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A proteome-wide protein interaction map for Campylobacter jejuni
Jodi R Parrish, Jingkai Yu, Guozhen Liu, Julie A Hines, Jason E Chan, Bernie A Mangiola, Huamei Zhang, Svetlana Pacifico, Farshad Fotouhi, Victor J DiRita, Trey Ideker, Phillip Andrews, Russell L Finley, Jr
Genome Biol. 2007; 8(7): R130. Published online 2007 July 5. doi: 10.1186/gb-2007-8-7-r130
PMCID:
PMC2323224
Abstract Full Text PDF–1.5M Supplementary Material
 Is Cited by the Following 27 Articles in this Archive:
Polar Flagellar Biosynthesis and a Regulator of Flagellar Number Influence Spatial Parameters of Cell Division in Campylobacter jejuni
Murat Balaban, David R. Hendrixson
PLoS Pathog. 2011 December; 7(12): e1002420. Published online 2011 December 1. doi: 10.1371/journal.ppat.1002420
PMCID:
PMC3228812
Abstract Full Text PDF–1.5M Supplementary Material
Dominating Biological Networks
Tijana Milenković, Vesna Memišević, Anthony Bonato, Nataša Pržulj
PLoS One. 2011; 6(8): e23016. Published online 2011 August 26. doi: 10.1371/journal.pone.0023016
PMCID:
PMC3162560
Abstract Full Text PDF–779K
The Campylobacter jejuni Transcriptional Regulator Cj1556 Plays a Role in the Oxidative and Aerobic Stress Response and Is Important for Bacterial Survival In Vivo
Ozan Gundogdu, Dominic C. Mills, Abdi Elmi, Melissa J. Martin, Brendan W. Wren, Nick Dorrell
J Bacteriol. 2011 August; 193(16): 4238–4249. doi: 10.1128/JB.05189-11
PMCID:
PMC3147681
Abstract Full Text PDF–902K
Genome Annotation and Intraviral Interactome for the Streptococcus pneumoniae Virulent Phage Dp-1
Mourad Sabri, Roman Häuser, Marc Ouellette, Jing Liu, Mohammed Dehbi, Greg Moeck, Ernesto García, Björn Titz, Peter Uetz, Sylvain Moineau
J Bacteriol. 2011 January; 193(2): 551–562. Published online 2010 November 19. doi: 10.1128/JB.01117-10
PMCID:
PMC3019816
Abstract Full Text PDF–1.3M Supplementary Material
Protein Networks Reveal Detection Bias and Species Consistency When Analysed by Information-Theoretic Methods
Luis P. Fernandes, Alessia Annibale, Jens Kleinjung, Anthony C. C. Coolen, Franca Fraternali
PLoS One. 2010; 5(8): e12083. Published online 2010 August 18. doi: 10.1371/journal.pone.0012083
PMCID:
PMC2923596
Abstract Full Text PDF–4.3M Supplementary Material
Protein-protein interaction map is a key gateway into liver regeneration
Chao Xie, Jin Gao, Run-Zhi Zhu, Yun-Sheng Yuan, Hong-Lin He, Qiu-Shi Huang, Wei Han, Yan Yu
World J Gastroenterol. 2010 July 28; 16(28): 3491–3498. Published online 2010 July 28. doi: 10.3748/wjg.v16.i28.3491
PMCID:
PMC2909548
Abstract Full Text PDF–1023K
Reply to Robert et al.: Model criticism informs model choice and model comparison
Oliver Ratmann, Christophe Andrieu, Carsten Wiuf, Sylvia Richardson
Proc Natl Acad Sci U S A. 2010 January 19; 107(3): E6–E7. Published online 2010 January 14. doi: 10.1073/pnas.0912887107
PMCID:
PMC2824293
Full Text PDF–574K
Tailored graph ensembles as proxies or null models for real networks I: tools for quantifying structure
A Annibale, ACC Coolen, LP Fernandes, F Fraternali, J Kleinjung
J Phys A Math Gen. Author manuscript; available in PMC 2010 September 14.
Published in final edited form as: J Phys A Math Gen. 2009 December 4; 42(48): 485001. doi: 10.1088/1751-8113/42/48/485001
PMCID:
PMC2938474
Abstract Full Text PDF–2.6M
Computer applications for prediction of protein–protein interactions and rational drug design
Solène Grosdidier, Max Totrov, Juan Fernández-Recio
Adv Appl Bioinforma Chem. 2009; 2: 101–123. Published online 2009 November 10.
