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cjeans's library [832 articles]

Recent papers added to cjeans's library ordered by importance.
  • Getting the most from PSI-BLAST
    Trends in Biochemical Sciences, Vol. 27, No. 3. (1 March 2002), pp. 161-164.
    by David T Jones, Mark B Swindells
    posted to blast sequence by cjeans on 2007-10-17 11:11:31 as *****
  • Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs".
    Genome Res, Vol. 11, No. 12. (December 2001), pp. 2120-2126.
    by LR Matthews, P Vaglio, J Reboul, H Ge, BP Davis, J Garrels, S Vincent, M Vidal
    posted to ppi prediction by cjeans on 2007-10-16 09:24:14 as ***** along with 3 people and 1 group lfriedl nuke2005 bluto kdl
  • Correlated sequence-signatures as markers of protein-protein interaction.
    J Mol Biol, Vol. 311, No. 4. (24 August 2001), pp. 681-692.
    by E Sprinzak, H Margalit
    posted to ppi prediction by cjeans on 2007-10-16 09:23:44 as ***** along with 8 people bicko chad_davis maryee dyermd grahamc lilith wilbur Rhys
  • Predicting protein--protein interactions from primary structure.
    Bioinformatics, Vol. 17, No. 5. (May 2001), pp. 455-460.
    by JR Bock, DA Gough
    posted to ppi prediction by cjeans on 2007-10-16 09:22:52 as ***** along with 5 people wilbur iris_2001 maryee leelarcombe Evangelia
  • Predicted protein-protein interaction sites from local sequence information
    FEBS Letters, Vol. 544, No. 1-3. (5 June 2003), pp. 236-239.
    by Yanay Ofran, Burkhard Rost
    posted to ppi prediction by cjeans on 2007-10-16 09:21:56 as *****
  • Evidence for a clade of nematodes, arthropods and other moulting animals.
    Nature, Vol. 387, No. 6632. (29 May 1997), pp. 489-493.
    by AM Aguinaldo, JM Turbeville, LS Linford, MC Rivera, JR Garey, RA Raff, JA Lake
    posted to evolution by cjeans on 2007-06-30 15:25:40 as *****
  • Conservation of Regional Gene Expression in Mouse and Human Brain
    PLoS Genetics, Vol. 3, No. 4. (1 April 2007), e59.
    by Andrew D Strand, Aaron K Aragaki, Zachary C Baquet, Angela Hodges, Philip Cunningham, Peter Holmans, Kevin R Jones, Lesley Jones, Charles Kooperberg, James M Olson
    posted to expression tissue-specific transcriptome by cjeans on 2007-06-30 11:03:58 as ***** along with 5 people and 1 group nickluscombe Iden-J_GluR ghattem suizan ppark EBI-regulation
  • Evolutionary Conservation of Expression Profiles Between Human and Mouse Orthologous Genes
    Molecular Biology and Evolution, Vol. 23, No. 3. (March 2006), pp. 530-540.
    by Ben-Yang Liao, Jianzhi Zhang
    posted to evolution expression microarray by cjeans on 2007-06-30 11:01:18 as ***** along with 2 people and 1 group penka gjuggler Nie
  • Large-scale analysis of the human and mouse transcriptomes.
    Proc Natl Acad Sci U S A, Vol. 99, No. 7. (2 April 2002), pp. 4465-4470.
    by AI Su, MP Cooke, KA Ching, Y Hakak, JR Walker, T Wiltshire, AP Orth, RG Vega, LM Sapinoso, A Moqrich, A Patapoutian, GM Hampton, PG Schultz, JB Hogenesch
    posted to evolution tissue-specific transcriptome by cjeans on 2007-06-28 15:52:04 as ***** along with 3 people miguel cconboy eukfn
  • Coiled coil structures and transcription: an analysis of the S. cerevisiae coilome.
