TY - JOUR AU - Barabasi, A. -. L. AU - Oltvai, Z. N. PY - 2004 DA - 2004// TI - Network biology: understanding the cell’s functional organization JO - Nat Rev Genet VL - 5 UR - https://doi.org/10.1038/nrg1272 DO - 10.1038/nrg1272 ID - Barabasi2004 ER - TY - JOUR AU - Ideker, T. AU - Krogan, N. J. PY - 2012 DA - 2012// TI - Differential network biology JO - Mol Syst Biol VL - 8 UR - https://doi.org/10.1038/msb.2011.99 DO - 10.1038/msb.2011.99 ID - Ideker2012 ER - TY - JOUR AU - Ideker, T. AU - Thorsson, V. AU - Ranish, J. A. AU - Christmas, R. AU - Buhler, J. AU - Eng, J. K. AU - Bumgarner, R. AU - Goodlett, D. R. AU - Aebersold, R. AU - Hood, L. PY - 2001 DA - 2001// TI - Integrated genomic and proteomic analyses of a systematically perturbed metabolic network JO - Science VL - 292 UR - https://doi.org/10.1126/science.292.5518.929 DO - 10.1126/science.292.5518.929 ID - Ideker2001 ER - TY - JOUR AU - Ideker, T. AU - Ozier, O. AU - Schwikowski, B. AU - Siegel, A. F. PY - 2002 DA - 2002// TI - Discovering regulatory and signalling circuits in molecular interaction networks JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.suppl_1.S233 DO - 10.1093/bioinformatics/18.suppl_1.S233 ID - Ideker2002 ER - TY - JOUR AU - Luscombe, N. M. AU - Babu, M. M. AU - Yu, H. AU - Snyder, M. AU - Teichmann, S. A. AU - Gerstein, M. PY - 2004 DA - 2004// TI - Genomic analysis of regulatory network dynamics reveals large topological changes JO - Nature VL - 431 UR - https://doi.org/10.1038/nature02782 DO - 10.1038/nature02782 ID - Luscombe2004 ER - TY - JOUR AU - Lynch, M. AU - Conery, J. S. PY - 2003 DA - 2003// TI - The evolutionary demography of duplicate genes JO - J Struct Funct Genomics VL - 3 UR - https://doi.org/10.1023/A:1022696612931 DO - 10.1023/A:1022696612931 ID - Lynch2003 ER - TY - JOUR AU - Konrad, A. AU - Teufel, A. I. AU - Grahnen, J. A. AU - Liberles, D. A. PY - 2011 DA - 2011// TI - Toward a general model for the evolutionary dynamics of gene duplicates JO - Genome Biol Evol VL - 3 UR - https://doi.org/10.1093/gbe/evr093 DO - 10.1093/gbe/evr093 ID - Konrad2011 ER - TY - JOUR AU - Lynch, M. AU - Conery, J. S. PY - 2000 DA - 2000// TI - The evolutionary fate and consequences of duplicate genes JO - Science VL - 290 UR - https://doi.org/10.1126/science.290.5494.1151 DO - 10.1126/science.290.5494.1151 ID - Lynch2000 ER - TY - JOUR AU - Lynch, M. AU - Conery, J. S. PY - 2003 DA - 2003// TI - The origins of genome complexity JO - Science VL - 302 UR - https://doi.org/10.1126/science.1089370 DO - 10.1126/science.1089370 ID - Lynch2003 ER - TY - JOUR AU - Rzhetsky, A. AU - Gomez, S. M. PY - 2001 DA - 2001// TI - Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.10.988 DO - 10.1093/bioinformatics/17.10.988 ID - Rzhetsky2001 ER - TY - JOUR AU - Chung, F. AU - Lu, L. AU - Dewey, T. G. AU - Galas, D. J. PY - 2003 DA - 2003// TI - Duplication models for biological networks JO - J Comput Biol VL - 10 UR - https://doi.org/10.1089/106652703322539024 DO - 10.1089/106652703322539024 ID - Chung2003 ER - TY - JOUR AU - Fares, M. A. AU - Keane, O. M. AU - Toft, C. AU - Carretero-Paulet, L. AU - Jones, G. W. PY - 2013 DA - 2013// TI - The roles of whole-genome