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cjeans's evolution [149 articles]

Recent papers added to cjeans's library classified by the tag evolution. You can also see everyone's evolution.
  • Darwinian Evolution on a Chip
    PLoS Biology, Vol. 6, No. 4. (1 April 2008), e85.
    by Brian M Paegel, Gerald F Joyce
    posted to experiment evolution by cjeans on 2008-05-06 01:52:55 as ** along with 1 person biomcgary
  • The evolution of gene collectives: How natural selection drives chemical innovation
    Proceedings of the National Academy of Sciences (23 January 2008), 0709132105.
    by Michael A Fischbach, Christopher T Walsh, Jon Clardy
    posted to evolution by cjeans on 2008-01-24 08:27:21 as ** along with 3 people stevanspringer operon tomhebbron
  • Preferential protection of protein interaction network hubs in yeast: Evolved functionality of genetic redundancy
    Proceedings of the National Academy of Sciences (23 January 2008), 0711043105.
    by Ran Kafri, Orna Dahan, Jonathan Levy, Yitzhak Pilpel
    posted to evolution network pin by cjeans on 2008-01-24 08:26:19 as ** along with 4 people and 1 group zwang janek04 wsjames mclarenv Oxford Virology
  • Positive selection acting on splicing motifs reflects compensatory evolution
    Genome Res. (18 January 2008), gr.070268.107.
    by Shengdong Ke, Xiang H Zhang, Lawrence A Chasin
    posted to coevolution evolution by cjeans on 2008-01-22 00:43:06 as ** along with 4 people and 1 group bpcusack operon stajich gjuggler Berkeley Mycology
  • The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication
    Proceedings of the National Academy of Sciences (16 January 2008), 0707293105.
    by Aviva Presser, Michael B Elowitz, Manolis Kellis, Roy Kishony
    posted to duplication evolution module network pin ppi by cjeans on 2008-01-17 08:39:26 as ** along with 3 people zwang roys phoenixzxl
  • High-confidence prediction of global interactomes based on genome-wide coevolutionary networks
    Proceedings of the National Academy of Sciences (16 January 2008), 0709671105.
    by David Juan, Florencio Pazos, Alfonso Valencia
    posted to coevolution evolution mirrortree pin ppi profile by cjeans on 2008-01-17 08:07:50 as ** along with 12 people and 1 group paolomarcatili tmmurali brant balicea sebastien_vigneau bluto aconesa Katje roys friendpine huali mdstobbe microbiology_nijmegen
  • Functional evolution of the p53 regulatory network through its target response elements
    Proceedings of the National Academy of Sciences (10 January 2008), 0704694105.
    by Anil G Jegga, Alberto Inga, Daniel Menendez, Bruce J Aronow, Michael A Resnick
    posted to evolution network transcription by cjeans on 2008-01-14 05:28:50 as ** along with 5 people and 1 group brant zwang cisevol idonaldson renatomilani cis-regulatory-evolution
  • Evolution and Selection in Yeast Promoters: Analyzing the Combined Effect of Diverse Transcription Factor Binding Sites
    PLoS Computational Biology, Vol. 4, No. 1. (1 January 2008), e7.
    by Daniela Raijman, Ron Shamir, Amos Tanay
    posted to evolution tfbs transcription by cjeans on 2008-01-14 03:39:27 as **
  • Expression Profiles Reveal Parallel Evolution of Epistatic Interactions Involving the CRP regulon in Escherichia coli
    PLoS Genetics, Vol. preprint, No. 2008. (1 January 2008), e35.eor.
    by Tim F Cooper, Susanna Remold, Rich E Lenski, Dominique Schneider
    posted to evolution expression transcription by cjeans on 2008-01-14 03:17:17 as **
  • Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage.
    Mol Biol Evol (3 January 2008)
    by Ziheng Yang, Rasmus Nielsen
    posted to algorithm evolution by cjeans on 2008-01-11 06:01:13 as ** along with 2 people and 1 group stajich gjuggler Berkeley Mycology
  • Phylogeny of endocytic components yields insight into the process of nonendosymbiotic organelle evolution
    Proceedings of the National Academy of Sciences (8 January 2008), 0707318105.
    by Joel B Dacks, Pak P Poon, Mark C Field
    posted to evolution by cjeans on 2008-01-09 13:10:39 as ** along with 1 person renatomilani
  • Protein dispensability and rate of evolution.
