TY - JOUR AU - Przulj, N. PY - 2011 DA - 2011// TI - Protein-protein interactions: making sense of networks via graph-theoretic modeling JO - BioEssays VL - 33 UR - https://doi.org/10.1002/bies.201000044 DO - 10.1002/bies.201000044 ID - Przulj2011 ER - TY - JOUR AU - Bader, G. AU - Hogue, C. PY - 2002 DA - 2002// TI - Analyzing yeast protein-protein interaction data obtained from different sources JO - Nat Biotechnol VL - 20 UR - https://doi.org/10.1038/nbt1002-991 DO - 10.1038/nbt1002-991 ID - Bader2002 ER - TY - JOUR AU - Wang, C. AU - Ding, C. AU - Yang, Q. AU - Holbrook, S. PY - 2007 DA - 2007// TI - Consistent dissection of the protein interaction network by combining global and local metrics JO - Genome Biol VL - 8 UR - https://doi.org/10.1186/gb-2007-8-12-r271 DO - 10.1186/gb-2007-8-12-r271 ID - Wang2007 ER - TY - JOUR AU - King, A. AU - Przulj, N. AU - Jurisica, I. PY - 2004 DA - 2004// TI - Protein complex prediction via cost-based clustering JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth351 DO - 10.1093/bioinformatics/bth351 ID - King2004 ER - TY - JOUR AU - Asthana, S. AU - King, O. AU - Gibbons, F. AU - Roth, F. PY - 2004 DA - 2004// TI - Predicting protein complex membership using probabilistic network reliability JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.2203804 DO - 10.1101/gr.2203804 ID - Asthana2004 ER - TY - JOUR AU - Wang, J. AU - Li, M. AU - Deng, Y. AU - Pan, Y. PY - 2010 DA - 2010// TI - Recent advances in clustering methods for protein interaction networks JO - BMC Genomics VL - 11 UR - https://doi.org/10.1186/1471-2164-11-S3-S10 DO - 10.1186/1471-2164-11-S3-S10 ID - Wang2010 ER - TY - JOUR AU - Ulitsky, I. AU - Shamir, R. PY - 2009 DA - 2009// TI - Identifying functional modules using expression profiles and confidence-scored protein interactions JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp118 DO - 10.1093/bioinformatics/btp118 ID - Ulitsky2009 ER - TY - JOUR AU - Chua, H. N. AU - Sung, W. K. AU - Wong, L. PY - 2006 DA - 2006// TI - Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl145 DO - 10.1093/bioinformatics/btl145 ID - Chua2006 ER - TY - JOUR AU - Sharan, R. AU - Ulitsky, I. AU - Shamir, R. PY - 2007 DA - 2007// TI - Network-based prediction of protein function JO - Molecular Systems Biology VL - 3 UR - https://doi.org/10.1038/msb4100129 DO - 10.1038/msb4100129 ID - Sharan2007 ER - TY - JOUR AU - Friedel, C. AU - Krumsiek, J. AU - Zimmer, R. PY - 2009 DA - 2009// TI - Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast JO - Journal of Computational Biology VL - 16 UR - https://doi.org/10.1089/cmb.2009.0023 DO - 10.1089/cmb.2009.0023 ID - Friedel2009 ER - TY - JOUR AU - Lee, K. AU - Chuang, H. AU - Beyer, A. AU - Sung, M. AU - Huh, W. AU - Lee, B. AU - Ideker, T. PY - 2008 DA - 2008// TI - Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkn619 DO - 10.1093/nar/gkn619 ID - Lee2008 ER - TY - JOUR AU - Chuang, H. Y. AU - Lee, E. AU - Liu, Y. T. AU - Lee, D. AU - Ideker, T. PY - 2007 DA - 2007// TI - Network-based classification of breast cancer metastasis JO - Mol Syst Biol VL - 3 UR - https://doi.org/10.1038/msb4100180 DO - 10.1038/msb4100180 ID - Chuang2007 ER - TY - JOUR AU - Hannum, G. AU - Srivas, R. AU - Guenole, A. AU - van Attikum, H. AU - Krogan, N. AU - Karp, R. AU - Ideker, T. PY - 2009 DA - 2009// TI - Genome-wide association data reveal a global map of genetic interactions among protein complexes JO - PLoS Genet VL - 5 UR - https://doi.org/10.1371/journal.pgen.1000782 DO - 10.1371/journal.pgen.1000782 ID - Hannum2009 ER - TY - JOUR AU - Ideker, T. AU - Sharan, R. PY - 2008 DA - 2008// TI - Protein networks in disease JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.071852.107 DO - 10.1101/gr.071852.107 ID - Ideker2008 ER - TY - JOUR AU - Kim, Y. AU - Wuchty, S. AU - Przytycka, T. PY - 2011 DA - 2011// TI - Identifying causal genes and dysregulated pathways in complex diseases JO - PLoS Comput Biol VL - 7 UR - https://doi.org/10.1371/journal.pcbi.1001095 DO - 10.1371/journal.pcbi.1001095 ID - Kim2011 ER - TY - JOUR AU - Hidalgo, C. AU - Blumm, N. AU - Barabasi, A. AU - Christakis, N. PY - 2009 DA - 2009// TI - A dynamic network approach for the study of human phenotypes JO - PLoS Comput Biol VL - 5 UR - https://doi.org/10.1371/journal.pcbi.1000353 DO - 10.1371/journal.pcbi.1000353 ID - Hidalgo2009 ER - TY - JOUR AU - Huang, H. AU - Jedynak, B. M. AU - Bader, J. S. PY - 2007 DA - 2007// TI - Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps JO - PLoS Comput Biol VL - 3 UR - https://doi.org/10.1371/journal.pcbi.0030214 DO - 10.1371/journal.pcbi.0030214 ID - Huang2007 ER - TY - JOUR AU - Lei, C. AU - Ruan, J. PY - 2013 DA - 2013// TI - A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/bts688 DO - 10.1093/bioinformatics/bts688 ID - Lei2013 ER - TY - JOUR AU - Ruan, J. AU - Zhang, W. PY - 2008 DA - 2008// TI - Identifying network communities with a high resolution JO - Physical Review E VL - 77 UR - https://doi.org/10.1103/PhysRevE.77.016104 DO - 10.1103/PhysRevE.77.016104 ID - Ruan2008 ER - TY - JOUR AU - Newman, M. PY - 2006 DA - 2006// TI - Modularity and community structure in networks JO - Proc Natl Acad Sci USA VL - 103 UR - https://doi.org/10.1073/pnas.0601602103 DO - 10.1073/pnas.0601602103 ID - Newman2006 ER - TY - JOUR AU - Fortunato, S. AU - Barthelemy, M. PY - 2007 DA - 2007// TI - Resolution limit in community detection JO - Proc Natl Acad Sci USA VL - 104 UR - https://doi.org/10.1073/pnas.0605965104 DO - 10.1073/pnas.0605965104 ID - Fortunato2007 ER - TY - CHAP AU - Lei, C. AU - Ruan, J. PY - 2012 DA - 2012// TI - A random walk based approach for improving protein-protein interaction network and protein complex prediction BT - Bioinformatics and Biomedicine (BIBM), IEEE International Conference on 2012 UR - https://doi.org/10.1109/BIBM.2012.6392693 DO - 10.1109/BIBM.2012.6392693 ID - Lei2012 ER - TY - JOUR AU - Krogan, N. AU - Cagney, G. AU - Yu, H. AU - Zhong, G. AU - Guo, X. AU - Ignatchenko, A. AU - Li, J. AU - Pu, S. AU - Datta, N. AU - Tikuisis, A. P. AU - Punna, T. AU - Peregrn-Alvarez, J. AU - Sha les, M. AU - Zhang, X. AU - Davey, M. AU - Robinson, M. AU - Paccana ro, A. AU - Bray, J. AU - Sheung, A. AU - Beattie, B. AU - Richards, D. AU - Canadien, V. AU - Lalev, A. AU - Mena, F. AU - Wong, P. AU - Starostine, A. AU - Canete, M. AU - Vlasblom, J. AU - Wu, S. AU - Or si, C. AU - Collins, S. AU - Chandran, S. AU - Haw, R. AU - Rilstone, J. AU - Gandi, K. AU - Thompson, N. AU - Musso, G. AU - St Onge, P. AU - Ghanny, S. AU - Lam, M. AU - Butland, G. AU - Altaf-Ul, A. M. AU - Kanaya, S. AU - Shilatifard, A. AU - O'Shea, E. AU - Weissman, J. S. AU - Ingles, C. AU - Hughes, T. AU - Parkinson, J. AU - Gerstein, M. AU - Wodak, S. AU - Emili, A. AU - Greenblatt, J. PY - 2006 DA - 2006// TI - Global landscape of protein complexes in the yeast Saccharomyces cerevisiae JO - Nature VL - 440 UR - https://doi.org/10.1038/nature04670 DO - 10.1038/nature04670 ID - Krogan2006 ER - TY - JOUR AU - Fouss, F. AU - Pirotte, A. AU - Renders, J. M. AU - Saerens, M. PY - 2007 DA - 2007// TI - Random-Walk Computation of Similarities between Nodes of a Graph with Application to Collaborative Recommendation JO - IEEE Transactions on Knowledge and Data Engineering VL - 19 UR - https://doi.org/10.1109/TKDE.2007.46 DO - 10.1109/TKDE.2007.46 ID - Fouss2007 ER - TY - CHAP AU - Tong, H. AU - Faloutsos, C. AU - Pan, J. Y. PY - 2006 DA - 2006// TI - Fast Random Walk with Restart and Its Applications BT - Proceedings of the Sixth International Conference on Data Mining, ICDM '06 PB - IEEE Computer Society CY - Washington, DC, USA UR - https://doi.org/10.1109/ICDM.2006.70 DO - 10.1109/ICDM.2006.70 ID - Tong2006 ER - TY - JOUR AU - Kuchaiev, O. AU - Rasajski, M. AU - Higham, D. J. AU - Przulj, N. PY - 2009 DA - 2009// TI - Geometric De-noising of Protein-Protein Interaction Networks JO - PLoS Comput Biol VL - 5 UR - https://doi.org/10.1371/journal.pcbi.1000454 DO - 10.1371/journal.pcbi.1000454 ID - Kuchaiev2009 ER - TY - JOUR AU - Fang, Y. AU - Benjamin, W. AU - Sun, M. AU - Ramani, K. PY - 2011 DA - 2011// TI - Global Geometric Affinity for Revealing High Fidelity Protein Interaction Network JO - PLoS ONE VL - 6 UR - https://doi.org/10.1371/journal.pone.0019349 DO - 10.1371/journal.pone.0019349 ID - Fang2011 ER - TY - JOUR AU - Wang, J. AU - Du, Z. AU - Payattakool, R. AU - Yu, P. AU - Chen, C. PY - 2007 DA - 2007// TI - A new method to measure the semantic similarity of GO terms JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm087 DO - 10.1093/bioinformatics/btm087 ID - Wang2007 ER - TY - JOUR AU - Yu, G. AU - Li, F. AU - Qin, Y. AU - Bo, X. AU - Wu, Y. AU - Wang, S. PY - 2010 DA - 2010// TI - GOSemSim: an R package for measuring semantic similarity among GO terms and gene products JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq064 DO - 10.1093/bioinformatics/btq064 ID - Yu2010 ER - TY - JOUR AU - Gasch, A. AU - Spellman, P. AU - Kao, C. AU - Carmel-Harel, O. AU - Eisen, M. AU - Storz, G. AU - Botstein, D. AU - Brown, P. PY - 2000 DA - 2000// TI - Genomic expression programs in the response of yeast cells to environmental changes JO - Mol Biol Cell VL - 11 UR - https://doi.org/10.1091/mbc.11.12.4241 DO - 10.1091/mbc.11.12.4241 ID - Gasch2000 ER - TY - JOUR AU - Mewes, H. AU - Frishman, D. AU - Mayer, K. AU - Munsterkotter, M. AU - Noubibou, O. AU - Pagel, P. AU - Rattei, T. AU - Oesterheld, M. AU - Ruepp, A. AU - Stumpflen, V. PY - 2006 DA - 2006// TI - MIPS: analysis and annotation of proteins from whole genomes in 2005 JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkj148 DO - 10.1093/nar/gkj148 ID - Mewes2006 ER - TY - CHAP AU - Meila, M. PY - 2005 DA - 2005// TI - Comparing clusterings: an axiomatic view BT - ICML '05: Proceedings of the 22nd international conference on Machine learning PB - ACM Press CY - New York, NY, USA UR - https://doi.org/10.1145/1102351.1102424 DO - 10.1145/1102351.1102424 ID - Meila2005 ER - TY - JOUR AU - Fowlkes, E. AU - Mallows, C. PY - 1983 DA - 1983// TI - A method for comparing two hierarchical clusterings JO - J Amer Statist Assoc VL - 78 UR - https://doi.org/10.1080/01621459.1983.10478008 DO - 10.1080/01621459.1983.10478008 ID - Fowlkes1983 ER - TY - JOUR AU - Shannon, P. AU - Markiel, A. AU - Ozier, O. AU - Baliga, N. S. AU - Wang, J. T. AU - Ramage, D. AU - Amin, N. AU - Schwikowski, B. AU - Ideker, T. PY - 2003 DA - 2003// TI - Cytoscape: a software environment for integrated models of biomolecular interaction networks JO - Genome research VL - 13 UR - https://doi.org/10.1101/gr.1239303 DO - 10.1101/gr.1239303 ID - Shannon2003 ER -