Nitin S. Baliga, MSc, PhD

Senior Vice President, Director and Professor

Nitin S. Baliga, MSc, PhD

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

Download Baliga_CV

Im, Jinwoo, Dipankar Dwivedi, Andrew Putt, Kathleen F. Walker, James Marquis, Lauren M. Lui, Alex Carr, et al. 2023. “Reactive Transport Modeling of N Cycling for Prediction of N2O Emitted from the Subsurface Observatory at Area 3 under Rainfall Events.” In . AGU. https://agu.confex.com/agu/fm23/meetingapp.cgi/Paper/1443082. Cite
Kusebauch, Ulrike, Alan P. R. Lorenzetti, David S. Campbell, Min Pan, David Shteynberg, Charu Kapil, Mukul K. Midha, Adrián López García de Lomana, Nitin S. Baliga, and Robert L. Moritz. 2023. “A Comprehensive Spectral Assay Library to Quantify the Halobacterium Salinarum NRC-1 Proteome by DIA/SWATH-MS.” Scientific Data 10 (1): 697. https://doi.org/10.1038/s41597-023-02590-5. Cite Download
Lim, Joe J., Christian Diener, James Wilson, Jacob J. Valenzuela, Nitin S. Baliga, and Sean M. Gibbons. 2023. “Growth Phase Estimation for Abundant Bacterial Populations Sampled Longitudinally from Human Stool Metagenomes.” Nature Communications 14 (1): 5682. https://doi.org/10.1038/s41467-023-41424-1. Cite Download
Wang, Yaxi, Larry A. Gallagher, Pia A. Andrade, Andi Liu, Ian R. Humphreys, Serdar Turkarslan, Kevin J. Cutler, et al. 2023. “Genetic Manipulation of Patescibacteria Provides Mechanistic Insights into Microbial Dark Matter and the Epibiotic Lifestyle.” Cell, S0092-8674(23)00906-6. https://doi.org/10.1016/j.cell.2023.08.017. Cite Download
Peterson, Eliza J. R., Aaron N. Brooks, David J. Reiss, Amardeep Kaur, Julie Do, Min Pan, Wei-Ju Wu, et al. 2023. “MtrA Modulates Mycobacterium Tuberculosis Cell Division in Host Microenvironments to Mediate Intrinsic Resistance and Drug Tolerance.” Cell Reports 42 (8): 112875. https://doi.org/10.1016/j.celrep.2023.112875. Cite Download
Wang, Yaxi, Hannah E. Ledvina, Catherine A. Tower, Stanimir Kambarev, Elizabeth Liu, James C. Charity, Lieselotte S. M. Kreuk, et al. 2023. “Discovery of a Glutathione Utilization Pathway in Francisella That Shows Functional Divergence between Environmental and Pathogenic Species.” Cell Host & Microbe, S1931-3128(23)00261-5. https://doi.org/10.1016/j.chom.2023.06.010. Cite
Carr, Alex, Nitin S. Baliga, Christian Diener, and Sean M. Gibbons. 2023. “Personalized Clostridioides Difficile Engraftment Risk Prediction and Probiotic Therapy Assessment in the Human Gut.” BioRxiv: The Preprint Server for Biology, 2023.04.28.538771. https://doi.org/10.1101/2023.04.28.538771. Cite Download
Lorenzetti, Alan P. R., Ulrike Kusebauch, Lívia S. Zaramela, Wei-Ju Wu, João P. P. de Almeida, Serdar Turkarslan, Adrián L G de Lomana, et al. 2023. “A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon.” MSystems, e0081622. https://doi.org/10.1128/msystems.00816-22. Cite Download
Arrieta-Ortiz, Mario L., Min Pan, Amardeep Kaur, Evan Pepper-Tunick, Vivek Srinivas, Ananya Dash, Selva Rupa Christinal Immanuel, Aaron N. Brooks, Tyson R. Shepherd, and Nitin S. Baliga. 2023. “Disrupting the ArcA Regulatory Network Amplifies the Fitness Cost of Tetracycline Resistance in Escherichia Coli.” MSystems 8 (1): e0090422. https://doi.org/10.1128/msystems.00904-22. Cite Download
Xavier, Joao B., Jonathan M. Monk, Saugat Poudel, Charles J. Norsigian, Anand V. Sastry, Chen Liao, Jose Bento, et al. 2022. “Mathematical Models to Study the Biology of Pathogens and the Infectious Diseases They Cause.” IScience 25 (4). https://doi.org/10.1016/j.isci.2022.104079. Cite Download
Pavao, Aidan, Madeline Graham, Mario L. Arrieta-Ortiz, Selva Rupa Christinal Immanuel, Nitin S. Baliga, and Lynn Bry. 2022. “Reconsidering the in Vivo Functions of Clostridial Stickland Amino Acid Fermentations.” Anaerobe 76: 102600. https://doi.org/10.1016/j.anaerobe.2022.102600. Cite
