timflutre's bioinformatics [127 articles] Export

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	Probability landscapes for integrative genomics [My Copy] Theoretical Biology and Medical Modelling, Vol. 5, No. 1. (20 May 2008), 9. by Annick Lesne, Arndt Benecke posted to sequencing modeling methylation genomics bioinformatics annotation by timflutre on 2009-12-02 08:37:08 as
	Quantifying the local reliability of a sequence alignment. [My Copy] Protein engineering, Vol. 9, No. 2. (February 1996), pp. 127-132. by H. T. Mevissen, M. Vingron posted to bioinformatics alignment by timflutre on 2009-11-18 16:29:05 as
	Computation for ChIP-seq and RNA-seq studies [My Copy] Nature Methods In Nat Meth, Vol. 6, No. 11s. (15 October 2009), pp. S22-S32. by Shirley Pepke, Barbara Wold, Ali Mortazavi posted to sequencing bioinformatics algorithm by timflutre on 2009-11-17 20:53:33 as along with 25 people and 2 groups n00c ongenetics urgi Jporci pst epigenetics molnet-mna Vincent_Rouilly guhjy cajunsushi mpizbioinfo stubrown hzoltan robertrentzsch xingxu oannes74 tonamswish inesdesantiago Baschl polivares jwfoley druvus GeeSharpMinor chvlyl heliopais molnet-macs Orengo Group Journal Picks
	Dynamic Programming Alignment Accuracy [My Copy] Journal of Computational Biology, Vol. 5, No. 3. (January 1998), pp. 493-504. by I. A. N. Holmes, Richard Durbin posted to modeling bioinformatics alignment algorithm by timflutre on 2009-11-16 11:17:04 as
	Genome-wide identification of human functional DNA using a neutral indel model. [My Copy] PLoS computational biology, Vol. 2, No. 1. (13 January 2006) by Gerton Lunter, Chris P. Ponting, Jotun Hein posted to modeling indel human genomics bioinformatics by timflutre on 2009-11-10 14:01:49 as along with 12 people and 2 groups gjuggler nklee aprasad eckart_bindewald eweaver lhonigberg acidwizard juliettecolinas bpcusack Stew cisevol mailund EisenLab cis-regulatory-evolution
	Computational Identification and Characterization of Repeats in Sequenced Eukaryotic Genomes [My Copy] (December 2002) by Zhirong Bao posted to transposable_element thesis rice repeats eukaryote clustering bioinformatics by timflutre on 2009-11-10 13:04:52 as
	A Macaque's-Eye View of Human Insertions and Deletions: Differences in Mechanisms [My Copy] PLoS Comput Biol, Vol. 3, No. 9. (14 September 2007), e176. by Erika M. Kvikstad, Svitlana Tyekucheva, Francesca Chiaromonte, Kateryna D. Makova posted to statistics phylogeny indel human chimpanzee bioinformatics alignment by timflutre on 2009-11-10 12:58:06 as along with 4 people and 1 group Iden-J_GluR aprasad djkt cisevol cis-regulatory-evolution
	Generic eukaryotic core promoter prediction using structural features of DNA [My Copy] Genome Research, Vol. 18, No. 2. (20 February 2008), pp. 310-323. by Thomas Abeel, Yvan Saeys, Eric Bonnet, Pierre Rouze, Yves Van de Peer posted to transcription promoter genomics bioinformatics by timflutre on 2009-11-06 09:53:22 as along with 8 people chvlyl hagechouchin443 rsaito tonamswish cjeans cabbagezs maximilianh idonaldson
	REPuter: the manifold applications of repeat analysis on a genomic scale. [My Copy] Nucleic acids research, Vol. 29, No. 22. (15 November 2001), pp. 4633-4642. by S. Kurtz, J. V. Choudhuri, E. Ohlebusch, C. Schleiermacher, J. Stoye, R. Giegerich posted to repeats bioinformatics algorithm by timflutre on 2009-11-02 21:48:48 as along with 2 people druvus yoanjacquemin
