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sujaikumar's library [54 articles]

最近录入 sujaikumar's 文献库.
  • USING GRAPH CONCEPTS TO UNDERSTAND THE ORGANIZATION OF COMPLEX SYSTEMS
    International Journal of Bifurcation and Chaos, Vol. 17, No. 7. (July 2007), pp. 2201-2214.
    by Claire Christensen, Reka Albert
    posted to complex network by sujaikumar on 2007-10-05 16:41:23 as read
  • Web services at the European bioinformatics institute.
    Nucleic Acids Res, Vol. 35, No. Web Server issue. (1 July 2007)
    by A Labarga, F Valentin, M Anderson, R Lopez
    posted to no-tag by sujaikumar on 2007-08-22 22:04:37 as ** along with 7 people moborg dullhunk sgoetz niallhaslam sim82 alanrw tny
  • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    Nucleic Acids Res, Vol. 25, No. 17. (1 September 1997), pp. 3389-3402.
    by SF Altschul, TL Madden, AA Schäffer, J Zhang, Z Zhang, W Miller, DJ Lipman
    posted to algorithm alignment by sujaikumar on 2007-08-22 21:47:07 as ** along with 44 people and 4 groups knaseanka setar iakes miguel kaarsinogen bjorns bicko jmeppley chad_davis balajis nuke2005 eweaver david_parsons indigoviolet dullhunk robert dgront happy_manatee caporaso treangen kengg manzanita leelarcombe CitoJam jdelcampo aengisch rabio massivemayhem mirzazadeh azazello beatrizfernandez GustavoLacerda siebertm adijr viktor21614 mijam grottenolm bandrewfox edvin newton1234 mariakmejia granujilla marti CharlesM EisenLab biomedical-nlp Microbial-Ecology Plantandetc
  • A greedy algorithm for aligning DNA sequences.
    J Comput Biol, Vol. 7, No. 1-2. (r 2000), pp. 203-214.
    by Z Zhang, S Schwartz, L Wagner, W Miller
    posted to algorithm alignment by sujaikumar on 2007-08-22 10:40:22 as ** along with 4 people AaronDarling azazello benwei bozdagd
  • Identification of common molecular subsequences.
    J Mol Biol, Vol. 147, No. 1. (25 March 1981), pp. 195-197.
    by TF Smith, MS Waterman
    posted to algorithm alignment by sujaikumar on 2007-08-22 10:35:10 as ** along with 9 people creswick vavi bicko dgront rabio cjeans incovoma newton1234 bozdagd
  • Improved tools for biological sequence comparison.
    Proc Natl Acad Sci U S A, Vol. 85, No. 8. (April 1988), pp. 2444-2448.
    by WR Pearson, DJ Lipman
    posted to fasta by sujaikumar on 2007-08-21 01:06:24 as ** along with 9 people and 2 groups arcticrasta ffranca gurkanbebek bsmagic CitoJam lusk cjeans Ema bozdagd Bioinformatics bioinplant
  • FASTA format description
    posted to fasta by sujaikumar on 2007-08-21 01:01:20 as **
  • The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics
    PLoS Biology, Vol. 1, No. 2. (1 November 2003), e45.
    by Lincoln D Stein, Zhirong Bao, Darin Blasiar, Thomas Blumenthal, Michael R Brent, Nansheng Chen, Asif Chinwalla, Laura Clarke, Chris Clee, Avril Coghlan, Alan Coulson, Peter D'eustachio, David H Fitch, Lucinda A Fulton, Robert E Fulton, Sam Griffiths-Jones, Todd W Harris, Ladeana W Hillier, Ravi Kamath, Patricia E Kuwabara, Elaine R Mardis, Marco A Marra, Tracie L Miner, Patrick Minx, James C Mullikin, Robert W Plumb, Jane Rogers, Jacqueline E Schein, Marc Sohrmann, John Spieth, Jason E Stajich, Chaochun Wei, David Willey, Richard K Wilson, Richard Durbin, Robert H Waterston
    posted to briggsae comparative by sujaikumar on 2007-08-19 23:16:28 as ** along with 1 person and 1 group stajich Berkeley Mycology
  • Molecular Genealogy of Some Nematode Taxa as Based on Cytochrome c and Globin Amino Acid Sequences
    Molecular Phylogenetics and Evolution, Vol. 3, No. 2. (June 1994), pp. 92-101.
