneau R, Baliga N.
 Gaggle: An open-source software system for integrating bioinformatics software and data sources.
BMC Bioinformatics, 2006 Mar 28;7(1):176. PMID: 16569235 [PubMed - as supplied by publisher]

 

Bonneau R*, Reiss D, Shannon P, Facciotti MT, Hood L, Baliga NS, Thorsson V.
 The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data-sets.
Genome Biology, 2006 May 10;7(5):R36. PMID: 16686963

2005

Iyer R, Baliga NS, Camilli A.
 Catabolite control protein A (CcpA) contributes to virulence and regulation of sugar metabolism in Streptococcus pneumoniae.
Journal of Bacteriology, 2005 Dec;187(24):8340-9. PMID: 16321938 [PubMed - indexed for MEDLINE]

2004

Facciotti MT, Bonneau R, Hood L, and Baliga NS.
 Systems Biology Experimental Design - Considerations for Building Predictive Gene Regulatory Network Models for Prokaryotic Systems.
Current Genomics, 2004 5(7):527-544.

 

Baliga NS, Bonneau R, Facciotti MT, Pan M, Glusman G, Deutsch EW, Shannon P, Chiu Y, Weng RS, Gan RR, Hung P, Date SV, Marcotte E,
Hood L, Ng WV.
 Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea.
Genome Res. 2004 14:2221-2234. PMID: 15520287 [PubMed - indexed for MEDLINE]

 

Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MCH, Hood L, DiRuggiero J.
Systems Level Insights Into the Stress Response to UV Radiation in the Halophilic Archaeon Halobacterium NRC-1.
Genome Res. 2004 14:1025-1035. Published in Advance May 12, 2004, 10.1101/gr.1993504

 

Facciotti MT, Cheung VS, Lunde CS, Rouhani S, Baliga NS, Glaeser RM.
Specificity of anion binding in the substrate pocket of bacteriorhodopsin.
Biochemistry. 2004 May 4;43(17):4934-43. PMID: 15109251

 

Goo YA, Roach J, Glusman G, Baliga NS, Deutsch K, Pan M, Kennedy S, DasSarma S, Victor Ng W, Hood L.
Low-pass sequencing for microbial comparative genomics.
BMC Genomics. 2004 Jan 12;5(1):3. PMID: 14718067 [PubMed - as supplied by publisher]

 

Bonneau R, Baliga NS, Deutsch EW, Shannon P, Hood L.
Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1.
Genome Biology 2004, 5(8):R52-68. PMID: 15287974 [PubMed - indexed for MEDLINE]

2003

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T.
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Genome Res. 2003 Nov;13(11):2498-504. PMID: 14597658 [PubMed - indexed for MEDLINE]

 

Goo YA, Yi EC, Baliga NS, Tao WA, Pan M, Aebersold R, Goodlett DR, Hood L, Ng WV.
Proteomic Analysis of an Extreme Halophilic Archaeon, Halobacterium sp. NRC-1. Mol Cell Proteomics. 2003 Aug;2(8):506-24. Epub 2003 Jul 18. PMID: 12872007

 

Weston AD, Baliga NS, Bonneau R, Hood L.
Systems approaches applied to the study of Saccharomyces cerevisiae and Halobacterium sp.
Cold Spring Harbor Symposia on Quantitative Biology. 2003;68:345-57. PMID: 15338636 [PubMed - indexed for MEDLINE]

2002

Baliga NS, Pan M, Goo YA, Yi EC, Goodlett DR, Dimitrov K, Shannon P, Aebersold R, Ng WV, Hood L.
Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach.
Proc Natl Acad Sci U S A. 2002 Nov 12;99(23):14913-8. Epub 2002 Oct 28.
PMID: 12403819 [PubMed - indexed for MEDLINE]

2001

DasSarma S, Kennedy SP, Berquist B, Ng W-LV, Baliga NS, Spudich JL, Krebs MP, Eisen JA, Johnson CH, Hood L.
Genomic perspective on the photobiology of Halobacterium species NRC-1, a phototrophic, phototactic, and UV-tolerant haloarchaeon.
Photosynthesis Research. 2001;70(1):3-17. PMID: 16228359 [PubMed - as supplied by publisher]

 

Baliga NS.
Promoter analysis by saturation mutagenesis.
Biol Proced Online. 2001 Dec 22;3:64-69. PMID: 12734578 [PubMed - as supplied by publisher]

 

Baliga NS, Kennedy SP, Ng WV, Hood L, DasSarma S.
Genomic and genetic dissection of an archaeal regulon.
Proc Natl Acad Sci U S A. 2001 Feb 27;98(5):2521-5. Epub 2001 Feb 20.  PMID: 11226271 [PubMed - indexed for MEDLINE]

2000

Ng WV, Kennedy SP, Mahairas GG, Berquist B, Pan M, Shukla HD, Lasky SR, Baliga NS, Thorsson V, Sbrogna J, Swartzell S, Weir D, Hall J, Dahl TA, Welti R, Goo YA, Leithauser B, Keller K, Cruz R, Danson MJ, Hough DW, Maddocks DG, Jablonski PE, Krebs MP, Angevine CM, Dale H, Isenbarger TA, Peck RF, Pohlschroder M, Spudich JL, Jung KW, Alam M, Freitas T, Hou S, Daniels CJ, Dennis PP, Omer AD, Ebhardt H, Lowe TM, Liang P, Riley M, Hood L, DasSarma S.
Genome sequence of Halobacterium species NRC-1.
Proc Natl Acad Sci U S A. 2000 Oct 24;97(22):12176-81. PMID: 11016950 [PubMed - indexed for MEDLINE]

 

Baliga NS, Goo YA, Ng WV, Hood L, Daniels CJ, DasSarma S.
Is gene expression in Halobacterium NRC-1 regulated by multiple TBP and TFB transcription factors?
Mol Microbiol. 2000 Jun;36(5):1184-5. No abstract available.  PMID: 10844702 [PubMed - indexed for MEDLINE]

 

Baliga NS, Dassarma S.
Saturation mutagenesis of the haloarchaeal bop gene promoter:identification of DNA supercoiling sensitivity sites and absence of TFB recognition element and UAS enhancer activity.
Mol Microbiol. 2000 Jun;36(5):1175-83.  PMID: 10844701 [PubMed - indexed for MEDLINE]

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