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radek's library [53 articles]

Recent papers added to radek's library.
  • Emergence of a new disease as a result of interspecific virulence gene transfer
    Nature Genetics, Vol. 38, No. 8. (09 July 2006), pp. 953-956.
    by Timothy L Friesen, Eva H Stukenbrock, Zhaohui Liu, Steven Meinhardt, Hua Ling, Justin D Faris, Jack B Rasmussen, Peter S Solomon, Bruce A Mcdonald, Richard P Oliver
    posted to candida horizontal_transfer virulence by radek on 2006-08-15 21:03:30 as **
  • Genomic evidence for a complete sexual cycle in Candida albicans.
    Proc Natl Acad Sci U S A, Vol. 98, No. 6. (13 March 2001), pp. 3249-3253.
    by KW Tzung, RM Williams, S Scherer, N Federspiel, T Jones, N Hansen, V Bivolarevic, L Huizar, C Komp, R Surzycki, R Tamse, RW Davis, N Agabian
    posted to candida by radek on 2006-08-11 21:45:09 as **
  • Genomics of the fungal kingdom: insights into eukaryotic biology.
    Genome Res, Vol. 15, No. 12. (December 2005), pp. 1620-1631.
    by JE Galagan, MR Henn, LJ Ma, CA Cuomo, B Birren
    posted to evolution yeast by radek on 2006-08-08 23:33:35 as ** along with 1 person GustavoLacerda
  • Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae
    Nature, Vol. 438, No. 7071., pp. 1105-1115.
    by James E Galagan, Sarah E Calvo, Christina Cuomo, Li-Jun Ma, Jennifer R Wortman, Serafim Batzoglou, Su-In Lee, Meray Baştürkmen, Christina C Spevak, John Clutterbuck, Vladimir Kapitonov, Jerzy Jurka, Claudio Scazzocchio, Mark Farman, Jonathan Butler, Seth Purcell, Steve Harris, Gerhard H Braus, Oliver Draht, Silke Busch, Christophe D'Enfert, Christiane Bouchier, Gustavo H Goldman, Deborah Bell-Pedersen, Sam Griffiths-Jones, John H Doonan, Jaehyuk Yu, Kay Vienken, Arnab Pain, Michael Freitag, Eric U Selker, David B Archer, Miguel, Berl R Oakley, Michelle Momany, Toshihiro Tanaka, Toshitaka Kumagai, Kiyoshi Asai, Masayuki Machida, William C Nierman, David W Denning, Mark Caddick, Michael Hynes, Mathieu Paoletti, Reinhard Fischer, Bruce Miller, Paul Dyer, Matthew S Sachs, Stephen A Osmani, Bruce W Birren
    posted to genome by radek on 2006-08-08 23:32:52 as ** along with 1 person alexl
  • Metagenes and molecular pattern discovery using matrix factorization.
    Proc Natl Acad Sci U S A, Vol. 101, No. 12. (23 March 2004), pp. 4164-4169.
    by JP Brunet, P Tamayo, TR Golub, JP Mesirov
    posted to clustering gene-expression by radek on 2006-07-25 15:28:43 as ** along with 9 people and 1 group kentsis dragonrez yas balicea yama_tah aviad_work ivokwee GeeSharpMinor kintoki T_lab
  • Phosphoproteome analysis of capacitated human sperm. Evidence of tyrosine phosphorylation of a kinase-anchoring protein 3 and valosin-containing protein/p97 during capacitation.
    J Biol Chem, Vol. 278, No. 13. (28 March 2003), pp. 11579-11589.
    by S Ficarro, O Chertihin, VA Westbrook, F White, F Jayes, P Kalab, JA Marto, J Shabanowitz, JC Herr, DF Hunt, PE Visconti
    posted to protein_motifs by radek on 2006-06-13 21:58:24 as ** along with 1 person tmt
  • Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae.
    Nat Biotechnol, Vol. 20, No. 3. (March 2002), pp. 301-305.
    by SB Ficarro, ML McCleland, PT Stukenberg, DJ Burke, MM Ross, J Shabanowitz, DF Hunt, FM White
    posted to protein_motifs by radek on 2006-06-13 21:57:04 as **
  • Consistency matrices: quantified structure alignments for sets of related proteins.
