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Tag sequence [644 articles]

Recent papers classified by the tag sequence.
  • Mind the Gaps: Evidence of Bias in Estimates of Multiple Sequence Alignments.
    Mol Biol Evol (20 August 2007)
    by Tanya Golubchik, Michael J J Wise, Simon Easteal, Lars S S Jermiin
    posted to alignment sequence by zwang on 2007-11-07 07:45:42 as ** along with 3 people caseybrown lilou dandaman
  • Genome instability: a mechanistic view of its causes and consequences.
    Nat Rev Genet (29 January 2008)
    by Andrés Aguilera, Belén Gómez-González
    posted to genome mutation sequence by zwang on 2008-02-19 01:22:05 as **
  • Structure-Templated Predictions of Novel Protein Interactions from Sequence Information
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e182.
    by Doron Betel, Kevin E Breitkreuz, Ruth Isserlin, Danielle Dewar-Darch, Mike Tyers, Christopher W Hogue
    posted to interaction prediction protein sequence structure by zwang on 2007-10-22 05:11:20 as **** along with 2 people winterschlaefer cjeans
  • A fast structural multiple alignment method for long RNA sequences
    BMC Bioinformatics, Vol. 9 (23 January 2008), 33.
    by Yasuo Tabei, Hisanori Kiryu, Taishin Kin, Kiyoshi Asai
    posted to alignment rna sequence structure by zwang on 2008-02-24 13:44:59 as ***** along with 1 person mtagaya
  • Rapid selection of accessible and cleavable sites in RNA by Escherichia coli RNase P and random external guide sequences
    Proceedings of the National Academy of Sciences (8 February 2008), 0711977105.
    by Eirik W Lundblad, Gaoping Xiao, Jae-Hyeong Ko, Sidney Altman
    posted to disease ecoli rna rnasep selection sequence by zwang on 2008-02-17 10:56:28 as **** along with 1 person austin
  • Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data
    Mol Biol Evol, Vol. 25, No. 5. (1 May 2008), pp. 960-971.
    by Tae-Kun Seo
    posted to bootstrap evolution phylogeny sequence by zwang on 2008-04-15 05:10:40 as ** along with 1 person adacier
  • Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method
    Mol Syst Biol, Vol. 4 (12 February 2008)
    by Lukas Burger, Erik van Nimwegen
    posted to alignment bayesian interaction prediction protein sequence by zwang on 2008-02-17 10:10:43 as **** along with 10 people pansapiens kengg grahamc laughcry biomcgary cabbagezs roys cdeane gjuggler phoenixzxl
  • Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome
    Science (24 January 2008), 1151721.
    by Daniel G Gibson, Gwynedd A Benders, Cynthia Andrews-Pfannkoch, Evgeniya A Denisova, Holly Baden-Tillson, Jayshree Zaveri, Timothy B Stockwell, Anushka Brownley, David W Thomas, Mikkel A Algire, Chuck Merryman, Lei Young, Vladimir N Noskov, John I Glass, Craig J Venter, Clyde A Hutchison, Hamilton O Smith
    posted to assembly genome sequence by zwang on 2008-04-12 13:30:43 as ** along with 8 people austin operon neveaire grahamc GeeSharpMinor lisa1 renatomilani kevinchannon
  • Biclustering As A Method For RNA Local Multiple Sequence Alignment
    Bioinformatics (6 October 2007), btm485.
    by Shu Wang, Robin R Gutell, Daniel P Miranker
    posted to alignment clustering rna sequence by zwang on 2007-12-10 03:49:41 as ** along with 1 person cjeans
  • Single-Molecule DNA Sequencing of a Viral Genome
    Science, Vol. 320, No. 5872. (4 April 2008), pp. 106-109.
    by Timothy D Harris, Phillip R Buzby, Hazen Babcock, Eric Beer, Jayson Bowers, Ido Braslavsky, Marie Causey, Jennifer Colonell, James Dimeo, William J Efcavitch, Eldar Giladi, Jaime Gill, John Healy, Mirna Jarosz, Dan Lapen, Keith Moulton, Stephen R Quake, Kathleen Steinmann, Edward Thayer, Anastasia Tyurina, Rebecca Ward, Howard Weiss, Zheng Xie
    posted to dna genome sequence virus by zwang on 2008-04-07 15:57:43 as ** along with 13 people and 3 groups vmarshal ilyaf austin operon dchughes samjlord neils cabbagezs kinestetika benlin caseybrown kjglennie melting moernerlab Microbial-Ecology microbiology_nijmegen
  • Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments
    Proceedings of the National Academy of Sciences, Vol. 105, No. 14. (8 April 2008), pp. 5441-5446.
