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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Reiss, David J., Christopher L. Plaisier, Wei-Ju Wu, and Nitin S. Baliga. 2015. “cMonkey2: Automated, Systematic, Integrated Detection of Co-Regulated Gene Modules for Any Organism.” Nucleic Acids Res, April. doi:10.1093/nar/gkv300. Cite
Raman, A. V., and N. S. Baliga. 2015. “The Universe under a Microscope.” Environmental Microbiology Reports 7 (1): 11–12. Cite
Imam, Saheed, Sascha Schäuble, Aaron N. Brooks, Nitin S. Baliga, and Nathan D. Price. 2015. “Data-Driven Integration of Genome-Scale Regulatory and Metabolic Network Models.” Front Microbiol 6: 409. doi:10.3389/fmicb.2015.00409. Cite
Minch, Kyle J., Tige R. Rustad, Eliza J. R. Peterson, Jessica Winkler, David J. Reiss, Shuyi Ma, Mark Hickey, et al. 2015. “The DNA-Binding Network of Mycobacterium Tuberculosis.” Nat Commun 6: 5829. doi:10.1038/ncomms6829. Cite
Turkarslan, Serdar, Eliza J. R. Peterson, Tige R. Rustad, Kyle J. Minch, David J. Reiss, Robert Morrison, Shuyi Ma, Nathan D. Price, David R. Sherman, and Nitin S. Baliga. 2015. “A Comprehensive Map of Genome-Wide Gene Regulation in Mycobacterium Tuberculosis.” Sci Data 2: 150010. doi:10.1038/sdata.2015.10. Cite


Hillesland, K. L., S. Lim, J. J. Flowers, S. Turkarslan, N. Pinel, G. M. Zane, N. Elliott, 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, September. Cite
Peterson, Eliza J. R., David J. Reiss, Serdar Turkarslan, Kyle J. Minch, Tige Rustad, Christopher L. Plaisier, William J. R. Longabaugh, David R. Sherman, and Nitin S. Baliga. 2014. “A High-Resolution Network Model for Global Gene Regulation in Mycobacterium Tuberculosis.” Nucleic Acids Res, September. doi:10.1093/nar/gku777. Cite
Wurtmann, E. J., A. V. Ratushny, M. Pan, K. D. Beer, J. D. Aitchison, and N. S. Baliga. 2014. “An Evolutionarily Conserved RNase-Based Mechanism for Repression of Transcriptional Positive Autoregulation.” Molecular Microbiology 92 (2): 369–82. Cite
Beer, K. D., E. J. Wurtmann, N. Pinel, and N. S. Baliga. 2014. “Model Organisms Have Memory of Complex Ecologically-Relevant Environmental Variation.” Applied and Environmental Microbiology, January. Cite
Turkarslan, S., E. J. Wurtmann, W. J. Wu, N. Jiang, J. C. Bare, K. Foley, D. J. Reiss, P. Novichkov, and N. S. Baliga. 2014. “Network Portal: A Database for Storage, Analysis and Visualization of Biological Networks.” Nucleic Acids Res 42 (1): D184–90. Cite
Danziger, S. A., A. V. Ratushny, J. J. Smith, R. A. Saleem, Y. Wan, C. E. Arens, A. M. Armstrong, et al. 2014. “Molecular Mechanisms of System Responses to Novel Stimuli Are Predictable from Public Data.” Nucleic Acids Research 42 (3): 1442–60. Cite
Ekici, Seda, Serdar Turkarslan, Grzegorz Pawlik, Andrew Dancis, Nitin S. Baliga, Hans-Georg Koch, and Fevzi Daldal. 2014. “Intracytoplasmic Copper Homeostasis Controls Cytochrome c Oxidase Production.” mBio 5 (1): e01055–13. Cite
Muller, Emilie E. L., Nicolás Pinel, Cedric C. Laczny, Michael R. Hoopmann, Shaman Narayanasamy, Laura A. Lebrun, Hugo Roume, et al. 2014. “Community-Integrated Omics Links Dominance of a Microbial Generalist to Fine-Tuned Resource Usage.” Nat Commun 5: 5603. doi:10.1038/ncomms6603. Cite
Rustad, Tige R., Kyle J. Minch, Shuyi Ma, Jessica K. Winkler, Samuel Hobbs, Mark Hickey, William Brabant, et al. 2014. “Mapping and Manipulating the Mycobacterium Tuberculosis Transcriptome Using a Transcription Factor Overexpression-Derived Regulatory Network.” Genome Biol 15: 502. doi:10.1186/PREACCEPT-1701638048134699. Cite