    Mol Genet Genomics (3 May 2007)
    by Kellie E Barbara, Kristine A Willis, Terry M Haley, Stephen J Deminoff, George M Santangelo
    posted to coiled-coil transcription by cjeans on 2007-06-21 15:58:00 as ***** along with 1 person chgjb
  • The many faces of the helix-turn-helix domain: transcription regulation and beyond.
    FEMS Microbiol Rev, Vol. 29, No. 2. (April 2005), pp. 231-262.
    by L Aravind, V Anantharaman, S Balaji, MM Babu, LM Iyer
    posted to evolution network regulation transcription trn by cjeans on 2007-06-20 14:32:11 as *****
  • Co-evolution of transcription factors and their targets depends on mode of regulation
    Genome Biology, Vol. 7 (19 July 2006), R62.
    by Ruth Hershberg, Hanah Margalit
    posted to coevolution evolution network regulation transcription trn by cjeans on 2007-06-19 13:03:37 as ***** along with 4 people and 2 groups cisevol PetrovLab indigoviolet dpollard cis-regulatory-evolution EisenLab
  • Assessing performance of orthology detection strategies applied to eukaryotic genomes.
    PLoS ONE, Vol. 2 (2007)
    by F Chen, AJ Mackey, JK Vermunt, DS Roos
    posted to f1000 ortholog by cjeans on 2007-06-09 04:09:11 as ***** along with 7 people and 3 groups natstreet icases operon rvosa indigoviolet stajich winterschlaefer EisenLab FAB-lab TNT
  • In Search of the Biological Significance of Modular Structures in Protein Networks
    PLoS Computational Biology, Vol. 3, No. 6. (1 June 2007), e107.
    by Zhi Wang, Jianzhi Zhang
    posted to evolution network by cjeans on 2007-06-05 14:46:40 as ***** along with 6 people and 2 groups pinney jfr grahamc massivemayhem zwang cabbagezs Bioinformatics ParkinsonLab_at_MaRS
  • Distributive immunization of networks against viruses using the /`honey-pot/' architecture
    Nat Phys, Vol. 1, No. 3. (December 2005), pp. 184-188.
    by Jacob Goldenberg, Yuval Shavitt, Eran Shir, Sorin Solomon
    posted to network by cjeans on 2007-06-01 13:24:50 as ***** along with 1 person tomhebbron
  • Structure and evolution of transcriptional regulatory networks.
    Curr Opin Struct Biol, Vol. 14, No. 3. (June 2004), pp. 283-291.
    by MM Babu, NM Luscombe, L Aravind, M Gerstein, SA Teichmann
    posted to evolution trn by cjeans on 2007-05-25 10:55:38 as ***** along with 5 people and 2 groups tny kengg koller tvdbulck karfunkel Bioinformatics Plantandetc
  • Structure, function and evolution of multidomain proteins
    Current Opinion in Structural Biology, Vol. 14, No. 2. (April 2004), pp. 208-216.
    by Christine Vogel, Matthew Bashton, Nicola D Kerrison, Cyrus Chothia, Sarah A Teichmann
    posted to chothia domain evolution structure by cjeans on 2007-05-25 10:51:45 as *****
  • The origins and evolution of functional modules: lessons from protein complexes
    Philosophical Transactions of The Royal Society B Biological Sciences, Vol. 361, No. 1467. (29 March 2006), pp. 507-517.
    by Jose B Pereira-Leal, Emmanuel D Levy, Sarah A Teichmann
    posted to evolution structure by cjeans on 2007-05-25 10:48:26 as *****
  • Correlated mutations contain information about protein-protein interaction.
    J Mol Biol, Vol. 271, No. 4. (29 August 1997), pp. 511-523.
    by F Pazos, M Helmer-Citterich, G Ausiello, A Valencia
    posted to residues critical coevolution by cjeans on 2007-02-05 08:05:15 as ***** along with 2 people gurkanbebek tale
  • A Model-Based Approach for Detecting Co-evolving Positions in a Molecule.