    Proteins, Vol. 51, No. 1. (1 April 2003), pp. 1-9.
    by I Van Walle, I Lasters, L Wyns
    posted to alignment protein structure transitivity by radek on 2006-04-19 11:23:28 as **
  • Consistency of optimal sequence alignments.
    Bull Math Biol, Vol. 52, No. 4. (1990), pp. 509-525.
    by O Gotoh
    posted to alignment transitivity by radek on 2006-04-19 11:22:20 as **
  • ProbCons: Probabilistic consistency-based multiple sequence alignment.
    Genome Res, Vol. 15, No. 2. (February 2005), pp. 330-340.
    by CB Do, MS Mahabhashyam, M Brudno, S Batzoglou
    posted to alignment transitivity by radek on 2006-04-19 11:17:35 as ** along with 6 people and 1 group bpb balajis stajich olympos newton1234 gjuggler Berkeley Mycology
  • Development and validation of a consistency based multiple structure alignment algorithm
    Bioinformatics, Vol. 22, No. 9. (1 May 2006), pp. 1080-1087.
    by Jessica Ebert, Douglas Brutlag
    posted to alignment protein transitivity by radek on 2006-04-19 11:16:34 as ** along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • Alternative splicing: increasing diversity in the proteomic world.
    Trends Genet, Vol. 17, No. 2. (February 2001), pp. 100-107.
    by BR Graveley
    posted to alternative_splicing by radek on 2006-02-22 12:15:35 as *** along with 1 person and 1 group macowell BUiGEM
  • Low conservation of alternative splicing patterns in the human and mouse genomes.
    Hum Mol Genet, Vol. 12, No. 11. (1 June 2003), pp. 1313-1320.
    by RN Nurtdinov, II Artamonova, AA Mironov, MS Gelfand
    posted to alternative_splicing conserved by radek on 2006-01-25 11:14:25 as *** along with 1 person eoghanharr
  • The alternative genome.
    Sci Am, Vol. 292, No. 4. (April 2005), pp. 40-47.
    by G Ast
    posted to alternative_splicing evolution by radek on 2006-01-25 10:43:44 as read
  • Genome-wide detection of alternative splicing in expressed sequences using partial order multiple sequence alignment graphs.
    Pac Symp Biocomput (2004), pp. 29-41.
    by C Grasso, B Modrek, Y Xing, C Lee
    posted to alternative_splicing by radek on 2006-01-10 10:59:15 as *****
  • The importance of being divisible by three in alternative splicing.
    Nucleic Acids Res, Vol. 33, No. 17. (2005), pp. 5574-5582.
    by A Magen, G Ast
    posted to alternative_splicing frameshift by radek on 2006-01-10 10:57:21 as read
  • How did alternative splicing evolve?
    Nat Rev Genet, Vol. 5, No. 10. (October 2004), pp. 773-782.
    by G Ast
    posted to alternative_splicing evolution by radek on 2006-01-10 10:54:53 as read along with 7 people and 2 groups greg GloriaFu macowell setar Cortel balicea grahamc spliceml BUiGEM
  • A genome-wide study of dual coding regions in human alternatively spliced genes.
    Genome Res (19 December 2005)
    by Han Liang, Laura F F Landweber
    posted to alternative_splicing frameshift by radek on 2006-01-04 13:48:28 as *****
  • HyPhy: hypothesis testing using phylogenies
    Bioinformatics, Vol. 21, No. 5. (01 March 2005), pp. 676-679.
    by SLK Sergei, Simon DW Frost, Spencer V Muse
    posted to comparative_genomics evolution kaks tool by radek on 2005-12-16 10:50:32 as ** along with 4 people druvus operon Natasha Garamonfok
  • Protein Modularity of Alternatively Spliced Exons Is Associated with Tissue-Specific Regulation of Alternative Splicing.
