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nirfriedmans library [116 articles]

Senaste artiklarna i nirfriedmans bibliotek.
  • Phosphotransfer profiling: systematic mapping of two-component signal transduction pathways and phosphorelays.
    Methods Enzymol, Vol. 423 (2007), pp. 531-548.
    by MT Laub, EG Biondi, JM Skerker
    posted to coevolution by nirfriedman on 2007-11-01 07:13:44 as **
  • Using evolutionary Expectation Maximization to estimate indel rates.
    Bioinformatics, Vol. 21, No. 10. (15 May 2005), pp. 2294-2300.
    by I Holmes
    posted to coevolution by nirfriedman on 2007-10-31 21:46:22 as ** along with 1 person aprasad
  • A gamma mixture model better accounts for among site rate heterogeneity.
    Bioinformatics, Vol. 21 Suppl 2 (1 September 2005)
    by I Mayrose, N Friedman, T Pupko
    posted to coevolution by nirfriedman on 2007-10-31 21:43:59 as **
  • Distribution and intensity of constraint in mammalian genomic sequence.
    Genome Res, Vol. 15, No. 7. (July 2005), pp. 901-913.
    by GM Cooper, EA Stone, G Asimenos, ED Green, S Batzoglou, A Sidow
    posted to coevolution by nirfriedman on 2007-10-31 20:32:30 as ** along with 5 people operon aprasad JeffR100 Garamonfok tale
  • Inference of functional regions in proteins by quantification of evolutionary constraints.
    Proc Natl Acad Sci U S A, Vol. 99, No. 5. (5 March 2002), pp. 2912-2917.
    by AL Simon, EA Stone, A Sidow
    posted to coevolution by nirfriedman on 2007-10-31 20:27:02 as ** along with 1 person tale
  • Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?
    Protein Eng, Vol. 7, No. 3. (March 1994), pp. 349-358.
    by IN Shindyalov, NA Kolchanov, C Sander
    posted to coevolution by nirfriedman on 2007-10-31 10:06:48 as ** along with 2 people kieran101 gbart
  • Coevolving protein residues: maximum likelihood identification and relationship to structure.
    J Mol Biol, Vol. 287, No. 1. (19 March 1999), pp. 187-198.
    by DD Pollock, WR Taylor, N Goldman
    posted to coevolution by nirfriedman on 2007-10-30 20:20:26 as ** along with 1 person pradiptaray
  • Functional Coevolutionary Networks of the Hsp70HopHsp90 System Revealed through Computational Analyses
    Molecular Biology and Evolution, Vol. 24, No. 4. (April 2007), pp. 1032-1044.
    by Travers, AA Simon, Fares, A Mario
    posted to coevolution by nirfriedman on 2007-10-30 20:18:22 as ** along with 2 people tale mingzhi
  • Detecting coevolving amino acid sites using Bayesian mutational mapping.
    Bioinformatics, Vol. 21 Suppl 1 (June 2005)
    by MW Dimmic, MJ Hubisz, CD Bustamante, R Nielsen
    posted to coevolution by nirfriedman on 2007-10-30 20:16:26 as **
  • Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions.
    Biochemistry, Vol. 44, No. 19. (17 May 2005), pp. 7156-7165.
    by GB Gloor, LC Martin, LM Wahl, SD Dunn
    posted to coevolution by nirfriedman on 2007-10-30 20:12:43 as ** along with 1 person LeightonP
  • Determination of network of residues that regulate allostery in protein families using sequence analysis.
    Protein Sci, Vol. 15, No. 2. (February 2006), pp. 258-268.
    by RI Dima, D Thirumalai
    posted to coevolution by nirfriedman on 2007-10-30 20:04:18 as ** along with 5 people and 1 group xdeupi gbart choonpeng tale mingzhi LabCompMed
  • Evolutionarily conserved networks of residues mediate allosteric communication in proteins.
    Nat Struct Biol, Vol. 10, No. 1. (January 2003), pp. 59-69.
    by GM Süel, SW Lockless, MA Wall, R Ranganathan
    posted to coevolution by nirfriedman on 2007-10-30 20:03:21 as ** along with 15 people and 3 groups ca3295 lna dimka marcius eckart_bindewald gbart analogAI dgront caporaso choonpeng efge carlescorbi mingzhi yalexeev weisblum biomedical-nlp BioinfoCIPF SGU-CIPF
  • An efficient algorithm for large-scale detection of protein families.