    by Lei Xie, Philip E Bourne
    posted to alignment evolution profile sequence structure by zwang on 2008-04-09 03:58:23 as ** along with 1 person and 1 group sobolevnrm baker-group
  • Characterization of conserved sequence elements in eukaryotic RNase P RNA reveals roles in holoenzyme assembly and tRNA processing.
    RNA, Vol. 11, No. 6. (June 2005), pp. 885-896.
    by S Xiao, JJ Day-Storms, C Srisawat, CA Fierke, DR Engelke
    posted to element eukaryota rna rnasep sequence by zwang on 2007-07-26 11:40:48 as ****
  • Simulating DNA coding sequence evolution with EvolveAGene 3
    Mol Biol Evol (12 January 2008), msn008.
    by Barry G Hall
    posted to dna evolution sequence simulation by zwang on 2008-04-10 11:24:26 as *** along with 4 people adacier operon aprasad friendpine
  • A Maximum Likelihood Method for Detecting Directional Evolution in Protein Sequences and its Application to Influenza A Virus.
    Molecular biology and evolution (29 May 2008)
    by Sergei L L Kosakovsky Pond, Art F Y F Poon, Andrew J J Leigh Brown, Simon D W D Frost
    posted to sequence protein evolution by zwang on 2008-06-27 03:55:48 as ** along with 1 person and 1 group stajich Berkeley Mycology
  • The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data
    Nature, Vol. 452, No. 7183., pp. 51-55.
    by Marc Parisien, François Major
    posted to prediction rna sequence structure by zwang on 2008-03-07 02:48:26 as *** along with 3 people reyez austin elfar
  • Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes
    Nat Rev Genet, Vol. 9, No. 4. (April 2008), pp. 303-313.
    by Elliott H Margulies, Ewan Birney
    posted to comparativegenomics function genome sequence by zwang on 2008-03-20 13:01:59 as ** along with 5 people natstreet jyuh mingzhi phoenixzxl ptrobajo
  • Multiple protein sequence alignment
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Jimin Pei
    posted to sequence alignment by zwang on 2008-06-16 03:49:58 as ** along with 3 people marck paulschlesinger TOchi
  • Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e181.
    by Can Alkan, Mario Ventura, Nicoletta Archidiacono, Mariano Rocchi, Cenk S Sahinalp, Evan E Eichler
    posted to evolution genome sequence by zwang on 2007-11-02 08:09:50 as ** along with 1 person and 1 group hpaces Bioinformatics
  • Structure-Templated Predictions of Novel Protein Interactions from Sequence Information
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e182.
    by Doron Betel, Kevin E Breitkreuz, Ruth Isserlin, Danielle Dewar-Darch, Mike Tyers, Christopher W Hogue
    posted to interaction prediction protein sequence structure by zwang on 2007-11-02 08:05:43 as *** along with 3 people bicko chad_davis dquest
  • Specificity in protein interactions and its relationship with sequence diversity and coevolution.
    Proc Natl Acad Sci U S A (27 April 2007)
    by Luke Hakes, Simon C C Lovell, Stephen G G Oliver, David L L Robertson
    posted to co-evolution diversity interaction protein sequence by zwang on 2007-05-09 07:25:09 as **** along with 9 people and 2 groups stevanspringer bjorns cjeans Garamonfok cursonivel1 tale winterschlaefer phoenixzxl chrys FAB-lab cursonivel1
  • Complete genome sequence of the myxobacterium Sorangium cellulosum
    Nature Biotechnology, Vol. 25, No. 11. (28 October 2007), pp. 1281-1289.
