Baliga Lab Publications

2013

Orellana, M. V., Pang W. L., Durand P. M., Whitehead K., & Baliga N. S. (2013). A role for programmed cell death in the microbial loop.. PloS one. 8(5), e62595. Abstract

Ashworth, J., Coesel S., Lee A., Armbrust V. E., Orellana M. V., & Baliga N. S. (2013). Genome-wide diel growth state transitions in the diatom Thalassiosira pseudonana.. Proceedings of the National Academy of Sciences of the United States of America. 110(18), 7518-23. Abstract

Pang, L. W., Kaur A., Ratushny A. V., Cvetkovic A., Kumar S., Pan M., et al. (2013). Metallochaperones Regulate Intracellular Copper Levels. PLoS Comput BiolPLoS Comput Biol. 9(1), e1002880 - . Abstract

Costa, K. C., Yoon S. H., Pan M., Burn J. A., Baliga N. S., & Leigh J. A. (2013). Effects of H2 and formate on growth yield and regulation of methanogenesis in Methanococcus maripaludis.. Journal of bacteriology. Abstract

2012

Rustad, T. R., Minch K. J., Brabant W., Winkler J. K., Reiss D. J., Baliga N. S., et al. (2012). Global analysis of mRNA stability in Mycobacterium tuberculosis.. Nucleic acids research. Abstract

Bare, J. C., & Baliga N. S. (2012). Architecture for interoperable software in biology.. Briefings in bioinformatics. Abstract

Muller, E. E. L., Pinel N., Gillece J. D., Schupp J. M., Price L. B., Engelthaler D. M., et al. (2012). Genome Sequence of "Candidatus Microthrix parvicella" Bio17-1, a Long-Chain-Fatty-Acid-Accumulating Filamentous Actinobacterium from a Biological Wastewater Treatment Plant.. Journal of bacteriology. 194(23), 6670-1. Abstract

Plaisier, C. L., Pan M., & Baliga N. S. (2012). A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers.. Genome research. Abstract

Plaisier, C. L., & Baliga N. S. (2012). Harnessing the power of human tumor-derived cell lines for the rational design of cancer therapies. Pigment Cell & Melanoma Research. 25(4), 406 - 408.

Edgar, R. S., Green E. W., Zhao Y., van Ooijen G., Olmedo M., Qin X., et al. (2012). Peroxiredoxins are conserved markers of circadian rhythms.. Nature. 485(7399), 459-64. Abstract

2011

Ashworth, J., Wurtmann E. J., & Baliga N. S. (2011). Reverse engineering systems models of regulation: discovery, prediction and mechanisms.. Current opinion in biotechnology. Abstract

Turkarslan, S., Reiss D. J., Gibbins G., Su W. L., Pan M., Bare C. J., et al. (2011). Niche adaptation by expansion and reprogramming of general transcription factors.. Molecular systems biology. 7, 554. Abstract

Yoon, S. H., Reiss D. J., Bare C. J., Tenenbaum D., Pan M., Slagel J., et al. (2011). Parallel evolution of transcriptome architecture during genome reorganization.. Genome research. Abstract

Plaisier, C. L., Bare C. J., & Baliga N. S. (2011). miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling. Nucleic Acids Research. Abstract

Robinson, C. K., Webb K., Kaur A., Jaruga P., Dizdaroglu M., Baliga N. S., et al. (2011). A Major Role for Non-Enzymatic Antioxidant Processes in the Radioresistance of Halobacterium salinarum.. Journal of bacteriology. Abstract

Schmid, A. K., Pan M., Sharma K., & Baliga N. S. (2011). Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon.. Nucleic acids research. Abstract

Tautenhahn, R., Patti G. J., Kalisiak E., Miyamoto T., Schmidt M., Yin Lo F., et al. (2011). metaXCMS: Second-Order Analysis of Untargeted Metabolomics Data.. Analytical chemistry. Abstract

2010

Gehlenborg, N., O'Donoghue S. I., Baliga N. S., Goesmann A., Hibbs M. A., Kitano H., et al. (2010). Visualization of omics data for systems biology.. Nature methods. 7(3 Suppl), S56-68. Abstract

Kaur, A., Van P. T., Busch C. R., Robinson C. K., Pan M., Pang W. L., et al. (2010). Coordination of frontline defense mechanisms under severe oxidative stress.. Molecular systems biology. 6, 393. Abstract