    PLoS Genet, Vol. 1, No. 3. (16 September 2005)
    by Yi Xing, Christopher J J Lee
    posted to alternative_splicing by radek on 2005-12-12 12:43:31 as **
  • Changes in alternative splicing of human and mouse genes are accompanied by faster evolution of constitutive exons.
    Mol Biol Evol, Vol. 22, No. 11. (November 2005), pp. 2198-2208.
    by BP Cusack, KH Wolfe
    posted to alternative_splicing comparative_genomics conserved evolution kaks by radek on 2005-12-12 12:41:26 as ** along with 3 people inesdesantiago Cortel hpaces
  • Assessing the application of Ka/Ks ratio test to alternatively spliced exons.
    Bioinformatics (9 August 2005)
    by Yi Xing, Christopher Lee
    posted to alternative_splicing kaks by radek on 2005-11-23 15:33:21 as ** along with 2 people Cortel bpcusack
  • Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation
    Nucl. Acids Res., Vol. 32, No. 4. (24 February 2004), pp. 1261-1269.
    by Alissa Resch, Yi Xing, Alexander Alekseyenko, Barmak Modrek, Christopher Lee
    posted to alternative_splicing conserved frameshift by radek on 2005-11-23 11:01:43 as ** along with 1 person Cortel
  • Identification and analysis of alternative splicing events conserved in human and mouse
    PNAS, Vol. 102, No. 8. (22 February 2005), pp. 2850-2855.
    by Gene W Yeo, Eric Van Nostrand, Dirk Holste, Tomaso Poggio, Christopher B Burge
    posted to alternative_splicing conserved by radek on 2005-11-23 09:59:19 as ** along with 3 people and 1 group eoghanharr penka stajich Nie
  • Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles
    Nucl. Acids Res., Vol. 33, No. 17. (29 September 2005), pp. 5659-5666.
    by Zhengyan Kan, Philip W Garrett-Engele, Jason M Johnson, John C Castle
    posted to alternative_splicing conserved expression by radek on 2005-11-23 09:58:28 as ** along with 1 person Cortel
  • Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences.
    Proc Natl Acad Sci U S A, Vol. 102, No. 38. (20 September 2005), pp. 13526-13531.
    by Y Xing, C Lee
    posted to alternative_splicing conserved evolution by radek on 2005-11-23 09:57:43 as ** along with 3 people and 3 groups aprasad penka bsmagic Bioinformatics Nie bioinplant
  • Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss.
    Nat Genet, Vol. 34, No. 2. (June 2003), pp. 177-180.
    by B Modrek, CJ Lee
    posted to alternative_splicing conserved evolution by radek on 2005-11-11 15:47:03 as ** along with 2 people inesdesantiago frohike
  • Categorization and characterization of transcript-confirmed constitutively and alternatively spliced introns and exons from human.
    Hum Mol Genet, Vol. 11, No. 4. (15 February 2002), pp. 451-464.
    by F Clark, TA Thanaraj
    posted to alternative_splicing frameshift by radek on 2005-11-11 15:37:21 as ** along with 3 people and 1 group brl Cortel kaspermunch Bioinformatics
  • Tests for gene clustering.
    J Comput Biol, Vol. 10, No. 3-4. (2003), pp. 453-482.
    by D Durand, D Sankoff
    posted to conserved gene_clustering by radek on 2005-11-11 11:04:44 as **
  • The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome.
    Nucleic Acids Res, Vol. 32, No. 13. (2004), pp. 3977-3983.
    by J Leipzig, P Pevzner, S Heber
    posted to alternative_splicing alternative_splicing_database by radek on 2005-11-02 11:09:27 as ** along with 6 people and 1 group greg setar Cortel dchughes nedwards antonkratz spliceml
  • SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein.
    Nucleic Acids Res, Vol. 30, No. 1. (1 January 2002), pp. 299-300.
    by A Krause, SA Haas, E Coward, M Vingron
    posted to alternative_splicing alternative_splicing_database by radek on 2005-11-02 11:07:26 as ** along with 1 person and 1 group greg spliceml
  • Induction of changes in human behaviour by the parasitic protozoan Toxoplasma gondii.