	The functional repertoires of metazoan genomes [My Copy] Nat Rev Genet, Vol. 9, No. 9. (01 September 2008), pp. 689-698. by Chris P. Ponting posted to noncoding metazoan genomics bioinformatics by timflutre on 2009-10-20 15:53:03 as along with 3 people jo_davies dakelley bpcusack
	Fast Statistical Alignment [My Copy] PLoS Comput Biol, Vol. 5, No. 5. (29 May 2009), e1000392. by Robert K. Bradley, Adam Roberts, Michael Smoot, et al.Sudeep Juvekar, Jaeyoung Do, Colin Dewey, Ian Holmes, Lior Pachter posted to indel modeling bioinformatics alignment algorithm by timflutre on 2009-10-13 08:16:49 as along with 18 people and 1 group seb1 rdowell natstreet n00c yylin aprasad Gorzomagnificent guhjy dakelley reyez rec3141 farhat operon bmduggan nuin AlexBateman djkt druvus Journal picks
	Alignment-free sequence comparison-a review. [My Copy] Bioinformatics (Oxford, England), Vol. 19, No. 4. (1 March 2003), pp. 513-523. by Susana Vinga, Jonas Almeida posted to sequence_comparison modeling bioinformatics by timflutre on 2009-10-09 17:05:51 as along with 5 people akiii mox druvus treangen dario
	A novel genome-scale repeat finder geared towards transposons [My Copy] Bioinformatics, Vol. 24, No. 4. (15 February 2008), pp. 468-476. by Xuehui Li, Tamer Kahveci, A. Mark Settles posted to transposable_element bioinformatics annotation by timflutre on 2009-10-07 09:26:49 as along with 3 people and 1 group operon GustavoLacerda idonaldson BergmanLab
	Identification of repeat structure in large genomes using repeat probability clouds [My Copy] Analytical Biochemistry, Vol. 380, No. 1. (01 September 2008), pp. 77-83. by W. Gu, T. Castoe, D. Hedges, M. Batzer, D. Pollock posted to human repeats bioinformatics by timflutre on 2009-10-07 09:13:37 as along with 2 people orzenil operon
	ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements [My Copy] Genome Res. (19 October 2006), gr.4537706. by James Taylor, Svitlana Tyekucheva, David C. King, Ross C. Hardison, Webb Miller, Francesca Chiaromonte posted to statistics regulation noncoding modeling genomics bioinformatics alignment by timflutre on 2009-09-12 11:06:56 as along with 1 person kmdaily
	MOSAIC: segmenting multiple aligned DNA sequences [My Copy] Bioinformatics, Vol. 17, No. 2. (1 February 2001), pp. 196-197. by Cecile Andre, Pierre Vincens, Jean-Francois Boisvieux, Serge Hazout posted to bioinformatics alignment by timflutre on 2009-09-10 16:43:12 as
	How repetitive are genomes? [My Copy] BMC bioinformatics, Vol. 7 (22 December 2006), 541. by Bernhard Haubold, Thomas Wiehe posted to repeats genomics bioinformatics by timflutre on 2009-09-08 17:17:24 as along with 2 people treangen mtagaya
	Incorporating indel information into phylogeny estimation for rapidly emerging pathogens [My Copy] BMC Evolutionary Biology, Vol. 7, No. 1. (14 March 2007), 40. by Benjamin Redelings, Marc Suchard posted to indel phylogeny bioinformatics alignment by timflutre on 2009-08-23 10:39:53 as along with 5 people and 1 group druvus operon aprasad dpollard stajich EisenLab
	Statistical alignment based on fragment insertion and deletion models [My Copy] Bioinformatics, Vol. 19, No. 4. (1 March 2003), pp. 490-499. by Dirk Metzler posted to indel phylogeny bioinformatics alignment by timflutre on 2009-08-23 10:38:06 as along with 1 person druvus