    Mol Biol Evol (8 June 2005)
    by Julien Dutheil, Tal Pupko, Alain Jean-Marie, Nicolas Galtier
    posted to residues critical coevolution by cjeans on 2007-02-05 06:59:58 as ***** along with 2 people and 1 group stevanspringer RMGraze FAB-lab
  • Automatic Methods for Predicting Functionally Important Residues
    Journal of Molecular Biology, Vol. 326, No. 4. (28 February 2003), pp. 1289-1302.
    by A Del, Florencio Pazos, Alfonso Valencia
    posted to residues critical coevolution by cjeans on 2007-02-05 06:59:32 as ***** along with 2 people and 1 group mdimmic sriram_s TNT
  • Evolutionary Potential of a Duplicated Repressor-Operator Pair: Simulating Pathways Using Mutation Data
    PLoS Computational Biology, Vol. 2, No. 5. (1 May 2006), e58.
    by Frank J Poelwijk, Daniel J Kiviet, Sander J Tans
    posted to landscape fitness by cjeans on 2007-02-05 06:29:49 as ***** along with 1 person cckan
  • GAPWM: A Genetic Algorithm Method for Optimizing a Position Weight Matrix.
    Bioinformatics (6 March 2007)
    by Leping Li, Yu Liang, Robert L L Bass
    posted to sequence by cjeans on 2007-10-23 10:49:59 as **** along with 3 people and 2 groups dpollard grahamc ghattem EisenLab ParkinsonLab_at_MaRS
  • Machine Learning and Its Applications to Biology
    PLoS Computational Biology, Vol. 3, No. 6. (1 June 2007), e116.
    by Adi L Tarca, Vincent J Carey, Xue-Wen Chen, Roberto Romero, Sorin Drăghici
    posted to machine-learning by cjeans on 2007-07-09 14:52:48 as **** along with 7 people and 2 groups Borelli skhadar julius asddd ciga nklee kmdaily SysbioMPI-TCells Computational_Information_Geometry
  • An integrated approach to prognosis using protein microarrays and nonparametric methods
    Mol Syst Biol, Vol. 3 (26 June 2007)
    by Tanya Knickerbocker, Jiunn R Chen, Ravi Thadhani, Gavin Macbeath
    posted to integrative microarray by cjeans on 2007-07-04 09:00:56 as ****
  • Natural selection on gene expression
    Trends in Genetics, Vol. 22, No. 8. (August 2006), pp. 456-461.
    by Yoav Gilad, Alicia Oshlack, Scott A Rifkin
    posted to evolution expression by cjeans on 2007-07-01 12:39:35 as **** along with 4 people and 2 groups bpcusack dchughes calamar emarker G4ID Genetics-of-Gambling
  • Arthropods: developmental diversity within a (super) phylum.
    Proc Natl Acad Sci U S A, Vol. 97, No. 9. (25 April 2000), pp. 4438-4441.
    by M Akam
    posted to evolution by cjeans on 2007-06-30 15:23:24 as ****
  • The new animal phylogeny: reliability and implications.
    Proc Natl Acad Sci U S A, Vol. 97, No. 9. (25 April 2000), pp. 4453-4456.
    by A Adoutte, G Balavoine, N Lartillot, O Lespinet, B Prud'homme, R de Rosa
    posted to evolution phylogenetic by cjeans on 2007-06-30 15:22:46 as **** along with 3 people tanchize altotor hervelequere
  • Evolution of primate gene expression
    Nature Reviews Genetics, Vol. 7, No. 9., pp. 693-702.
    by Philipp Khaitovich, Wolfgang Enard, Michael Lachmann, Svante Pääbo
    posted to evolution expression by cjeans on 2007-06-30 15:07:24 as **** along with 4 people balicea usagi-kirin Manchester emarker
  • Neurogenomics: at the intersection of neurobiology and genome sciences
    Nat Neurosci, Vol. 7, No. 5. (May 2004), pp. 429-433.
    by Mark S Boguski, Allan R Jones
    posted to nervous-system by cjeans on 2007-06-30 15:06:29 as ****
  • Evolutionary significance of gene expression divergence.
