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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López García de Lomana, Adrián, Ulrike Kusebauch, Arjun V. Raman, Min Pan, Serdar Turkarslan, Alan P. R. Lorenzetti, Robert L. Moritz, and Nitin S. Baliga. 2020. “Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium Salinarum.” MSystems 5 (4). https://doi.org/10.1128/mSystems.00329-20. Cite Download
Flores-Valdez, Mario Alberto, Michel de Jesús Aceves-Sánchez, Eliza J. R. Peterson, Nitin Baliga, Jorge Bravo-Madrigal, Miguel Ángel De la Cruz-Villegas, Miguel A. Ares, et al. 2020. “Transcriptional Portrait of M. Bovis BCG during Biofilm Production Shows Genes Differentially Expressed during Intercellular Aggregation and Substrate Attachment.” Scientific Reports 10 (1): 12578. https://doi.org/10.1038/s41598-020-69152-2. Cite Download
Peterson, Eliza J. R., Abrar A. Abidi, Mario L. Arrieta-Ortiz, Boris Aguilar, James T. Yurkovich, Amardeep Kaur, Min Pan, Vivek Srinivas, Ilya Shmulevich, and Nitin S. Baliga. 2020. “Intricate Genetic Programs Controlling Dormancy in Mycobacterium Tuberculosis.” Cell Reports 31 (4): 107577. https://doi.org/10.1016/j.celrep.2020.107577. Cite Download
Arrieta-Ortiz, Mario L., Christoph Hafemeister, Bentley Shuster, Nitin S. Baliga, Richard Bonneau, and Patrick Eichenberger. 2020. “Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks.” MSystems 5 (3). https://doi.org/10.1128/mSystems.00057-20. Cite Download
Mast, Fred D., Arti T. Navare, Almer M. van der Sloot, Jasmin Coulombe-Huntington, Michael P. Rout, Nitin S. Baliga, Alexis Kaushansky, et al. 2020. “Crippling Life Support for SARS-CoV-2 and Other Viruses through Synthetic Lethality.” The Journal of Cell Biology 219 (10). https://doi.org/10.1083/jcb.202006159. Cite
Vega-Dominguez, Perla, Eliza Peterson, Min Pan, Alessandro Di Maio, Saumya Singh, Siva Umapathy, Deepak K. Saini, Nitin Baliga, and Apoorva Bhatt. 2020. “Biofilms of the Non-Tuberculous Mycobacterium Chelonae Form an Extracellular Matrix and Display Distinct Expression Patterns.” Cell Surface (Amsterdam, Netherlands) 6: 100043. https://doi.org/10.1016/j.tcsw.2020.100043. Cite Download
Midha, Mukul K., Ulrike Kusebauch, David Shteynberg, Charu Kapil, Samuel L. Bader, Panga Jaipal Reddy, David S. Campbell, Nitin S. Baliga, and Robert L. Moritz. 2020. “A Comprehensive Spectral Assay Library to Quantify the Escherichia Coli Proteome by DIA/SWATH-MS.” Scientific Data 7 (1): 389. https://doi.org/10.1038/s41597-020-00724-7. Cite
Idso, Matthew N., Ajay Suresh Akhade, Mario L. Arrieta-Ortiz, Bert T. Lai, Vivek Srinivas, James P. Hopkins, Ana Oliveira Gomes, Naeha Subramanian, Nitin Baliga, and James R. Heath. 2020. “Antibody-Recruiting Protein-Catalyzed Capture Agents to Combat Antibiotic-Resistant Bacteria.” Chemical Science 11 (11): 3054–67. https://doi.org/10.1039/C9SC04842A. Cite Download
Sathe, Santosh, Mónica V. Orellana, Nitin S. Baliga, and Pierre M. Durand. 2019. “Temporal and Metabolic Overlap between Lipid Accumulation and Programmed Cell Death Due to Nitrogen Starvation in the Unicellular Chlorophyte Chlamydomonas Reinhardtii.” Phycological Research 67 (3): 173–83. https://doi.org/10.1111/pre.12368. Cite
Carr, Alex, Christian Diener, Nitin S. Baliga, and Sean M. Gibbons. 2019. “Use and Abuse of Correlation Analyses in Microbial Ecology.” The ISME Journal, 1. https://doi.org/10.1038/s41396-019-0459-z. Cite
Zengler, Karsten, Kirsten Hofmockel, Nitin S. Baliga, Scott W. Behie, Hans C. Bernstein, James B. Brown, José R. Dinneny, et al. 2019. “EcoFABs: Advancing Microbiome Science through Standardized Fabricated Ecosystems.” Nature Methods. https://doi.org/10.1038/s41592-019-0465-0. Cite
Peterson, Eliza Jr, Rebeca Bailo, Alissa C. Rothchild, Mario L. Arrieta-Ortiz, Amardeep Kaur, Min Pan, Dat Mai, et al. 2019. “Path-Seq Identifies an Essential Mycolate Remodeling Program for Mycobacterial Host Adaptation.” Molecular Systems Biology 15 (3): e8584. https://doi.org/10.15252/msb.20188584. Cite Download
Otwell, Anne E., Adrián López García de Lomana, Sean M. Gibbons, Mónica V. Orellana, and Nitin S. Baliga. 2018. “Systems Biology Approaches towards Predictive Microbial Ecology.” Environmental Microbiology. https://doi.org/10.1111/1462-2920.14378. Cite
