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Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1
Richard Bonneau, Nitin S Baliga, Eric W Deutsch, Paul Shannon, Leroy Hood
Genome Biol. 2004; 5(8): R52. Published online 2004 July 12. doi: 10.1186/gb-2004-5-8-r52
PMCID:
PMC507877
Abstract Full Text PDF–809K

Is Cited by the Following 17 Articles in this Archive:

The Proteome Folding Project: Proteome-scale prediction of structure and function
Kevin Drew, Patrick Winters, Glenn L. Butterfoss, Viktors Berstis, Keith Uplinger, Jonathan Armstrong, Michael Riffle, Erik Schweighofer, Bill Bovermann, David R. Goodlett, Trisha N. Davis, Dennis Shasha, Lars Malmström, Richard Bonneau
Genome Res. 2011 November; 21(11): 1981–1994. doi: 10.1101/gr.121475.111
PMCID:
PMC3205581
Abstract Full Text PDF–1.1M
Synergistic use of plant-prokaryote comparative genomics for functional annotations
Svetlana Gerdes, Basma El Yacoubi, Marc Bailly, Ian K Blaby, Crysten E Blaby-Haas, Linda Jeanguenin, Aurora Lara-Núñez, Anne Pribat, Jeffrey C Waller, Andreas Wilke, Ross Overbeek, Andrew D Hanson, Valérie de Crécy-Lagard
BMC Genomics. 2011; 12(Suppl 1): S2. Published online 2011 June 15. doi: 10.1186/1471-2164-12-S1-S2
PMCID:
PMC3223725
Abstract Full Text PDF–718K Supplementary Material
Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon
Amy K. Schmid, Min Pan, Kriti Sharma, Nitin S. Baliga
Nucleic Acids Res. 2011 April; 39(7): 2519–2533. Published online 2010 November 24. doi: 10.1093/nar/gkq1211
PMCID:
PMC3074139
Abstract Full Text PDF–4.4M Supplementary Material
Coordination of frontline defense mechanisms under severe oxidative stress
Amardeep Kaur, Phu T Van, Courtney R Busch, Courtney K Robinson, Min Pan, Wyming Lee Pang, David J Reiss, Jocelyne DiRuggiero, Nitin S Baliga
Mol Syst Biol. 2010; 6: 393. Published online 2010 July 27. doi: 10.1038/msb.2010.50
PMCID:
PMC2925529
Abstract Full Text PDF–2.6M Supplementary Material
Innate immune detection of the type III secretion apparatus through the NLRC4 inflammasome
Edward A. Miao, Dat P. Mao, Natalya Yudkovsky, Richard Bonneau, Cynthia G. Lorang, Sarah E. Warren, Irina A. Leaf, Alan Aderem
Proc Natl Acad Sci U S A. 2010 February 16; 107(7): 3076–3080. Published online 2010 February 1. doi: 10.1073/pnas.0913087107
PMCID:
PMC2840275
Abstract Full Text PDF–1.3M Supplementary Material
PSPP: A Protein Structure Prediction Pipeline for Computing Clusters
Michael S. Lee, Rajkumar Bondugula, Valmik Desai, Nela Zavaljevski, In-Chul Yeh, Anders Wallqvist, Jaques Reifman
PLoS One. 2009; 4(7): e6254. Published online 2009 July 16. doi: 10.1371/journal.pone.0006254
PMCID:
PMC2707601
Abstract Full Text PDF–919K
A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability
Amy K Schmid, David J Reiss, Min Pan, Tie Koide, Nitin S Baliga
Mol Syst Biol. 2009; 5: 282. Published online 2009 June 16. doi: 10.1038/msb.2009.40
PMCID:
PMC2710871
Abstract Full Text PDF–1.7M Supplementary Material
Halobacterium salinarum NRC-1 PeptideAtlas: strategies for targeted proteomics
Phu T. Van, Amy K. Schmid, Nichole L. King, Amardeep Kaur, Min Pan, Kenia Whitehead, Tie Koide, Marc T. Facciotti, Young-Ah Goo, Eric W. Deutsch, David J. Reiss, Parag Mallick, Nitin S. Baliga
J Proteome Res. Author manuscript; available in PMC 2009 September 1.
