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Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach
Michael Strong, Parag Mallick, Matteo Pellegrini, Michael J Thompson, David Eisenberg
Genome Biol. 2003; 4(9): R59. Published online 2003 August 29.
PMCID:
PMC193659
Abstract Full Text PDF–302K

Is Cited by the Following 29 Articles in this Archive:

The TB Structural Genomics Consortium: A decade of progress
Nicholas Chim, Jeff E. Habel, Jodie M. Johnston, Inna Krieger, Linda Miallau, Ramasamy Sankaranarayanan, Robert P. Morse, John Bruning, Stephanie Swanson, Haelee Kim, Chang-Yub Kim, Hongye Li, Esther M. Bulloch, Richard J. Payne, Alexandra Manos-Turvey, Li-Wei Hung, Edward N. Baker, J. Shaun Lott, Michael N.G. James, Thomas C. Terwilliger, David S. Eisenberg, James C. Sacchettini, Celia W. Goulding
Tuberculosis (Edinb) Author manuscript; available in PMC 2012 March 22.
Published in final edited form as: Tuberculosis (Edinb). 2011 March; 91(2): 155–172. Published online 2011 January 17. doi: 10.1016/j.tube.2010.11.009
PMCID:
PMC3310434
Abstract Full Text PDF–2.5M
A systematic study of genome context methods: calibration, normalization and combination
Luciana Ferrer, Joseph M Dale, Peter D Karp
BMC Bioinformatics. 2010; 11: 493. Published online 2010 October 1. doi: 10.1186/1471-2105-11-493
PMCID:
PMC3247869
Abstract Full Text PDF–4.0M Supplementary Material
An extracellular disulfide bond forming protein (DsbF) from Mycobacterium tuberculosis: Structural, biochemical and gene expression analysis
Nicholas Chim, Robert Riley, Juliana The, Soyeon Im, Brent Segelke, Tim Lekin, Minmin Yu, Li Wei Hung, Tom Terwilliger, Julian P. Whitelegge, Celia W. Goulding
J Mol Biol. Author manuscript; available in PMC 2011 March 12.
Published in final edited form as: J Mol Biol. 2010 March 12; 396(5): 1211–1226. Published online 2010 January 11. doi: 10.1016/j.jmb.2009.12.060
PMCID:
PMC2883863
Abstract Full Text PDF–3.2M
The Symbiosis Interactome: a computational approach reveals novel components, functional interactions and modules in Sinorhizobium meliloti
Ignacio Rodriguez-Llorente, Miguel A Caviedes, Mohammed Dary, Antonio J Palomares, Francisco M Cánovas, José M Peregrín-Alvarez
BMC Syst Biol. 2009; 3: 63. Published online 2009 June 16. doi: 10.1186/1752-0509-3-63
PMCID:
PMC2701930
Abstract Full Text PDF–1.2M Supplementary Material
A Complex-based Reconstruction of the Saccharomyces cerevisiae Interactome
Haidong Wang, Boyko Kakaradov, Sean R. Collins, Lena Karotki, Dorothea Fiedler, Michael Shales, Kevan M. Shokat, Tobias C. Walther, Nevan J. Krogan, Daphne Koller
Mol Cell Proteomics. 2009 June; 8(6): 1361–1381. doi: 10.1074/mcp.M800490-MCP200
PMCID:
PMC2690481
Abstract Full Text
Uncovering new signaling proteins and potential drug targets through the interactome analysis of Mycobacterium tuberculosis
Tao Cui, Lei Zhang, Xizhou Wang, Zheng-Guo He
BMC Genomics. 2009; 10: 118. Published online 2009 March 19. doi: 10.1186/1471-2164-10-118
PMCID:
PMC2671525
Abstract Full Text PDF–1.5M Supplementary Material
Bioinformatics Resources for the Study of Gene Regulation in Bacteria
Julio Collado-Vides, Heladia Salgado, Enrique Morett, Socorro Gama-Castro, Verónica Jiménez-Jacinto, Irma Martínez-Flores, Alejandra Medina-Rivera, Luis Muñiz-Rascado, Martín Peralta-Gil, Alberto Santos-Zavaleta
J Bacteriol. 2009 January; 191(1): 23–31. Published online 2008 October 31. doi: 10.1128/JB.01017-08
PMCID:
PMC2612416
Full Text PDF–2.4M
Predicting protein linkages in bacteria: Which method is best depends on task
Anis Karimpour-Fard, Sonia M Leach, Ryan T Gill, Lawrence E Hunter
BMC Bioinformatics. 2008; 9: 397. Published online 2008 September 24. doi: 10.1186/1471-2105-9-397
