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Author Details

Nitin S Baliga
Institute for Systems Biology
1999
141
43
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37162960Personalized <i>Clostridioides difficile</i> engraftment risk prediction and probiotic therapy assessment in the human gut.bioRxiv2024
37162960Personalized <i>Clostridioides difficile</i> engraftment risk prediction and probiotic therapy assessment in the human gut.bioRxiv2024
36537814Disrupting the ArcA Regulatory Network Amplifies the Fitness Cost of Tetracycline Resistance in Escherichia coli.mSystems2023
37833331A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS.Sci Data2023
37709733Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes.Nat Commun2023
37683634Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle.Cell2023
36912639A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon.mSystems2023
37453420Discovery of a glutathione utilization pathway in Francisella that shows functional divergence between environmental and pathogenic species.Cell Host Microbe2023
36537814Disrupting the ArcA Regulatory Network Amplifies the Fitness Cost of Tetracycline Resistance in Escherichia coli.mSystems2023
37542718MtrA modulates Mycobacterium tuberculosis cell division in host microenvironments to mediate intrinsic resistance and drug tolerance.Cell Rep2023
37709733Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes.Nat Commun2023
37833331A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS.Sci Data2023
37542718MtrA modulates Mycobacterium tuberculosis cell division in host microenvironments to mediate intrinsic resistance and drug tolerance.Cell Rep2023
37683634Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle.Cell2023
37453420Discovery of a glutathione utilization pathway in Francisella that shows functional divergence between environmental and pathogenic species.Cell Host Microbe2023
36912639A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon.mSystems2023
35165190MadR mediates acyl CoA-dependent regulation of mycolic acid desaturation in mycobacteria.Proc Natl Acad Sci U S A2022
35709938Reconsidering the in vivo functions of Clostridial Stickland amino acid fermentations.Anaerobe2022
35941215A single-cell based precision medicine approach using glioblastoma patient-specific models.NPJ Precis Oncol2022
35359802Mathematical models to study the biology of pathogens and the infectious diseases they cause.iScience2022
35165190MadR mediates acyl CoA-dependent regulation of mycolic acid desaturation in mycobacteria.Proc Natl Acad Sci U S A2022
35709938Reconsidering the in vivo functions of Clostridial Stickland amino acid fermentations.Anaerobe2022
35359802Mathematical models to study the biology of pathogens and the infectious diseases they cause.iScience2022
35941215A single-cell based precision medicine approach using glioblastoma patient-specific models.NPJ Precis Oncol2022
33450011A systems-level gene regulatory network model for Plasmodium falciparum.Nucleic Acids Res2021
33912773Mycobacterium abscessus biofilms produce an extracellular matrix and have a distinct mycolic acid profile.Cell Surf2021
33841364Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology.Front Microbiol2021
33841175History and Future Perspectives on the Discipline of Quantitative Systems Pharmacology Modeling and Its Applications.Front Physiol2021
33621265Lettuce (Lactuca sativa) productivity influenced by microbial inocula under nitrogen-limited conditions in aquaponics.PLoS One2021
33612833Synergistic epistasis enhances the co-operativity of mutualistic interspecies interactions.ISME J2021
33563788Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification.mSystems2021
34202449A Systems Approach to Brain Tumor Treatment.Cancers (Basel)2021
33450011A systems-level gene regulatory network model for Plasmodium falciparum.Nucleic Acids Res2021
34133939Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis.Cell Rep2021
34342082Contrasting heat stress response patterns of coral holobionts across the Red Sea suggest distinct mechanisms of thermal tolerance.Mol Ecol2021
34183722Genetic program activity delineates risk, relapse, and therapy responsiveness in multiple myeloma.NPJ Precis Oncol2021
34566920Autophagy as a Mechanism for Adaptive Prediction-Mediated Emergence of Drug Resistance.Front Microbiol2021
34977849Transcriptome signature of cell viability predicts drug response and drug interaction in <i>Mycobacterium tuberculosis</i>.Cell Rep Methods2021
34873198Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks using PRIME.NPJ Syst Biol Appl2021
34637781In vivo commensal control of Clostridioides difficile virulence.Cell Host Microbe2021
34637780Predictive regulatory and metabolic network models for systems analysis of Clostridioides difficile.Cell Host Microbe2021
33621265Lettuce (Lactuca sativa) productivity influenced by microbial inocula under nitrogen-limited conditions in aquaponics.PLoS One2021
33563788Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification.mSystems2021
33841364Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology.Front Microbiol2021
33841175History and Future Perspectives on the Discipline of Quantitative Systems Pharmacology Modeling and Its Applications.Front Physiol2021
33612833Synergistic epistasis enhances the co-operativity of mutualistic interspecies interactions.ISME J2021
33912773Mycobacterium abscessus biofilms produce an extracellular matrix and have a distinct mycolic acid profile.Cell Surf2021
34977849Transcriptome signature of cell viability predicts drug response and drug interaction in <i>Mycobacterium tuberculosis</i>.Cell Rep Methods2021
34873198Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks using PRIME.NPJ Syst Biol Appl2021
34637781In vivo commensal control of Clostridioides difficile virulence.Cell Host Microbe2021
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Collaborators

Christopher L Plaisier
Arizona State University
Co-authored papers 15
Leroy Hood
Center for Phenomic Health, The Buck Institute for Research on Aging
Co-authored papers 15
Richard Bonneau
Center for Computational Biology (CCB), Flatiron Institute, Simons Foundation
Co-authored papers 11
James Christopher Bare
Institute for Systems Biology
Co-authored papers 10
Paul Shannon
Institute for Systems Biology
Co-authored papers 9
John D Aitchison
Center for Global Infectious Disease Research, Seattle Children's Research Institute
Co-authored papers 9
David A Stahl
University of Washington
Co-authored papers 9
Nathan D Price
Institute for Systems Biology
Co-authored papers 8
Robert L Moritz
Institute for Systems Biology
Co-authored papers 7
David R Sherman
University of Washington
Co-authored papers 6
Sean M Gibbons
Institute for Systems Biology
Co-authored papers 6
Ulrike Kusebauch
Institute for Systems Biology
Co-authored papers 4
Eric W Deutsch
Institute for Systems Biology
Co-authored papers 4
Dan Tenenbaum
Fred Hutchinson Cancer Research Center
Co-authored papers 4
Jennifer J Smith
Institute for Systems Biology
Co-authored papers 4
Ruedi Aebersold
Institute of Molecular Systems Biology, ETH Zurich
Co-authored papers 3
Ricardo Z N V??ncio
University of Sao Paulo
Co-authored papers 3
Jizhong Zhou
Institute for Environmental Genomics, University of Oklahoma
Co-authored papers 3
Gary Siuzdak
Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute
Co-authored papers 3
Ilya Shmulevich
Institute for Systems Biology
Co-authored papers 3
Lynn Bry
Co-authored papers 3
Kristina L Hillesland
University of Washington Bothell
Co-authored papers 3
Vesteinn Thorsson
Institute for Systems Biology
Co-authored papers 3
John A Leigh
University of Washingtongrid.34477.33
Co-authored papers 3
Alan Aderem
Seattle Children's Research Institute
Co-authored papers 3
Alexis Kaushansky
Seattle Children's Research Institute, University of Washington
Co-authored papers 2
Gustavo Glusman
Institute for Systems Biology
Co-authored papers 2
Grant M Zane
University of Missouri
Co-authored papers 2
Trent R Northen
Co-authored papers 2
Brady Bernard
Co-authored papers 2
Release 1.2