caporaso's sequence [24 articles] Export

Recent papers added to caporaso's library classified by the tag sequence. You can also see everyone's sequence.

	MAFFT version 5: improvement in accuracy of multiple sequence alignment. [My Copy] Nucleic acids research, Vol. 33, No. 2. (2005), pp. 511-518. by K. Katoh, K. Kuma, H. Toh, T. Miyata posted to alignment sequence by caporaso on 2006-12-08 08:45:07 as along with 8 people and 1 group hryk BioNica druvus treangen CharlesM rabio timflutre urgi biomedical-nlp
	MUSCLE: a multiple sequence alignment method with reduced time and space complexity [My Copy] BMC Bioinformatics, Vol. 5, No. 1. (19 August 2004), 113. by Robert Edgar posted to compare comps evolution major-proposal sequence by caporaso on 2006-11-13 20:28:08 as along with 30 people and 5 groups tomatoe45 rneches gwallau OscarLopez ivanffcc Helenita Joaquin kmma13 khlevy Pal tomjad mgomes hryk BioNica natstreet Md_2007 sebk wallacei knaseanka chrn jwm balajis gbart sriram_s cdallett sanchezbuelna timflutre gisle urgi Ema LabDros References for 3DSim paper Radiation_Damage Stressosome biomedical-nlp
	Correlated mutations contain information about protein-protein interaction [My Copy] J Mol Biol, Vol. 271, No. 4. (Aug 1997), pp. 511-523. by F. Pazos, Helmer M. Citterich, G. Ausiello, A. Valencia posted to evolution from-sandra major-proposal sequence by caporaso on 2006-10-10 15:02:49 as along with 1 group biomedical-nlp
	Coevolving protein residues: maximum likelihood identification and relationship to structure [My Copy] J Mol Biol, Vol. 287, No. 1. (Mar 1999), pp. 187-198. by D. D. Pollock, W. R. Taylor, N. Goldman posted to evolution from-sandra major-proposal sequence by caporaso on 2006-10-10 15:02:49 as along with 1 group biomedical-nlp
	Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap [My Copy] Proc Natl Acad Sci U S A, Vol. 97, No. 7. (Mar 2000), pp. 3288-3291. by K. R. Wollenberg, W. R. Atchley posted to evolution from-sandra major-proposal sequence by caporaso on 2006-10-10 15:02:49 as along with 1 group biomedical-nlp
	Exploring a phylogenetic approach for the detection of correlated substitutions in proteins [My Copy] Mol Biol Evol, Vol. 17, No. 11. (Nov 2000), pp. 1753-1759. by P. Tuff, P. Darlu posted to evolution from-sandra major-proposal sequence by caporaso on 2006-10-10 15:02:49 as along with 1 group biomedical-nlp
	Correlated mutation analyses on very large sequence families [My Copy] Chembiochem, Vol. 3, No. 10. (Oct 2002), pp. 1010-1017. by L. Oliveira, A. C. Paiva, G. Vriend posted to evolution from-sandra major-proposal sequence by caporaso on 2006-10-10 15:02:49 as along with 1 group biomedical-nlp
	Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments [My Copy] Bioinformatics, Vol. 19, No. 6. (Apr 2003), pp. 750-755. by E. R. Tillier, T. W. Lui posted to evolution from-sandra major-proposal sequence by caporaso on 2006-10-10 15:02:49 as along with 1 group biomedical-nlp
	Using multiple sequence correlation analysis to characterize functionally important protein regions [My Copy] Protein Eng, Vol. 16, No. 6. (Jun 2003), pp. 397-406. by M. C. Saraf, G. L. Moore, C. D. Maranas posted to evolution from-sandra major-proposal sequence by caporaso on 2006-10-10 15:02:49 as along with 1 group biomedical-nlp
	Evaluating the predictability of conformational switching in RNA [My Copy] Bioinformatics, Vol. 20, No. 10. (Jul 2004), pp. 1573-1582. by B. Voss, C. Meyer, R. Giegerich posted to evolution from-sandra major-proposal sequence by caporaso on 2006-10-10 15:02:49 as along with 1 group biomedical-nlp
	On evolutionary conservation of thermodynamic coupling in proteins [My Copy] J Biol Chem, Vol. 279, No. 18. (Apr 2004), pp. 19046-19050. by A. A. Fodor, R. W. Aldrich posted to evolution from-sandra major-proposal sequence by caporaso on 2006-10-10 15:02:49 as along with 1 group biomedical-nlp