Brooks, A. N., Turkarslan S., Beer K. D., Yin Lo F., & Baliga N. S. (2010). Adaptation of cells to new environments.. Wiley interdisciplinary reviews. Systems biology and medicine. Abstract

Facciotti, M. T., Pang W. L., Lo F. -yin, Whitehead K., Koide T., Masumura K. -ichi, et al. (2010). Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis.. BMC systems biology. 4, 64. Abstract

Bare, C. J., Koide T., Reiss D. J., Tenenbaum D., & Baliga N. S. (2010). Integration and visualization of systems biology data in context of the genome.. BMC bioinformatics. 11, 382. Abstract

Tenenbaum, D., Bare C. J., & Baliga N. S. (2010). GTC: A web server for integrating systems biology data with web tools and desktop applications.. Source code for biology and medicine. 5, 7. Abstract

2009

Koide, T., Pang W. L., & Baliga N. S. (2009). The role of predictive modelling in rationally re-engineering biological systems.. Nature reviews. Microbiology. 7(4), 297-305. Abstract

Koide, T., Reiss D. J., Bare C. J., Pang W. L., Facciotti M. T., Schmid A. K., et al. (2009). Prevalence of transcription promoters within archaeal operons and coding sequences.. Molecular systems biology. 5, 285. Abstract

Schmid, A. K., Reiss D. J., Pan M., Koide T., & Baliga N. S. (2009). A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability.. Molecular systems biology. 5, 282. Abstract

Whitehead, K., Pan M., Masumura K. -ichi, Bonneau R., & Baliga N. S. (2009). Diurnally entrained anticipatory behavior in archaea.. PloS one. 4(5), e5485. Abstract

2008

Van, P. T., Schmid A. K., King N. L., Kaur A., Pan M., Whitehead K., et al. (2008). Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage.. Journal of proteome research. 7(9), 3755-64. Abstract

Baliga, N. S. (2008). Systems biology. The scale of prediction.. Science (New York, N.Y.). 320(5881), 1297-8.

Rubio, E. D., Reiss D. J., Welcsh P. L., Disteche C. M., Filippova G. N., Baliga N. S., et al. (2008). CTCF physically links cohesin to chromatin.. Proceedings of the National Academy of Sciences of the United States of America. 105(24), 8309-14. Abstract

Reiss, D. J., Facciotti M. T., & Baliga N. S. (2008). Model-based deconvolution of genome-wide DNA binding.. Bioinformatics (Oxford, England). 24(3), 396-403. Abstract

2007

Schmid, A. K., Reiss D. J., Kaur A., Pan M., King N., Van P. T., et al. (2007). The anatomy of microbial cell state transitions in response to oxygen.. Genome research. 17(10), 1399-413. Abstract

Facciotti, M. T., Reiss D. J., Pan M., Kaur A., Vuthoori M., Bonneau R., et al. (2007). General transcription factor specified global gene regulation in archaea.. Proceedings of the National Academy of Sciences of the United States of America. 104(11), 4630-5. Abstract

Bonneau, R., Facciotti M. T., Reiss D. J., Schmid A. K., Pan M., Kaur A., et al. (2007). A predictive model for transcriptional control of physiology in a free living cell.. Cell. 131(7), 1354-65. Abstract

Bare, C. J., Shannon P. T., Schmid A. K., & Baliga N. S. (2007). The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications.. BMC bioinformatics. 8, 456. Abstract

2006

Kaur, A., Pan M., Meislin M., Facciotti M. T., El-Gewely R., & Baliga N. S. (2006). A systems view of haloarchaeal strategies to withstand stress from transition metals.. Genome research. 16(7), 841-54. Abstract

Shannon, P. T., Reiss D. J., Bonneau R., & Baliga N. S. (2006). The Gaggle: an open-source software system for integrating bioinformatics software and data sources.. BMC bioinformatics. 7, 176. Abstract

Reiss, D. J., Baliga N. S., & Bonneau R. (2006). Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks.. BMC bioinformatics. 7, 280. Abstract

Whitehead, K., Kish A., Pan M., Kaur A., Reiss D. J., King N., et al. (2006). An integrated systems approach for understanding cellular responses to gamma radiation.. Molecular systems biology. 2, 47. Abstract

Bonneau, R., Reiss D. J., Shannon P., Facciotti M., Hood L., Baliga N. S., et al. (2006). The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo.. Genome biology. 7(5), R36. Abstract

2005

Iyer, R., Baliga N. S., & Camilli A. (2005). Catabolite control protein A (CcpA) contributes to virulence and regulation of sugar metabolism in Streptococcus pneumoniae.. Journal of bacteriology. 187(24), 8340-9. Abstract