    by Susanne Schneiker, Olena Perlova, Olaf Kaiser, Klaus Gerth, Aysel Alici, Matthias O Altmeyer, Daniela Bartels, Thomas Bekel, Stefan Beyer, Edna Bode, Helge B Bode, Christoph J Bolten, Jomuna V Choudhuri, Sabrina Doss, Yasser A Elnakady, Bettina Frank, Lars Gaigalat, Alexander Goesmann, Carolin Groeger, Frank Gross, Lars Jelsbak, Lotte Jelsbak, Jörn Kalinowski, Carsten Kegler, Tina Knauber, Sebastian Konietzny, Maren Kopp, Lutz Krause, Daniel Krug, Bukhard Linke, Taifo Mahmud, Rosa Martinez-Arias, Alice C Mchardy, Michelle Merai, Folker Meyer, Sascha Mormann, Jose Muñoz-Dorado, Juana Perez, Silke Pradella, Shwan Rachid, Günter Raddatz, Frank Rosenau, Christian Rückert, Florenz Sasse, Maren Scharfe, Stephan C Schuster, Garret Suen, Anke Treuner-Lange, Gregory J Velicer, Frank-Jörg Vorhölter, Kira J Weissman, Roy D Welch, Silke C Wenzel, David E Whitworth, Susanne Wilhelm, Christoph Wittmann, Helmut Blöcker, Alfred Pühler, Rolf Müller
    posted to genome sequence by zwang on 2007-11-09 08:44:44 as * along with 3 people and 1 group neils blobbybirdman kroos Myxo group
  • Recent Evolutions of Multiple Sequence Alignment Algorithms
    PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e123.
    by Cédric Notredame
    posted to algorithm alignment evolution sequence by zwang on 2007-09-01 17:08:49 as ** along with 9 people and 2 groups smbe2008 mdimmic rvosa timflutre stajich cabbagezs groepl yoanjacquemin marti Bioinformatics FAB-lab
  • Alignment Uncertainty and Genomic Analysis
    Science, Vol. 319, No. 5862. (25 January 2008), pp. 473-476.
    by Karen M Wong, Marc A Suchard, John P Huelsenbeck
    posted to alignment genome sequence by zwang on 2008-02-18 11:09:28 as ** along with 23 people and 2 groups pradiptaray jdelcampo timflutre gracio adacier jyuh bpb aprasad dayjm dpollard tny djkt cjeans lisa1 cactus biomcgary lilou kinestetika dandaman gjuggler renatomilani mclarenv youdon EisenLab microbiology_nijmegen
  • Systematic Identification of cis-Regulatory Sequences Active in Mouse and Human Embryonic Stem Cells
    PLoS Genetics, Vol. 3, No. 8. (1 August 2007), e145.
    by Marica Grskovic, Christina Chaivorapol, Alexandre Gaspar-Maia, Hao Li, Miguel Ramalho-Santos
    posted to human motif prediction regulatory sequence systematic by zwang on 2007-09-03 04:40:58 as **
  • Protein-Protein Interaction Hotspots Carved into Sequences.
    PLoS Comput Biol, Vol. 3, No. 7. (13 July 2007)
    by Yanay Ofran, Burkhard Rost
    posted to insilico interaction prediction protein sequence by zwang on 2007-08-29 02:25:39 as *** along with 7 people and 3 groups higueruelo bicko dchughes grahamc cjeans Jporci Pao-Yang G4ID ParkinsonLab_at_MaRS Genetics-of-Gambling
  • LINKER: a program to generate linker sequences for fusion proteins
    Protein Eng., Vol. 13, No. 5. (1 May 2000), pp. 309-312.
    by Chiquito J Crasto, Jin-An Feng
    posted to linker protein sequence by zwang on 2007-08-30 05:25:33 as **
  • Coevolution of a Homing Endonuclease and Its Host Target Sequence
    Journal of Molecular Biology, Vol. 372, No. 5. (5 October 2007), pp. 1305-1319.
    by Michelle Scalley-Kim, Audrey Mcconnell-Smith, Barry L Stoddard
    posted to co-evolution protein sequence by zwang on 2007-11-01 07:33:43 as **
  • Accuracy of structure-based sequence alignments of automatic methods
    BMC Bioinformatics, Vol. 8 (20 September 2007), 355.
    by Changhoon Kim, Byungkook Lee
    posted to accuracy algorithm alignment sequence structure by zwang on 2007-11-01 07:29:02 as *** along with 3 people rabio dimka chad_davis
  • Predicting protein function from sequence and structure
    Nat Rev Mol Cell Biol, Vol. 8, No. 12. (December 2007), pp. 995-1005.