    Nature, Vol. 411, No. 6841. (28 June 2001), pp. 1046-1049.
    by AE Hirsh, HB Fraser
    posted to evolution fitness phenotype by cjeans on 2007-12-29 08:50:04 as ** along with 5 people and 1 group tfogal bjorns balicea penka bluto Nie
  • A simple method for estimating the parameter of substitution rate variation among sites
    Mol Biol Evol, Vol. 14, No. 11. (1 November 1997), pp. 1106-1113.
    by X Gu, J Zhang
    posted to evolution substitution by cjeans on 2007-12-26 04:15:27 as **
  • Determining divergence times with a protein clock: Update and<img src="corehtml/pmc/pmcents/x2009.gif" border="0" alt=" " />reevaluation
    posted to evolution by cjeans on 2007-12-26 04:11:12 as **
  • Comparative analysis of the Saccharomyces cerevisiae and Caenorhabditis elegans protein interaction networks
    BMC Evolutionary Biology, Vol. 5, No. 1. (2005)
    by Ino Agrafioti, Jonathan Swire, James Abbott, Derek Huntley, Sarah Butcher, Michael Stumpf
    posted to compare-genomics evolution pin by cjeans on 2007-12-25 12:39:35 as **
  • A Single Determinant Dominates the Rate of Yeast Protein Evolution
    Molecular Biology and Evolution, Vol. 23, No. 2. (20 February 2006), pp. 327-337.
    by Allan D Drummond, Alpan Raval, Claus O Wilke
    posted to evolution pin ppi by cjeans on 2007-12-25 12:34:18 as **
  • Integration of Horizontally Transferred Genes into Regulatory Interaction Networks Takes Many Million Years
    Mol Biol Evol (24 December 2007), msm283.
    by Martin J Lercher, Csaba Pal
    posted to evolution network by cjeans on 2007-12-25 12:03:06 as ** along with 4 people and 1 group cisevol cambray marcio dquest cis-regulatory-evolution
  • Deriving structure from evolution: metazoan segmentation
    Mol Syst Biol, Vol. 3 (18 December 2007)
    by Paul Francois, Vincent Hakim, Eric D Siggia
    posted to evolution network system-biology by cjeans on 2007-12-20 00:41:22 as ** along with 3 people grahamc biomcgary Ema
  • Double Dutch for duplications
    Nature Genetics, Vol. 39, No. 11., pp. 1303-1304.
    by Ewan Birney
    posted to duplication evolution genetics by cjeans on 2007-12-17 00:57:10 as **
  • Evolutionary Analysis of Amino Acid Repeats Across the Genomes of 12 Drosophila Species
    Mol Biol Evol (7 December 2007), msm129.
    by Melanie A Huntley, Andrew G Clark
    posted to compare-genomics evolution by cjeans on 2007-12-16 04:42:40 as **
  • Positive selection at the protein network periphery: Evaluation in terms of structural constraints and cellular context
    Proceedings of the National Academy of Sciences (12 December 2007), 0710183104.
    by Philip M Kim, Jan O Korbel, Mark B Gerstein
    posted to evolution network by cjeans on 2007-12-14 00:28:33 as ** along with 6 people wilbur jyuh tmmurali grahamc mingzhi minostro
  • Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements
    Proceedings of the National Academy of Sciences (11 December 2007), 0705658104.
    by Sergey I Nikolaev, Juan I Montoya-Burgos, Konstantin Popadin, Leila Parand, Elliott H Margulies, National, Stylianos E Antonarakis
    posted to evolution by cjeans on 2007-12-12 10:24:10 as ** along with 4 people and 1 group aprasad djkt zwang cisevol cis-regulatory-evolution
  • Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets
    Nature Genetics, Vol. 38, No. 3. (24 February 2006), pp. 285-293.
    by TKB Gandhi, Jun Zhong, Suresh Mathivanan, L Karthick, KN Chandrika, Sujatha S Mohan, Salil Sharma, Stefan Pinkert, Shilpa Nagaraju, Balamurugan Periaswamy, Goparani Mishra, Kannabiran Nandakumar, Beiyi Shen, Nandan Deshpande, Rashmi Nayak, Malabika Sarker, Jef D Boeke, Giovanni Parmigiani, Jörg Schultz, Joel S Bader, Akhilesh Pandey
    posted to evolution pin ppi by cjeans on 2007-12-10 10:24:26 as ** along with 11 people and 2 groups TheresaNiederberger cerca carlk balajis indigoviolet tny spavey alwinpremanand dejori Pao-Yang pmendes EisenLab FAB-lab
  • Tests for comparing related amino-acid sequences. Cytochrome c and cytochrome c551
    Journal of Molecular Biology, Vol. 61, No. 2. (28 October 1971), pp. 409-424.
    by AD Mclachlan
    posted to correlated-mutation evolution by cjeans on 2007-12-02 11:17:13 as ** along with 1 person Lombardo_7
  • Molecular evolution in large genetic networks: does connectivity equal constraint?
    J Mol Evol, Vol. 58, No. 2. (February 2004), pp. 203-211.
    by MW Hahn, GC Conant, A Wagner
    posted to evolution network by cjeans on 2007-12-02 11:14:36 as ** along with 1 person and 1 group penka Nie
  • Two types of amino acid substitutions in protein evolution.