    by Jacques R Vanfleteren, Yves Van De Peer, Mark L Blaxter, Susan A Tweedie, Clive Trotman, Liu Lu, Marie-Louise Van Hauwaert, Luc Moens
    posted to celegans nematodes by sujaikumar on 2007-08-19 23:08:37 as ***
  • EVOLUTION: An Embarrassment of Switches
    Science, Vol. 317, No. 5839. (10 August 2007), pp. 758-759.
    by Leonid Kruglyak, David L Stern
    posted to alignment cis-regulatory cne identity by sujaikumar on 2007-08-17 09:00:42 as **
  • Divergence of Transcription Factor Binding Sites Across Related Yeast Species
    Science, Vol. 317, No. 5839. (10 August 2007), pp. 815-819.
    by Anthony R Borneman, Tara A Gianoulis, Zhengdong D Zhang, Haiyuan Yu, Joel Rozowsky, Michael R Seringhaus, Lu Y Wang, Mark Gerstein, Michael Snyder
    posted to binding-site divergence yeast by sujaikumar on 2007-08-17 08:16:06 as ** along with 17 people and 2 groups bryankr aalibes chad_davis dpollard djkt mikaelhuss lusk cjeans zwang GustavoLacerda Jporci maximilianh cisevol njcitulike emptyhb nklee anka EisenLab cis-regulatory-evolution
  • BLASTCLUST - BLAST score-based single-linkage clustering
    posted to algorithm blast by sujaikumar on 2007-08-16 18:33:57 as **
  • GFF (General Feature Format) Specifications Document
    by Richard Durbin, David Haussler, Lincoln Stein, Suzanna Lewis, Anders Krogh
    posted to gff by sujaikumar on 2007-08-14 11:45:37 as **
  • RepeatMasker Open-3.0
    (1996-2004)
    by AFA Smit, R Hubley, P Green
    posted to repeat repeatmasker software tool by sujaikumar on 2007-08-13 18:59:48 as ** along with 1 person dandaman
  • Having a BLAST with bioinformatics (and avoiding BLASTphemy).
    Genome Biol, Vol. 2, No. 10. (2001)
    by A Pertsemlidis, JW Fondon
    posted to algorithm blast by sujaikumar on 2007-08-12 16:16:16 as ** along with 8 people and 2 groups karbak ziquje prtmht textoris shantanu cjeans scottstensland hpaces Bioinformatics MathBio
  • Into the heart of darkness: large-scale clustering of human non-coding DNA
    by Gill Bejerano
    posted to clustering non-coding by sujaikumar on 2007-07-31 18:30:39 as ***
  • Active Conservation of Noncoding Sequences Revealed by Three-Way Species Comparisons
    Genome Res., Vol. 10, No. 9. (1 September 2000), pp. 1304-1306.
    by Inna Dubchak, Michael Brudno, Gabriela G Loots, Lior Pachter, Chris Mayor, Edward M Rubin, Kelly A Frazer
    posted to genome percentage_identity by sujaikumar on 2007-07-11 10:11:39 as **
  • Quantification of the variation in percentage identity for protein sequence alignments
    BMC Bioinformatics, Vol. 7 (19 September 2006), 415.
    by Ps G Raghava, Geoffrey J Barton
    posted to genome percentage_identity by sujaikumar on 2007-07-11 10:10:58 as ** along with 5 people and 1 group pansapiens bicko dpollard rabio medic0747 EisenLab
  • What is a gene, post-ENCODE? History and updated definition.
    Genome Res, Vol. 17, No. 6. (June 2007), pp. 669-681.
    by MB Gerstein, C Bruce, JS Rozowsky, D Zheng, J Du, JO Korbel, O Emanuelsson, ZD Zhang, S Weissman, M Snyder
    posted to encode gene genome by sujaikumar on 2007-06-22 13:34:51 as *** along with 26 people and 4 groups jyuh carolh12 eweaver dpollard balicea dchughes dullhunk madhadron cottrell grahamc egonw ghattem Garamonfok PunkRock jasonbobe PredictER cabbagezs Jporci kmdaily krokicki antonkratz Minty hpaces tharris altotor mjoach Bioinformatics EisenLab G4ID Genetics-of-Gambling
  • Computational Maps in the Visual Cortex
    (2005)
    by Risto Miikkulainen, James A Bednar, Yoonsuck Choe, Joseph Sirosh
    posted to cnv2 oblique by sujaikumar on 2007-04-08 15:09:06 as **
  • A controlled, mirror-image study of second-generation antipsychotics in the treatment of schizophrenia.
