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Baliga Lab Publications

2015

Imam, S., Schäuble S., Brooks A. N., Baliga N. S., & Price N. D. (2015).  Data-driven integration of genome-scale regulatory and metabolic network models.. Frontiers in microbiology. 6, 409. Abstract
Danziger, S. A., Reiss D. J., Ratushny A. V., Smith J. J., Plaisier C. L., Aitchison J. D., et al. (2015).  Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions.. BMC systems biology. 9 Suppl 2, S1. Abstract
Reiss, D. J., Plaisier C. L., Wu W. - J., & Baliga N. S. (2015).  cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism.. Nucleic acids research. Abstract
Turkarslan, S., Peterson E. J. R., Rustad T. R., Minch K. J., Reiss D. J., Morrison R., et al. (2015).  A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis. Scientific Data. 2, 150010.
Gomes-Filho, J. V., Zaramela L. S., da Italiani V. C. S., Baliga N. S., Vêncio R. Z. N., & Koide T. (2015).  Sense overlapping transcripts in IS 1341-type transposase genes are functional non-coding RNAs in archaea.. RNA biology. Abstract
Raman, A. V., & Baliga N. S. (2015).  The universe under a microscope.. Environmental microbiology reports. 7(1), 11-2.
Minch, K. J., Rustad T. R., Peterson E. J. R., Winkler J., Reiss D. J., Ma S., et al. (2015).  The DNA-binding network of Mycobacterium tuberculosis.. Nature communications. 6, 5829. Abstract

2014

Muller, E. E. L., Pinel N., Laczny C. C., Hoopmann M. R., Narayanasamy S., Lebrun L. A., et al. (2014).  Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage.. Nature communications. 5, 5603. Abstract
Ashworth, J., Bernard B., Reynolds S., Plaisier C. L., Shmulevich I., & Baliga N. S. (2014).  Structure-based predictions broadly link transcription factor mutations to gene expression changes in cancers.. Nucleic acids research. Abstract
Plaisier, C. L., Lo F. -yin, Ashworth J., Brooks A. N., Beer K. D., Kaur A., et al. (2014).  Evolution of context dependent regulation by expansion of feast/famine regulatory proteins.. BMC systems biology. 8(1), 122. Abstract
Rustad, T. R., Minch K. J., Ma S., Winkler J. K., Hobbs S., Hickey M., et al. (2014).  Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network.. Genome biology. 15(11), 502. Abstract
Peterson, E. J. R., Reiss D. J., Turkarslan S., Minch K. J., Rustad T., Plaisier C. L., et al. (2014).  A high-resolution network model for global gene regulation in Mycobacterium tuberculosis.. Nucleic acids research. 42(18), 11291-303. Abstract
Hillesland, K. L., Lim S., Flowers J. J., Turkarslan S., Pinel N., Zane G. M., et al. (2014).  Erosion of functional independence early in the evolution of a microbial mutualism.. Proceedings of the National Academy of Sciences of the United States of America. 111(41), 14822-7. Abstract
Ashworth, J., Plaisier C. L., Yin Lo F., Reiss D. J., & Baliga N. S. (2014).  Inference of expanded lrp-like feast/famine transcription factor targets in a non-model organism using protein structure-based prediction.. PloS one. 9(9), e107863. Abstract
Brooks, A. N., Reiss D. J., Allard A., Wu W. - J., Salvanha D. M., Plaisier C. L., et al. (2014).  A system-level model for the microbial regulatory genome.. Molecular systems biology. 10(7), 740. Abstract
Zaramela, L. S., Vêncio R. Z. N., Ten-Caten F., Baliga N. S., & Koide T. (2014).  Transcription Start Site Associated RNAs (TSSaRNAs) Are Ubiquitous in All Domains of Life.. PloS one. 9(9), e107680. Abstract
Beer, K. D., Wurtmann E. J., Pinel N., & Baliga N. S. (2014).  Model organisms retain an "ecological memory" of complex ecologically relevant environmental variation.. Applied and environmental microbiology. 80(6), 1821-31. Abstract
Wurtmann, E. J., Ratushny A. V., Pan M., Beer K. D., Aitchison J. D., & Baliga N. S. (2014).  An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation.. Molecular microbiology. 92(2), 369-82. Abstract
Ekici, S., Turkarslan S., Pawlik G., Dancis A., Baliga N. S., Koch H. - G., et al. (2014).  Intracytoplasmic copper homeostasis controls cytochrome C oxidase production.. mBio. 5(1),  Abstract
Turkarslan, S., Wurtmann E. J., Wu W. - J., Jiang N., Bare C. J., Foley K., et al. (2014).  Network portal: a database for storage, analysis and visualization of biological networks.. Nucleic acids research. Abstract
Danziger, S. A., Ratushny A. V., Smith J. J., Saleem R. A., Wan Y., Arens C. E., et al. (2014).  Molecular mechanisms of system responses to novel stimuli are predictable from public data.. Nucleic acids research. Abstract

2013

Beer, K. D., Orellana M. V., & Baliga N. S. (2013).  Modeling the evolution of C4 photosynthesis.. Cell. 153(7), 1427-9. Abstract
Yoon, S. H., Turkarslan S., Reiss D. J., Pan M., Burn J. A., Costa K. C., et al. (2013).  A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen.. Genome research. Abstract
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., & 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
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
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
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

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
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
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

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., 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