Valenzuela, Jacob J., Adrián López García de Lomana, Allison Lee, E. V. Armbrust, Mónica V. Orellana, and Nitin S. Baliga. 2018. “Ocean Acidification Conditions Increase Resilience of Marine Diatoms.” Nature Communications 9 (1): 2328. https://doi.org/10.1038/s41467-018-04742-3. Cite
Flores-Valdez, Mario A., César Pedroza-Roldán, Michel de Jesús Aceves-Sánchez, Eliza J. R. Peterson, Nitin S. Baliga, Rogelio Hernández-Pando, JoLynn Troudt, et al. 2018. “The BCGΔBCG1419c Vaccine Candidate Reduces Lung Pathology, IL-6, TNF-α, and IL-10 During Chronic TB Infection.” Frontiers in Microbiology 9: 1281. https://doi.org/10.3389/fmicb.2018.01281. Cite
Ament, Seth A., Jocelynn R. Pearl, Jeffrey P. Cantle, Robert M. Bragg, Peter J. Skene, Sydney R. Coffey, Dani E. Bergey, et al. 2018. “Transcriptional Regulatory Networks Underlying Gene Expression Changes in Huntington’s Disease.” Molecular Systems Biology 14 (3): e7435. Cite
Flowers, Jason J., Matthew A. Richards, Nitin Baliga, Birte Meyer, and David A. Stahl. 2018. “Constraint-Based Modelling Captures the Metabolic Versatility of Desulfovibrio Vulgaris.” Environmental Microbiology Reports. https://doi.org/10.1111/1758-2229.12619. Cite
Turkarslan, Serdar, Arjun V. Raman, Anne W. Thompson, Christina E. Arens, Mark A. Gillespie, Frederick von Netzer, Kristina L. Hillesland, et al. 2017. “Mechanism for Microbial Population Collapse in a Fluctuating Resource Environment.” Molecular Systems Biology 13 (3): 919. Cite
Wang, Zhuo, Samuel A. Danziger, Benjamin D. Heavner, Shuyi Ma, Jennifer J. Smith, Song Li, Thurston Herricks, et al. 2017. “Combining Inferred Regulatory and Reconstructed Metabolic Networks Enhances Phenotype Prediction in Yeast.” PLoS Computational Biology 13 (5): e1005489. https://doi.org/10.1371/journal.pcbi.1005489. Cite
Thompson, Anne W., Serdar Turkarslan, Christina E. Arens, Adrián López García de Lomana, Arjun V. Raman, David A. Stahl, and Nitin S. Baliga. 2017. “Robustness of a Model Microbial Community Emerges from Population Structure among Single Cells of a Clonal Population.” Environmental Microbiology. https://doi.org/10.1111/1462-2920.13764. Cite
López García de Lomana, Adrián, Amardeep Kaur, Serdar Turkarslan, Karlyn D. Beer, Fred D. Mast, Jennifer J. Smith, John D. Aitchison, and Nitin S. Baliga. 2017. “Adaptive Prediction Emerges Over Short Evolutionary Time Scales.” Genome Biology and Evolution. https://doi.org/10.1093/gbe/evx116. Cite Download
Qin, Wei, Shady A. Amin, Rachel A. Lundeen, Katherine R. Heal, Willm Martens-Habbena, Serdar Turkarslan, Hidetoshi Urakawa, et al. 2017. “Stress Response of a Marine Ammonia-Oxidizing Archaeon Informs Physiological Status of Environmental Populations.” The ISME Journal. https://doi.org/10.1038/ismej.2017.186. Cite
Patra, Biranchi, Yoshiko Kon, Gitanjali Yadav, Anthony W. Sevold, Jesse P. Frumkin, Ravishankar R. Vallabhajosyula, Arend Hintze, et al. 2017. “A Genome Wide Dosage Suppressor Network Reveals Genomic Robustness.” Nucleic Acids Research 45 (1): 255–70. https://doi.org/10.1093/nar/gkw1148. Cite
Plaisier, Christopher L., Sofie O’Brien, Brady Bernard, Sheila Reynolds, Zac Simon, Chad M. Toledo, Yu Ding, David J. Reiss, Patrick J. Paddison, and Nitin S. Baliga. 2016. “Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis.” Cell Systems 3 (2): 172–86. https://doi.org/10.1016/j.cels.2016.06.006. Cite
Keller, Mark P., Pradyut K. Paul, Mary E. Rabaglia, Donnie S. Stapleton, Kathryn L. Schueler, Aimee Teo Broman, Shuyun Isabella Ye, et al. 2016. “The Transcription Factor Nfatc2 Regulates β-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets.” PLoS Genetics 12 (12): e1006466. https://doi.org/10.1371/journal.pgen.1006466. Cite
Rothchild, Alissa C., James R. Sissons, Shahin Shafiani, Christopher Plaisier, Deborah Min, Dat Mai, Mark Gilchrist, et al. 2016. “MiR-155-Regulated Molecular Network Orchestrates Cell Fate in the Innate and Adaptive Immune Response to Mycobacterium Tuberculosis.” Proceedings of the National Academy of Sciences of the United States of America 113 (41): E6172–81. https://doi.org/10.1073/pnas.1608255113. Cite