    Int Clin Psychopharmacol, Vol. 22, No. 3. (May 2007), pp. 133-136.
    by D Taylor, K Hayhurst, R Kerwin
    posted to schizy by sujaikumar on 2007-04-07 20:57:49 as **
  • The world from a cat's perspective--statistics of natural videos.
    Biol Cybern, Vol. 90, No. 1. (January 2004), pp. 41-50.
    by BY Betsch, W Einhäuser, KP Körding, P König
    posted to cnv2 oblique by sujaikumar on 2007-04-06 20:27:38 as **
  • A horizontal bias in human visual processing of orientation and its correspondence to the structural components of natural scenes.
    J Vis, Vol. 4, No. 12. (10 December 2004), pp. 1044-1060.
    by BC Hansen, EA Essock
    posted to cnv2 oblique by sujaikumar on 2007-04-06 19:00:10 as **
  • An oblique effect in human primary visual cortex.
    Nat Neurosci, Vol. 3, No. 6. (June 2000), pp. 535-536.
    by CS Furmanski, SA Engel
    posted to cnv2 oblique by sujaikumar on 2007-04-06 18:40:51 as ** along with 1 person mrkrause
  • Unequal representation of cardinal vs. oblique orientations in the middle temporal visual area
    PNAS, Vol. 103, No. 46. (14 November 2006), pp. 17490-17495.
    by Xiangmin Xu, Christine E Collins, Ilya Khaytin, Jon H Kaas, Vivien A Casagrande
    posted to cnv2 oblique by sujaikumar on 2007-04-06 18:39:15 as **
  • Oblique Effect: A Neural Basis in the Visual Cortex
    J Neurophysiol, Vol. 90, No. 1. (1 July 2003), pp. 204-217.
    by Baowang Li, Matthew R Peterson, Ralph D Freeman
    posted to cnv2 oblique by sujaikumar on 2007-04-06 18:37:54 as **
  • An oblique effect for transparent-motion detection caused by variation in global-motion direction-tuning bandwidths
    Vision Research, Vol. In Press, Corrected Proof
    by John A Greenwood, Mark Edwards
    posted to cnv2 oblique by sujaikumar on 2007-04-06 18:37:34 as ** along with 1 person fcalabro
  • Anisotropic local contrast normalization: The role of stimulus orientation and spatial frequency bandwidths in the oblique and horizontal effect perceptual anisotropies
    Vision Research, Vol. 46, No. 26. (December 2006), pp. 4398-4415.
    by Bruce C Hansen, Edward A Essock
    posted to cnv2 oblique by sujaikumar on 2007-04-06 18:37:08 as **
  • An oblique effect for local motion: psychophysics and natural movie statistics.
    J Vis, Vol. 5, No. 10. (2005), pp. 878-887.
    by SC Dakin, I Mareschal, PJ Bex
    posted to cnv2 oblique by sujaikumar on 2007-04-06 18:36:50 as **
  • Ultrasensitivity in the mitogen-activated protein kinase cascade.
    Proc Natl Acad Sci U S A, Vol. 93, No. 19. (17 September 1996), pp. 10078-10083.
    by CY Huang, JE Ferrell
    posted to csb by sujaikumar on 2007-03-27 03:14:32 as ** along with 1 person rklancer
  • Quantification of Short Term Signaling by the Epidermal Growth Factor Receptor
    J. Biol. Chem., Vol. 274, No. 42. (15 October 1999), pp. 30169-30181.
    by Boris N Kholodenko, Oleg V Demin, Gisela Moehren, Jan B Hoek
    posted to csb by sujaikumar on 2007-03-27 03:12:46 as ** along with 2 people and 2 groups imouthesmp rhem1224 TCR_Signaling SysbioMPI-TCells
  • Differential feedback regulation of the MAPK cascade underlies the quantitative differences in EGF and NGF signalling in PC12 cells
    FEBS Letters, Vol. 482, No. 3. (6 October 2000), pp. 169-174.
    by Frances A Brightman, David A Fell
    posted to csb by sujaikumar on 2007-03-27 03:12:04 as **
  • Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors.
