Nitin Baliga, PhD

Senior Vice President and Director

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(206) 732-1266


Interaction with the environment is central to how information within our DNA is decoded into observable phenotypes. Dr. Baliga and his laboratory are using a multidisciplinary systems approach to understand this process. Once delineated, the engineering principles governing assembly of biological systems will help unlock potentials within diverse organisms. By responsibly using this information we will be able to power spectacular solutions for problems in environment and medicine. Dr. Baliga holds an undergraduate degree in Microbiology from Ruia College, India, and a MSc in Marine Biotechnology from Goa University, India. Dr. Baliga conducted his doctoral studies in Microbiology at University of Massachusetts at Amherst and his postdoctoral studies in systems biology with Dr. Leroy Hood at ISB. During his predoctoral studies, he won two competitive awards from the government of India: the Council for Scientific and Industrial Research Fellowship, and a fellowship from the Department of Biotechnology. Dr. Baliga has also made significant contributions to high school science education throughout Washington. His primary goal is to develop mind-stimulating lessons that will prepare a new generation of scientists. Research in Dr. Baliga’s laboratory is supported by research grants from the NSF, NIH, NASA and DOE. Learn more about research and education efforts in the Baliga Laboratory by going here.

PhD, Microbiology University of Massachusetts at Amherst

MSc, Marine Biotechnology Goa University, India

Systems biology of organism-environment interactions

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 Imam, S., Schäuble, S., Brooks, A. N., Baliga, N. S. & Price, N. D. Data-driven integration of genome-scale regulatory and metabolic network models. Front Microbiol 6, 409.

Raman A.V, Baliga NS.  2015.  The universe under a microscope. Environmental microbiology reports. 7:11-2.

Gomes-Filho, J. V. et al. Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea. RNA Biol 12, 490–500.

Turkarslan, S. et al. A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis. Sci Data 2, 150010.

Reiss, D. J., Plaisier, C. L., Wu, W.-J. & Baliga, N. S. cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism. Nucleic Acids Res. doi:10.1093/nar/gkv300.

Danziger, S. A. et al. Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions. BMC Syst Biol 9 Suppl 2, S1.

Minch, K. J. et al. The DNA-binding network of Mycobacterium tuberculosis. Nat Commun 6, 5829.

Peterson, E. J. R. et al. A high-resolution network model for global gene regulation in Mycobacterium tuberculosis. Nucleic acids research 42, 11291–11303.


Hillesland K.L, Lim S, Flowers J.J, Turkarslan S, Pinel N, Zane G.M, Elliott N.,Qin Y., Wu L., Baliga NS et al..  2014.  Erosion of functional independence early in the evolution of a microbial mutualism. Proceedings of the National Academy of Sciences of the United States of America.

Wurtmann EJ, Ratushny AV, Pan M, Beer K.D, Aitchison JD, Baliga NS.  2014.  An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation. Molecular microbiology. 92:369-82.

Beer K.D, Wurtmann EJ, Pinel N, Baliga NS.  2014.  Model organisms have memory of complex ecologically-relevant environmental variation. Applied and environmental microbiology.

Danziger S.A, Ratushny AV, Smith JJ, Saleem RA, Wan Y, Arens CE, Armstrong AM, Sitko K, Chen WM, Chiang JH et al..  2014.  Molecular mechanisms of system responses to novel stimuli are predictable from public data. Nucleic acids research. 42:1442-60.

Turkarslan S, Wurtmann EJ, Wu W.J, Jiang N., Bare JC, Foley K, Reiss DJ,Novichkov P., Baliga NS.  2014.  Network portal: a database for storage, analysis and visualization of biological networks. Nucleic Acids Res. 42:D184-90.


Costa KC, Yoon SH, Pan M, Burn JA, Baliga NS, Leigh JA.  2013.  Effects of H2 and formate on growth yield and regulation of methanogenesis in Methanococcus maripaludis.Journal of bacteriology.

Pang WL, Kaur A, Ratushny AV, Cvetkovic A, Kumar S, Pan M, Arkin AP,Aitchison JD, Adams MW, Baliga NS.  2013.  Metallochaperones regulate intracellular copper levels. PLoS computational biology. 9:e1002880.

Beer K.D, Orellana MV, Baliga NS.  2013.  Modeling the evolution of C4 photosynthesis. Cell. 153:1427-9.

Danziger S.A, Ratushny AV, Smith JJ, Saleem RA, Wan Y, Arens CE, Armstrong AM, Sitko K, Chen WM, Chiang JH et al..  2013.  Molecular mechanisms of system responses to novel stimuli are predictable from public data. Nucleic Acids Res.

Orellana MV, Pang WL, Durand P.M, Whitehead K, Baliga NS.  2013.  A role for programmed cell death in the microbial loop. PLoS One. 8:e62595.

Yoon SH, Turkarslan S, Reiss DJ, Pan M, Burn JA, Costa KC, Lie T.J, Slagel J,Moritz RL, Hackett M et al..  2013.  A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen. Genome Res. 23:1839-51.


Bare JC, Baliga NS.  2012.  Architecture for interoperable software in biology. Briefings in bioinformatics.

Muller EE, Pinel N, Gillece JD, Schupp JM, Price LB, Engelthaler DM, Levantesi C,Tandoi V, Luong K, Baliga NS et al..  2012.  Genome Sequence of “Candidatus Microthrix parvicella” Bio17-1, a Long-Chain-Fatty-Acid-Accumulating Filamentous Actinobacterium from a Biological Wastewater Treatment Plant. Journal of bacteriology. 194:6670-1.

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.

Plaisier CL, Baliga NS.  2012.  Harnessing the power of human tumor-derived cell lines for the rational design of cancer therapies. Pigment cell & melanoma research. 25:406-8.