    Nucleic Acids Res, Vol. 30, No. 7. (1 April 2002), pp. 1575-1584.
    by AJ Enright, S Van Dongen, CA Ouzounis
    posted to p2p by nirfriedman on 2007-06-19 12:24:38 as ** along with 12 people and 2 groups Borelli camster operon knaseanka indigoviolet skhadar dgront entropy gcalda GustavoLacerda hpaces RebeccaHamer dbk-lab EisenLab
  • Evaluation of clustering algorithms for protein-protein interaction networks
    BMC Bioinformatics, Vol. 7 (06 November 2006), 488.
    by Sylvain Brohee, Jacques van Helden
    posted to p2p by nirfriedman on 2007-06-19 12:22:45 as ** along with 15 people and 1 group ethkim cerca AbnerCYH Borelli carlk pdelosri jfr chad_davis balajis dquest grahamc cjeans hpaces Pao-Yang oktie EPFL_SB_ITP_LBS
  • An automated method for finding molecular complexes in large protein interaction networks.
    BMC Bioinformatics, Vol. 4, No. 1. (13 January 2003)
    by GD Bader, CW Hogue
    posted to p2p by nirfriedman on 2007-06-19 12:22:13 as ** along with 5 people and 1 group ethkim carlk dragonrez lfriedl massivemayhem kdl
  • SWI/SNF is required for transcriptional memory at the yeast GAL gene cluster.
    Genes Dev, Vol. 21, No. 8. (15 April 2007), pp. 997-1004.
    by S Kundu, PJ Horn, CL Peterson
    posted to chromatin by nirfriedman on 2007-05-23 18:03:40 as **
  • Do disparate mechanisms of duplication add similar genes to the genome?
    Trends in Genetics, Vol. In Press, Corrected Proof
    by Jerel C Davis, Dmitri A Petrov
    posted to duplication by nirfriedman on 2006-12-22 09:04:04 as ** along with 5 people and 2 groups bpcusack PetrovLab Retchless dchughes mikemacpherson G4ID Genetics-of-Gambling
  • Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution.
    Genetics, Vol. 169, No. 2. (February 2005), pp. 1157-1164.
    by X He, J Zhang
    posted to duplication genome by nirfriedman on 2006-12-22 09:00:51 as ** along with 3 people pansapiens ushishir bluto
  • Transcriptional Regulation by Competing Transcription Factor Modules
    PLoS Computational Biology, Vol. 2, No. 12. (1 December 2006), e164.
    by Rutger Hermsen, Sander Tans, Ten
    posted to no-tag by nirfriedman on 2006-12-16 15:40:19 as ** along with 3 people wnpx zwang nklee
  • Global Mapping of Transposon Location
    PLoS Genetics, Vol. 2, No. 12. (1 December 2006), e212.
    by Abram Gabriel, Johannes Dapprich, Mark Kunkel, David Gresham, Stephen C Pratt, Maitreya J Dunham
    posted to no-tag by nirfriedman on 2006-12-16 15:36:18 as ** along with 1 person and 2 groups dchughes G4ID Genetics-of-Gambling
  • Transcriptional regulatory code of a eukaryotic genome
    Nature, Vol. 431, No. 7004. (2004), pp. 99-104.
    by Christopher T Harbison, Benjamin D Gordon, Tong I Lee, Nicola J Rinaldi, Kenzie D Macisaac, Timothy W Danford, Nancy M Hannett, Jean-Bosco Tagne, David B Reynolds, Jane Yoo, Ezra G Jennings, Julia Zeitlinger, Dmitry K Pokholok, Manolis Kellis, Alex P Rolfe, Ken T Takusagawa, Eric S Lander, David K Gifford, Ernest Fraenkel, Richard A Young
    posted to chip-chip by nirfriedman on 2006-11-15 00:10:38 as ** along with 24 people and 8 groups aalibes snow_dragon kristallreiner mariakmejia brant alokm tuck chad_davis lyongu kaspermunch dpollard balicea kt dchughes cmm nickluscombe kengg gespim koller lusk nklee cisevol njcitulike xili03 Bioinformatics EisenLab FAB-lab G4ID EBI-regulation Plantandetc Genetics-of-Gambling BergmanLab
  • Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
    Nat Genet, Vol. 25, No. 1. (May 2000), pp. 25-29.
    by M Ashburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel-Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, G Sherlock
    posted to no-tag by nirfriedman on 2006-11-15 00:08:54 as ** along with 34 people and 6 groups fongenae rvosa roys dgront marck carlk pablomendes CitoJam aalibes miguel dragonrez lfriedl chad_davis yas balajis indigoviolet benny dullhunk fisherp caporaso helliontroy zlu gurkanbebek djkt massivemayhem incovoma leechuck aconesa sgoetz javamint bootsy PunkRock natstreet naegele FAB-lab kdl Bioinformatics EisenLab T_lab biomedical-nlp
  • Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network.