    Nat Biotechnol, Vol. 20, No. 4. (April 2002), pp. 370-375.
    by B Schoeberl, C Eichler-Jonsson, ED Gilles, G Müller
    posted to csb by sujaikumar on 2007-03-27 03:09:08 as ** along with 3 people tuck lukaswindhager renatomilani
  • Prediction and validation of the distinct dynamics of transient and sustained ERK activation
    Nature Cell Biology, Vol. 7, No. 4. (27 March 2005), pp. 365-373.
    by Satoru Sasagawa, Yu-Ichi Ozaki, Kazuhiro Fujita, Shinya Kuroda
    posted to csb by sujaikumar on 2007-03-24 12:28:44 as ** along with 2 people and 1 group camster js229 dbk-lab
  • Genome sequence of the nematode C. elegans: a platform for investigating biology.
    Science, Vol. 282, No. 5396. (11 December 1998), pp. 2012-2018.
    by
    posted to celegans nematodes worms by sujaikumar on 2007-03-22 17:04:00 as ** along with 8 people sdinka Cortel treangen antonkratz jeanfamily wormbase_ant CitoJam hsekiguc
  • Gene regulatory networks and the evolution of animal body plans.
    Science, Vol. 311, No. 5762. (10 February 2006), pp. 796-800.
    by EH Davidson, DH Erwin
    posted to evolution grn regulatory_network by sujaikumar on 2007-03-22 10:45:47 as read along with 14 people and 4 groups eldan bayesian dpollard xico dchughes brixtonmc Liusha margaritis josepe cjeans Garamonfok jtomasch Ema natstreet EisenLab WetBiology G4ID Genetics-of-Gambling
  • Developmental gene regulatory network architecture across 500 million years of echinoderm evolution
    PNAS, Vol. 100, No. 23. (11 November 2003), pp. 13356-13361.
    by Veronica F Hinman, Albert T Nguyen, Andrew R Cameron, Eric H Davidson
    posted to evolution regulatory_network by sujaikumar on 2007-03-22 10:43:58 as ***
  • Synthetic biology: new engineering rules for an emerging discipline
    Mol Syst Biol, Vol. 2 (2006), pp. msb4100073-E1-msb4100073-E14.
    by Ernesto Andrianantoandro, Subhayu Basu, David K Karig, Ron Weiss
    posted to grn regulatory_network by sujaikumar on 2007-03-22 10:34:05 as ** along with 10 people sharatjv johncumbers mmt margaritis jrbanga jbchang nicholasflann kevinchannon jonsta247 grahamc
  • Identification and characterization of multi-species conserved sequences.
    Genome Res, Vol. 13, No. 12. (December 2003), pp. 2507-2518.
    by EH Margulies, M Blanchette, D Haussler, ED Green,
    posted to algorithm cne identification by sujaikumar on 2007-03-20 14:01:02 as ** along with 5 people and 1 group operon ujh brant bezdan nklee EisenLab
  • CONSERVED NON-GENIC SEQUENCES - AN UNEXPECTED FEATURE OF MAMMALIAN GENOMES
    Nat Rev Genet, Vol. 6, No. 2. (February 2005), pp. 151-157.
    by Emmanouil T Dermitzakis, Alexandre Reymond, Stylianos E Antonarakis
    posted to cne mammals by sujaikumar on 2007-03-20 13:56:34 as ** along with 1 person djkt
  • Ultraconserved elements in insect genomes: A highly conserved intronic sequence implicated in the control of homothorax mRNA splicing.
    Genome Res (17 May 2005)
    by Evgeny A A Glazov, Michael Pheasant, Elizabeth A A McGraw, Gill Bejerano, John S S Mattick
    posted to cne drosophila insect by sujaikumar on 2007-03-19 20:38:29 as ** along with 2 people and 1 group ujh Stew EisenLab
  • Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
    Genome Res, Vol. 15, No. 8. (August 2005), pp. 1034-1050.
    by A Siepel, G Bejerano, JS Pedersen, AS Hinrichs, M Hou, K Rosenbloom, H Clawson, J Spieth, LW Hillier, S Richards, GM Weinstock, RK Wilson, RA Gibbs, WJ Kent, W Miller, D Haussler
    posted to cne comparative insects non-coding phastcons vertebrates worms yeast by sujaikumar on 2007-03-19 09:53:45 as *** along with 15 people and 3 groups bpb aprasad balajis eckart_bindewald indigoviolet brant pradiptaray adepace djkt olympos Stew cisevol dmc elfar AlexanderPico EisenLab cis-regulatory-evolution ConklinLab
  • Defining a genomic radius for long-range enhancer action: duplicated conserved non-coding elements hold the key
    Trends in Genetics, Vol. 22, No. 1. (January 2006), pp. 5-10.