	Influence of conservation on calculations of amino acid covariance in multiple sequence alignments [My Copy] Proteins, Vol. 56, No. 2. (Aug 2004), pp. 211-221. by A. A. Fodor, R. W. Aldrich posted to evolution from-sandra major-proposal sequence by caporaso on 2006-10-10 15:02:48 as along with 1 group biomedical-nlp
	CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. [My Copy] Nucleic acids research, Vol. 22, No. 22. (11 November 1994), pp. 4673-4680. by J. D. Thompson, D. G. Higgins, T. J. Gibson posted to alignment comps evolution major-proposal sequence by caporaso on 2006-09-19 18:06:21 as along with 34 people and 1 group biomcgary vprieto tomjad oceanwind Blackbeard db344 udivi daforerog Md_2007 sebk cen4ik usagi-kirin jmw greger_halltorp jshapiro mercaptan evaf caldavis miguel onlyrey bjorns aprasad RMGraze moborg arcticrasta dullhunk ahanora Haggan BioNica timflutre adijr xingxu newton1234 Lombardo_7 biomedical-nlp
	Multiple sequence alignment [My Copy] Current Opinion in Structural Biology In Nucleic acids/Sequences and topology - Anna Marie Pyle and Jonathan Widom/Nick V Grishin and Sarah A Teichmann, Vol. 16, No. 3. (June 2006), pp. 368-373. by R. Edgar, S. Batzoglou posted to alignment comps evolution major-proposal sequence by caporaso on 2006-09-19 18:03:29 as along with 10 people and 1 group natstreet carlk treangen druvus CharlesM rabio cjeans mingzhi edvin nklee biomedical-nlp
	Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements [My Copy] Nucl. Acids Res., Vol. 29, No. 14. (15 July 2001), pp. 2994-3005. by Alejandro A. Schaffer, L. Aravind, Thomas L. Madden, et al.Sergei Shavirin, John L. Spouge, Yuri I. Wolf, Eugene V. Koonin, Stephen F. Altschul posted to alignment comps major-proposal sequence by caporaso on 2006-09-19 18:01:22 as along with 1 group biomedical-nlp
	Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. [My Copy] Nucleic acids research, Vol. 25, No. 17. (1 September 1997), pp. 3389-3402. by S. F. Altschul, T. L. Madden, A. A. Schäffer, et al.J. Zhang, Z. Zhang, W. Miller, D. J. Lipman posted to alignment bioinformatics sequence by caporaso on 2006-09-13 01:52:34 as along with 68 people and 5 groups rshe niallhaslam ucbcjbm timhubbard parnell tfuji maria_hauser jbhiatt yylin mgomes BioNica idoerg pjcite swp09 kgutwin mcbla cpwardell johanviklund daforerog nlapalu sebk tjimenez shung pwais dakelley knaseanka setar iakes miguel kaarsinogen bjorns bicko jmeppley chad_davis balajis nuke2005 eweaver david_parsons indigoviolet dullhunk robert dgront happy_manatee treangen kengg manzanita CitoJam jdelcampo aengisch rabio massivemayhem mirzazadeh azazello sujaikumar beatrizfernandez GustavoLacerda siebertm adijr viktor21614 mijam grottenolm bandrewfox edvin newton1234 mariakmejia granujilla marti CharlesM References for 3DSim paper EisenLab biomedical-nlp Microbial-Ecology Plantandetc
	Basic local alignment search tool. [My Copy] Journal of molecular biology, Vol. 215, No. 3. (5 October 1990), pp. 403-410. by S. F. Altschul, W. Gish, W. Miller, E. W. Myers, D. J. Lipman posted to alignment bioinformatics sequence by caporaso on 2006-09-13 01:52:11 as along with 77 people and 6 groups VGreiff richter80 krapnik azazello rshe mtaschuk sjcockell niallhaslam djohnson thegoose humburg timhubbard pachorip n00c maria_hauser rpetrenko parnell yylin esyoun APRegier idoerg Neeperando robert85 thegoose2 daforerog mcbla coela alessandroparini bertelsen Blackbeard florisbuijzen laurabailey treangen pwais mmartin tharris dmp camster davidng evaf dragonrez jwm jmeppley Ayest RMGraze ea yas balajis alexg indigoviolet moborg arcticrasta dullhunk dgront michC myui BioNica CitoJam rabio timflutre lusk cjeans incovoma beatrizfernandez wenhan jtomasch GustavoLacerda sgoetz siebertm ichbins81 jofiel Thaverkamp shung marti ashaytan benwei granujilla C. elegans / WormBase dbk-lab EisenLab T_lab biomedical-nlp Microbial-Ecology
