Prolinks: a database of protein functional linkages derived from coevolution
-
* Corresponding author: David Eisenberg david@mbi.ucla.edu
Genome Biology 2004, 5:R35 doi:
Accesses
- Last 30 days: 64 accesses
- Last year: 1046 accesses
- All time: 17795 accesses
Cited by
BioMed Central: 33 citations
|
Research
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 (2 November 2010) |
|
Review
Construction and analysis of protein–protein interaction networks Karthik Raman Automated Experimentation 2010, 2:2 (15 February 2010) |
|
Research article
Discovering local patterns of co - evolution: computational aspects and biological examples Tamir Tuller, Yifat Felder, Martin Kupiec BMC Bioinformatics 2010, 11:43 (22 January 2010) |
|
Proceedings
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 (3 December 2009) |
|
Research
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 Biology 2009, 10:R97 (16 September 2009) The first computational interaction network built from |
|
Research article
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 (9 September 2009) |
|
Proceedings
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 (14 July 2009) |
|
Research article
Ignacio Rodriguez-Llorente, Miguel A Caviedes, Mohammed Dary, Antonio J Palomares, Francisco M Cánovas, José M Peregrín-Alvarez BMC Systems Biology 2009, 3:63 (16 June 2009) |
|
Research
Co-evolutionary networks of genes and cellular processes across fungal species Tamir Tuller, Martin Kupiec, Eytan Ruppin Genome Biology 2009, 10:R48 (5 May 2009) Two new measures of evolution are used to study co-evolutionary networks of fungal genes and cellular processes; links between co-evolution and co-functionality are revealed. |
|
Research article
Tao Cui, Lei Zhang, Xizhou Wang, Zheng-Guo He BMC Genomics 2009, 10:118 (19 March 2009) |
|
Research article
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 (24 September 2008) |
|
Research article
Anis Karimpour-Fard, Sonia M Leach, Lawrence E Hunter, Ryan T Gill BMC Genomics 2008, 9:313 (30 June 2008) |
|
Research article
Improving protein function prediction methods with integrated literature data Aaron P Gabow, Sonia M Leach, William A Baumgartner, Lawrence E Hunter, Debra S Goldberg BMC Bioinformatics 2008, 9:198 (15 April 2008) |
|
Software
PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes Christine Fong, Laurence Rohmer, Matthew Radey, Michael Wasnick, Mitchell J Brittnacher BMC Bioinformatics 2008, 9:170 (26 March 2008) |
|
Research article
High-precision high-coverage functional inference from integrated data sources Bolan Linghu, Evan S Snitkin, Dustin T Holloway, Adam M Gustafson, Yu Xia, Charles DeLisi BMC Bioinformatics 2008, 9:119 (25 February 2008) |
|
Research article
Evidence of probabilistic behaviour in protein interaction networks Joseph Ivanic, Anders Wallqvist, Jaques Reifman BMC Systems Biology 2008, 2:11 (31 January 2008) |
|
Method
Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes Kriston L McGary, Insuk Lee, Edward M Marcotte Genome Biology 2007, 8:R258 (5 December 2007) Loss-of-function phenotypes of yeast genes can be predicted from the loss-of-function phenotypes of their neighbours in functional gene networks. This could potentially be applied to the prediction of human disease genes. |
|
Research article
Anis Karimpour-Fard, Lawrence Hunter, Ryan T Gill BMC Genomics 2007, 8:393 (29 October 2007) |
|
Methodology article
Jingchun Sun, Yan Sun, Guohui Ding, Qi Liu, Chuan Wang, Youyu He, Tieliu Shi, Yixue Li, Zhongming Zhao BMC Bioinformatics 2007, 8:414 (26 October 2007) |
|
Research article
William A McLaughlin, Ken Chen, Tingjun Hou, Wei Wang BMC Bioinformatics 2007, 8:390 (16 October 2007) |
|
Method
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 Biology 2007, 8:R185 (5 September 2007) Cluster Co-Conservation (CCC) has been extended to a method for developing protein interaction networks based on co-conservation between protein pairs across multiple species, Cross-Species Cluster Co-Conservation (CS-CCC). |
|
Research
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 Genome Biology 2007, 8:R130 (5 July 2007) 'Systematic identification of protein interactions for the bacterium |
|
Research article
Raja Jothi, Teresa M Przytycka, L Aravind BMC Bioinformatics 2007, 8:173 (23 May 2007) |
|
Proceedings
An improved method for identifying functionally linked proteins using phylogenetic profiles Shawn Cokus, Sayaka Mizutani, Matteo Pellegrini BMC Bioinformatics 2007, 8(Suppl 4):S7 (22 May 2007) |
|
Methodology article
David J Reiss, Nitin S Baliga, Richard Bonneau BMC Bioinformatics 2006, 7:280 (2 June 2006) |
|
Method
Richard Bonneau, David J Reiss, Paul Shannon, Marc Facciotti, Leroy Hood, Nitin S Baliga, Vesteinn Thorsson Genome Biology 2006, 7:R36 (10 May 2006) The Inferelator, a method for deriving genome-wide transcriptional regulatory interactions, successfully predicted global expression in Halobacterium under novel perturbations.
|
|
Methodology article
Identifying metabolic enzymes with multiple types of association evidence Peter Kharchenko, Lifeng Chen, Yoav Freund, Dennis Vitkup, George M Church BMC Bioinformatics 2006, 7:177 (29 March 2006) |
|
Software
The Gaggle: An open-source software system for integrating bioinformatics software and data sources Paul T Shannon, David J Reiss, Richard Bonneau, Nitin S Baliga BMC Bioinformatics 2006, 7:176 (28 March 2006) |
|
Methodology article
Gene annotation and network inference by phylogenetic profiling Jie Wu, Zhenjun Hu, Charles DeLisi BMC Bioinformatics 2006, 7:80 (17 February 2006) |
|
Method
Predicting genes for orphan metabolic activities using phylogenetic profiles Lifeng Chen, Dennis Vitkup Genome Biology 2006, 7:R17 (15 February 2006) A method that combines local structure of a metabolic network with phylogenetic profiles is described and used to assign genes to orphan metabolic activities in yeast and |
|
Research article
Maria Persico, Arnaud Ceol, Caius Gavrila, Robert Hoffmann, Arnaldo Florio, Gianni Cesareni BMC Bioinformatics 2005, 6(Suppl 4):S21 (1 December 2005) |
|
Software
Phydbac "Gene Function Predictor" : a gene annotation tool based on genomic context analysis François Enault, Karsten Suhre, Jean-Michel Claverie BMC Bioinformatics 2005, 6:247 (12 October 2005) Gene Function Predictor, included in the updated Phydbac tool compares well with other genomic context servers in proposing putative associations between Escherichia coli K-12 proteins, demonstrating an accuracy of over 70% in the linkage of these predictions to gene ontology terms.
|
|
Research article
Phylogenetic detection of conserved gene clusters in microbial genomes Yu Zheng, Brian P Anton, Richard J Roberts, Simon Kasif BMC Bioinformatics 2005, 6:243 (3 October 2005) |