Peterson, Eliza J. R., Shuyi Ma, David R. Sherman, and Nitin S. Baliga. 2016. “Network Analysis Identifies Rv0324 and Rv0880 as Regulators of Bedaquiline Tolerance in Mycobacterium Tuberculosis.” Nature Microbiology 1 (8): 16078. https://doi.org/10.1038/nmicrobiol.2016.78. Cite
Toledo, C. M., Y. Ding, P. Hoellerbauer, R. J. Davis, R. Basom, E. J. Girard, E. Lee, et al. 2015. “Genome-Wide CRISPR-Cas9 Screens Reveal Loss of Redundancy between PKMYT1 and WEE1 in Glioblastoma Stem-like Cells.” Cell Reports 13 (December): 2425–39. https://doi.org/10.1016/j.celrep.2015.11.021. Cite
Imam, S., S. Schauble, J. Valenzuela, A. Lopez Garcia de Lomana, W. Carter, N. D. Price, and N. S. Baliga. 2015. “A Refined Genome-Scale Reconstruction of Chlamydomonas Metabolism Provides a Platform for Systems-Level Analyses.” The Plant Journal : For Cell and Molecular Biology 84 (December): 1239–56. https://doi.org/10.1111/tpj.13059. Cite
Ashworth, J., S. Turkarslan, M. Harris, M. V. Orellana, and N. S. Baliga. 2015. “Pan-Transcriptomic Analysis Identifies Coordinated and Orthologous Functional Modules in the Diatoms Thalassiosira Pseudonana and Phaeodactylum Tricornutum.” Marine Genomics, November. https://doi.org/10.1016/j.margen.2015.10.011. Cite
Thompson, Anne W., Matthew J. Crow, Brian Wadey, Christina Arens, Serdar Turkarslan, Sergey Stolyar, Nicholas Elliott, et al. 2015. “A Method to Analyze, Sort, and Retain Viability of Obligate Anaerobic Microorganisms from Complex Microbial Communities.” Journal of Microbiological Methods 117 (October): 74–77. https://doi.org/10.1016/j.mimet.2015.07.009. Cite Download
Hennon, Gwenn M. M., Justin Ashworth, Ryan D. Groussman, Chris Berthiaume, Rhonda L. Morales, Nitin S. Baliga, Mónica V. Orellana, and E. V. Armbrust. 2015. “Diatom Acclimation to Elevated CO2 via CAMP Signalling and Coordinated Gene Expression.” Nature Climate Change 5 (8): 761–65. https://doi.org/10.1038/nclimate2683. Cite
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 Research 43 (13): e87. https://doi.org/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
Ludwig, Claudia, Monica Orellana, DeVault, Megan, Zac Simon, and Nitin Baliga. 2015. “Ocean Acidification.” The Science Teacher 082 (06). https://doi.org/10.2505/4/tst15_082_06_41. 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.” Nature Communications 6. https://doi.org/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.” Scientific Data 2: 150010. https://doi.org/10.1038/sdata.2015.10. Cite
Imam, Saheed, Sascha Schauble, Aaron N. Brooks, Nitin S. Baliga, and Nathan D. Price. 2015. “Data-Driven Integration of Genome-Scale Regulatory and Metabolic Network Models.” Frontiers in Microbiology 6. https://doi.org/10.3389/fmicb.2015.00409. Cite
Lopez Garcia de Lomana, A., S. Schauble, J. Valenzuela, S. Imam, W. Carter, D. D. Bilgin, C. B. Yohn, et al. 2015. “Transcriptional Program for Nitrogen Starvation-Induced Lipid Accumulation in Chlamydomonas Reinhardtii.” Biotechnology for Biofuels 8: 207. https://doi.org/10.1186/s13068-015-0391-z. Cite
Gomes-Filho, José Vicente, Livia Soares Zaramela, Valéria Cristina da Silva Italiani, Nitin S. Baliga, Ricardo Z. N. Vêncio, and Tie Koide. 2015. “Sense Overlapping Transcripts in IS1341-Type Transposase Genes Are Functional Non-Coding RNAs in Archaea.” RNA Biology 12 (5): 490–500. https://doi.org/10.1080/15476286.2015.1019998. 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 Research 42 (18): 11291–303. https://doi.org/10.1093/nar/gku777. 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
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
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. https://doi.org/10.1093/nar/gkt938. 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
Muller, Emilie E. L., Nicolás Pinel, Cédric 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.” Nature Communications 5: 5603. https://doi.org/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 Biology 15 (11). https://doi.org/10.1186/PREACCEPT-1701638048134699. 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
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