Published in final edited form as: J Proteome Res. 2008 September; 7(9): 3755–3764. Published online 2008 July 25. doi: 10.1021/pr800031f
PMCID:
PMC2643335
Abstract Full Text PDF–585K Supplementary Material
The anatomy of microbial cell state transitions in response to oxygen
Amy K. Schmid, David J. Reiss, Amardeep Kaur, Min Pan, Nichole King, Phu T. Van, Laura Hohmann, Daniel B. Martin, Nitin S. Baliga
Genome Res. 2007 October; 17(10): 1399–1413. doi: 10.1101/gr.6728007
PMCID:
PMC1987344
Abstract Full Text PDF–1.0M
Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment
Raja Jothi, Teresa M Przytycka, L Aravind
BMC Bioinformatics. 2007; 8: 173. Published online 2007 May 23. doi: 10.1186/1471-2105-8-173
PMCID:
PMC1904249
Abstract Full Text PDF–2.9M Supplementary Material
Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology
Lars Malmström, Michael Riffle, Charlie E. M Strauss, Dylan Chivian, Trisha N Davis, Richard Bonneau, David Baker
PLoS Biol. 2007 April; 5(4): e76. Published online 2007 March 20. doi: 10.1371/journal.pbio.0050076
PMCID:
PMC1828141
Abstract Full Text PDF–592K Supplementary Material
The Rab6 Effector Bicaudal D1 Associates with Chlamydia trachomatis Inclusions in a Biovar-Specific Manner
A. R. Moorhead, K. A. Rzomp, M. A. Scidmore
Infect Immun. 2007 February; 75(2): 781–791. Published online 2006 November 13. doi: 10.1128/IAI.01447-06
PMCID:
PMC1828475
Abstract Full Text PDF–535K
A systems view of haloarchaeal strategies to withstand stress from transition metals
Amardeep Kaur, Min Pan, Megan Meislin, Marc T. Facciotti, Raafat El-Gewely, Nitin S. Baliga
Genome Res. 2006 July; 16(7): 841–854. doi: 10.1101/gr.5189606
PMCID:
PMC1484451
Abstract Full Text PDF–1.4M
The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
Richard Bonneau, David J Reiss, Paul Shannon, Marc Facciotti, Leroy Hood, Nitin S Baliga, Vesteinn Thorsson
Genome Biol. 2006; 7(5): R36. Published online 2006 May 10. doi: 10.1186/gb-2006-7-5-r36
PMCID:
PMC1779511
Abstract Full Text PDF–829K Supplementary Material
Post-genomics of the model haloarchaeon Halobacterium sp. NRC-1
Shiladitya DasSarma, Brian R Berquist, James A Coker, Priya DasSarma, Jochen A Müller
Saline Systems. 2006; 2: 3. Published online 2006 March 16. doi: 10.1186/1746-1448-2-3
PMCID:
PMC1447603
Abstract Full Text PDF–1.0M
The Haloferax volcanii FtsY Homolog Is Critical for Haloarchaeal Growth but Does Not Require the A Domain
Alex Haddad, R. Wesley Rose, Mechthild Pohlschröder
J Bacteriol. 2005 June; 187(12): 4015–4022. doi: 10.1128/JB.187.12.4015-4022.2005
PMCID:
PMC1151737
Abstract Full Text PDF–174K
Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea
Nitin S. Baliga, Richard Bonneau, Marc T. Facciotti, Min Pan, Gustavo Glusman, Eric W. Deutsch, Paul Shannon, Yulun Chiu, Rueyhung Sting Weng, Rueichi Richie Gan, Pingliang Hung, Shailesh V. Date, Edward Marcotte, Leroy Hood, Wailap Victor Ng
Genome Res. 2004 November; 14(11): 2221–2234. doi: 10.1101/gr.2700304
Correction in:
Genome Res. 2004 December; 14(12): 2510.
PMCID:
PMC525680
Abstract Full Text PDF–472K Correction
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