NITIN BALIGA

Summary

Affiliation: Institute for Systems Biology
Country: USA

Publications

  1. pmc A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability
    Amy K Schmid
    Institute for Systems Biology, Seattle, WA 98103 8904, USA
    Mol Syst Biol 5:282. 2009
  2. pmc An integrated systems approach for understanding cellular responses to gamma radiation
    Kenia Whitehead
    Institute for Systems Biology, Seattle, WA 98103 8904, USA
    Mol Syst Biol 2:47. 2006
  3. pmc Diurnally entrained anticipatory behavior in archaea
    Kenia Whitehead
    Institute for Systems Biology, Seattle, Washington, United States of America
    PLoS ONE 4:e5485. 2009
  4. pmc Prevalence of transcription promoters within archaeal operons and coding sequences
    Tie Koide
    Institute for Systems Biology, Seattle, WA 98103, USA
    Mol Syst Biol 5:285. 2009
  5. pmc miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling
    Christopher L Plaisier
    Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109 5234, USA
    Nucleic Acids Res 39:W125-31. 2011
  6. pmc The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
    Richard Bonneau
    New York University, Biology Department, Center for Comparative Functional Genomics, New York, NY 10003, USA
    Genome Biol 7:R36. 2006
  7. pmc Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1
    Richard Bonneau
    Institute for Systems Biology, Seattle, WA 98103 8904, USA
    Genome Biol 5:R52. 2004
  8. pmc Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis
    Marc T Facciotti
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    BMC Syst Biol 4:64. 2010
  9. pmc Low-pass sequencing for microbial comparative genomics
    Young Ah Goo
    Institute for Systems Biology, Seattle, Washington 98103, USA
    BMC Genomics 5:3. 2004
  10. pmc The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications
    J Christopher Bare
    Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
    BMC Bioinformatics 8:456. 2007