and small-scale duplications in the functional specialization of Saccharomyces cerevisiae genes JO - PLoS Genet VL - 9 UR - https://doi.org/10.1371/journal.pgen.1003176 DO - 10.1371/journal.pgen.1003176 ID - Fares2013 ER - TY - JOUR AU - Wagner, A. PY - 2002 DA - 2002// TI - Asymmetric functional divergence of duplicate genes in yeast JO - Mol Biol Evol VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003998 DO - 10.1093/oxfordjournals.molbev.a003998 ID - Wagner2002 ER - TY - JOUR AU - Alvarez-Ponce, D. AU - Fares, M. A. PY - 2012 DA - 2012// TI - Evolutionary rate and duplicability in the Arabidopsis thaliana protein-protein interaction network JO - Genome Biol Evol VL - 4 UR - https://doi.org/10.1093/gbe/evs101 DO - 10.1093/gbe/evs101 ID - Alvarez-Ponce2012 ER - TY - JOUR AU - Eanes, W. F. PY - 2011 DA - 2011// TI - Molecular population genetics and selection in the glycolytic pathway JO - J Exp Biol VL - 214 UR - https://doi.org/10.1242/jeb.046458 DO - 10.1242/jeb.046458 ID - Eanes2011 ER - TY - JOUR AU - Wagner, A. PY - 2012 DA - 2012// TI - Metabolic networks and their evolution JO - Adv Exp Med Biol VL - 751 UR - https://doi.org/10.1007/978-1-4614-3567-9_2 DO - 10.1007/978-1-4614-3567-9_2 ID - Wagner2012 ER - TY - JOUR AU - Conant, G. C. AU - Wolfe, K. H. PY - 2006 DA - 2006// TI - Functional partitioning of yeast co-expression networks after genome duplication JO - PLoS Biol VL - 4 UR - https://doi.org/10.1371/journal.pbio.0040109 DO - 10.1371/journal.pbio.0040109 ID - Conant2006 ER - TY - JOUR AU - Cork, J. M. AU - Purugganan, M. D. PY - 2004 DA - 2004// TI - The evolution of molecular genetic pathways and networks JO - Bioessays VL - 26 UR - https://doi.org/10.1002/bies.20026 DO - 10.1002/bies.20026 ID - Cork2004 ER - TY - JOUR AU - Huynen, M. A. AU - van Nimwegen, E. PY - 1998 DA - 1998// TI - The frequency distribution of gene family sizes in complete genomes JO - Mol Biol Evol VL - 15 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025959 DO - 10.1093/oxfordjournals.molbev.a025959 ID - Huynen1998 ER - TY - JOUR AU - Karev, G. P. AU - Wolf, Y. I. AU - Rzhetsky, A. Y. AU - Berezovskaya, F. S. AU - Koonin, E. V. PY - 2002 DA - 2002// TI - Birth and death of protein domains: a simple model of evolution explains power law behavior JO - BMC Evol Biol VL - 2 UR - https://doi.org/10.1186/1471-2148-2-18 DO - 10.1186/1471-2148-2-18 ID - Karev2002 ER - TY - JOUR AU - Koonin, E. V. PY - 2011 DA - 2011// TI - Are there laws of genome evolution? JO - PLoS Comput Biol VL - 7 UR - https://doi.org/10.1371/journal.pcbi.1002173 DO - 10.1371/journal.pcbi.1002173 ID - Koonin2011 ER - TY - JOUR AU - Padawer, T. AU - Leighty, R. E. AU - Wang, D. PY - 2012 DA - 2012// TI - Duplicate gene enrichment and expression pattern diversification in multicellularity JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gks464 DO - 10.1093/nar/gks464 ID - Padawer2012 ER - TY - JOUR AU - Wuchty, S. PY - 2001 DA - 2001// TI - Scale-free behavior in protein domain networks JO - Mol Biol Evol VL - 18 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003957 DO - 10.1093/oxfordjournals.molbev.a003957 ID - Wuchty2001 ER - TY - JOUR AU - Qian, J. AU - Luscombe, N. M. AU - Gerstein, M. PY - 2001 DA - 2001// TI - Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model JO - J Mol Biol VL - 313 UR - https://doi.org/10.1006/jmbi.2001.5079 DO - 10.1006/jmbi.2001.5079 ID - Qian2001 ER - TY - JOUR AU - D’Antonio, M. AU - Ciccarelli, F. D. PY - 2011 DA - 2011// TI - Modification of gene duplicability during the evolution of protein interaction network JO - PLoS Comput Biol VL - 7 UR - https://doi.org/10.1371/journal.pcbi.1002029 DO - 10.1371/journal.pcbi.1002029 ID - D’Antonio2011 ER - TY - JOUR AU - He, X. AU - Zhang, J. PY - 2005 DA - 2005// TI - Gene complexity and gene duplicability JO - Curr Biol VL - 15 UR - https://doi.org/10.1016/j.cub.2005.04.035 DO - 10.1016/j.cub.2005.04.035 ID - He2005 ER - TY - JOUR AU - Yang, J. AU - Lusk, R. AU - Li, W. H. PY - 2003 DA - 2003// TI - Organismal complexity, protein complexity, and gene duplicability JO - Proc Natl Acad Sci U S A VL - 100 UR - https://doi.org/10.1073/pnas.2536672100 DO - 10.1073/pnas.2536672100 ID - Yang2003 ER - TY - JOUR AU - Liang, H. AU - Fernandez, A. PY - 2008 DA - 2008// TI - Evolutionary constraints imposed by gene dosage balance JO - Front Biosci VL - 13 UR - https://doi.org/10.2741/3010 DO - 10.2741/3010 ID - Liang2008 ER - TY - JOUR AU - Hase, T. AU - Niimura, Y. AU - Tanaka, H. PY - 2010 DA - 2010// TI - Difference in gene duplicability may explain the difference in overall structure of protein-protein interaction networks among eukaryotes JO - BMC Evol Biol VL - 10 UR - https://doi.org/10.1186/1471-2148-10-358 DO - 10.1186/1471-2148-10-358 ID - Hase2010 ER - TY - JOUR AU - Pink, R. C. AU - Wicks, K. AU - Caley, D. P. AU - Punch, E. K. AU - Jacobs, L. AU - Carter, D. R. PY - 2011 DA - 2011// TI - Pseudogenes: pseudo-functional or key regulators in health and disease? JO - RNA VL - 17 UR - https://doi.org/10.1261/rna.2658311 DO - 10.1261/rna.2658311 ID - Pink2011 ER - TY - JOUR AU - Balakirev, E. S. AU - Chechetkin, V. R. AU - Lobzin, V. V. AU - Ayala, F. J. PY - 2003 DA - 2003// TI - DNA polymorphism in the beta-Esterase gene cluster of Drosophila melanogaster JO - Genetics VL - 164 ID - Balakirev2003 ER - TY - JOUR AU - Gu, Z. AU - Rifkin, S. A. AU - White, K. P. AU - Li, W. H. PY - 2004 DA - 2004// TI - Duplicate genes increase gene expression diversity within and between species JO - Nat Genet VL - 36 UR - https://doi.org/10.1038/ng1355 DO - 10.1038/ng1355 ID - Gu2004 ER - TY - JOUR AU - Papp, B. AU - Pal, C. AU - Hurst, L. D. PY - 2003 DA - 2003// TI - Dosage sensitivity and the evolution of gene families in yeast JO - Nature VL - 424 UR - https://doi.org/10.1038/nature01771 DO - 10.1038/nature01771 ID - Papp2003 ER - TY - JOUR AU - Qian, W. AU - Zhang, J. PY - 2008 DA - 2008// TI - Gene dosage and gene duplicability JO - Genetics VL - 179 UR - https://doi.org/10.1534/genetics.108.090936 DO - 10.1534/genetics.108.090936 ID - Qian2008 ER - TY - JOUR AU - Carmel, L. AU - Rogozin, I. B. AU - Wolf, Y. I. AU - Koonin, E. V. PY - 2007 DA - 2007// TI - Evolutionarily conserved genes preferentially accumulate introns JO - Genome Res VL - 17 UR - https://doi.org/10.1101/gr.5978207 DO - 10.1101/gr.5978207 ID - Carmel2007 ER - TY - JOUR AU - Ivessa, A. S. AU - Zhou, J. Q. AU - Zakian, V. A. PY - 2000 DA - 2000// TI - The Saccharomyces Pif1p DNA helicase and the highly related Rrm3p have opposite effects on replication fork progression in ribosomal DNA JO - Cell VL - 100 UR - https://doi.org/10.1016/S0092-8674(00)80683-2 DO - 10.1016/S0092-8674(00)80683-2 ID - Ivessa2000 ER - TY - JOUR AU - Kerrien, S. AU - Aranda, B. AU - Breuza, L. AU - Bridge, A. AU - Broackes-Carter, F. AU - Chen, C. AU - Duesbury, M. AU - Dumousseau, M. AU - Feuermann, M. AU - Hinz, U. AU - Jandrasits, C. AU - Jimenez, R. C. AU - Khadake, J. AU - Mahadevan, U. AU - Masson, P. AU - Pedruzzi, I. AU - Pfeiffenberger, E. AU - Porras, P. AU - Raghunath, A. AU - Roechert, B. AU - Orchard, S. AU - Hermjakob, H. PY - 2012 DA - 2012// TI - The IntAct molecular interaction database in 2012 JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr1088 DO - 10.1093/nar/gkr1088 ID - Kerrien2012 ER - TY - JOUR AU - Carretero-Paulet, L. AU - Fares, M. A. PY - 2012 DA - 2012// TI - Evolutionary dynamics and functional specialization of plant paralogs formed by whole and small-scale genome duplications JO - Mol Biol Evol VL - 29 UR - https://doi.org/10.1093/molbev/mss162 DO - 10.1093/molbev/mss162 ID - Carretero-Paulet2012 ER - TY - JOUR AU - Morris, R. T. AU - Drouin, G. PY - 2011 DA - 2011// TI - Ectopic gene conversions in the genome of ten hemiascomycete yeast species JO - Int J Evol Biol VL - 2011 UR - https://doi.org/10.4061/2011/970768 DO - 10.4061/2011/970768 ID - Morris2011 ER - TY - JOUR AU - Satake, M. AU - Kawata, M. AU - McLysaght, A. AU - Makino, T. PY - 2012 DA - 2012// TI - Evolution of vertebrate tissues driven by differential modes of gene duplication JO - DNA Res VL - 19 UR - https://doi.org/10.1093/dnares/dss012 DO - 10.1093/dnares/dss012 ID - Satake2012 ER - TY - JOUR AU - Singh, P. P. AU - Affeldt, S. AU - Cascone, I. AU - Selimoglu, R. AU - Camonis, J. AU - Isambert, H. PY - 2012 DA - 2012// TI - On the expansion of “dangerous” gene repertoires by whole-genome duplications in early vertebrates JO - Cell Rep VL - 2 UR - https://doi.org/10.1016/j.celrep.2012.09.034 DO - 10.1016/j.celrep.2012.09.034 ID - Singh2012 ER - TY - JOUR AU - Ravasz, E. AU - Somera, A. L. AU - Mongru, D. A. AU - Oltvai, Z. N. AU - Barabasi, A. L. PY - 2002 DA - 2002// TI - Hierarchical organization of modularity in metabolic networks JO - Science VL - 297 UR - https://doi.org/10.1126/science.1073374 DO - 10.1126/science.1073374 ID - Ravasz2002 ER - TY - JOUR AU - Onnela, J. -. P. AU - Saramaki, J. AU - Kertesz, J. AU - Kaski, K. PY - 2005 DA - 2005// TI - Intensity and coherence of motifs in weighted complex networks JO - Phys Rev E Stat Nonlin Soft Matter Phys VL - 71 UR - https://doi.org/10.1103/PhysRevE.71.065103 DO - 10.1103/PhysRevE.71.065103 ID - Onnela2005 ER - TY - JOUR AU - Cheng, X. AU - Qin, Y. AU - Ivessa, A. S. PY - 2009 DA - 2009// TI - Loss of mitochondrial DNA under genotoxic stress conditions in the absence of the yeast DNA helicase Pif1p occurs independently of the DNA helicase Rrm3p JO - Mol Genet Genomics VL - 281 UR - https://doi.org/10.1007/s00438-009-0438-6 DO - 10.1007/s00438-009-0438-6 ID - Cheng2009 ER - TY - JOUR AU - Yu, L. AU - Qi, M. AU - Sheff, M. A. AU - Elion, E. A. PY - 2008 DA - 2008// TI - Counteractive control of polarized morphogenesis during mating by mitogen-activated protein kinase Fus3 and G1 cyclin-dependent kinase JO - Mol Biol Cell VL - 19 UR - https://doi.org/10.1091/mbc.E07-08-0757 DO - 10.1091/mbc.E07-08-0757 ID - Yu2008 ER - TY - JOUR AU - Wagner, A. PY - 2001 DA - 2001// TI - The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes JO - Mol Biol Evol VL - 18 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003913 DO - 10.1093/oxfordjournals.molbev.a003913 ID - Wagner2001 ER - TY - JOUR AU - Wapinski, I. AU - Pfeffer, A. AU - Friedman, N. AU - Regev, A. PY - 2007 DA - 2007// TI - Natural history and evolutionary principles of gene duplication in fungi JO - Nature VL - 449 UR - https://doi.org/10.1038/nature06107 DO - 10.1038/nature06107 ID - Wapinski2007 ER - TY - JOUR AU - Manning, G. AU - Whyte, D. B. AU - Martinez, R. AU - Hunter, T. AU - Sudarsanam, S. PY - 2002 DA - 2002// TI - The protein kinase complement of the human genome JO - Science VL - 298 UR - https://doi.org/10.1126/science.1075762 DO - 10.1126/science.1075762 ID - Manning2002 ER - TY - JOUR AU - Wang, D. AU - Harper, J. F. AU - Gribskov, M. PY - 2003 DA - 2003// TI - Systematic trans-genomic comparison of protein kinases between Arabidopsis and Saccharomyces cerevisiae JO - Plant Physiol VL - 132 UR - https://doi.org/10.1104/pp.103.021485 DO - 10.1104/pp.103.021485 ID - Wang2003 ER - TY - JOUR AU - Searls, D. B. PY - 1997 DA - 1997// TI - Linguistic approaches to biological sequences JO - Comput Appl Biosci VL - 13 ID - Searls1997 ER - TY - JOUR AU - Searls, D. B. PY - 2002 DA - 2002// TI - The language of genes JO - Nature VL - 420 UR - https://doi.org/10.1038/nature01255 DO - 10.1038/nature01255 ID - Searls2002 ER - TY - JOUR AU - Cherry, J. M. AU - Hong, E. L. AU - Amundsen, C. AU - Balakrishnan, R. AU - Binkley, G. AU - Chan, E. T. AU - Christie, K. R. AU - Costanzo, M. C. AU - Dwight, S. S. AU - Engel, S. R. AU - Fisk, D. G. AU - Hirschman, J. E. AU - Hitz, B. C. AU - Karra, K. AU - Krieger, C. J. AU - Miyasato, S. R. AU - Nash, R. S. AU - Park, J. AU - Skrzypek, M. S. AU - Simison, M. AU - Weng, S. AU - Wong, E. D. PY - 2012 DA - 2012// TI - Saccharomyces Genome Database: the genomics resource of budding yeast JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr1029 DO - 10.1093/nar/gkr1029 ID - Cherry2012 ER - TY - JOUR AU - Camacho, C. AU - Coulouris, G. AU - Avagyan, V. AU - Ma, N. AU - Papadopoulos, J. AU - Bealer, K. AU - Madden, T. L. PY - 2009 DA - 2009// TI - BLAST+: architecture and applications JO - BMC Bioinformatics VL - 10 UR - https://doi.org/10.1186/1471-2105-10-421 DO - 10.1186/1471-2105-10-421 ID - Camacho2009 ER - TY - JOUR AU - Byrne, K. P. AU - Wolfe, K. H. PY - 2006 DA - 2006// TI - Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkj041 DO - 10.1093/nar/gkj041 ID - Byrne2006 ER - TY - JOUR AU - Byrne, K. P. AU - Wolfe, K. H. PY - 2005 DA - 2005// TI - The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species JO - Genome Res VL - 15 UR - https://doi.org/10.1101/gr.3672305 DO - 10.1101/gr.3672305 ID - Byrne2005 ER -