Plaisier CL, Pan M, Baliga NS.  2012.  A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers. Genome research.


Robinson CK, Webb K, Kaur A, Jaruga P, Dizdaroglu M, Baliga NS, Place A,DiRuggiero J.  2011.  A Major Role for Nonenzymatic Antioxidant Processes in the Radioresistance of Halobacterium salinarum. J Bacteriol. 193:1653-62.

Tautenhahn R, Patti GJ, Kalisiak E, Miyamoto T, Schmidt M, Lo FY, McBee J,Baliga NS, Siuzdak G.  2011.  metaXCMS: second-order analysis of untargeted metabolomics data. Anal Chem. 83:696-700.

Plaisier CL, Bare JC, Baliga NS.  2011.  miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling. Nucleic Acids Res.

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.

Ashworth J, Wurtmann EJ, Baliga NS.  2011.  Reverse engineering systems models of regulation: discovery, prediction and mechanisms. Current opinion in biotechnology.


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.

Tenenbaum D, Bare JC, Baliga NS.  2010.  GTC: A web server for integrating systems biology data with web tools and desktop applications. Source Code Biol Med. 5:7.

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.

Schmid AK, Pan M, Sharma K, Baliga NS.  2010.  Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon. Nucleic Acids Res.

Gehlenborg N, O’Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H,Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D et al..  2010.  Visualization of omics data for systems biology. Nat Methods. 7:S56-68.


Whitehead K, Pan M, Masumura K, Bonneau R, Baliga NS.  2009.  Diurnally entrained anticipatory behavior in archaea. PLoS ONEPLoS ONE. 4:e5485.

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.

Koide T, Pang WL, Baliga NS.  2009.  The role of predictive modelling in rationally re-engineering biological systems. Nat Rev Microbiol. 7:297-305.

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.


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

Baliga NS.  2008.  Systems biology. The scale of prediction. Science. 320:1297-8.

Ludwig C, Baliga NS.  2008.  Systems Concepts Effectively Taught Using Systems Practices. Science Scope. 31:16-20.


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.

Bare JC, Shannon P, Schmid AK, Baliga NS.  2007.  The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications. BMC Bioinformatics. 8:456.

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.


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.

Schmid A, Baliga NS.  2006.  Prokaryotic Systems Biology. Cell Engineering. 5

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


Iyer R, Baliga NS, Camilli A.  2005.  Catabolite control protein A (CcpA) contributes to virulence and regulation of sugar metabolism in Streptococcus pneumoniae. J Bacteriol. 187:8340-9.


Bonneau R, Baliga NS, Deutsch EW, Shannon P, Hood L.  2004.  Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1. Genome Biol. 5:R52.

Baliga NS, Bonneau R, Facciotti MT, Pan M, Glusman G, Deutsch EW, Shannon P, Chiu Y, Weng RS, Gan RR et al..  2004.  Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res. 14:2221-34.

Goo YA, Roach J, Glusman G, Baliga NS, Deutsch K, Pan M, Kennedy S,DasSarma S, Ng WV, Hood L.  2004.  Low-pass sequencing for microbial comparative genomics. BMC Genomics. 5:3.

Facciotti MT, Cheung VS, Lunde CS, Rouhani S, Baliga NS, Glaeser RM.  2004.  Specificity of anion binding in the substrate pocket of bacteriorhodopsin.Biochemistry. 43:4934-43.

Facciotti MT, Bonneau R, Hood L, Baliga NS.  2004.  Systems Biology Experimental Design – Considerations for Building Predictive Gene Regulatory Network Models for Prokaryotic Systems. Current Genomics. 5:527-544(18).

Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L,DiRuggiero J.  2004.  Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. Genome Res. 14:1025-35.


Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N,Schwikowski B, Ideker T.  2003.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13:2498-504.

Goo YA, Yi EC, Baliga NS, Tao WA, Pan M, Aebersold R, Goodlett DR, Hood L, Ng WV.  2003.  Proteomic analysis of an extreme halophilic archaeon, Halobacterium sp. NRC-1. Mol Cell Proteomics. 2:506-24.

Weston AD, Baliga NS, Bonneau R, Hood L.  2003.  Systems approaches applied to the study of Saccharomyces cerevisiae and Halobacterium sp. Cold Spring Harb Symp Quant Biol. 68:345-57.


Baliga NS, Pan M, Goo YA, Yi EC, Goodlett DR, Dimitrov K, Shannon P,Aebersold R, Ng WV, Hood L.  2002.  Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proc Natl Acad Sci U S A. 99:14913-8.


Baliga NS, Kennedy SP, Ng WV, Hood L, DasSarma S.  2001.  Genomic and genetic dissection of an archaeal regulon. Proc Natl Acad Sci U S A. 98:2521-5..

DasSarma S, Kennedy SP, Berquist B, Victor Ng W, Baliga NS, Spudich JL, Krebs MP, Eisen JA, Johnson CH, Hood L.  2001.  Genomic perspective on the photobiology of Halobacterium species NRC-1, a phototrophic, phototactic, and UV-tolerant haloarchaeon. Photosynth Res. 70:3-17.

Baliga NS.  2001.  Promoter analysis by saturation mutagenesis. Biol Proced Online. 3:64-69.


Baliga NS, Goo YA, Ng WV, Hood L, Daniels CJ, DasSarma S.  2000.  Is gene expression in Halobacterium NRC-1 regulated by multiple TBP and TFB transcription factors? Mol Microbiol. 36:1184-5.

Ng WV, Kennedy SP, Mahairas GG, Berquist B, Pan M, Shukla HD, Lasky SR,Baliga NS, Thorsson V, Sbrogna J et al..  2000.  Genome sequence of Halobacterium species NRC-1. Proc Natl Acad Sci U S A. 97:12176-81.