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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
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 Is Cited by the Following 76 Articles in this Archive:
SAFE Software and FED Database to Uncover Protein-Protein Interactions using Gene Fusion Analysis
Dimosthenis Tsagrasoulis, Vasilis Danos, Maria Kissa, Philip Trimpalis, V. Lila Koumandou, Amalia D. Karagouni, Athanasios Tsakalidis, Sophia Kossida
Evol Bioinform Online. 2012; 8: 47–60. Published online 2011 December 18. doi: 10.4137/EBO.S8018
PMCID:
PMC3256994
Abstract Full Text PDF–3.3M Supplementary Material
Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters
Thadeous Kacmarczyk, Peter Waltman, Ashley Bate, Patrick Eichenberger, Richard Bonneau
PLoS Comput Biol. 2011 December; 7(12): e1002228. Published online 2011 December 1. doi: 10.1371/journal.pcbi.1002228
PMCID:
PMC3228777
Abstract Full Text PDF–4.3M Supplementary Material
Global protein interactome exploration through mining genome-scale data in Arabidopsis thaliana
Feng Xu, Guang Li, Chen Zhao, Yuhua Li, Peng Li, Jian Cui, Youping Deng, Tieliu Shi
BMC Genomics. 2010; 11(Suppl 2): S2. Published online 2010 November 2. doi: 10.1186/1471-2164-11-S2-S2
PMCID:
PMC2975419
Abstract Full Text PDF–637K Supplementary Material
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
Multi-species integrative biclustering
Peter Waltman, Thadeous Kacmarczyk, Ashley R Bate, Daniel B Kearns, David J Reiss, Patrick Eichenberger, Richard Bonneau
Genome Biol. 2010; 11(9): R96. Published online 2010 September 29. doi: 10.1186/gb-2010-11-9-r96
PMCID:
PMC2965388
Abstract Full Text PDF–2.6M Supplementary Material
Finding the “Dark Matter” in Human and Yeast Protein Network Prediction and Modelling
Juan A. G. Ranea, Ian Morilla, Jon G. Lees, Adam J. Reid, Corin Yeats, Andrew B. Clegg, Francisca Sanchez-Jimenez, Christine Orengo
PLoS Comput Biol. 2010 September; 6(9): e1000945. Published online 2010 September 23. doi: 10.1371/journal.pcbi.1000945
PMCID:
PMC2944794
Abstract Full Text PDF–3.4M Supplementary Material
Synthetic Lethal Screen of an EGFR-Centered Network to Improve Targeted Therapies
Igor Astsaturov, Vladimir Ratushny, Anna Sukhanova, Margret B. Einarson, Tetyana Bagnyukova, Yan Zhou, Karthik Devarajan, Joshua S. Silverman, Nadezhda Tikhmyanova, Natalya Skobeleva, Anna Pecherskaya, Rochelle E. Nasto, Catherine Sharma, Sandra A. Jablonski, Ilya G. Serebriiskii, Louis M. Weiner, Erica A. Golemis
Sci Signal. Author manuscript; available in PMC 2011 September 21.
Published in final edited form as: Sci Signal. 2010 September 21; 3(140): ra67. doi: 10.1126/scisignal.2001083
PMCID:
PMC2950064
Abstract Full Text PDF–2.4M Supplementary Material
Predicting genetic modifier loci using functional gene networks
Insuk Lee, Ben Lehner, Tanya Vavouri, Junha Shin, Andrew G. Fraser, Edward M. Marcotte
Genome Res. 2010 August; 20(8): 1143–1153. doi: 10.1101/gr.102749.109
PMCID:
PMC2909577
Abstract Full Text PDF–1.1M
CODA: Accurate Detection of Functional Associations between Proteins in Eukaryotic Genomes Using Domain Fusion
Adam J. Reid, Juan A. G. Ranea, Andrew B. Clegg, Christine A. Orengo
PLoS One. 2010; 5(6): e10908. Published online 2010 June 1. doi: 10.1371/journal.pone.0010908
PMCID:
PMC2879367
Abstract Full Text PDF–351K Supplementary Material
DUFs: families in search of function
Alex Bateman, Penny Coggill, Robert D. Finn
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 October 1; 66(Pt 10): 1148–1152. Published online 2010 March 5. doi: 10.1107/S1744309110001685
PMCID:
PMC2954198
Abstract Full Text PDF–527K
Construction and analysis of protein–protein interaction networks
Karthik Raman
Autom Exp. 2010; 2: 2. Published online 2010 February 15. doi: 10.1186/1759-4499-2-2
PMCID:
PMC2834675
Abstract Full Text PDF–440K
Prediction of human functional genetic networks from heterogeneous data using RVM-based ensemble learning
Chia-Chin Wu, Shahab Asgharzadeh, Timothy J. Triche, David Z. D'Argenio
Bioinformatics. 2010 March 15; 26(6): 807–813. Published online 2010 February 4. doi: 10.1093/bioinformatics/btq044
PMCID:
PMC2832827
Abstract Full Text PDF–307K Supplementary Material
Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana
Insuk Lee, Bindu Ambaru, Pranjali Thakkar, Edward M. Marcotte, Seung Y. Rhee
Nat Biotechnol. Author manuscript; available in PMC 2010 April 20.