Yoon, S. H., S. Turkarslan, D. J. Reiss, M. Pan, J. A. Burn, K. C. Costa, T. J. Lie, et al. 2013. “A Systems Level Predictive Model for Global Gene Regulation of Methanogenesis in a Hydrogenotrophic Methanogen.” Genome Res 23 (11): 1839–51. Cite
Danziger, S. A., A. V. Ratushny, J. J. Smith, R. A. Saleem, Y. Wan, C. E. Arens, A. M. Armstrong, et al. 2013. “Molecular Mechanisms of System Responses to Novel Stimuli Are Predictable from Public Data.” Nucleic Acids Res, October. Cite
Beer, K. D., M. V. Orellana, and N. S. Baliga. 2013. “Modeling the Evolution of C4 Photosynthesis.” Cell 153 (7): 1427–29. Cite
Costa, K. C., S. H. Yoon, M. Pan, J. A. Burn, N. S. Baliga, and J. A. Leigh. 2013. “Effects of H2 and Formate on Growth Yield and Regulation of Methanogenesis in Methanococcus Maripaludis.” Journal of Bacteriology, January. Cite
Pang, W. L., A. Kaur, A. V. Ratushny, A. Cvetkovic, S. Kumar, M. Pan, A. P. Arkin, J. D. Aitchison, M. W. Adams, and N. S. Baliga. 2013. “Metallochaperones Regulate Intracellular Copper Levels.” PLoS Computational Biology 9 (1): e1002880. Cite
Orellana, M. V., W. L. Pang, P. M. Durand, K. Whitehead, and N. S. Baliga. 2013. “A Role for Programmed Cell Death in the Microbial Loop.” PLoS One 8 (5): e62595. Cite


Bare, J. C., and N. S. Baliga. 2012. “Architecture for Interoperable Software in Biology.” Briefings in Bioinformatics, December. Cite
Muller, E. E., N. Pinel, J. D. Gillece, J. M. Schupp, L. B. Price, D. M. Engelthaler, C. Levantesi, 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 (23): 6670–71. Cite
Rustad, T. R., K. J. Minch, W. Brabant, J. K. Winkler, D. J. Reiss, N. S. Baliga, and D. R. Sherman. 2012. “Global Analysis of mRNA Stability in Mycobacterium Tuberculosis.” Nucleic Acids Research, November. Cite
Plaisier, C. L., and N. S. Baliga. 2012. “Harnessing the Power of Human Tumor-Derived Cell Lines for the Rational Design of Cancer Therapies.” Pigment Cell & Melanoma Research 25 (4): 406–8. Cite
Plaisier, C. L., M. Pan, and N. S. Baliga. 2012. “A miRNA-Regulatory Network Explains How Dysregulated miRNAs Perturb Oncogenic Processes across Diverse Cancers.” Genome Research, June. Cite
Edgar, Rachel S., Edward W. Green, Yuwei Zhao, Gerben van Ooijen, Maria Olmedo, Ximing Qin, Yao Xu, et al. 2012. “Peroxiredoxins Are Conserved Markers of Circadian Rhythms.” Nature 485 (May): 459–64. doi:10.1038/nature11088. Cite


Ashworth, J., E. J. Wurtmann, and N. S. Baliga. 2011. “Reverse Engineering Systems Models of Regulation: Discovery, Prediction and Mechanisms.” Current Opinion in Biotechnology, December. Cite
Yoon, S. H., D. J. Reiss, J. C. Bare, D. Tenenbaum, M. Pan, J. Slagel, R. L. Moritz, et al. 2011. “Parallel Evolution of Transcriptome Architecture during Genome Reorganization.” Genome Research 21 (11): 1892–1904. Cite
Plaisier, C. L., J. C. Bare, and N. S. Baliga. 2011. “miRvestigator: Web Application to Identify miRNAs Responsible for Co-Regulated Gene Expression Patterns Discovered through Transcriptome Profiling.” Nucleic Acids Res, May. Cite
Robinson, C. K., K. Webb, A. Kaur, P. Jaruga, M. Dizdaroglu, N. S. Baliga, A. Place, and J. DiRuggiero. 2011. “A Major Role for Nonenzymatic Antioxidant Processes in the Radioresistance of Halobacterium Salinarum.” J Bacteriol 193 (7): 1653–62. Cite
Tautenhahn, R., G. J. Patti, E. Kalisiak, T. Miyamoto, M. Schmidt, F. Y. Lo, J. McBee, N. S. Baliga, and G. Siuzdak. 2011. “metaXCMS: Second-Order Analysis of Untargeted Metabolomics Data.” Anal Chem 83 (3): 696–700. Cite
Turkarslan, S., D. J. Reiss, G. Gibbins, W. L. Su, M. Pan, J. C. Bare, C. L. Plaisier, and N. S. Baliga. 2011. “Niche Adaptation by Expansion and Reprogramming of General Transcription Factors.” Molecular Systems Biology 7: 554. Cite