    Gene, Vol. 345, No. 1. (17 January 2005), pp. 119-126.
    by IK Jordan, L Mariño-Ramírez, EV Koonin
    posted to evolution expression by cjeans on 2007-06-30 15:04:43 as **** along with 1 person emarker
  • Tissue-specific transcriptional regulation has diverged significantly between human and mouse
    Nature Genetics, Vol. 39, No. 6. (21 May 2007), pp. 730-732.
    by Duncan T Odom, Robin D Dowell, Elizabeth S Jacobsen, William Gordon, Timothy W Danford, Kenzie D Macisaac, Alexander P Rolfe, Caitlin M Conboy, David K Gifford, Ernest Fraenkel
    posted to expression regulation tissue-specific transcription by cjeans on 2007-06-30 11:04:51 as **** along with 9 people and 4 groups dpollard gpalidwor dchughes cwbrown djkt maximilianh fpattyn caseybrown yevishere EisenLab G4ID Genetics-of-Gambling cis-regulatory-evolution
  • Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression.
    Genome Res, Vol. 9, No. 10. (October 1999), pp. 950-959.
    by RM Ewing, A Ben Kahla, O Poirot, F Lopez, S Audic, JM Claverie
    posted to est expression by cjeans on 2007-06-30 11:00:10 as **** along with 1 person dandaman
  • EST databases as multi-conditional gene expression datasets.
    Pac Symp Biocomput (2000), pp. 430-442.
    by RM Ewing, JM Claverie
    posted to est expression by cjeans on 2007-06-30 10:59:29 as ****
  • Extensive and divergent circadian gene expression in liver and heart.
    Nature, Vol. 417, No. 6884. (2 May 2002), pp. 78-83.
    by KF Storch, O Lipan, I Leykin, N Viswanathan, FC Davis, WH Wong, CJ Weitz
    posted to expression tissue-specific by cjeans on 2007-06-30 10:38:31 as ****
  • Cell cycle: Complex evolution
    Nature, Vol. 443, No. 7111. (04 October 2006), pp. 513-515.
    by Gavin Sherlock
    posted to cell-cycle by cjeans on 2007-06-30 10:14:28 as ****
  • A genetic signature of interspecies variations in gene expression
    Nature Genetics, Vol. 38, No. 7. (18 June 2006), pp. 830-834.
    by Itay Tirosh, Adina Weinberger, Miri Carmi, Naama Barkai
    posted to expression tissue-specific by cjeans on 2007-06-30 10:12:06 as **** along with 4 people and 2 groups adepace nickluscombe aswin caseybrown EisenLab EBI-regulation
  • Similar gene expression profiles do not imply similar tissue functions.
    Trends Genet, Vol. 22, No. 3. (March 2006), pp. 132-138.
    by I Yanai, JO Korbel, S Boue, SK McWeeney, P Bork, MJ Lercher
    posted to expression microarray tissue-specific by cjeans on 2007-06-30 10:11:15 as **** along with 1 person and 1 group nickluscombe EBI-regulation
  • Comparative genome analyses of nervous system-specific genes.
    Gene, Vol. 365 (3 January 2006), pp. 130-136.
    by AO Noda, K Ikeo, T Gojobori
    posted to tissue-specific by cjeans on 2007-06-30 10:10:18 as **** along with 1 person and 1 group dpollard EisenLab
  • Systems biology: Many things from one
    Nature (19 November 2006)
    by John RS Newman, Jonathan S Weissman
    posted to noise system-biology by cjeans on 2007-06-30 08:06:03 as **** along with 2 people manduca totolee
  • A gene atlas of the mouse and human protein-encoding transcriptomes.