    Genome Res, Vol. 13, No. 2. (February 2003), pp. 244-253.
    by J Förster, I Famili, P Fu, BØ Palsson, J Nielsen
    posted to no-tag by nirfriedman on 2006-11-14 23:58:34 as ** along with 7 people and 3 groups opheliav wnpx JeremyZucker bsmagic gcalda jpoyatos edwardmorrissey Bioinformatics bioinplant MetabolicModeling
  • Advances in flux balance analysis.
    Curr Opin Biotechnol, Vol. 14, No. 5. (October 2003), pp. 491-496.
    by KJ Kauffman, P Prakash, JS Edwards
    posted to no-tag by nirfriedman on 2006-11-14 23:57:51 as ** along with 4 people and 5 groups beapen wnpx bsmagic edwardmorrissey Bioinformatics Atopic_and_Seborrhoeic_Dermatitis Skin_Deep Applied_Bimatics bioinplant
  • Test of synergistic interactions among deleterious mutations in bacteria.
    Nature, Vol. 390, No. 6658. (27 November 1997), pp. 395-398.
    by SF Elena, RE Lenski
    posted to genettic-interactions by nirfriedman on 2006-11-14 23:54:28 as **
  • Principles for the buffering of genetic variation.
    Science, Vol. 291, No. 5506. (9 February 2001), pp. 1001-1004.
    by JL Hartman, B Garvik, L Hartwell
    posted to genettic-interactions by nirfriedman on 2006-11-14 23:51:29 as ** along with 1 person patrycja_missiuro
  • Functional classification of drugs by properties of their pairwise interactions
    Nature Genetics, Vol. 38, No. 4. (19 March 2006), pp. 489-494.
    by Pamela Yeh, Ariane I Tschumi, Roy Kishony
    posted to genettic-interactions by nirfriedman on 2006-11-14 23:40:09 as ** along with 3 people and 1 group lingchong madhadron nickluscombe EBI-regulation
  • A global view of pleiotropy and phenotypically derived gene function in yeast
    Molecular Systems Biology, Vol. 1, No. 1. (29 March 2005), pp. msb4100004-E1-msb4100004-E11.
    by Aimée M Dudley, Daniel M Janse, Amos Tanay, Ron Shamir, George M Church
    posted to genettic-interactions by nirfriedman on 2006-11-14 23:39:09 as ** along with 5 people balajis balicea i41m koller jiny
  • Inferring cellular networks using probabilistic graphical models.
    Science, Vol. 303, No. 5659. (6 February 2004), pp. 799-805.
    by N Friedman
    posted to gene-expression by nirfriedman on 2006-11-14 23:20:59 as ** along with 16 people and 1 group jo_davies saman_vp srp33 ldfu ujh lfriedl opheliav ryang wnpx neveaire koller helsley dimatura edwardmorrissey vietanh0 Yumyai kdl
  • Towards an integrated protein-protein interaction network: a relational markov network approach.
    J Comput Biol, Vol. 13, No. 2. (March 2006), pp. 145-164.
    by A Jaimovich, G Elidan, H Margalit, N Friedman
    posted to p2p by nirfriedman on 2006-11-14 23:20:19 as ** along with 5 people and 1 group lfriedl wnpx koller rsantana iris_2001 kdl
  • Forensic genetics and ethical, legal and social implications beyond the clinic.
    Nat Genet, Vol. 36, No. 11 Suppl. (November 2004)
    by MK Cho, P Sankar
    posted to gene-expression by nirfriedman on 2006-11-14 23:19:32 as ** along with 2 people and 1 group ladygoat balajis CGREL
  • From signatures to models: understanding cancer using microarrays.
    Nat Genet, Vol. 37 Suppl (June 2005)
    by E Segal, N Friedman, N Kaminski, A Regev, D Koller
    posted to gene-expression by nirfriedman on 2006-11-14 23:19:08 as ** along with 8 people and 1 group srp33 aalibes textoris troels_marstrand wnpx rdiaz sampath shikin GeneGo
  • Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast.