    Parasitology, Vol. 113 ( Pt 1) (July 1996), pp. 49-54.
    by D Frynta, P Kodym, S Zitková, J Flegr
    posted to behaviour toxoplasma by radek on 2005-09-28 11:34:44 as ** along with 2 people flegr craigtalbert
  • Probable neuroimmunological link between Toxoplasma and cytomegalovirus infections and personality changes in the human host.
    BMC Infect Dis, Vol. 5 (6 July 2005)
    by M Novotná, J Hanusova, J Klose, M Preiss, J Havlicek, K Roubalová, J Flegr
    posted to behaviour toxoplasma by radek on 2005-09-28 11:25:16 as ** along with 2 people craigtalbert ascidiacea
  • Identification of nine human-specific frameshift mutations by comparative analysis of the human and the chimpanzee genome sequences.
    Bioinformatics, Vol. 21 Suppl 1 (1 June 2005)
    by Y Hahn, B Lee
    posted to conserved frameshift by radek on 2005-09-24 13:41:01 as ****
  • Functional divergence of proteins through frameshift mutations
    Trends in Genetics, Vol. 21, No. 8. (August 2005), pp. 428-431.
    by Jeroen Raes, Yves Van de Peer
    posted to alternative_splicing evolution frameshift by radek on 2005-09-24 13:40:19 as **** along with 2 people Cortel alexl
  • Vesicle trafficking: pleasure and pain from SM genes.
    Trends Cell Biol, Vol. 13, No. 4. (April 2003), pp. 177-186.
    by RF Toonen, M Verhage
    posted to munc18 sm_genes vesicle_docking by radek on 2005-09-13 11:31:21 as **** along with 1 person moborg
  • Intronic sequences flanking alternatively spliced exons are conserved between human and mouse.
    Genome Res, Vol. 13, No. 7. (July 2003), pp. 1631-1637.
    by R Sorek, G Ast
    posted to alternative_splicing conserved by radek on 2005-09-12 16:19:58 as *** along with 1 person maryee
  • ASD: the Alternative Splicing Database.
    Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004)
    by TA Thanaraj, S Stamm, F Clark, JJ Riethoven, V Le Texier, J Muilu
    posted to alternative_splicing alternative_splicing_database conserved by radek on 2005-09-12 16:17:15 as ** along with 1 person Cortel
  • Conservation of human alternative splice events in mouse.
    Nucleic Acids Res, Vol. 31, No. 10. (15 May 2003), pp. 2544-2552.
    by TA Thanaraj, F Clark, J Muilu
    posted to alternative_splicing conserved ests frameshift by radek on 2005-09-12 16:15:56 as ****
  • Genome wide identification and classification of alternative splicing based on EST data.
    Bioinformatics, Vol. 20, No. 16. (1 November 2004), pp. 2579-2585.
    by S Gupta, D Zink, B Korn, M Vingron, SA Haas
    posted to alternative_splicing ests splicing by radek on 2005-09-12 13:35:25 as *** along with 2 people and 1 group greg cantupaz spliceml
  • Transcriptome and genome conservation of alternative splicing events in humans and mice.
    Pac Symp Biocomput (2004), pp. 66-77.
    by CW Sugnet, WJ Kent, M Ares, D Haussler
    posted to alternative_splicing conserved ests splicing by radek on 2005-09-12 13:26:00 as *****
  • Comparative analyses of multi-species sequences from targeted genomic regions.
    Nature, Vol. 424, No. 6950. (14 August 2003), pp. 788-793.