2004

Baliga, N. S., Bonneau R., Facciotti M. T., Pan M., Glusman G., Deutsch E. W., et al. (2004). Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea.. Genome research. 14(11), 2221-34. Abstract

Facciotti, M. T., Cheung V. S., Lunde C. S., Rouhani S., Baliga N. S., & Glaeser R. M. (2004). Specificity of anion binding in the substrate pocket of bacteriorhodopsin.. Biochemistry. 43(17), 4934-43. Abstract

Baliga, N. S., Bjork S. J., Bonneau R., Pan M., Iloanusi C., Kottemann M. C. H., et al. (2004). Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.. Genome research. 14(6), 1025-35. Abstract

Goo, Y. A., Roach J., Glusman G., Baliga N. S., Deutsch K., Pan M., et al. (2004). Low-pass sequencing for microbial comparative genomics.. BMC genomics. 5(1), 3. Abstract

Bonneau, R., Baliga N. S., Deutsch E. W., Shannon P., & Hood L. (2004). Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1.. Genome biology. 5(8), R52. Abstract

2003

Shannon, P., Markiel A., Ozier O., Baliga N. S., Wang J. T., Ramage D., et al. (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks.. Genome research. 13(11), 2498-504. Abstract

Goo, Y. A., Yi E. C., Baliga N. S., Tao W. A., Pan M., Aebersold R., et al. (2003). Proteomic analysis of an extreme halophilic archaeon, Halobacterium sp. NRC-1.. Molecular & cellular proteomics : MCP. 2(8), 506-24. Abstract

Weston, A. D., Baliga N. S., Bonneau R., & Hood L. (2003). Systems approaches applied to the study of Saccharomyces cerevisiae and Halobacterium sp.. Cold Spring Harbor symposia on quantitative biology. 68, 345-57.

2002

Baliga, N. S., Pan M., Goo Y. A., Yi E. C., Goodlett D. R., Dimitrov K., et al. (2002). Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach.. Proceedings of the National Academy of Sciences of the United States of America. 99(23), 14913-8. Abstract

2001

Baliga, N. S., Kennedy S. P., Ng W. V., Hood L., & Dassarma S. (2001). Genomic and genetic dissection of an archaeal regulon.. Proceedings of the National Academy of Sciences of the United States of America. 98(5), 2521-5. Abstract

Baliga, N. S. (2001). Promoter analysis by saturation mutagenesis.. Biological procedures online. 3, 64-69. Abstract

Dassarma, S., Kennedy S. P., Berquist B., Victor Ng W., Baliga N. S., Spudich J. L., et al. (2001). Genomic perspective on the photobiology of Halobacterium species NRC-1, a phototrophic, phototactic, and UV-tolerant haloarchaeon.. Photosynthesis research. 70(1), 3-17. Abstract

2000

Ng, W. V., Kennedy S. P., Mahairas G. G., Berquist B., Pan M., Shukla H. D., et al. (2000). Genome sequence of Halobacterium species NRC-1.. Proceedings of the National Academy of Sciences of the United States of America. 97(22), 12176-81. Abstract

Baliga, N. S., & Dassarma S. (2000). Saturation mutagenesis of the haloarchaeal bop gene promoter: identification of DNA supercoiling sensitivity sites and absence of TFB recognition element and UAS enhancer activity.. Molecular microbiology. 36(5), 1175-83. Abstract

Baliga, N. S., Goo Y. A., Ng W. V., Hood L., Daniels C. J., & Dassarma S. (2000). Is gene expression in Halobacterium NRC-1 regulated by multiple TBP and TFB transcription factors?. Molecular microbiology. 36(5), 1184-5.

1999

Baliga, N. S., & Dassarma S. (1999). Saturation mutagenesis of the TATA box and upstream activator sequence in the haloarchaeal bop gene promoter.. Journal of bacteriology. 181(8), 2513-8. Abstract

Featured

Bonneau R, Facciotti MT, Reiss DJ, Schmid AK, Pan M, Kaur A, et al. A predictive model for transcriptional control of physiology in a free living cell. Cell. 2007;131(7):1354-65. Abstract

Facciotti MT, Reiss DJ, Pan M, Kaur A, Vuthoori M, Bonneau R, et al. General transcription factor specified global gene regulation in archaea. Proc Natl Acad Sci USA. 2007;104(11):4630-5. Abstract

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