	AAindex: Amino Acid index database [My Copy] Nucl. Acids Res., Vol. 28, No. 1. (1 January 2000), 374. by Shuichi Kawashima, Minoru Kanehisa posted to data-mining protein sequence by caporaso on 2006-09-10 01:43:54 as along with 2 people and 1 group kshameer BioNica biomedical-nlp
	Sequence clustering strategies improve remote homology recognitions while reducing search times. [My Copy] Protein engineering, Vol. 15, No. 8. (August 2002), pp. 643-649. by Weizhong Li, Lukasz Jaroszewski, Adam Godzik posted to clustering protein sequence by caporaso on 2006-09-01 22:02:35 as along with 1 person and 1 group maria_hauser biomedical-nlp
	Clustering of highly homologous sequences to reduce the size of large protein databases. [My Copy] Bioinformatics (Oxford, England), Vol. 17, No. 3. (1 March 2001), pp. 282-283. by W. Li, L. Jaroszewski, A. Godzik posted to clustering comps major-proposal protein sequence by caporaso on 2006-09-01 22:00:52 as along with 4 people and 1 group maria_hauser TLVincent yylin Cortel biomedical-nlp
	Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. [My Copy] Bioinformatics, Vol. 22, No. 13. (1 July 2006), pp. 1658-1659. by W. Li, A. Godzik posted to alignment clustering compare protein sequence by caporaso on 2006-09-01 21:10:40 as along with 6 people and 2 groups saunders pablocarb guhjy eweaver indigoviolet gisle EisenLab biomedical-nlp
	The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties. [My Copy] Genome Biol, Vol. 3, No. 8. (25 July 2002) by N. M. Luscombe, J. Qian, Z. Zhang, T. Johnson, M. Gerstein posted to alignment compare comps major-proposal protein sequence by caporaso on 2006-08-23 22:38:59 as along with 1 group biomedical-nlp
	A comparative study of machine-learning methods to predict the effects of single nucleotide polymorphisms on protein function. [My Copy] Bioinformatics, Vol. 19, No. 17. (22 November 2003), pp. 2199-2209. by V. G. Krishnan, D. R. Westhead posted to function machine-learning mutation protein sequence structural-biology by caporaso on 2006-04-26 16:56:32 as along with 5 people and 3 groups chrn marcius eweaver rlhsiao rsantana biomedical-nlp BioinfoCIPF SGU-CIPF
	Combining text mining and sequence analysis to discover protein functional regions. [My Copy] Pac Symp Biocomput (2004), pp. 288-299. by E. Eskin, E. Agichtein posted to biomedical full-text machine-learning protein sequence structural-biology by caporaso on 2006-03-26 03:18:31 as along with 1 person and 1 group tuck biomedical-nlp

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major-proposal	81
nlp	73
protein	72
comps	63
structural-biology	41
evolution	40
drug-design	38
mutation	33
bibtex-import	30
minor-proposal	30
machine-learning	24
sequence	24
druggability	23
biomedical	22
bioinformatics	17
data-mining	17
function	17
compensatory	16
ai	13
pdb	13
alignment	11
cross-validation	10
from-sandra	10
screening	9
compare	8
cs	7
database	7
math	7
coevolution	6
statistics	6
trec	6
clustering	5
dmap	5
high-throughput	5
hunter-lab	5
information-retrieval	5
myosin	5
reading-group	5
structural-genomics-consortium	5
structure	5
information-theory	4
sca	4
bioi7712	3
fold-space	3
protein-structure-initiative	3
zone	3
amyloid	2
chemistry	2
genetic-code	2
hiv	2
knight-lab	2
nomenclature	2
ontology	2
semantic-web	2
structure-classification	2
svd	2
topic-modeling	2
yarus-lab	2
aggregation	1
biochem	1
conservation	1
feature-selection	1
full-text	1
genome	1
genomics	1
lsa	1
optimization	1
pas	1
query-expansion	1
rna	1
unix	1

caporaso's sequence [24 articles] Export

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