PMCID:
PMC3169948
Abstract Full Text PDF–15M
From evidence to inference: probing the evolution of protein interaction networks
Oliver Ratmann, Carsten Wiuf, John W. Pinney
HFSP J. 2009 October; 3(5): 290–306. Published online 2009 October 19. doi: 10.2976/1.3167215
PMCID:
PMC2801530
Abstract Full Text PDF–380K
Evolutionarily Conserved Herpesviral Protein Interaction Networks
Even Fossum, Caroline C. Friedel, Seesandra V. Rajagopala, Björn Titz, Armin Baiker, Tina Schmidt, Theo Kraus, Thorsten Stellberger, Christiane Rutenberg, Silpa Suthram, Sourav Bandyopadhyay, Dietlind Rose, Albrecht von Brunn, Mareike Uhlmann, Christine Zeretzke, Yu-An Dong, Hélène Boulet, Manfred Koegl, Susanne M. Bailer, Ulrich Koszinowski, Trey Ideker, Peter Uetz, Ralf Zimmer, Jürgen Haas
PLoS Pathog. 2009 September; 5(9): e1000570. Published online 2009 September 4. doi: 10.1371/journal.ppat.1000570
PMCID:
PMC2731838
Abstract Full Text PDF–1.5M Supplementary Material
Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins
Pingzhao Hu, Sarath Chandra Janga, Mohan Babu, J. Javier Díaz-Mejía, Gareth Butland, Wenhong Yang, Oxana Pogoutse, Xinghua Guo, Sadhna Phanse, Peter Wong, Shamanta Chandran, Constantine Christopoulos, Anaies Nazarians-Armavil, Negin Karimi Nasseri, Gabriel Musso, Mehrab Ali, Nazila Nazemof, Veronika Eroukova, Ashkan Golshani, Alberto Paccanaro, Jack F Greenblatt, Gabriel Moreno-Hagelsieb, Andrew Emili
PLoS Biol. 2009 April; 7(4): e1000096. Published online 2009 April 28. doi: 10.1371/journal.pbio.1000096
PMCID:
PMC2672614
Abstract Full Text Supplementary Material
A Rice Kinase-Protein Interaction Map
Xiaodong Ding, Todd Richter, Mei Chen, Hiroaki Fujii, Young Su Seo, Mingtang Xie, Xianwu Zheng, Siddhartha Kanrar, Rebecca A. Stevenson, Christopher Dardick, Ying Li, Hao Jiang, Yan Zhang, Fahong Yu, Laura E. Bartley, Mawsheng Chern, Rebecca Bart, Xiuhua Chen, Lihuang Zhu, William G. Farmerie, Michael Gribskov, Jian-Kang Zhu, Michael E. Fromm, Pamela C. Ronald, Wen-Yuan Song
Plant Physiol. 2009 March; 149(3): 1478–1492. doi: 10.1104/pp.108.128298
PMCID:
PMC2649385
Abstract Full Text PDF–717K Supplementary Material
The development of an affinity evaluation and prediction system by using protein–protein docking simulations and parameter tuning
Koki Tsukamoto, Tatsuya Yoshikawa, Kiyonobu Yokota, Yuichiro Hourai, Kazuhiko Fukui
Adv Appl Bioinforma Chem. 2009; 2: 1–15. Published online 2009 January 12.
PMCID:
PMC3169950
Abstract Full Text PDF–1.2M
Michigan molecular interactions r2: from interacting proteins to pathways
V. Glenn Tarcea, Terry Weymouth, Alex Ade, Aaron Bookvich, Jing Gao, Vasudeva Mahavisno, Zach Wright, Adriane Chapman, Magesh Jayapandian, Arzucan Özgür, Yuanyuan Tian, Jim Cavalcoli, Barbara Mirel, Jignesh Patel, Dragomir Radev, Brian Athey, David States, H. V. Jagadish
Nucleic Acids Res. 2009 January; 37(Database issue): D642–D646. Published online 2009 January. doi: 10.1093/nar/gkn722
PMCID:
PMC2686565
Abstract Full Text PDF–3.5M
Cost effective strategies for completing the Interactome
Ariel S. Schwartz, Jingkai Yu, Kyle R. Gardenour, Russell L. Finley, Jr., Trey Ideker
Nat Methods. Author manuscript; available in PMC 2009 July 1.
