Nitin S. Baliga, MSc, PhD

Senior Vice President, Director and Professor

Nitin Baliga
Nitin Baliga leads a cross-disciplinary team of scientists to address complex problems relevant to global health, personalized medicine, energy, and environment. His team uses a systems approach to construct predictive models of cellular and molecular networks within pathogens, cancer cells, and environmental microbes to enable biotechnologies to overcome drug resistance, find new drugs, predict consequence of climate change, and manufacture biorenewables. Dr. Baliga is also actively engaged in science education, and is passionate about developing and disseminating current science curriculum and authentic cross-disciplinary practices to schools. His contributions to HS education have had worldwide impact, and have won awards including the Alvin J. Thompson award. As a Professor at the Institute for Systems Biology, he was one of the founding members, and currently serves as the Director and Senior Vice President.

Dr. Baliga did his early schooling in Mumbai, India, where he received a B.Sc. in Microbiology (1992) from Ruia College within the Mumbai University system. In 1992, Dr. Baliga entered a national competition and won the highly coveted Central Government of India sponsored Department of Biotechnology studentship, which supported his graduate studies in Marine Biotechnology at Goa University. After getting a M.Sc. in Marine Biotechnology in 1994, Dr. Baliga won the prestigious Council for Scientific and Industrial Research fellowship through another Central Government of India-sponsored national competition. After completing his Ph.D. in Microbiology in 2000 at the University of Massachusetts at Amherst, Dr. Baliga moved to Seattle for postdoctoral training with Dr. Leroy Hood at the Institute for Systems Biology.

In 2007, Dr. Baliga published a landmark paper that demonstrated how to accurately predict the response of an organism to a new environment. This breakthrough was made possible by a suite of technologies, experimental strategies and computational tools that Dr. Baliga and his team developed to reverse engineer the complete gene regulatory network of a free-living organism. This study uncovered the theory and fundamental principles that underlie the evolution and predictability of biological responses.

Applying this approach to environmental issues, Dr. Baliga has discovered how some extremophiles might explore life in a new environment, revised a >5 decade old “operon” paradigm of gene regulation in prokaryotes, discovered diurnal anticipatory behavior in archaea, uncovered the role of programmed cell death in unicellular chlorophytes, elucidated how cells maintain copper ions at a safe concentration and discovered the role of RNases in adaptation to rapid environmental changes. Together with collaborators at the University of Washington, and the Lawrence Berkeley Laboratories, he is now elucidating the biological networks underlying response to ocean acidification, social interactions, and fuel production in microbes.

Dr. Baliga has also expanded his research program to complex human disease to elucidate dysfunctional networks in cancers and the basis for latency, drug tolerance, and altered immune responses in TB infections. His work has identified regulatory drivers across multiple cancers, and are aiding academic organizations and pharmaceutical companies in drug target discovery, drug repositioning, and combinatorial therapeutics. Dr. Baliga’s work has been published in top international journals including Cell, Science and Nature. He has been invited to the Google SciFoo Camp, and has been profiled by The Scientist, Genome Web, Wired Magazine, Genetic Engineering News, Ars Technica, Xconomy, and Nature Methods, among many others. Research in Dr. Baliga’s laboratory has been supported by the National Science Foundation, National Institutes of Health, NASA, Department of Energy, and the Department of Defense. He is the Section Editor of BMC Systems Biology and Nature Scientific Data, serves on scientific advisory boards of numerous academic and industrial organizations, and been instrumental in research program planning for the NSF and DOE.

Dr. Baliga has also made transformative contributions to science education. He founded the Systems Education Experiences (SEE) program that has offered internship opportunities to dozens of students and teachers from underrepresented groups and of disadvantaged backgrounds. Science curriculum developed by Dr. Baliga’s SEE program has impacted >2 million students in over one hundred countries.