	RNAmmer: consistent and rapid annotation of ribosomal RNA genes [My Copy] Nucl. Acids Res., Vol. 35, No. 9. (14 May 2007), pp. 3100-3108. by Karin Lagesen, Peter Hallin, Einar A. Rodland, Hans-Henrik Staerfeldt, Torbjorn Rognes, David W. Ussery posted to bioinformatics hmm rna by timflutre on 2009-08-04 09:15:13 as along with 2 people tfuji mcox
	RAP: a new computer program for de novo identification of repeated sequences in whole genomes [My Copy] Bioinformatics, Vol. 21, No. 5. (1 March 2005), pp. 582-588. by Davide Campagna, Chiara Romualdi, Nicola Vitulo, et al.Micky Del Favero, Matej Lexa, Nicola Cannata, Giorgio Valle posted to algorithm bioinformatics genomics repeats by timflutre on 2009-07-23 17:32:45 as along with 1 person operon
	MCALIGN2: Faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (08 June 2006), 292. by Jun Wang, Peter Keightley, Toby Johnson posted to indel algorithm bioinformatics evolution hmm modeling noncoding by timflutre on 2009-07-20 15:34:36 as along with 6 people and 1 group druvus gjuggler Ayest dpollard papamicd bozdagd EisenLab
	Model-based identification of Helitrons results in a new classification of their families in Arabidopsis thaliana [My Copy] Gene, Vol. 403, No. 1-2. (15 November 2007), pp. 18-28. by Sébastien Tempel, Jacques Nicolas, Abdelhak El Amrani, Ivan Couée posted to helitron transposable_element bioinformatics repeats by timflutre on 2009-07-10 09:58:25 as
	Automated paleontology of repetitive DNA with REANNOTATE [My Copy] BMC Genomics, Vol. 9, No. 1. (2008), 614. by Vini Pereira posted to transposable_element annotation bioinformatics by timflutre on 2009-06-26 14:52:12 as along with 3 people natstreet LHON druvus
	Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees [My Copy] Science, Vol. 324, No. 5934. (19 June 2009), pp. 1561-1564. by Kevin Liu, Sindhu Raghavan, Serita Nelesen, C. Randal Linder, Tandy Warnow posted to alignment bioinformatics phylogeny by timflutre on 2009-06-22 12:34:02 as along with 26 people and 4 groups gjuggler parnell kinestetika robertrentzsch xianjun gdb jbhiatt stajich operon biomcgary kieran101 zwang michaelbarton vingron tatman303 hryk lizbiogen pkonings ppgardne dokky aprasad inquil TRHvidsten djkt fenghezi phoenixzxl Orengo Group Journal Picks Mycology Journal picks iSEEM
	Lossless filter for multiple repeats with bounded edit distance [My Copy] Algorithms for Molecular Biology, Vol. 4, No. 1. (30 January 2009), 3. by Pierre Peterlongo, Gustavo A. Sacomoto, Pereira, Nadia Pisanti, Marie-France Sagot posted to algorithm bioinformatics repeats by timflutre on 2009-06-17 13:35:20 as along with 4 people renatocarmo gwallau svenrahmann druvus
	Joint Bayesian estimation of alignment and phylogeny. [My Copy] Systematic biology, Vol. 54, No. 3. (June 2005), pp. 401-418. by Benjamin Redelings, Marc Suchard posted to statistics alignment bioinformatics evolution modeling molecular phylogeny by timflutre on 2009-06-04 22:41:40 as along with 3 people cmzmasek aprasad AaronDarling
	BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data [My Copy] Mol Biol Evol, Vol. 14, No. 7. (1 July 1997), pp. 685-695. by O. Gascuel posted to bioinformatics modeling phylogeny by timflutre on 2009-05-29 11:37:52 as along with 7 people darian vingron BioNica lizbiogen swp09 Haggan matsen
	Identification of common molecular subsequences. [My Copy] Journal of molecular biology, Vol. 147, No. 1. (25 March 1981), pp. 195-197. by T. F. Smith, M. S. Waterman posted to alignment bioinformatics by timflutre on 2009-05-19 21:43:29 as along with 21 people rshe jengeldk maria_hauser jmanning2k cmor parnell adamnellis heliopais mcbla alessandroparini usagi-kirin creswick vavi bicko dgront rabio cjeans incovoma sujaikumar newton1234 bozdagd