    by David Lee, Oliver Redfern, Christine Orengo
    posted to function prediction protein review sequence structure by zwang on 2007-12-08 08:55:16 as *** along with 8 people kluck skhadar neils cjeans Evangelia hpaces Ema renatomilani
  • Heads or Tails: A Simple Reliability Check for Multiple Sequence Alignments
    Mol Biol Evol, Vol. 24, No. 6. (1 June 2007), pp. 1380-1383.
    by Giddy Landan, Dan Graur
    posted to alignment reliability sequence by zwang on 2007-06-14 02:10:16 as *** along with 7 people and 1 group aprasad rvosa BioNica stajich cjeans lilou mailund FAB-lab
  • The Hill–Robertson effect: evolutionary consequences of weak selection and linkage in finite populations
    Heredity, Vol. aop, No. current.
    by JM Comeron, A Williford, RM Kliman
    posted to evolution selection sequence by zwang on 2007-12-19 13:22:00 as *
  • A comprehensive comparison of multiple sequence alignment programs
    Nucl. Acids Res., Vol. 27, No. 13. (1 July 1999), pp. 2682-2690.
    by Jd Thompson, F Plewniak, O Poch
    posted to alignment evolution methods multiple sequence by zmasek on 2006-07-27 04:02:42 as ** along with 1 person treangen
  • DNA sequence analysis linguistic tools: contrast vocabularies, compositional spectra and linguistic complexity.
    Appl Bioinformatics, Vol. 2, No. 2. (2003), pp. 103-112.
    by A Bolshoy
    posted to analysis linguistics sequence by ziquje on 2005-05-16 16:48:06 as *****
  • fMRI investigation of cortical and subcortical networks in the learning of abstract and effector-specific representations of motor sequences.
    Neuroimage, Vol. 32, No. 2. (15 August 2006), pp. 714-727.
    by RS Bapi, KP Miyapuram, FX Graydon, K Doya
    posted to bob brian imitation nichola sequence by yigal on 2007-02-17 02:15:15 as ** along with 1 person and 2 groups oamg Glimcher_Lab VisionLab
  • Using BLAST for identifying gene and protein names in journal articles
    Gene, Vol. 259, No. 1-2. (23 December 2000), pp. 245-252.
    by Michael Krauthammer, Andrey Rzhetsky, Pavel Morozov, Carol Friedman
    posted to sequence ner alignment by yggdrasil on 2008-05-15 10:49:16 as ** along with 3 people and 1 group yas bhaddow vlachmore T_lab
  • The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors.
    Proc Natl Acad Sci U S A, Vol. 101, No. 4. (27 January 2004), pp. 959-963.
    by S Yohannan, S Faham, D Yang, JP Whitelegge, JU Bowie
    posted to evolution helix mutation pro-kink sequence structure transmembrane by xdeupi on 2006-05-15 15:16:00 as ** along with 1 person and 1 group thaliana LabCompMed
  • Helix-packing motifs in membrane proteins.
    Proc Natl Acad Sci U S A (5 September 2006)
    by R F S F Walters, W F F Degrado
    posted to folding helix membrane modeling sequence structure transmembrane by xdeupi on 2006-09-13 10:25:08 as **** along with 4 people and 1 group thaliana dgront sebk chgjb LabCompMed
  • Helix packing moments reveal diversity and conservation in membrane protein structure.
    J Mol Biol, Vol. 337, No. 3. (26 March 2004), pp. 713-729.
    by W Liu, M Eilers, AB Patel, SO Smith
    posted to gpcr helix membrane_proteins rhodopsin sequence ser structure transmembrane by xdeupi on 2007-04-26 13:49:38 as ***** along with 1 group LabCompMed
  • How strongly do sequence conservation patterns and empirical scales correlate with exposure patterns of transmembrane helices of membrane proteins?
    Biopolymers (12 July 2006)
    by Yungki Park, Volkhard Helms
    posted to helix sequence transmembrane by xdeupi on 2006-07-24 11:46:23 as ** along with 1 person and 1 group thaliana LabCompMed
  • A two-entropies analysis to identify functional positions in the transmembrane region of class A G protein-coupled receptors.
