Genetic manipulation of candidate phyla radiation bacteria provides functional insights into microbial dark matter
- Yaxi Wang, Larry A Gallagher, Pia A Andrade, …, Nitin S Baliga, S Brook Peterson, Joseph D Mougous
- None, 10.1101/2023.05.02.539146
Personalized Clostridioides difficile engraftment risk prediction and probiotic therapy assessment in the human gut
- Alex Carr, Nitin S Baliga, Christian Diener, …, Nitin S Baliga, Christian Diener, Sean M Gibbons
- None, 10.1101/2023.04.28.538771
Disrupting the ArcA Regulatory Network Amplifies the Fitness Cost of Tetracycline Resistance in Escherichia coli
- Mario L Arrieta-Ortiz, Min Pan, Amardeep Kaur, …, Aaron N Brooks, Tyson R Shepherd, Nitin S Baliga
- mSystems, 10.1128/msystems.00904-22
A single-cell based precision medicine approach using glioblastoma patient-specific models
- James H Park, Abdullah H Feroze, Samuel N Emerson, …, Serdar Turkarslan, Nitin S Baliga, Anoop P Patel
- None, 10.1038/s41698-022-00294-4
Reconsidering the in vivo functions of Clostridial Stickland amino acid fermentations
- Aidan Pavao, Madeline Graham, Mario L Arrieta-Ortiz, …, Selva Rupa Christinal Immanuel, Nitin S Baliga, Lynn Bry
- Anaerobe, 10.1016/j.anaerobe.2022.102600
MadR mediates acyl CoA-dependent regulation of mycolic acid desaturation in mycobacteria
- Charlotte Cooper, Eliza J R Peterson, Rebeca Bailo, …, Nagatoshi Fujiwara, Nitin Baliga, Apoorva Bhatt
- Proc Natl Acad Sci U S A, 10.1073/pnas.2111059119
Transcriptome signature of cell viability predicts drug response and drug interaction in Mycobacterium tuberculosis
- Vivek Srinivas, Rene A Ruiz, Min Pan, Selva Rupa Christinal Immanuel, Eliza J R Peterson, Nitin S Baliga
- Cell Rep Methods, 10.1016/j.crmeth.2021.100123
Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks using PRIME
- Selva Rupa Christinal Immanuel, Mario L Arrieta-Ortiz, Rene A Ruiz, …, Adrian Lopez Garcia de Lomana, Eliza J R Peterson, Nitin S Baliga
- NPJ Syst Biol Appl, 10.1038/s41540-021-00205-6
In vivo commensal control of Clostridioides difficile virulence
- Brintha P Girinathan, Nicholas DiBenedetto, Jay N Worley, …, Nitin S Baliga, Bruno Dupuy, Lynn Bry
- Cell Host Microbe, 10.1016/j.chom.2021.09.007
Contrasting heat stress response patterns of coral holobionts across the Red Sea suggest distinct mechanisms of thermal tolerance
- Christian R Voolstra, Jacob J Valenzuela, Serdar Turkarslan, …, Maoz Fine, Sarah Frias-Torres, Daniel J Barshis
- Mol Ecol, 10.1111/mec.16064
A Systems Approach to Brain Tumor Treatment
- James H Park, Adrian Lopez Garcia de Lomana, Diego M Marzese, …, Santosh Kesari, Sui Huang, Nitin S Baliga
- None, 10.3390/cancers13133152
Mycobacterium abscessus biofilms produce an extracellular matrix and have a distinct mycolic acid profile
- Anja Dokic, Eliza Peterson, Mario L Arrieta-Ortiz, …, Alessandro Di Maio, Nitin Baliga, Apoorva Bhatt
- None, 10.1016/j.tcsw.2021.100051
Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology
- Lauren M Lui, Erica L-W Majumder, Heidi J Smith, …, Nitin S Baliga, Paul D Adams, Adam P Arkin
- None, 10.3389/fmicb.2021.642422
History and Future Perspectives on the Discipline of Quantitative Systems Pharmacology Modeling and Its Applications
- Karim Azer, Chanchala D Kaddi, Jeffrey S Barrett, …, Silvia Parolo, Selva Rupa Christinal Immanuel, Nitin S Baliga
- None, 10.3389/fphys.2021.637999
Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification
- Anne E Otwell, Alex V Carr, Erica L W Majumder, …, David A Stahl, Gary Siuzdak, Nitin S Baliga
- mSystems, 10.1128/msystems.01025-20
A comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS
- Mukul K Midha, Ulrike Kusebauch, David Shteynberg, …, David S Campbell, Nitin S Baliga, Robert L Moritz
- Sci Data, 10.1038/s41597-020-00724-7
Biofilms of the non-tuberculous Mycobacterium chelonae form an extracellular matrix and display distinct expression patterns
- Perla Vega-Dominguez, Eliza Peterson, Min Pan, …, Deepak K Saini, Nitin Baliga, Apoorva Bhatt
- None, 10.1016/j.tcsw.2020.100043
Crippling life support for SARS-CoV-2 and other viruses through synthetic lethality
- Fred D Mast, Arti T Navare, Almer M van der Sloot, …, Andrej Sali, Mike Tyers, John D Aitchison
- J Cell Biol, 10.1083/jcb.202006159
Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium salinarum
- Adrián López García de Lomana, Ulrike Kusebauch, Arjun V Raman, …, Alan P R Lorenzetti, Robert L Moritz, Nitin S Baliga
- mSystems, 10.1128/msystems.00329-20
Transcriptional portrait of M. bovis BCG during biofilm production shows genes differentially expressed during intercellular aggregation and substrate attachment
- Mario Alberto Flores-Valdez, Michel de Jesús Aceves-Sánchez, Eliza J R Peterson, …, Mirna Burciaga-Flores, Tanya Amanda Camacho-Villegas, María Guadalupe Espinoza-Jorge
- Sci Rep, 10.1038/s41598-020-69152-2
Use and abuse of correlation analyses in microbial ecology
- Alex Carr, Christian Diener, Nitin S Baliga, Sean M Gibbons
- ISME J, 10.1038/s41396-019-0459-z
EcoFABs: advancing microbiome science through standardized fabricated ecosystems
- Karsten Zengler, Kirsten Hofmockel, Nitin S Baliga, …, Matthew D Wallenstein, Elizabeth A Shank, Trent R Northen
- Nat Methods, 10.1038/s41592-019-0465-0
Systems biology approaches towards predictive microbial ecology
- Anne E Otwell, Adrián López García de Lomana, Sean M Gibbons, Mónica V Orellana, Nitin S Baliga
- Environ Microbiol, 10.1111/1462-2920.14378
Ocean acidification conditions increase resilience of marine diatoms
- Jacob J Valenzuela, Adrián López García de Lomana, Allison Lee, E V Armbrust, Mónica V Orellana, Nitin S Baliga
- Nat Commun, 10.1038/s41467-018-04742-3
Transcriptional regulatory networks underlying gene expression changes in Huntington’s disease
- Seth A Ament, Jocelynn R Pearl, Jeffrey P Cantle, …, Leroy E Hood, Jeffrey B Carroll, Nathan D Price
- Mol Syst Biol, 10.15252/msb.20167435
Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations
- Wei Qin, Shady A Amin, Rachel A Lundeen, …, E Virginia Armbrust, Anitra E Ingalls, David A Stahl
- ISME J, 10.1038/ismej.2017.186
Cytoscape: a software environment for integrated models of biomolecular interaction networks
- Paul Shannon, Andrew Markiel, Owen Ozier, …, Nada Amin, Benno Schwikowski, Trey Ideker
- Genome Res, 10.1101/gr.1239303