    J Mol Evol, Vol. 12, No. 3. (15 March 1979), pp. 219-236.
    by T Miyata, S Miyazawa, T Yasunaga
    posted to evolution by cjeans on 2007-12-02 11:13:17 as ** along with 1 person Iden-J_GluR
  • A pair-to-pair amino acids substitution matrix and its applications for protein structure prediction.
    Proteins, Vol. 67, No. 1. (1 April 2007), pp. 142-153.
    by E Eyal, M Frenkel-Morgenstern, V Sobolev, S Pietrokovski
    posted to coevolution correlated-mutation evolution by cjeans on 2007-12-02 10:45:50 as ** along with 2 people Lombardo_7 bicko
  • Gene conversion as a focusing mechanism for correlated mutations: a hypothesis.
    Mol Gen Genet, Vol. 251, No. 5. (19 July 1996), pp. 503-508.
    by J Ninio
    posted to correlated-mutation evolution hypothesis by cjeans on 2007-12-01 08:22:07 as **
  • Single and coincident intragenic mutations attributable to gene conversion in a human cell line.
    Genetics, Vol. 146, No. 4. (August 1997), pp. 1429-1439.
    by CR Giver, AJ Grosovsky
    posted to correlated-mutation evolution by cjeans on 2007-12-01 07:49:53 as **
  • Evolution of Two-Component Signal Transduction
    Mol Biol Evol, Vol. 17, No. 12. (1 December 2000), pp. 1956-1970.
    by Kristin K Koretke, Andrei N Lupas, Patrick V Warren, Martin Rosenberg, James R Brown
    posted to coevolution evolution by cjeans on 2007-12-01 07:29:46 as ** along with 1 person tale
  • Sequence evolution and the mechanism of protein folding.
    Biophys J, Vol. 79, No. 4. (October 2000), pp. 1787-1799.
    by AR Ortiz, J Skolnick
    posted to evolution sequence structure by cjeans on 2007-12-01 07:16:13 as ** along with 2 people and 2 groups marcius penka BioinfoCIPF SGU-CIPF
  • The Effect of Stochasticity on the Lac Operon: An Evolutionary Perspective
    PLoS Computational Biology, Vol. 3, No. 6. (1 June 2007), e111.
    by Milan van Hoek, Paulien Hogeweg
    posted to evolution simulation by cjeans on 2007-12-01 02:53:45 as ** along with 3 people Retchless madhadron proulx
  • POINT: a database for the prediction of protein-protein interactions based on the orthologous interactome
    Bioinformatics, Vol. 20, No. 17. (22 November 2004), pp. 3273-3276.
    by Tao-Wei Huang, An-Chi Tien, Wen-Shien Huang, Yuan-Chii G Lee, Chin-Lin Peng, Huei-Hun Tseng, Cheng-Yan Kao, Chi-Ying F Huang
    posted to evolution ortholog ppi by cjeans on 2007-11-30 06:47:59 as ** along with 1 person cerca
  • Evolutionary predictions of binding surfaces and interactions
    Current Opinion in Structural Biology, Vol. 12, No. 1. (1 February 2002), pp. 21-27.
    by Olivier Lichtarge, Mathew E Sowa
    posted to evolution interface ppi by cjeans on 2007-11-30 01:14:28 as ** along with 1 person Pao-Yang
  • Protein interaction networks from yeast to human.
    Curr Opin Struct Biol, Vol. 14, No. 3. (June 2004), pp. 292-299.
    by P Bork, LJ Jensen, C von Mering, AK Ramani, I Lee, EM Marcotte
    posted to evolution pin ppi by cjeans on 2007-11-30 00:58:27 as ** along with 7 people kuhn koller grahamc lpfernandes selrac Evangelia larsjuhljensen
  • Determination of protein function, evolution and interactions by structural genomics
    Current Opinion in Structural Biology, Vol. 11, No. 3. (1 June 2001), pp. 354-363.
    by Sarah A Teichmann, Alexey G Murzin, Cyrus Chothia
    posted to evolution genome ppi structure by cjeans on 2007-11-28 09:47:51 as **
  • From the Cover: Conserved patterns of protein interaction in multiple species.
    Proc Natl Acad Sci U S A, Vol. 102, No. 6. (8 February 2005), pp. 1974-1979.
    by R Sharan, S Suthram, RM Kelley, T Kuhn, S McCuine, P Uetz, T Sittler, RM Karp, T Ideker
    posted to evolution ppi by cjeans on 2007-11-28 00:40:00 as ** along with 11 people and 1 group sza dragonrez okarsligil balajis nuke2005 maryee gurkanbebek koller iris_2001 maralena mdstobbe Bioinformatics
  • Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?