	A general method applicable to the search for similarities in the amino acid sequence of two proteins. [My Copy] Journal of molecular biology, Vol. 48, No. 3. (March 1970), pp. 443-453. by S. B. Needleman, C. D. Wunsch posted to alignment bioinformatics by timflutre on 2009-05-19 21:39:53 as along with 16 people windman83 esyoun stsaft mcbla BioNica db344 DarkMars cawelsh9 sebk jwm dgront rabio incovoma yylin newton1234 Ema
	The estimation of statistical parameters for local alignment score distributions. [My Copy] Nucleic Acids Res, Vol. 29, No. 2. (15 January 2001), pp. 351-361. by S. F. Altschul, R. Bundschuh, R. Olsen, T. Hwa posted to statistics alignment bioinformatics by timflutre on 2009-05-19 21:08:15 as along with 3 people catmat treangen newton1234
	Statistical Composition of High-Scoring Segments from Molecular Sequences [My Copy] The Annals of Statistics, Vol. 18, No. 2. (1990), pp. 571-581. by Samuel Karlin, Amir Dembo, Tsutomu Kawabata posted to statistics alignment bioinformatics modeling by timflutre on 2009-05-17 22:00:59 as
	Transcriptionally active gene fragments derived from potentially fast-evolving donor genes in the rice genome [My Copy] Bioinformatics, Vol. 25, No. 10. (15 May 2009), pp. 1215-1218. by Xiangfeng Wang, Zhihui Yu, Xiaozeng Yang, Xing-Wang Deng, Lei Li posted to plant bioinformatics rice transcription by timflutre on 2009-05-14 16:39:15 as along with 1 person reyez
	TEclass--a tool for automated classification of unknown eukaryotic transposable elements [My Copy] Bioinformatics, Vol. 25, No. 10. (15 May 2009), pp. 1329-1330. by Gyorgy Abrusan, Norbert Grundmann, Luc Demester, Wojciech Makalowski posted to transposable_element rpt bioinformatics by timflutre on 2009-05-13 10:10:07 as along with 3 people operon gwallau natstreet
	BlastAlign: a program that uses blast to align problematic nucleotide sequences [My Copy] Bioinformatics, Vol. 21, No. 1., 122. by Robert Belshaw, Aris Katzourakis posted to alignment bioinformatics by timflutre on 2009-05-11 10:52:02 as along with 1 person natstreet
	Wavelets in bioinformatics and computational biology: state of art and perspectives [My Copy] Bioinformatics, Vol. 19, No. 1. (1 January 2003), pp. 2-9. by Pietro Lio posted to bioinformatics genomics wavelets by timflutre on 2009-03-21 20:27:33 as along with 4 people and 1 group reyntjesr humburg polivares groepl BergmanLab
	Identification of higher-order functional domains in the human ENCODE regions [My Copy] Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 917-927. by Robert E. Thurman, Nathan Day, William S. Noble, John A. Stamatoyannopoulos posted to bioinformatics chromatin encode genomics wavelets by timflutre on 2009-03-21 20:23:11 as along with 3 people and 1 group ghattem epigenetics jasonflannick Bioinformatics
	Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome [My Copy] Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 760-774. by Elliott H. Margulies, Gregory M. Cooper, George Asimenos, et al.Daryl J. Thomas, Colin N. Dewey, Adam Siepel, Ewan Birney, Damian Keefe, Ariel S. Schwartz, Minmei Hou, James Taylor, Sergey Nikolaev, Juan I. Montoya-Burgos, Ari Loytynoja, Simon Whelan, Fabio Pardi, Tim Massingham, James B. Brown, Peter Bickel, Ian Holmes, James C. Mullikin, Abel Ureta-Vidal, Benedict Paten, Eric A. Stone, Kate R. Rosenbloom, James W. Kent, Gerard G. Bouffard, Xiaobin Guan, Nancy F. Hansen, Jacquelyn R. Idol, Valerie V. Maduro, Baishali Maskeri, Jennifer C. Mcdowell, Morgan Park, Pamela J. Thomas, Alice C. Young, Robert W. Blakesley, Donna M. Muzny, Erica Sodergren, David A. Wheeler, Kim C. Worley, Huaiyang Jiang, George M. Weinstock, Richard A. Gibbs, Tina Graves, Robert Fulton, Elaine R. Mardis, Richard K. Wilson, Michele Clamp, James Cuff, Sante Gnerre, David B. Jaffe, Jean L. Chang, Kerstin Lindblad-Toh, Eric S. Lander, Angie Hinrichs, Heather Trumbower, Hiram Clawson, Ann Zweig, Robert M. Kuhn, Galt Barber, Rachel Harte, Donna Karolchik, Matthew A. Field, Richard A. Moore, Carrie A. Matthewson, Jacqueline E. Schein, Marco A. Marra, Stylianos E. Antonarakis, Serafim Batzoglou, Nick Goldman, Ross Hardison, David Haussler, Webb Miller, Lior Pachter, Eric D. Green, Arend Sidow posted to human alignment bioinformatics encode evolution genomics mammals molecular by timflutre on 2009-03-21 20:13:08 as along with 11 people and 5 groups daveGerrard polivares aprasad dpollard dchughes AaronDarling djkt ghattem Garamonfok gjuggler elfar BergmanLab Bioinformatics EisenLab G4ID Genetics-of-Gambling
	Parametric Alignment of Drosophila Genomes [My Copy] (2 Dec 2005) by Colin Dewey, Peter Huggins, Kevin Woods, Bernd Sturmfels, Lior Pachter posted to drosophila alignment bioinformatics genomics modeling by timflutre on 2009-03-12 10:01:33 as
	Parametric inference for biological sequence analysis. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 46. (16 November 2004), pp. 16138-16143. by L. Pachter, B. Sturmfels posted to bioinformatics modeling by timflutre on 2009-03-11 13:40:11 as
	Parametric sequence comparisons. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 89, No. 13. (1 July 1992), pp. 6090-6093. by M. S. Waterman, M. Eggert, E. Lander posted to alignment bioinformatics modeling by timflutre on 2009-03-11 09:29:36 as
	An introduction to reconstructing ancestral genomes [My Copy] eprint arXiv:q-bio/0612046 (December 2006) by L. Pachter posted to alignment bioinformatics genomics modeling phylogeny by timflutre on 2009-03-10 22:40:58 as along with 1 person liguoliang
	The many faces of sequence alignment [My Copy] Brief Bioinform, Vol. 6, No. 1. (1 January 2005), pp. 6-22. by Serafim Batzoglou posted to alignment bioinformatics by timflutre on 2009-03-09 15:07:32 as along with 11 people and 2 groups nuttpo druvus n00c pimmy BioNica treangen balajis dpollard sdvillal gjuggler yoanjacquemin Bioinformatics EisenLab
	A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes [My Copy] BMC Genomics, Vol. 9, No. 1. (31 October 2008), 517. by Stefan Kurtz, Apurva Narechania, Joshua C. Stein, Doreen Ware posted to transposable_element plant annotation bioinformatics genomics repeats by timflutre on 2009-03-04 16:08:50 as along with 5 people nklee skembel malcook operon treangen
	Quantitative Measures for the Management and Comparison of Annotated Genomes [My Copy] BMC Bioinformatics, Vol. 10 (23 February 2009), 67. by Karen, Mark Yandell posted to annotation bioinformatics genomics by timflutre on 2009-03-04 11:14:52 as along with 3 people and 1 group jmeppley stajich druvus Mycology
	Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats [My Copy] BMC Genomics, Vol. 9, No. 1. (31 October 2008), 518. by Thomas Wicker, Apurva Narechania, Francois Sabot, et al.Joshua Stein, Giang T. H. Vu, Andreas Graner, Doreen Ware, Nils Stein posted to plant barley bioinformatics genomics repeats by timflutre on 2009-03-03 19:18:40 as along with 5 people operon orzenil usagi-kirin natstreet abizar
	The evolution of biology. A shift towards the engineering of prediction-generating tools and away from traditional research practice [My Copy] EMBO Reports, Vol. aop, No. current. (14 November 2008) by Lawrence Kelley, Michael Scott posted to miscellanee bioinformatics epistemology by timflutre on 2009-02-20 18:55:57 as
	Chemistry. Pulling strings. [My Copy] Science (New York, N.Y.), Vol. 314, No. 5805. (8 December 2006), pp. 1552-1553. by W. Fontana posted to bioinformatics modeling by timflutre on 2009-02-20 18:53:45 as
	Detecting microsatellites within genomes: significant variation among algorithms [My Copy] BMC Bioinformatics, Vol. 8 (18 April 2007), 125. by Sebastien Leclercq, Eric Rivals, Philippe Jarne posted to bioinformatics microsatellites by timflutre on 2009-02-06 00:34:58 as along with 1 person druvus
	Jalview Version 2--a multiple sequence alignment editor and analysis workbench [My Copy] Bioinformatics, Vol. 25, No. 9. (1 May 2009), pp. 1189-1191. by Andrew M. Waterhouse, James B. Procter, David M. A. Martin, Michele Clamp, Geoffrey J. Barton posted to alignment bioinformatics rpt by timflutre on 2009-01-29 02:04:31 as along with 7 people tomjad calderonv dimka Thaverkamp jamselem nuin jmeppley

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transposable_element	149
bioinformatics	127
modeling	119
evolution	110
genomics	104
genetics	88
population	78
plant	57
molecular	55
network	51
expression	43
alignment	43
gene	42
phylogeny	39
repeats	31
duplication	30
rpt	30
drosophila	27
miscellanee	24
arabidopsis	24
recombination	24
epigenetics	21
thaliana	20
classic	19
rice	19
human	19
domestication	18
indel	18
coalescence	17
silencing	14
robustness	14
wheat	14
behaviour	13
rna	13
statistics	12
ecology	12
algorithm	11
philosophy	11
polyploidy	11
misconduct	10
annotation	10
maize	9
review	9
genome_size	9
selection	8
sex	7
cell	7
chromatin	7
mammals	7
dna	6
stress	6
complexity	6
sequencing	6
noncoding	5
thesis	5
ecoli	5
regulation	5
diffusion	5
evolvability	5
evo_devo	5
reaction	5
quasispecies	5
speciation	4
chaos	4
single	4
mutation	4
hmm	4
news	4
rearrangement	4
wavelets	4
function	4
transcription	4
cereal	4
retrotransposon	4
helitron	4
cycle	3
methylation	3
encode	3
metabolism	3
horizontal	3
eukaryote	3
biodiversity	3
stat_phy	3
biology	3
transfer	3
quantitative_trait	3
nucleosome	3
bacteria	3
sines	3
centromere	2
epistemology	2
drift	2
yeast	2
codon	2
clustering	2
cooperation	2
barley	2
programming	2
epidemiology	2
celegans	2
information	2
agriculture	2
haplotype	2
mouse	2
bias	2
disease	1
deletions	1
segmental	1
phylogeography	1
tomato	1
medicago	1
demography	1
structure	1
grasses	1
epistasis	1
vertebrate	1
proteomics	1
kinetics	1
homeobox	1
association	1
discretization	1
simulation	1
sympatry	1
tutorial	1
mites	1
sequence_comparison	1
crop	1
development	1
allometry	1
psychology	1
book	1
lines	1
mapping	1
synteny	1
brassica	1
flowering	1
spatialization	1
gcskew	1
pathway	1
promoter	1
chimpanzee	1
3d	1
histone	1
microsatellites	1
ethics	1
angiosperms	1
parasitism	1
creativity	1
metazoan	1
linkage	1
imprinting	1
pseudogenes	1

timflutre's bioinformatics [127 articles] Export

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