Schmid, A. K., M. Pan, K. Sharma, and N. S. Baliga. 2010. “Two Transcription Factors Are Necessary for Iron Homeostasis in a Salt-Dwelling Archaeon.” Nucleic Acids Res, November. Cite
Kaur, A., P. T. Van, C. R. Busch, C. K. Robinson, M. Pan, W. L. Pang, D. J. Reiss, J. DiRuggiero, and N. S. Baliga. 2010. “Coordination of Frontline Defense Mechanisms under Severe Oxidative Stress.” Mol Syst Biol 6 (July): 393. Cite
Gehlenborg, N., S. I. O’Donoghue, N. S. Baliga, A. Goesmann, M. A. Hibbs, H. Kitano, O. Kohlbacher, et al. 2010. “Visualization of Omics Data for Systems Biology.” Nat Methods 7 (3 Suppl): S56–68. Cite
Bare, J. C., T. Koide, D. J. Reiss, D. Tenenbaum, and N. S. Baliga. 2010. “Integration and Visualization of Systems Biology Data in Context of the Genome.” BMC Bioinformatics 11: 382. Cite
Facciotti, M. T., W. L. Pang, F. Y. Lo, K. Whitehead, T. Koide, K. Masumura, M. Pan, et al. 2010. “Large Scale Physiological Readjustment during Growth Enables Rapid, Comprehensive and Inexpensive Systems Analysis.” BMC Syst Biol 4: 64. Cite
Tenenbaum, D., J. C. Bare, and N. S. Baliga. 2010. “GTC: A Web Server for Integrating Systems Biology Data with Web Tools and Desktop Applications.” Source Code Biol Med 5: 7. Cite


Koide, T., W. L. Pang, and N. S. Baliga. 2009. “The Role of Predictive Modelling in Rationally Re-Engineering Biological Systems.” Nat Rev Microbiol 7 (4): 297–305. Cite
Koide, T., D. J. Reiss, J. C. Bare, W. L. Pang, M. T. Facciotti, A. K. Schmid, M. Pan, et al. 2009. “Prevalence of Transcription Promoters within Archaeal Operons and Coding Sequences.” Mol Syst Biol 5: 285. Cite
Schmid, A. K., D. J. Reiss, M. Pan, T. Koide, and N. S. Baliga. 2009. “A Single Transcription Factor Regulates Evolutionarily Diverse but Functionally Linked Metabolic Pathways in Response to Nutrient Availability.” Mol Syst Biol 5: 282. Cite
Whitehead, K., M. Pan, K. Masumura, R. Bonneau, and N. S. Baliga. 2009. “Diurnally Entrained Anticipatory Behavior in Archaea.” PLoS ONEPLoS ONE 4 (5): e5485. Cite


Van, P. T., A. K. Schmid, N. L. King, A. Kaur, M. Pan, K. Whitehead, T. Koide, et al. 2008. “Halobacterium Salinarum NRC-1 PeptideAtlas: Toward Strategies for Targeted Proteomics and Improved Proteome Coverage.” J Proteome Res 7 (9): 3755–64. Cite
Baliga, N. S. 2008. “Systems Biology. The Scale of Prediction.” Science 320 (5881): 1297–98. Cite
Rubio, E. D., D. J. Reiss, P. L. Welcsh, C. M. Disteche, G. N. Filippova, N. S. Baliga, R. Aebersold, J. Ranish, and A. Krumm. 2008. “CTCF Physically Links Cohesin to Chromatin.” Proc Natl Acad Sci U S A 105 (24): 8309–14. Cite
Reiss, D. J., M. T. Facciotti, and N. S. Baliga. 2008. “Model-Based Deconvolution of Genome-Wide DNA Binding.” Bioinformatics 24 (3): 396–403. Cite
Ludwig, C., and N. S. Baliga. 2008. “Systems Concepts Effectively Taught Using Systems Practices.” Science Scope 31 (9): 16–20. Cite