    Proteins, Vol. 63, No. 4. (1 June 2006), pp. 1018-1030.
    by K Ye, EW Lameijer, MW Beukers, AP Ijzerman
    posted to activation gpcr sequence transmembrane by xdeupi on 2006-07-24 10:21:33 as **** along with 2 people and 1 group cen4ik cat_worth LabCompMed
  • Folding of helical membrane proteins: the role of polar, GxxxG-like and proline motifs.
    Curr Opin Struct Biol, Vol. 14, No. 4. (August 2004), pp. 465-479.
    by A Senes, DE Engel, WF DeGrado
    posted to folding gly membrane pro-kink sequence ser structure transmembrane by xdeupi on 2006-05-22 10:55:10 as **** along with 1 person and 1 group thaliana LabCompMed
  • The relation between the divergence of sequence and structure in proteins.
    EMBO J, Vol. 5, No. 4. (April 1986), pp. 823-826.
    by C Chothia, AM Lesk
    posted to sequence structure theory by xdeupi on 2008-04-02 15:48:23 as ** along with 7 people and 6 groups ana pansapiens jwm Einat marcius ffranca insectopalo structural_bioinformatics Radiation_Damage Stressosome Bioinformatics BioinfoCIPF SGU-CIPF
  • The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints.
    Mol Pharmacol, Vol. 63, No. 6. (June 2003), pp. 1256-1272.
    by R Fredriksson, MC Lagerström, LG Lundin, HB Schiöth
    posted to evolution genome gpcr sequence by xdeupi on 2006-05-29 12:28:55 as read along with 2 people and 1 group happy_manatee adamsdi LabCompMed
  • An amino acid "transmembrane tendency" scale that approaches the theoretical limit to accuracy for prediction of transmembrane helices: relationship to biological hydrophobicity.
    Protein Sci, Vol. 15, No. 8. (August 2006), pp. 1987-2001.
    by G Zhao, E London
    posted to helix sequence transmembrane by xdeupi on 2006-10-27 09:46:58 as ** along with 1 group LabCompMed
  • Evolutionary trace of G protein-coupled receptors reveals clusters of residues that determine global and class-specific functions.
    J Biol Chem, Vol. 279, No. 9. (27 February 2004), pp. 8126-8132.
    by S Madabushi, AK Gross, A Philippi, EC Meng, TG Wensel, O Lichtarge
    posted to activation binding gpcr sequence switch by xdeupi on 2005-11-01 20:03:29 as read along with 2 people and 1 group gbart sriram_s LabCompMed
  • Sequence analyses of G-protein-coupled receptors: similarities to rhodopsin.
    Biochemistry, Vol. 42, No. 10. (18 March 2003), pp. 2759-2767.
    by T Mirzadegan, G Benkö, S Filipek, K Palczewski
    posted to activation gpcr rhodopsin sequence by xdeupi on 2005-11-01 19:50:18 as read along with 1 group LabCompMed
  • From Interactions of Single Transmembrane Helices to Folding of alpha-Helical Membrane Proteins: Analyzing Transmembrane Helix-Helix Interactions in Bacteria.
    Curr Protein Pept Sci, Vol. 8, No. 1. (February 20067), pp. 45-61.
    by Dirk Schneider, Carmen Finger, Alexander Prodöhl, Thomas Volkmer
    posted to helix membrane_proteins review sequence structure transmembrane by xdeupi on 2007-02-26 09:06:23 as ** along with 1 group LabCompMed
  • 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 genome paper sequence by wormbase_ant on 2008-02-18 16:53:05 as ** along with 7 people CitoJam sdinka Cortel treangen sujaikumar antonkratz jeanfamily
  • Protein consensus sequence motifs.
    Mol Biotechnol, Vol. 12, No. 3. (October 1999), pp. 241-253.
    by A Aitken
    posted to motif sequence by winterschlaefer on 2008-03-31 21:57:57 as **
  • Conservation of Orientation and Sequence in Protein Domain-Domain Interactions
    Journal of Molecular Biology, Vol. 345, No. 5. (2005), pp. 1265-1279.
    by Stephen J Littler, Simon J Hubbard
    posted to conservation ddi sequence structure by winterschlaefer on 2008-02-21 13:41:57 as ** along with 5 people and 2 groups ana bicko Schmidtc cjeans wilbur structural_bioinformatics Bioinformatics
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