Akhade, Ajay Suresh, Gabriela Verdezoto Mosquera, Mario L Arrieta-Ortiz, Amardeep Kaur, Eliza J.R Peterson, Nitin S Baliga, Kelly T Hughes, and Naeha Subramanian. 2022. “A Non-Canonical Role of Caspase-1 in Regulating Bacterial Physiology and Antimicrobial Resistance.” The Journal of Immunology 208 (1_Supplement): 51.05. https://doi.org/10.4049/jimmunol.208.Supp.51.05. Cite
Lorenzetti, Alan P. R., Ulrike Kusebauch, Lívia S. Zaramela, Wei-Ju Wu, João P. P. de Almeida, Serdar Turkarslan, Adrián L. G. de Lomana, et al. 2022. “A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon.” bioRxiv. https://doi.org/10.1101/2022.08.31.505529. Cite Download
Stuhlmiller, Timothy, Serdar Turkarslan, Julie Friedland, Mark Shapiro, Santosh Kesari, Anoop Patel, and Nitin Baliga. 2022. “SYSTEMS BIOLOGY-BASED THERAPEUTIC PREDICTIONS WITH GBMSYGNAL AND CLINICAL CORRELATES IN THE REAL-WORLD LONGITUDINAL OUTCOMES REGISTRY XCELSIOR.” In NEURO-ONCOLOGY, 24:117–117. OXFORD UNIV PRESS INC JOURNALS DEPT, 2001 EVANS RD, CARY, NC 27513 USA. Cite
Park, James H., Abdullah H. Feroze, Samuel N. Emerson, Anca B. Mihalas, C. Dirk Keene, Patrick J. Cimino, Adrian Lopez Garcia de Lomana, et al. 2022. “A Single-Cell Based Precision Medicine Approach Using Glioblastoma Patient-Specific Models.” NPJ Precision Oncology 6 (1): 55. https://doi.org/10.1038/s41698-022-00294-4. Cite Download
Cooper, Charlotte, Eliza J. R. Peterson, Rebeca Bailo, Min Pan, Albel Singh, Patrick Moynihan, Makoto Nakaya, Nagatoshi Fujiwara, Nitin Baliga, and Apoorva Bhatt. 2022. “MadR Mediates Acyl CoA-Dependent Regulation of Mycolic Acid Desaturation in Mycobacteria.” Proceedings of the National Academy of Sciences 119 (8): e2111059119. https://doi.org/10.1073/pnas.2111059119. Cite Download
Immanuel, Selva Rupa Christinal, Mario L. Arrieta-Ortiz, Rene A. Ruiz, Min Pan, Adrian Lopez Garcia de Lomana, Eliza J. R. Peterson, and Nitin S. Baliga. 2021. “Quantitative Prediction of Conditional Vulnerabilities in Regulatory and Metabolic Networks Using PRIME.” NPJ Systems Biology and Applications 7 (1): 43. https://doi.org/10.1038/s41540-021-00205-6. Cite Download
Srinivas, Vivek, Rene A. Ruiz, Min Pan, Selva Rupa Christinal Immanuel, Eliza J. R. Peterson, and Nitin S. Baliga. 2021. “Transcriptome Signature of Cell Viability Predicts Drug Response and Drug Interaction in Mycobacterium Tuberculosis.” Cell Reports Methods 1 (8): None. https://doi.org/10.1016/j.crmeth.2021.100123. Cite Download
Arrieta-Ortiz, Mario L., Selva Rupa Christinal Immanuel, Serdar Turkarslan, Wei-Ju Wu, Brintha P. Girinathan, Jay N. Worley, Nicholas DiBenedetto, et al. 2021. “Predictive Regulatory and Metabolic Network Models for Systems Analysis of Clostridioides Difficile.” Cell Host & Microbe, S1931-3128(21)00424-8. https://doi.org/10.1016/j.chom.2021.09.008. Cite
Girinathan, Brintha P., Nicholas DiBenedetto, Jay N. Worley, Johann Peltier, Mario L. Arrieta-Ortiz, Selva Rupa Christinal Immanuel, Richard Lavin, et al. 2021. “In Vivo Commensal Control of Clostridioides Difficile Virulence.” Cell Host & Microbe, S1931-3128(21)00423-6. https://doi.org/10.1016/j.chom.2021.09.007. Cite
Park, James H., Adrian Lopez Garcia de Lomana, Diego M. Marzese, Tiffany Juarez, Abdullah Feroze, Parvinder Hothi, Charles Cobbs, et al. 2021. “A Systems Approach to Brain Tumor Treatment.” Cancers 13 (13): 3152. https://doi.org/10.3390/cancers13133152. Cite Download
Wall, Matthew A., Serdar Turkarslan, Wei-Ju Wu, Samuel A. Danziger, David J. Reiss, Mike J. Mason, Andrew P. Dervan, et al. 2021. “Genetic Program Activity Delineates Risk, Relapse, and Therapy Responsiveness in Multiple Myeloma.” NPJ Precision Oncology 5 (1): 60. https://doi.org/10.1038/s41698-021-00185-0. Cite Download