    by JW Thomas, JW Touchman, RW Blakesley, GG Bouffard, SM Beckstrom-Sternberg, EH Margulies, M Blanchette, AC Siepel, PJ Thomas, JC McDowell, B Maskeri, NF Hansen, MS Schwartz, RJ Weber, WJ Kent, D Karolchik, TC Bruen, R Bevan, DJ Cutler, S Schwartz, L Elnitski, JR Idol, AB Prasad, SQ Lee-Lin, VV Maduro, TJ Summers, ME Portnoy, NL Dietrich, N Akhter, K Ayele, B Benjamin, K Cariaga, CP Brinkley, SY Brooks, S Granite, X Guan, J Gupta, P Haghighi, SL Ho, MC Huang, E Karlins, PL Laric, R Legaspi, MJ Lim, QL Maduro, CA Masiello, SD Mastrian, JC McCloskey, R Pearson, S Stantripop, EE Tiongson, JT Tran, C Tsurgeon, JL Vogt, MA Walker, KD Wetherby, LS Wiggins, AC Young, LH Zhang, K Osoegawa, B Zhu, B Zhao, CL Shu, PJ De Jong, CE Lawrence, AF Smit, A Chakravarti, D Haussler, P Green, W Miller, ED Green
    posted to comparative_genomics by radek on 2005-09-06 09:35:44 as read along with 3 people and 1 group aprasad adepace AaronDarling EisenLab
  • The objects of selection
    Proc Natl Acad Sci USA, Vol. 94 (1997), pp. 2091-2094.
    by Ernst Mayr
    posted to evolution by radek on 2005-09-06 09:32:53 as ** along with 1 person dayjm
  • Coevolution of gene expression among interacting proteins.
    Proc Natl Acad Sci U S A, Vol. 101, No. 24. (15 June 2004), pp. 9033-9038.
    by HB Fraser, AE Hirsh, DP Wall, MB Eisen
    posted to evolution expression gene interaction protein by radek on 2005-09-06 09:32:33 as ** along with 6 people and 2 groups stevanspringer lfriedl dayjm cmm Garamonfok pradiptaray kdl FAB-lab
  • Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements.
    PLoS Biol, Vol. 2, No. 3. (March 2004)
    by M Wu, LV Sun, J Vamathevan, M Riegler, R Deboy, JC Brownlie, EA McGraw, W Martin, C Esser, N Ahmadinejad, C Wiegand, R Madupu, MJ Beanan, LM Brinkac, SC Daugherty, AS Durkin, JF Kolonay, WC Nelson, Y Mohamoud, P Lee, K Berry, MB Young, T Utterback, J Weidman, WC Nierman, IT Paulsen, KE Nelson, H Tettelin, SL O'Neill, JA Eisen
    posted to bacteria evolution genome reduction by radek on 2005-09-05 10:01:06 as **** along with 3 people and 1 group operon knaseanka wrowell Cline_lab
  • Computational inference of scenarios for alpha-proteobacterial genome evolution.
    Proc Natl Acad Sci U S A, Vol. 101, No. 26. (29 June 2004), pp. 9722-9727.
    by B Boussau, EO Karlberg, AC Frank, BA Legault, SG Andersson
    posted to bacteria evolution genome reduction by radek on 2005-09-02 16:26:52 as **** along with 2 people knaseanka bjorns
  • Comparative genomics, minimal gene-sets and the last universal common ancestor.
    Nat Rev Microbiol, Vol. 1, No. 2. (November 2003), pp. 127-136.
    by EV Koonin
    posted to bacteria comparative_genomics evolution genome minimal by radek on 2005-09-02 14:00:21 as *** along with 4 people and 2 groups ana dayjm Ayest gbart structural_bioinformatics Bioinformatics
  • Genome reduction in the alpha-Proteobacteria.
    Curr Opin Microbiol (11 August 2005)
    by Björn Sällström, Siv Ge G Andersson
    posted to bacteria evolution genome reduction by radek on 2005-09-02 13:53:09 as ***** along with 3 people operon knaseanka bjorns
  • Genomes on the shrink.
    Proc Natl Acad Sci U S A, Vol. 102, No. 34. (23 August 2005), pp. 11959-11960.
    by H Ochman
    posted to bacteria evolution genome reduction by radek on 2005-09-02 10:43:07 as read along with 1 person aprasad
  • From The Cover: Bacterial genome size reduction by experimental evolution.
    Proc Natl Acad Sci U S A, Vol. 102, No. 34. (23 August 2005), pp. 12112-12116.
    by AI Nilsson, S Koskiniemi, S Eriksson, E Kugelberg, JC Hinton, DI Andersson
    posted to bacteria genome reduction by radek on 2005-09-02 10:42:24 as **** along with 4 people operon bjorns aprasad dayjm
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