Research Topics
| NITIN BALIGASummaryAffiliation: Institute for Systems Biology Country: USA Publications
Research Grants
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Detail Information
Publications
The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novoRichard 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...- Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1Richard 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... 
Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysisMarc 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...- Low-pass sequencing for microbial comparative genomicsYoung 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... - The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applicationsJ 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... - Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networksDavid 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... - Integration and visualization of systems biology data in context of the genomeJ 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... - The Gaggle: an open-source software system for integrating bioinformatics software and data sourcesPaul 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... - Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approachNitin 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... - Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead SeaNitin 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... 
Systems biology. The scale of predictionNitin S Baliga
Institute for Systems Biology, 1441 N. 34th Street, Seattle, WA 98103, USA
Science 320:1297-8. 2008- GTC: A web server for integrating systems biology data with web tools and desktop applicationsDan Tenenbaum
Institute for Systems Biology, 1441 N, 34th St, Seattle, WA USA
Source Code Biol Med 5:7. 2010.... - Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1Nitin S Baliga
Institute for Systems Biology, Seattle, Washington 98103, USA
Genome Res 14:1025-35. 2004.... - A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availabilityAmy 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... - Cytoscape: a software environment for integrated models of biomolecular interaction networksPaul Shannon
Institute for Systems Biology, Seattle, Washington 98103, USA
Genome Res 13:2498-504. 2003.... - Prevalence of transcription promoters within archaeal operons and coding sequencesTie 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... - Model-based deconvolution of genome-wide DNA bindingDavid J Reiss
Institute for Systems Biology, 1441 N 34th St Seattle, WA 98103 8904, USA
Bioinformatics 24:396-403. 2008.... - General transcription factor specified global gene regulation in archaeaMarc 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.... - Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coveragePhu 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... - An integrated systems approach for understanding cellular responses to gamma radiationKenia Whitehead
Institute for Systems Biology, Seattle, WA 98103-8904, USA
Mol Syst Biol 2:47. 2006.... - The anatomy of microbial cell state transitions in response to oxygenAmy 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... - A systems view of haloarchaeal strategies to withstand stress from transition metalsAmardeep Kaur
Institute for Systems Biology, Seattle, Washington 98103-8904, USA
Genome Res 16:841-54. 2006.... - Proteomic analysis of an extreme halophilic archaeon, Halobacterium sp. NRC-1Young Ah Goo
Institute for Systems Biology, Seattle, WA 98103, USA
Mol Cell Proteomics 2:506-24. 2003.... - Coordination of frontline defense mechanisms under severe oxidative stressAmardeep Kaur
Institute for Systems Biology, Seattle, WA 98103, USA
Mol Syst Biol 6:393. 2010.... - Diurnally entrained anticipatory behavior in archaeaKenia Whitehead
Institute for Systems Biology, Seattle, Washington, United States of America
PLoS ONE 4:e5485. 2009.... - The role of predictive modelling in rationally re-engineering biological systemsTie 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... - Catabolite control protein A (CcpA) contributes to virulence and regulation of sugar metabolism in Streptococcus pneumoniaeRamkumar 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... - Specificity of anion binding in the substrate pocket of bacteriorhodopsinMarc 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... - CTCF physically links cohesin to chromatinEric 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... - A predictive model for transcriptional control of physiology in a free living cellRichard 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...
Research Grants
- Interrogation of systems level mechanisms controlling DNA repair processesNITIN 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. ..
- Interrogation of systems level mechanisms controlling DNA repair processesNITIN 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. ..
- Interrogation of systems level mechanisms controlling DNA repair processesNitin 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. ..