Published in final edited form as: Nat Biotechnol. 2010 February; 28(2): 149–156. Published online 2010 January 31. doi: 10.1038/nbt.1603
PMCID:
PMC2857375
Abstract Full Text PDF–2.5M Supplementary Material
Discovering local patterns of co - evolution: computational aspects and biological examples
Tamir Tuller, Yifat Felder, Martin Kupiec
BMC Bioinformatics. 2010; 11: 43. Published online 2010 January 22. doi: 10.1186/1471-2105-11-43
PMCID:
PMC3224649
Abstract Full Text PDF–858K 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
PutidaNET: Interactome database service and network analysis of Pseudomonas putida KT2440
Seong-Jin Park, Jong-Soon Choi, Byoung-Chul Kim, Seong-Woong Jho, Jea-Woon Ryu, Daeui Park, Kyung-A Lee, Jong Bhak, Seung Il Kim
BMC Genomics. 2009; 10(Suppl 3): S18. Published online 2009 December 3. doi: 10.1186/1471-2164-10-S3-S18
PMCID:
PMC2788370
Abstract Full Text PDF–997K Supplementary Material
The Modular Organization of Protein Interactions in Escherichia coli
José M. Peregrín-Alvarez, Xuejian Xiong, Chong Su, John Parkinson
PLoS Comput Biol. 2009 October; 5(10): e1000523. Published online 2009 October 2. doi: 10.1371/journal.pcbi.1000523
PMCID:
PMC2739439
Abstract Full Text PDF–1.0M Supplementary Material
Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data
Yong Wang, Xiang-Sun Zhang, Yu Xia
Nucleic Acids Res. 2009 October; 37(18): 5943–5958. Published online 2009 October. doi: 10.1093/nar/gkp625
PMCID:
PMC2764433
Abstract Full Text PDF–3.1M Supplementary Material
Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function
James C Costello, Mehmet M Dalkilic, Scott M Beason, Jeff R Gehlhausen, Rupali Patwardhan, Sumit Middha, Brian D Eads, Justen R Andrews
Genome Biol. 2009; 10(9): R97. Published online 2009 September 16. doi: 10.1186/gb-2009-10-9-r97
PMCID:
PMC2768986
Abstract Full Text PDF–2.6M Supplementary Material
RRW: repeated random walks on genome-scale protein networks for local cluster discovery
Kathy Macropol, Tolga Can, Ambuj K Singh
BMC Bioinformatics. 2009; 10: 283. Published online 2009 September 9. doi: 10.1186/1471-2105-10-283
PMCID:
PMC2748087
Abstract Full Text PDF–312K
Mining gene functional networks to improve mass-spectrometry-based protein identification
Smriti R. Ramakrishnan, Christine Vogel, Taejoon Kwon, Luiz O. Penalva, Edward M. Marcotte, Daniel P. Miranker
Bioinformatics. 2009 November 15; 25(22): 2955–2961. Published online 2009 July 24. doi: 10.1093/bioinformatics/btp461
PMCID:
PMC2773251
Abstract Full Text PDF–302K
BioNetBuilder2.0: bringing systems biology to chicken and other model organisms
Jay H Konieczka, Kevin Drew, Alex Pine, Kevin Belasco, Sean Davey, Tatiana A Yatskievych, Richard Bonneau, Parker B Antin
BMC Genomics. 2009; 10(Suppl 2): S6. Published online 2009 July 14. doi: 10.1186/1471-2164-10-S2-S6
PMCID:
PMC2966329
Abstract Full Text PDF–408K Supplementary Material
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
SpaK/SpaR Two-component System Characterized by a Structure-driven Domain-fusion Method and in Vitro Phosphorylation Studies
Anu Chakicherla, Carol L. Ecale Zhou, Martha Ligon Dang, Virginia Rodriguez, J. Norman Hansen, Adam Zemla
PLoS Comput Biol. 2009 June; 5(6): e1000401. Published online 2009 June 5. doi: 10.1371/journal.pcbi.1000401
PMCID:
PMC2686270
Abstract Full Text PDF–796K Supplementary Material
Co-evolutionary networks of genes and cellular processes across fungal species
Tamir Tuller, Martin Kupiec, Eytan Ruppin
Genome Biol. 2009; 10(5): R48. Published online 2009 May 5. doi: 10.1186/gb-2009-10-5-r48
PMCID:
PMC2718514
Abstract Full Text PDF–724K 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
Biomedical Discovery Acceleration, with Applications to Craniofacial Development
Sonia M. Leach, Hannah Tipney, Weiguo Feng, William A. Baumgartner, Jr., Priyanka Kasliwal, Ronald P. Schuyler, Trevor Williams, Richard A. Spritz, Lawrence Hunter
PLoS Comput Biol. 2009 March; 5(3): e1000215. Published online 2009 March 27. doi: 10.1371/journal.pcbi.1000215
PMCID:
PMC2653649
Abstract Full Text PDF–1.6M Supplementary Material
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
EcID. A database for the inference of functional interactions in E. coli
Eduardo Andres Leon, Iakes Ezkurdia, Beatriz García, Alfonso Valencia, David Juan
Nucleic Acids Res. 2009 January; 37(Database issue): D629–D635. Published online 2009 January. doi: 10.1093/nar/gkn853
PMCID:
PMC2686479
Abstract Full Text PDF–2.5M
Genome-scale models of bacterial metabolism: reconstruction and applications
Maxime Durot, Pierre-Yves Bourguignon, Vincent Schachter
FEMS Microbiol Rev. 2009 January; 33(1): 164–190. Published online 2008 December. doi: 10.1111/j.1574-6976.2008.00146.x
PMCID:
PMC2704943
Abstract Full Text PDF–520K
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