Voolstra, Christian R., Jacob J. Valenzuela, Serdar Turkarslan, Anny Cárdenas, Benjamin C. C. Hume, Gabriela Perna, Carol Buitrago-López, et al. 2021. “Contrasting Heat Stress Response Patterns of Coral Holobionts across the Red Sea Suggest Distinct Mechanisms of Thermal Tolerance.” Molecular Ecology 30 (18): 4466–80. https://doi.org/10.1111/mec.16064. Cite Download
Nivedita, Nivedita, John D. Aitchison, and Nitin S. Baliga. 2021. “Autophagy as a Mechanism for Adaptive Prediction-Mediated Emergence of Drug Resistance.” Frontiers in Microbiology 12: 712631. https://doi.org/10.3389/fmicb.2021.712631. Cite Download
Dokic, Anja, Eliza Peterson, Mario L. Arrieta-Ortiz, Min Pan, Alessandro Di Maio, Nitin Baliga, and Apoorva Bhatt. 2021. “Mycobacterium Abscessus Biofilms Produce an Extracellular Matrix and Have a Distinct Mycolic Acid Profile.” Cell Surface (Amsterdam, Netherlands) 7: 100051. https://doi.org/10.1016/j.tcsw.2021.100051. Cite Download
Azer, Karim, Chanchala D. Kaddi, Jeffrey S. Barrett, Jane P. F. Bai, Sean T. McQuade, Nathaniel J. Merrill, Benedetto Piccoli, et al. 2021. “History and Future Perspectives on the Discipline of Quantitative Systems Pharmacology Modeling and Its Applications.” Frontiers in Physiology 12: 637999. https://doi.org/10.3389/fphys.2021.637999. Cite Download
Lui, Lauren M., Erica L.-W. Majumder, Heidi J. Smith, Hans K. Carlson, Frederick von Netzer, Matthew W. Fields, David A. Stahl, et al. 2021. “Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology.” Frontiers in Microbiology 12: 642422. https://doi.org/10.3389/fmicb.2021.642422. Cite Download
Turkarslan, Serdar, Nejc Stopnisek, Anne W. Thompson, Christina E. Arens, Jacob J. Valenzuela, James Wilson, Kristopher A. Hunt, et al. 2021. “Synergistic Epistasis Enhances the Co-Operativity of Mutualistic Interspecies Interactions.” The ISME Journal. https://doi.org/10.1038/s41396-021-00919-9. Cite Download
Neal, Maxwell L., Ling Wei, Eliza Peterson, Mario L. Arrieta-Ortiz, Samuel A. Danziger, Nitin S. Baliga, Alexis Kaushansky, and John D. Aitchison. 2021. “A Systems-Level Gene Regulatory Network Model for Plasmodium Falciparum.” Nucleic Acids Research. https://doi.org/10.1093/nar/gkaa1245. Cite Download
Otwell, Anne E., Alex V. Carr, Erica L. W. Majumder, Maryann K. Ruiz, Regina L. Wilpiszeski, Linh T. Hoang, Bill Webb, et al. 2021. “Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification.” MSystems 6 (1). https://doi.org/10.1128/mSystems.01025-20. Cite Download
Day, Jessica A., Christian Diener, Anne E. Otwell, Kourtney E. Tams, Brad Bebout, Angela M. Detweiler, Michael D. Lee, et al. 2021. “Lettuce (Lactuca Sativa) Productivity Influenced by Microbial Inocula under Nitrogen-Limited Conditions in Aquaponics.” PloS One 16 (2): e0247534. https://doi.org/10.1371/journal.pone.0247534. Cite Download
Day, JA, CM Ludwig, and NS Baliga. 2021. “Cultivating Environmental Sustainable Food through a Community Ambassador Program.” Clearing: Journal of Community-Based Environmental Literacy Education Winter Edition: 12–16. Cite
Orellana, Mónica, Claudia Ludwig, Anne Thompson, and Nitin Baliga. 2020. “Integrating Oceanographic Research into High School Curricula: Achieving Broader Impacts Through Systems Education Experiences Modules.” Oceanography 33 (3). https://doi.org/10.5670/oceanog.2020.304. Cite Download
Srinivas, Vivek, Mario L. Arrieta-Ortiz, Amardeep Kaur, Eliza J. R. Peterson, and Nitin S. Baliga. 2020. “PerSort Facilitates Characterization and Elimination of Persister Subpopulation in Mycobacteria.” MSystems 5 (6). https://doi.org/10.1128/mSystems.01127-20. Cite Download
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 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