PMCID:
PMC2570368
Abstract Full Text PDF–1.7M
Identifying Cognate Binding Pairs among a Large Set of Paralogs: The Case of PE/PPE Proteins of Mycobacterium tuberculosis
Robert Riley, Matteo Pellegrini, David Eisenberg
PLoS Comput Biol. 2008 September; 4(9): e1000174. Published online 2008 September 12. doi: 10.1371/journal.pcbi.1000174
PMCID:
PMC2519833
Abstract Full Text PDF–954K Supplementary Material
The topology of the bacterial co-conserved protein network and its implications for predicting protein function
Anis Karimpour-Fard, Sonia M Leach, Lawrence E Hunter, Ryan T Gill
BMC Genomics. 2008; 9: 313. Published online 2008 June 30. doi: 10.1186/1471-2164-9-313
PMCID:
PMC2488357
Abstract Full Text PDF–687K Supplementary Material
Investigation of factors affecting prediction of protein-protein interaction networks by phylogenetic profiling
Anis Karimpour-Fard, Lawrence Hunter, Ryan T Gill
BMC Genomics. 2007; 8: 393. Published online 2007 October 29. doi: 10.1186/1471-2164-8-393
PMCID:
PMC2204017
Abstract Full Text PDF–797K Supplementary Material
InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes
Jingchun Sun, Yan Sun, Guohui Ding, Qi Liu, Chuan Wang, Youyu He, Tieliu Shi, Yixue Li, Zhongming Zhao
BMC Bioinformatics. 2007; 8: 414. Published online 2007 October 26. doi: 10.1186/1471-2105-8-414
PMCID:
PMC2238723
Abstract Full Text PDF–588K
Cross-species cluster co-conservation: a new method for generating protein interaction networks
Anis Karimpour-Fard, Corrella S Detweiler, Kimberly D Erickson, Lawrence Hunter, Ryan T Gill
Genome Biol. 2007; 8(9): R185. Published online 2007 September 5. doi: 10.1186/gb-2007-8-9-r185
PMCID:
PMC2375023
Abstract Full Text PDF–1.9M Supplementary Material
False positive reduction in protein-protein interaction predictions using gene ontology annotations
Mahmoud A Mahdavi, Yen-Han Lin
BMC Bioinformatics. 2007; 8: 262. Published online 2007 July 23. doi: 10.1186/1471-2105-8-262
PMCID:
PMC1941744
Abstract Full Text PDF–327K Supplementary Material
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
Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners
Benjamin A Shoemaker, Anna R Panchenko
PLoS Comput Biol. 2007 April; 3(4): e43. Published online 2007 April 27. doi: 10.1371/journal.pcbi.0030043
PMCID:
PMC1857810
Full Text PDF–315K
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families
Shibu Yooseph, Granger Sutton, Douglas B Rusch, Aaron L Halpern, Shannon J Williamson, Karin Remington, Jonathan A Eisen, Karla B Heidelberg, Gerard Manning, Weizhong Li, Lukasz Jaroszewski, Piotr Cieplak, Christopher S Miller, Huiying Li, Susan T Mashiyama, Marcin P Joachimiak, Christopher van Belle, John-Marc Chandonia, David A Soergel, Yufeng Zhai, Kannan Natarajan, Shaun Lee, Benjamin J Raphael, Vineet Bafna, Robert Friedman, Steven E Brenner, Adam Godzik, David Eisenberg, Jack E Dixon, Susan S Taylor, Robert L Strausberg, Marvin Frazier, J. Craig Venter
PLoS Biol. 2007 March; 5(3): e16. Published online 2007 March 13. doi: 10.1371/journal.pbio.0050016
PMCID:
PMC1821046
Abstract Full Text PDF–1.8M Supplementary Material
Operon Prediction for Sequenced Bacterial Genomes without Experimental Information
Nicholas H. Bergman, Karla D. Passalacqua, Philip C. Hanna, Zhaohui S. Qin
Appl Environ Microbiol. 2007 February; 73(3): 846–854. Published online 2006 November 22. doi: 10.1128/AEM.01686-06
PMCID:
PMC1800777
Abstract Full Text PDF–288K Supplementary Material
The Life-Cycle of Operons
Morgan N Price, Adam P Arkin, Eric J Alm
PLoS Genet. 2006 June; 2(6): e96. Published online 2006 June 23. doi: 10.1371/journal.pgen.0020096
Correction in:
PLoS Genet. 2006 July; 2(7): e126.