Collaborators

Detail Information

Publications32

  1. pmc A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability
    Amy K Schmid
    Institute for Systems Biology, Seattle, WA 98103 8904, USA
    Mol Syst Biol 5:282. 2009
    ..Simultaneous analysis of metabolic and gene regulatory network architectures suggests an ongoing process of co-evolution in which TrmB integrates the expression of metabolic enzyme-coding genes of diverse origins...
  2. pmc An integrated systems approach for understanding cellular responses to gamma radiation
    Kenia Whitehead
    Institute for Systems Biology, Seattle, WA 98103 8904, USA
    Mol Syst Biol 2:47. 2006
    ....
  3. pmc Diurnally entrained anticipatory behavior in archaea
    Kenia Whitehead
    Institute for Systems Biology, Seattle, Washington, United States of America
    PLoS ONE 4:e5485. 2009
    ....
  4. pmc Prevalence of transcription promoters within archaeal operons and coding sequences
    Tie Koide
    Institute for Systems Biology, Seattle, WA 98103, USA
    Mol Syst Biol 5:285. 2009
    ..Using experimental validation, we illustrate the prevalence of overlapping genomic signals in archaeal transcription, casting doubt on the general perception of rigid boundaries between coding sequences and regulatory elements...
  5. pmc miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling
    Christopher L Plaisier
    Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109 5234, USA
    Nucleic Acids Res 39:W125-31. 2011
    ..The miRvestigator is freely available at http://mirvestigator.systemsbiology.net...
  6. pmc The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
    Richard Bonneau
    New York University, Biology Department, Center for Comparative Functional Genomics, New York, NY 10003, USA
    Genome Biol 7:R36. 2006
    ..Several specific regulatory predictions were experimentally tested and verified...
  7. pmc Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1
    Richard Bonneau
    Institute for Systems Biology, Seattle, WA 98103 8904, USA
    Genome Biol 5:R52. 2004
    ..The work reported here demonstrates that de novo structure prediction is now a viable option for providing general function information for many proteins of unknown function...
  8. pmc Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis
    Marc T Facciotti
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    BMC Syst Biol 4:64. 2010
    ..Therefore, a relatively quick and inexpensive strategy for observing changes in large fractions of the genetic elements is highly desirable...
  9. pmc Low-pass sequencing for microbial comparative genomics
    Young Ah Goo
    Institute for Systems Biology, Seattle, Washington 98103, USA
    BMC Genomics 5:3. 2004
    ..NRC-1 genome as a reference. Low-pass shotgun sequencing is a simple, inexpensive, and rapid approach that can readily be performed on any cultured microbe...
  10. pmc The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications
    J Christopher Bare
    Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
    BMC Bioinformatics 8:456. 2007
    ..Opportunities for new ways of combining and re-using data are arising as a result of the increasing use of web protocols to transmit structured data...
  11. pmc Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks
    David J Reiss
    Institute for Systems Biology, 1441 N, 34th St, Seattle, WA 98103 8904, USA
    BMC Bioinformatics 7:280. 2006
    ..In organisms where these motifs are not known, their de novo detection, integrated into the clustering algorithm, can help to guide the process towards more biologically parsimonious solutions...
  12. pmc Integration and visualization of systems biology data in context of the genome
    J Christopher Bare
    Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
    BMC Bioinformatics 11:382. 2010
    ..Visualization and exploration of this data is critical to understanding the regulatory logic encoded in the genome by which the cell dynamically affects its physiology and interacts with its environment...
  13. pmc The Gaggle: an open-source software system for integrating bioinformatics software and data sources
    Paul T Shannon
    Institute for Systems Biology, Seattle, WA 98103, USA
    BMC Bioinformatics 7:176. 2006
    ..A solution to this problem should recognize that data types, formats and software in this high throughput age of biology are constantly changing...
  14. doi request reprint Systems biology. The scale of prediction
    Nitin S Baliga
    Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
    Science 320:1297-8. 2008
  15. pmc GTC: A web server for integrating systems biology data with web tools and desktop applications
    Dan Tenenbaum
    Institute for Systems Biology, 1441 N, 34th St, Seattle, WA USA
    Source Code Biol Med 5:7. 2010
    ....
  16. pmc Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach
    Nitin S Baliga
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103 8904, USA
    Proc Natl Acad Sci U S A 99:14913-8. 2002
    ..phototrophy and arginine fermentation, are inversely regulated, presumably to achieve a balance in ATP production under anaerobic conditions...
  17. pmc Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1
    Nitin S Baliga
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Genome Res 14:1025-35. 2004
    ....
  18. pmc Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea
    Nitin S Baliga
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Genome Res 14:2221-34. 2004
    ..Finally, as expected from the larger genome, H. marismortui encodes many more functions and seems to have fewer nutritional requirements for survival than does Halobacterium sp. NRC-1...
  19. pmc Cytoscape: a software environment for integrated models of biomolecular interaction networks
    Paul Shannon
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Genome Res 13:2498-504. 2003
    ....
  20. pmc General transcription factor specified global gene regulation in archaea
    Marc T Facciotti
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98121, USA
    Proc Natl Acad Sci U S A 104:4630-5. 2007
    ....
  21. ncbi request reprint Model-based deconvolution of genome-wide DNA binding
    David J Reiss
    Institute for Systems Biology, 1441 N 34th St Seattle, WA 98103 8904, USA
    Bioinformatics 24:396-403. 2008
    ....
  22. pmc The anatomy of microbial cell state transitions in response to oxygen
    Amy K Schmid
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Genome Res 17:1399-413. 2007
    ..Dynamic temporal analysis of relationships between transcription and translation of key genes suggests several important mechanisms for cellular sustenance under anoxia as well as specific instances of post-transcriptional regulation...
  23. pmc Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage
    Phu T Van
    Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA
    J Proteome Res 7:3755-64. 2008
    ..Therefore, despite identifying at least one proteotypic peptide for almost all proteins in the PA, a context-dependent selection of proteotypic peptides appears to be the most effective approach for targeted proteomics...
  24. pmc A systems view of haloarchaeal strategies to withstand stress from transition metals
    Amardeep Kaur
    Institute for Systems Biology, Seattle, Washington 98103 8904, USA
    Genome Res 16:841-54. 2006
    ....
  25. ncbi request reprint Proteomic analysis of an extreme halophilic archaeon, Halobacterium sp. NRC-1
    Young Ah Goo
    Institute for Systems Biology, Seattle, WA 98103, USA
    Mol Cell Proteomics 2:506-24. 2003
    ....
  26. pmc Coordination of frontline defense mechanisms under severe oxidative stress
    Amardeep Kaur
    Institute for Systems Biology, Seattle, WA 98103, USA
    Mol Syst Biol 6:393. 2010
    ....
  27. pmc The role of predictive modelling in rationally re-engineering biological systems
    Tie Koide
    Institute for Systems Biology, 1441 N 34th Street, Seattle, Washington 98103, USA
    Nat Rev Microbiol 7:297-305. 2009
    ..Here, we review the status of these rapidly developing interdisciplinary fields of biology and provide a perspective on plausible venues for their merger...
  28. pmc CTCF physically links cohesin to chromatin
    Eric D Rubio
    Department of Radiation Oncology, University of Washington School of Medicine, Seattle WA 98195, USA
    Proc Natl Acad Sci U S A 105:8309-14. 2008
    ..These results have implications for the functional role of cohesin subunits in the pathogenesis of Cornelia de Lange syndrome and Roberts syndromes...
  29. ncbi request reprint Specificity of anion binding in the substrate pocket of bacteriorhodopsin
    Marc T Facciotti
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Biochemistry 43:4934-43. 2004
    ..Experimental comparison of the dissociation constants, K(d), for a variety of anions confirms this prediction and demonstrates, in addition, that the binding affinity is dramatically improved by the D212N substitution...
  30. ncbi request reprint A predictive model for transcriptional control of physiology in a free living cell
    Richard Bonneau
    Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA Courant Institute of Mathematical Sciences, Department of Computer Science, New York University, New York, NY 10003, USA
    Cell 131:1354-65. 2007
    ..This study supports the claim that the high degree of connectivity within biological and EF networks will enable the construction of similar models for any organism from relatively modest numbers of experiments...
  31. pmc Catabolite control protein A (CcpA) contributes to virulence and regulation of sugar metabolism in Streptococcus pneumoniae
    Ramkumar Iyer
    Department of Molecular Biology and Microbiology, Tufts University, 136 Harrison Avenue, Boston, MA 02111, USA
    J Bacteriol 187:8340-9. 2005
    ..Our results demonstrate that CcpA, though not a global regulator of CCR in S. pneumoniae, is required for colonization of the nasopharynx and survival and multiplication in the lung...

Research Grants4

  1. Interrogation of systems level mechanisms controlling DNA repair processes
    NITIN BALIGA; Fiscal Year: 2007
    ..e. a predictive model for regulatory mechanisms for repair. This basic model will serve as a template for designing systems approaches to model higher complexities of eukaryotic repair processes. ..
  2. Interrogation of systems level mechanisms controlling DNA repair processes
    NITIN BALIGA; Fiscal Year: 2009
    ..e. a predictive model for regulatory mechanisms for repair. This basic model will serve as a template for designing systems approaches to model higher complexities of eukaryotic repair processes. ..
  3. Interrogation of systems level mechanisms controlling DNA repair processes
    Nitin S Baliga; Fiscal Year: 2010
    ..e. a predictive model for regulatory mechanisms for repair. This basic model will serve as a template for designing systems approaches to model higher complexities of eukaryotic repair processes. ..