PhD, Microbiology University of Massachusetts at Amherst

MSc, Marine Biotechnology Goa University, India

Systems Biology, Microbial Ecology, Cancer, Tuberculosis

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Baliga, N. S., Y. A. Goo, W. V. Ng, L. Hood, C. J. Daniels, and S. DasSarma. 2000. “Is Gene Expression in Halobacterium NRC-1 Regulated by Multiple TBP and TFB Transcription Factors?” Mol Microbiol 36 (5): 1184–85. Cite
Ng, W. V., S. P. Kennedy, G. G. Mahairas, B. Berquist, M. Pan, H. D. Shukla, S. R. Lasky, et al. 2000. “Genome Sequence of Halobacterium Species NRC-1.” Proc Natl Acad Sci U S A 97 (22): 12176–81. Cite
Baliga, N. S., S. P. Kennedy, W. V. Ng, L. Hood, and S. DasSarma. 2001. “Genomic and Genetic Dissection of an Archaeal Regulon.” Proc Natl Acad Sci U S A 98 (5): 2521-5. Cite
DasSarma, S., S. P. Kennedy, B. Berquist, W. Victor Ng, N. S. Baliga, J. L. Spudich, M. P. Krebs, J. A. Eisen, C. H. Johnson, and L. Hood. 2001. “Genomic Perspective on the Photobiology of Halobacterium Species NRC-1, a Phototrophic, Phototactic, and UV-Tolerant Haloarchaeon.” Photosynth Res 70 (1): 3–17. Cite
Baliga, N. S. 2001. “Promoter Analysis by Saturation Mutagenesis.” Biol Proced Online 3 (December): 64–69. Cite
Baliga, N. S., M. Pan, Y. A. Goo, E. C. Yi, D. R. Goodlett, K. Dimitrov, P. Shannon, R. Aebersold, W. V. Ng, and L. Hood. 2002. “Coordinate Regulation of Energy Transduction Modules in Halobacterium Sp. Analyzed by a Global Systems Approach.” Proc Natl Acad Sci U S A 99 (23): 14913–18. Cite
Weston, A. D., N. S. Baliga, R. Bonneau, and L. Hood. 2003. “Systems Approaches Applied to the Study of Saccharomyces Cerevisiae and Halobacterium Sp.” Cold Spring Harb Symp Quant Biol 68: 345–57. Cite
Goo, Y. A., E. C. Yi, N. S. Baliga, W. A. Tao, M. Pan, R. Aebersold, D. R. Goodlett, L. Hood, and W. V. Ng. 2003. “Proteomic Analysis of an Extreme Halophilic Archaeon, Halobacterium Sp. NRC-1.” Mol Cell Proteomics 2 (8): 506–24. Cite
Shannon, P., A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang, D. Ramage, N. Amin, B. Schwikowski, and T. Ideker. 2003. “Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks.” Genome Res 13 (11): 2498–2504. Cite
Bonneau, R., N. S. Baliga, E. W. Deutsch, P. Shannon, and L. Hood. 2004. “Comprehensive de Novo Structure Prediction in a Systems-Biology Context for the Archaea Halobacterium Sp. NRC-1.” Genome Biol 5 (8): R52. Cite
Goo, Y. A., J. Roach, G. Glusman, N. S. Baliga, K. Deutsch, M. Pan, S. Kennedy, S. DasSarma, W. V. Ng, and L. Hood. 2004. “Low-Pass Sequencing for Microbial Comparative Genomics.” BMC Genomics 5 (1): 3. Cite
Facciotti, M. T., V. S. Cheung, C. S. Lunde, S. Rouhani, N. S. Baliga, and R. M. Glaeser. 2004. “Specificity of Anion Binding in the Substrate Pocket of Bacteriorhodopsin.” Biochemistry 43 (17): 4934–43. Cite
Baliga, N. S., S. J. Bjork, R. Bonneau, M. Pan, C. Iloanusi, M. C. Kottemann, L. Hood, and J. DiRuggiero. 2004. “Systems Level Insights into the Stress Response to UV Radiation in the Halophilic Archaeon Halobacterium NRC-1.” Genome Res 14 (6): 1025–35. Cite
Baliga, N. S., R. Bonneau, M. T. Facciotti, M. Pan, G. Glusman, E. W. Deutsch, P. Shannon, et al. 2004. “Genome Sequence of Haloarcula Marismortui: A Halophilic Archaeon from the Dead Sea.” Genome Res 14 (11): 2221–34. Cite
Facciotti, M. T., R. Bonneau, L. Hood, and N. S. Baliga. 2004. “Systems Biology Experimental Design - Considerations for Building Predictive Gene Regulatory Network Models for Prokaryotic Systems.” Current Genomics 5 (7): 527-544(18). Cite
Iyer, R., N. S. Baliga, and A. Camilli. 2005. “Catabolite Control Protein A (CcpA) Contributes to Virulence and Regulation of Sugar Metabolism in Streptococcus Pneumoniae.” J Bacteriol 187 (24): 8340–49. Cite
Shannon, P., D. J. Reiss, R. Bonneau, and N. S. Baliga. 2006. “The Gaggle: An Open-Source Software System for Integrating Bioinformatics Software and Data Sources.” BMC Bioinformatics 7: 176. Cite
Whitehead, K., A. Kish, M. Pan, A. Kaur, D. J. Reiss, N. King, L. Hohmann, J. DiRuggiero, and N. S. Baliga. 2006. “An Integrated Systems Approach for Understanding Cellular Responses to Gamma Radiation.” Mol Syst Biol 2: 47. Cite
Schmid, A., and N. S. Baliga. 2006. “Prokaryotic Systems Biology.” In Cell Engineering. Vol. 5. Springer. Cite
Bonneau, R., D. J. Reiss, P. Shannon, M. Facciotti, L. Hood, N. S. Baliga, and V. Thorsson. 2006. “The Inferelator: An Algorithm for Learning Parsimonious Regulatory Networks from Systems-Biology Data Sets de Novo.” Genome Biol 7 (5): R36. Cite
Kaur, A., M. Pan, M. Meislin, M. T. Facciotti, R. El-Geweley, and N. S. Baliga. 2006. “A Systems View of Haloarchaeal Strategies to Withstand Stress from Transition Metals.” Genome Res 16 (June): 841–54. Cite
Reiss, D. J., N. S. Baliga, and R. Bonneau. 2006. “Integrated Biclustering of Heterogeneous Genome-Wide Datasets for the Inference of Global Regulatory Networks.” BMC Bioinformatics 7 (1): 280. Cite
Facciotti, M. T., D. J. Reiss, M. Pan, A. Kaur, M. Vuthoori, R. Bonneau, P. Shannon, et al. 2007. “General Transcription Factor Specified Global Gene Regulation in Archaea.” Proc Natl Acad Sci U S A 104 (11): 4630–35. 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
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
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
Ludwig, C., and N. S. Baliga. 2008. “Systems Concepts Effectively Taught Using Systems Practices.” Science Scope 31 (9): 16–20. 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
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
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
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
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
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
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. 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
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
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
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
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
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
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
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
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. 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
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