Published in final edited form as: Nat Methods. 2009 January; 6(1): 55–61. Published online 2008 December 14. doi: 10.1038/nmeth.1283
PMCID:
PMC2613168
Abstract Full Text PDF–2.5M Supplementary Material
Functional Proteomics of Arabidopsis thaliana Guard Cells Uncovers New Stomatal Signaling Pathways
Zhixin Zhao, Wei Zhang, Bruce A. Stanley, Sarah M. Assmann
Plant Cell. 2008 December; 20(12): 3210–3226. doi: 10.1105/tpc.108.063263
PMCID:
PMC2630442
Abstract Full Text PDF–856K Supplementary Material
Combining multiple positive training sets to generate confidence scores for protein–protein interactions
Jingkai Yu, Russell L. Finley, Jr
Bioinformatics. 2009 January 1; 25(1): 105–111. Published online 2008 November 14. doi: 10.1093/bioinformatics/btn597
PMCID:
PMC2638943
Abstract Full Text PDF–256K Supplementary Material
The prediction of protein-protein interaction networks in rice blast fungus
Fei He, Yan Zhang, Hao Chen, Ziding Zhang, You-Liang Peng
BMC Genomics. 2008; 9: 519. Published online 2008 November 2. doi: 10.1186/1471-2164-9-519
PMCID:
PMC2601049
Abstract Full Text PDF–1.1M Supplementary Material
DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions
Jingkai Yu, Svetlana Pacifico, Guozhen Liu, Russell L Finley, Jr
BMC Genomics. 2008; 9: 461. Published online 2008 October 7. doi: 10.1186/1471-2164-9-461
PMCID:
PMC2572628
Abstract Full Text PDF–860K
iRefIndex: A consolidated protein interaction database with provenance
Sabry Razick, George Magklaras, Ian M Donaldson
BMC Bioinformatics. 2008; 9: 405. Published online 2008 September 30. doi: 10.1186/1471-2105-9-405
PMCID:
PMC2573892
Abstract Full Text PDF–555K
MPI-LIT: a literature-curated dataset of microbial binary protein--protein interactions
Seesandra V. Rajagopala, Johannes Goll, N.D. Deve Gowda, Kumar C. Sunil, Björn Titz, Arnab Mukherjee, Sharmila S. Mary, Naresh Raviswaran, Chetan S. Poojari, Srinivas Ramachandra, Svetlana Shtivelband, Stephen M. Blazie, Julia Hofmann, Peter Uetz
Bioinformatics. 2008 November 15; 24(22): 2622–2627. Published online 2008 September 11. doi: 10.1093/bioinformatics/btn481
PMCID:
PMC2720748
Abstract Full Text PDF–124K Supplementary Material
Characterization of CetA and CetB, a bipartite energy taxis system in Campylobacter jejuni
Kathryn T Elliott, Victor J DiRita
Mol Microbiol. 2008 September; 69(5): 1091–1103. Published online 2008 July 23. doi: 10.1111/j.1365-2958.2008.06357.x
PMCID:
PMC2628428
Abstract Full Text PDF–438K
Probing the Extent of Randomness in Protein Interaction Networks
Joseph Ivanic, Anders Wallqvist, Jaques Reifman
PLoS Comput Biol. 2008 July; 4(7): e1000114. Published online 2008 July 11. doi: 10.1371/journal.pcbi.1000114
PMCID:
PMC2527968
Abstract Full Text PDF–462K Supplementary Material
The Binary Protein Interactome of Treponema pallidum – The Syphilis Spirochete
Björn Titz, Seesandra V. Rajagopala, Johannes Goll, Roman Häuser, Matthew T. McKevitt, Timothy Palzkill, Peter Uetz
PLoS ONE. 2008; 3(5): e2292. Published online 2008 May 28. doi: 10.1371/journal.pone.0002292
PMCID:
PMC2386257
Abstract Full Text PDF–1.1M Supplementary Material
Bacteriome.org—an integrated protein interaction database for E. coli
Chong Su, Jose M. Peregrin-Alvarez, Gareth Butland, Sadhna Phanse, Vincent Fong, Andrew Emili, John Parkinson
Nucleic Acids Res. 2008 January; 36(Database issue): D632–D636. Published online 2008 January. doi: 10.1093/nar/gkm807
PMCID:
PMC2238847
Abstract Full Text PDF–492K
A Large-scale Protein–protein Interaction Analysis in Synechocystis sp. PCC6803
Shusei Sato, Yoshikazu Shimoda, Akiko Muraki, Mitsuyo Kohara, Yasukazu Nakamura, Satoshi Tabata
DNA Res. 2007; 14(5): 207–216. Published online 2007 November 13. doi: 10.1093/dnares/dsm021
PMCID:
PMC2779905
Abstract Full Text PDF–718K
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