    Protein Sci, Vol. 13, No. 1. (January 2004), pp. 190-202.
    by DR Caffrey, S Somaroo, JD Hughes, J Mintseris, ES Huang
    posted to evolution interface ppi by cjeans on 2007-11-28 00:20:51 as ** along with 3 people higueruelo bicko Evangelia
  • Phenotypic Mutation Rates and the Abundance of Abnormal Proteins in Yeast
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e203.
    by Martin Willensdorfer, Reinhard Bürger, Martin A Nowak
    posted to evolution by cjeans on 2007-11-27 01:50:13 as **
  • On evolutionary conservation of thermodynamic coupling in proteins.
    J Biol Chem, Vol. 279, No. 18. (30 April 2004), pp. 19046-19050.
    by AA Fodor, RW Aldrich
    posted to correlated-mutation evolution by cjeans on 2007-11-26 08:38:08 as ** along with 7 people and 2 groups Lombardo_7 ca3295 friendpine ana barry gbart tale structural_bioinformatics Bioinformatics
  • Structural divergence and distant relationships in proteins: evolution of the globins.
    Curr Opin Struct Biol, Vol. 15, No. 3. (June 2005), pp. 290-301.
    by JT Lecomte, DA Vuletich, AM Lesk
    posted to evolution sequence structure by cjeans on 2007-11-26 06:46:33 as **
  • Scoring docking models with evolutionary information.
    Proteins, Vol. 60, No. 2. (1 August 2005), pp. 275-280.
    by M Tress, D de Juan, O Graña, MJ Gómez, P Gómez-Puertas, JM González, G López, A Valencia
    posted to docking evolution ppi structure by cjeans on 2007-11-26 06:38:20 as ** along with 3 people and 2 groups bicko marcius ameetsoni BioinfoCIPF SGU-CIPF
  • Exploring a Phylogenetic Approach for the Detection of Correlated Substitutions in Proteins
    Mol Biol Evol, Vol. 17, No. 11. (1 November 2000), pp. 1753-1759.
    by Pierre Tuff, Pierre Darlu
    posted to coevolution evolution sequence by cjeans on 2007-11-26 06:33:55 as ** along with 1 person tale
  • An insight into domain combinations.
    Bioinformatics, Vol. 17 Suppl 1 (2001)
    by G Apic, J Gough, SA Teichmann
    posted to domain evolution by cjeans on 2007-11-26 02:30:40 as ** along with 1 person choonpeng
  • Structure, function and evolution of multidomain proteins.
    Curr Opin Struct Biol, Vol. 14, No. 2. (April 2004), pp. 208-216.
    by C Vogel, M Bashton, ND Kerrison, C Chothia, SA Teichmann
    posted to domain evolution structure by cjeans on 2007-11-26 02:30:13 as ** along with 3 people and 1 group Einat Schmidtc cmzmasek structural_bioinformatics
  • The linked conservation of structure and function in a family of high diversity: the monomeric cupredoxins.
    Structure, Vol. 12, No. 6. (June 2004), pp. 917-925.
    by J Gough, C Chothia
    posted to domain evolution by cjeans on 2007-11-26 02:29:50 as ** along with 1 person and 1 group Einat structural_bioinformatics
  • The Relationship Between Domain Duplication and Recombination
    Journal of Molecular Biology, Vol. 346, No. 1. (11 February 2005), pp. 355-365.
    by Christine Vogel, Sarah A Teichmann, Jose Pereira-Leal
    posted to domain evolution by cjeans on 2007-11-26 02:29:29 as ** along with 5 people and 4 groups ana marcius tny martainn mdimon structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • Relative rates of gene fusion and fission in multi-domain proteins.
    Trends Genet, Vol. 21, No. 1. (January 2005), pp. 25-30.
    by SK Kummerfeld, SA Teichmann
    posted to domain evolution by cjeans on 2007-11-26 02:29:14 as ** along with 1 person mingzhi
  • The evolution of domain arrangements in proteins and interaction networks.
    Cell Mol Life Sci, Vol. 62, No. 4. (February 2005), pp. 435-445.
    by E Bornberg-Bauer, F Beaussart, SK Kummerfeld, SA Teichmann, J Weiner
    posted to domain evolution by cjeans on 2007-11-26 02:28:57 as ** along with 2 people choonpeng cmzmasek
  • The properties of protein family space depend on experimental design
    Bioinformatics, Vol. 21, No. 11. (1 June 2005), pp. 2618-2622.
    by Victor Kunin, Sarah A Teichmann, Martijn A Huynen, Christos A Ouzounis
    posted to domain evolution structure by cjeans on 2007-11-26 02:28:37 as ** along with 2 people and 2 groups ana barry structural_bioinformatics Bioinformatics
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