    BMC Bioinformatics, Vol. 6 (2005)
    by P Ye, BD Peyser, FA Spencer, JS Bader
    posted to genettic-interactions by nirfriedman on 2006-11-14 07:11:40 as **
  • Gene function prediction from congruent synthetic lethal interactions in yeast
    Molecular Systems Biology, Vol. 1, No. 1. (22 November 2005), pp. msb4100034-E1-msb4100034-E12.
    by Ping Ye, Brian D Peyser, Xuewen Pan, Jef D Boeke, Forrest A Spencer, Joel S Bader
    posted to genettic-interactions by nirfriedman on 2006-11-14 07:11:03 as ** along with 1 person tresch
  • The underlying pathway structure of biochemical reaction networks.
    Proc Natl Acad Sci U S A, Vol. 95, No. 8. (14 April 1998), pp. 4193-4198.
    by CH Schilling, BO Palsson
    posted to genettic-interactions by nirfriedman on 2006-11-13 21:13:54 as **
  • The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation.
    Science, Vol. 298, No. 5596. (8 November 2002), pp. 1241-1245.
    by A Hoffmann, A Levchenko, ML Scott, D Baltimore
    posted to genettic-interactions by nirfriedman on 2006-11-13 21:08:57 as ** along with 1 person mhucka
  • Robustness in bacterial chemotaxis.
    Nature, Vol. 397, No. 6715. (14 January 1999), pp. 168-171.
    by U Alon, MG Surette, N Barkai, S Leibler
    posted to genettic-interactions by nirfriedman on 2006-11-13 21:04:59 as ** along with 5 people cerca rklancer monod nsamways balajis
  • Cells as computation.
    Nature, Vol. 419, No. 6905. (26 September 2002)
    by A Regev, E Shapiro
    posted to genettic-interactions by nirfriedman on 2006-11-13 20:20:59 as ** along with 1 person dullhunk
  • Representation and simulation of biochemical processes using the pi-calculus process algebra.
    Pac Symp Biocomput (2001), pp. 459-470.
    by A Regev, W Silverman, E Shapiro
    posted to genettic-interactions by nirfriedman on 2006-11-13 20:19:27 as **
  • Computational insights into Caenorhabditis elegans vulval development.
    Proc Natl Acad Sci U S A, Vol. 102, No. 6. (8 February 2005), pp. 1951-1956.
    by J Fisher, N Piterman, EJ Hubbard, MJ Stern, D Harel
    posted to genettic-interactions by nirfriedman on 2006-11-13 20:14:27 as ** along with 1 person Ema
  • Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis
    Nature, Vol. 436, No. 7052., pp. 861-865.
    by Kristin C Gunsalus, Hui Ge, Aaron J Schetter, Debra S Goldberg, Jing-Dong J Han, Tong Hao, Gabriel F Berriz, Nicolas Bertin, Jerry Huang, Ling-Shiang Chuang, Ning Li, Ramamurthy Mani, Anthony A Hyman, Birte Sönnichsen, Christophe J Echeverri, Frederick P Roth, Marc Vidal, Fabio Piano
    posted to genome p2p by nirfriedman on 2006-11-13 17:56:15 as ** along with 7 people ksiek carlk Doug koller patrycja_missiuro mingzhi jiny
  • Systematic genetic analysis with ordered arrays of yeast deletion mutants.
    Science, Vol. 294, No. 5550. (14 December 2001), pp. 2364-2368.
    by AH Tong, M Evangelista, AB Parsons, H Xu, GD Bader, N Pagé, M Robinson, S Raghibizadeh, CW Hogue, H Bussey, B Andrews, M Tyers, C Boone
    posted to genettic-interactions by nirfriedman on 2006-11-13 17:53:18 as ** along with 7 people and 1 group carlk shivaram lfriedl balajis opheliav blaine_5 ruvido kdl
  • Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network.
    J Biol, Vol. 4, No. 2. (2005)
    by LV Zhang, OD King, SL Wong, DS Goldberg, AH Tong, G Lesage, B Andrews, H Bussey, C Boone, FP Roth
    posted to genettic-interactions p2p by nirfriedman on 2006-11-13 17:52:12 as ** along with 10 people and 1 group ksiek carlk lfriedl marcora jjray ssb benny koller iris_2001 gwcarter kdl
  • Analysis of optimality in natural and perturbed metabolic networks.