    by Tanya Vavouri, Gayle K Mcewen, Adam Woolfe, Walter R Gilks, Greg Elgar
    posted to cne enhancer radius by sujaikumar on 2007-03-19 01:15:00 as *** along with 3 people and 1 group maximilianh cisevol brant cis-regulatory-evolution
  • Highly conserved non-coding sequences are associated with vertebrate development.
    PLoS Biol, Vol. 3, No. 1. (January 2005)
    by A Woolfe, M Goodson, DK Goode, P Snell, GK McEwen, T Vavouri, SF Smith, P North, H Callaway, K Kelly, K Walter, I Abnizova, W Gilks, YJ Edwards, JE Cooke, G Elgar
    posted to cne development vertebrate by sujaikumar on 2007-03-19 01:05:43 as *** along with 8 people and 2 groups bryankr awoolfe djkt Stew maximilianh cisevol rrhudson gelgar EisenLab cis-regulatory-evolution
  • Mastering seeds for genomic size nucleotide BLAST searches
    Nucl. Acids Res., Vol. 31, No. 23. (1 December 2003), pp. 6935-6941.
    by Valer Gotea, Vamsi Veeramachaneni, Wojciech Makalowski
    posted to alignment blast by sujaikumar on 2007-03-17 07:42:35 as **
  • Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis.
    Genome Res (13 March 2006)
    by Gayle K K McEwen, Adam Woolfe, Debbie Goode, Tanya Vavouri, Heather Callaway, Greg Elgar
    posted to cne evolution vertebrates by sujaikumar on 2007-03-13 19:52:27 as *** along with 4 people and 3 groups dpollard dchughes tabu maximilianh EisenLab G4ID Genetics-of-Gambling
  • The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics
    PLoS Biology, Vol. 1, No. 2. (1 November 2003), e45.
    by Lincoln D Stein, Zhirong Bao, Darin Blasiar, Thomas Blumenthal, Michael R Brent, Nansheng Chen, Asif Chinwalla, Laura Clarke, Chris Clee, Avril Coghlan, Alan Coulson, Peter D'eustachio, David H Fitch, Lucinda A Fulton, Robert E Fulton, Sam Griffiths-Jones, Todd W Harris, Ladeana W Hillier, Ravi Kamath, Patricia E Kuwabara, Elaine R Mardis, Marco A Marra, Tracie L Miner, Patrick Minx, James C Mullikin, Robert W Plumb, Jane Rogers, Jacqueline E Schein, Marc Sohrmann, John Spieth, Jason E Stajich, Chaochun Wei, David Willey, Richard K Wilson, Richard Durbin, Robert H Waterston
    posted to briggsae comparative evolution by sujaikumar on 2007-03-13 19:43:44 as *** along with 2 people and 1 group indigoviolet stajich EisenLab
  • Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes.
    BMC Genomics, Vol. 5, No. 1. (2004)
    by A Sandelin, P Bailey, S Bruce, PG Engström, JM Klos, WW Wasserman, J Ericson, B Lenhard
    posted to cne developmental vertebrates by sujaikumar on 2007-03-11 22:58:39 as *** along with 1 person fpattyn
  • Glocal alignment: finding rearrangements during alignment.
    Bioinformatics, Vol. 19 Suppl 1 (2003)
    by M Brudno, S Malde, A Poliakov, CB Do, O Couronne, I Dubchak, S Batzoglou
    posted to alignment glocal by sujaikumar on 2007-03-11 14:38:01 as ** along with 1 person Neeperando
  • A combined computational and experimental analysis of two families of snoRNA genes from Caenorhabditis elegans, revealing the expression and evolution pattern of snoRNAs in nematodes
    Genomics, Vol. In Press, Corrected Proof
    by Zhan-Peng Huang, Chong-Jian Chen, Hui Zhou, Bei-Bei Li, Liang-Hu Qu
    posted to celegans evolution nematodes snorna worms by sujaikumar on 2007-03-11 14:25:51 as ***
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