PMCID:
PMC1480536
Abstract Full Text PDF–536K Supplementary Material Correction
Toward the structural genomics of complexes: Crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis
Michael Strong, Michael R. Sawaya, Shuishu Wang, Martin Phillips, Duilio Cascio, David Eisenberg
Proc Natl Acad Sci U S A. 2006 May 23; 103(21): 8060–8065. Published online 2006 May 11. doi: 10.1073/pnas.0602606103
PMCID:
PMC1472429
Abstract Full Text PDF–1.7M Supplementary Material
Unique Transcriptome Signature of Mycobacterium tuberculosis in Pulmonary Tuberculosis
Helmy Rachman, Michael Strong, Timo Ulrichs, Leander Grode, Johannes Schuchhardt, Hans Mollenkopf, George A. Kosmiadi, David Eisenberg, Stefan H. E. Kaufmann
Infect Immun. 2006 February; 74(2): 1233–1242. doi: 10.1128/IAI.74.2.1233-1242.2006
PMCID:
PMC1360294
Abstract Full Text PDF–1.1M Supplementary Material
Phylogenetic detection of conserved gene clusters in microbial genomes
Yu Zheng, Brian P Anton, Richard J Roberts, Simon Kasif
BMC Bioinformatics. 2005; 6: 243. Published online 2005 October 3. doi: 10.1186/1471-2105-6-243
PMCID:
PMC1266350
Abstract Full Text PDF–352K
Assessing the limits of genomic data integration for predicting protein networks
Long J. Lu, Yu Xia, Alberto Paccanaro, Haiyuan Yu, Mark Gerstein
Genome Res. 2005 July; 15(7): 945–953. doi: 10.1101/gr.3610305
PMCID:
PMC1172038
Abstract Full Text PDF–1.3M
A universally applicable method of operon map prediction on minimally annotated genomes using conserved genomic context
Martin T. Edwards, Stuart C. G. Rison, Neil G. Stoker, Lorenz Wernisch
Nucleic Acids Res. 2005; 33(10): 3253–3262. Published online 2005 June 7. doi: 10.1093/nar/gki634
PMCID:
PMC1143694
Abstract Full Text PDF–261K
A novel method for accurate operon predictions in all sequenced prokaryotes
Morgan N. Price, Katherine H. Huang, Eric J. Alm, Adam P. Arkin
Nucleic Acids Res. 2005; 33(3): 880–892. Published online 2005 February 8. doi: 10.1093/nar/gki232
PMCID:
PMC549399
Abstract Full Text PDF–263K Supplementary Material
PredictRegulon: a web server for the prediction of the regulatory protein binding sites and operons in prokaryote genomes
Sailu Yellaboina, Jayashree Seshadri, M. Senthil Kumar, Akash Ranjan
Nucleic Acids Res. 2004 July 1; 32(Web Server issue): W318–W320. doi: 10.1093/nar/gkh364
PMCID:
PMC441502
Abstract Full Text PDF–58K
Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns
Galina V Glazko, Arcady R Mushegian
Genome Biol. 2004; 5(5): R32. Published online 2004 April 27.
PMCID:
PMC416468
Abstract Full Text PDF–609K Supplementary Material
Prolinks: a database of protein functional linkages derived from coevolution
Peter M Bowers, Matteo Pellegrini, Mike J Thompson, Joe Fierro, Todd O Yeates, David Eisenberg
Genome Biol. 2004; 5(5): R35. Published online 2004 April 16.
PMCID:
PMC416471
Abstract Full Text PDF–855K
Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps
Michael Strong, Thomas G. Graeber, Morgan Beeby, Matteo Pellegrini, Michael J. Thompson, Todd O. Yeates, David Eisenberg
Nucleic Acids Res. 2003 December 15; 31(24): 7099–7109. doi: 10.1093/nar/gkg924
PMCID:
PMC291866
Abstract Full Text PDF–457K Supplementary Material
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