    Proc Natl Acad Sci U S A, Vol. 99, No. 23. (12 November 2002), pp. 15112-15117.
    by D Segrè, D Vitkup, GM Church
    posted to genettic-interactions by nirfriedman on 2006-11-13 17:50:45 as ** along with 7 people JeremyZucker carlk rklancer koller gcalda kdang roys
  • Modular epistasis in yeast metabolism
    Nature Genetics, Vol. 37, No. 1. (12 December 2004), 77.
    by Daniel Segrè, Alexander Deluna, George M Church, Roy Kishony
    posted to genettic-interactions by nirfriedman on 2006-11-13 17:49:39 as ** along with 6 people tmmurali RMGraze balajis i41m koller edwardmorrissey
  • Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles.
    Science, Vol. 287, No. 5454. (4 February 2000), pp. 873-880.
    by CJ Roberts, B Nelson, MJ Marton, R Stoughton, MR Meyer, HA Bennett, YD He, H Dai, WL Walker, TR Hughes, M Tyers, C Boone, SH Friend
    posted to gene-expression genettic-interactions by nirfriedman on 2006-11-13 17:46:32 as ** along with 3 people carlk noano koller
  • Functional discovery via a compendium of expression profiles.
    Cell, Vol. 102, No. 1. (7 July 2000), pp. 109-126.
    by TR Hughes, MJ Marton, AR Jones, CJ Roberts, R Stoughton, CD Armour, HA Bennett, E Coffey, H Dai, YD He, MJ Kidd, AM King, MR Meyer, D Slade, PY Lum, SB Stepaniants, DD Shoemaker, D Gachotte, K Chakraburtty, J Simon, M Bard, SH Friend
    posted to gene-expression genettic-interactions by nirfriedman on 2006-11-13 17:45:53 as ** along with 9 people and 3 groups TheresaNiederberger roys chasmand camster lfriedl nickluscombe patrycjam patrycja_missiuro naegele dbk-lab kdl EBI-regulation
  • Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors.
    Mol Cell Biol, Vol. 24, No. 12. (June 2004), pp. 5534-5547.
    by J Grigull, S Mnaimneh, J Pootoolal, MD Robinson, TR Hughes
    posted to gene-expression genome by nirfriedman on 2006-11-13 17:44:57 as **
  • The synthetic genetic interaction spectrum of essential genes
    Nat Genet, Vol. 37, No. 10. (October 2005), pp. 1147-1152.
    by Armaity P Davierwala, Jennifer Haynes, Zhijian Li, Renee L Brost, Mark D Robinson, Lisa Yu, Sanie Mnaimneh, Huiming Ding, Hongwei Zhu, Yiqun Chen, Xin Cheng, Grant W Brown, Charles Boone, Brenda J Andrews, Timothy R Hughes
    posted to genettic-interactions by nirfriedman on 2006-11-13 17:43:39 as ** along with 7 people and 2 groups tmmurali textoris okarsligil nickluscombe koller patrycjam patrycja_missiuro Bioinformatics EBI-regulation
  • Functional profiling of the Saccharomyces cerevisiae genome.
    Nature, Vol. 418, No. 6896. (25 July 2002), pp. 387-391.
    by G Giaever, AM Chu, L Ni, C Connelly, L Riles, S Véronneau, S Dow, A Lucau-Danila, K Anderson, B André, AP Arkin, A Astromoff, M El-Bakkoury, R Bangham, R Benito, S Brachat, S Campanaro, M Curtiss, K Davis, A Deutschbauer, KD Entian, P Flaherty, F Foury, DJ Garfinkel, M Gerstein, D Gotte, U Güldener, JH Hegemann, S Hempel, Z Herman, DF Jaramillo, DE Kelly, SL Kelly, P Kötter, D LaBonte, DC Lamb, N Lan, H Liang, H Liao, L Liu, C Luo, M Lussier, R Mao, P Menard, SL Ooi, JL Revuelta, CJ Roberts, M Rose, P Ross-Macdonald, B Scherens, G Schimmack, B Shafer, DD Shoemaker, S Sookhai-Mahadeo, RK Storms, JN Strathern, G Valle, M Voet, G Volckaert, CY Wang, TR Ward, J Wilhelmy, EA Winzeler, Y Yang, G Yen, E Youngman, K Yu, H Bussey, JD Boeke, M Snyder, P Philippsen, RW Davis, M Johnston
    posted to genettic-interactions genome by nirfriedman on 2006-11-13 17:41:53 as ** along with 11 people and 2 groups dylanwalker chasmand pcahan1 lfriedl balajis rebeccahainess koller raiyar cjeans jiny hplatero kdl steinmetzlab
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