Bonneau, R., M. T. Facciotti, D. J. Reiss, A. K. Schmid, M. Pan, A. Kaur, V. Thorsson, et al. 2007. “A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell.” Cell 131 (7): 1354–65. Cite
Bare, J. C., P. Shannon, A. K. Schmid, and N. S. Baliga. 2007. “The Firegoose: Two-Way Integration of Diverse Data from Different Bioinformatics Web Resources with Desktop Applications.” BMC Bioinformatics 8 (1): 456. Cite
Schmid, A. K., D. J. Reiss, A. Kaur, M. Pan, N. King, P. T. Van, L. Hohmann, D. B. Martin, and N. S. Baliga. 2007. “The Anatomy of Microbial Cell State Transitions in Response to Oxygen.” Genome Res 17 (10): 1399–1413. Cite
Facciotti, M. T. et al. General transcription factor specified global gene regulation in archaea. Proc Natl Acad Sci U S A 104, 4630–5 (2007). Cite


Kaur, A. et al. A systems view of haloarchaeal strategies to withstand stress from transition metals. Genome Res 16, 841–854 (2006). Cite
Reiss, D. J., Baliga, N. S. & Bonneau, R. Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformatics 7, 280 (2006). Cite
Bonneau, R. et al. The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol 7, R36 (2006). Cite
Schmid, A. & Baliga, N. S. in Cell Engineering 5, (Springer, 2006). Cite
Shannon, P., Reiss, D. J., Bonneau, R. & Baliga, N. S. The Gaggle: an open-source software system for integrating bioinformatics software and data sources. BMC Bioinformatics 7, 176 (2006). Cite
Whitehead, K. et al. An integrated systems approach for understanding cellular responses to gamma radiation. Mol Syst Biol 2, 47 (2006). Cite


Iyer, R., Baliga, N. S. & Camilli, A. Catabolite control protein A (CcpA) contributes to virulence and regulation of sugar metabolism in Streptococcus pneumoniae. J Bacteriol 187, 8340–9 (2005). Cite


Baliga, N. S. et al. Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res 14, 2221–34 (2004). Cite
Facciotti, M. T., Bonneau, R., Hood, L. & Baliga, N. S. Systems Biology Experimental Design - Considerations for Building Predictive Gene Regulatory Network Models for Prokaryotic Systems. Current Genomics 5, 527–544(18) (2004). Cite
Baliga, N. S. et al. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. Genome Res 14, 1025–35 (2004). Cite
Facciotti, M. T. et al. Specificity of anion binding in the substrate pocket of bacteriorhodopsin. Biochemistry 43, 4934–43 (2004). Cite
Goo, Y. A. et al. Low-pass sequencing for microbial comparative genomics. BMC Genomics 5, 3 (2004). Cite
Bonneau, R., Baliga, N. S., Deutsch, E. W., Shannon, P. & Hood, L. Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1. Genome Biol 5, R52 (2004). Cite


Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13, 2498–504 (2003). Cite
Goo, Y. A. et al. Proteomic analysis of an extreme halophilic archaeon, Halobacterium sp. NRC-1. Mol Cell Proteomics 2, 506–24 (2003). Cite
Weston, A. D., Baliga, N. S., Bonneau, R. & Hood, L. Systems approaches applied to the study of Saccharomyces cerevisiae and Halobacterium sp. Cold Spring Harb Symp Quant Biol 68, 345–57 (2003). Cite


Baliga, N. S. et al. 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 (2002). Cite


Baliga, N. S. Promoter analysis by saturation mutagenesis. Biol Proced Online 3, 64–69 (2001). Cite
Baliga, N. S., Kennedy, S. P., Ng, W. V., Hood, L. & DasSarma, S. Genomic and genetic dissection of an archaeal regulon. Proc Natl Acad Sci U S A 98, 2521–5. (2001). Cite
DasSarma, S. et al. Genomic perspective on the photobiology of Halobacterium species NRC-1, a phototrophic, phototactic, and UV-tolerant haloarchaeon. Photosynth Res 70, 3–17 (2001). Cite


Ng, W. V. et al. Genome sequence of Halobacterium species NRC-1. Proc Natl Acad Sci U S A 97, 12176–81 (2000). Cite
Baliga, N. S. et al. Is gene expression in Halobacterium NRC-1 regulated by multiple TBP and TFB transcription factors? Mol Microbiol 36, 1184–5 (2000). Cite