    Proc Natl Acad Sci U S A, Vol. 101, No. 16. (20 April 2004), pp. 6062-6067.
    by AI Su, T Wiltshire, S Batalov, H Lapp, KA Ching, D Block, J Zhang, R Soden, M Hayakawa, G Kreiman, MP Cooke, JR Walker, JB Hogenesch
    posted to tissue-specific transcriptome by cjeans on 2007-06-30 04:08:50 as **** along with 11 people and 2 groups gjuggler dragonrez nickluscombe jeremymiller eukfn usagi-kirin asu shikin jdiezperezj caseybrown maralena EBI-regulation GeschwindLab
  • Noise in transcription negative feedback loops: simulation and experimental analysis
    Mol Syst Biol, Vol. 2 (2006)
    by Yann Dublanche, Konstantinos Michalodimitrakis, Nico Kummerer, Mathilde Foglierini, Luis Serrano
    posted to noise system-biology by cjeans on 2007-06-28 07:36:39 as **** along with 4 people marcio aalibes balabu johncumbers
  • Evolution of early development of the nervous system: a comparison between arthropods.
    Bioessays, Vol. 27, No. 9. (September 2005), pp. 874-883.
    by A Stollewerk, P Simpson
    posted to evolution nervous-system by cjeans on 2007-06-27 13:59:44 as ****
  • A human phenome-interactome network of protein complexes implicated in genetic disorders
    Nature Biotechnology, Vol. 25, No. 3. (07 March 2007), pp. 309-316.
    by Kasper Lage, Olof E Karlberg, Zenia M Størling, Páll, Anders G Pedersen, Olga Rigina, Anders M Hinsby, Zeynep Tümer, Flemming Pociot, Niels Tommerup, Yves Moreau, Søren Brunak
    posted to integrative system-biology by cjeans on 2007-06-27 13:34:17 as **** along with 7 people and 2 groups jyuh kuhn jfr ealloza JBEgwa01 grahamc jiny BioinfoCIPF ParkinsonLab_at_MaRS
  • A network of multiple regulatory layers shapes gene expression in fission yeast.
    Mol Cell, Vol. 26, No. 1. (13 April 2007), pp. 145-155.
    by DH Lackner, TH Beilharz, S Marguerat, J Mata, S Watt, F Schubert, T Preiss, J Bähler
    posted to integrative system-biology by cjeans on 2007-06-27 10:32:45 as **** along with 1 person and 1 group kengg Plantandetc
  • Noise in Gene Expression Determines Cell Fate in Bacillus subtilis.
    Science (14 June 2007)
    by Hédia Maamar, Arjun Raj, David Dubnau
    posted to noise by cjeans on 2007-06-27 10:24:04 as **** along with 4 people jjray sebastien_vigneau margaritis cabbagezs
  • A wiring of the human nucleolus.
    Mol Cell, Vol. 22, No. 2. (21 April 2006), pp. 285-295.
    by AM Hinsby, L Kiemer, EO Karlberg, K Lage, A Fausbøll, AS Juncker, JS Andersen, M Mann, S Brunak
    posted to integrative system-biology by cjeans on 2007-06-27 08:36:45 as **** along with 1 person arrak
  • Dynamic complex formation during the yeast cell cycle.
    Science, Vol. 307, No. 5710. (4 February 2005), pp. 724-727.
    by U de Lichtenberg, LJ Jensen, S Brunak, P Bork
    posted to cell-cycle integrative system-biology by cjeans on 2007-06-27 08:34:25 as **** along with 11 people and 1 group gjuggler carlk mdimmic chad_davis balajis wnpx koller massivemayhem arne phoenixzxl larsjuhljensen dIEMoSIRIS
  • Co-evolution of transcriptional and post-translational cell-cycle regulation
    Nature (27 September 2006)
    by Lars J Jensen, Thomas S Jensen, Ulrik de Lichtenberg, Søren Brunak, Peer Bork
    posted to cell-cycle coevolution integrative system-biology transcription by cjeans on 2007-06-27 08:22:23 as **** along with 7 people and 1 group JAShapiro adepace koller olympos ccr kluck larsjuhljensen EisenLab
  • Phylogenetic analysis in molecular evolutionary genetics.
    Annu Rev Genet, Vol. 30 (1996), pp. 371-403.
    by M Nei
    posted to classic evolution by cjeans on 2007-06-26 11:11:50 as ****
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