caporaso's library 303 articles Export

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	Lonesome George : The Life and Loves of a Conservation Icon [My Copy] (04 April 2006) by Henry Nicholls posted to conservation by caporaso on 2007-04-27 13:45:11 as along with 3 people and 2 groups dayjm cmm Fin FAB-lab biomedical-nlp
	Bolstered Error Estimation [My Copy] by Ulisses B. Neto, Edward Dougherty posted to cross-validation machine-learning by caporaso on 2007-03-30 14:53:27 as along with 1 group biomedical-nlp
	Prediction error estimation: a comparison of resampling methods [My Copy] Bioinformatics, Vol. 21, No. 15. (1 August 2005), pp. 3301-3307. by Annette M. Molinaro, Richard Simon, Ruth M. Pfeiffer posted to cross-validation data-mining machine-learning statistics by caporaso on 2007-03-19 23:33:34 as along with 3 people and 1 group srp33 rdiaz winterschlaefer biomedical-nlp
	Genomic biodiversity, phylogenetics and coevolution in proteins. [My Copy] Appl Bioinformatics, Vol. 1, No. 2. (2002), pp. 81-92. by D. D. Pollock posted to coevolution by caporaso on 2007-02-26 18:02:10 as along with 1 person and 1 group chrys biomedical-nlp
	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
	Chemical space and biology [My Copy] Nature, Vol. 432, No. 7019. (16 December 2004), pp. 824-828. by Christopher M. Dobson posted to chemistry minor-proposal by caporaso on 2006-12-07 01:08:17 as along with 6 people and 3 groups jxl VGreiff bertelsen LamBras kuhn marcius biomedical-nlp BioinfoCIPF SGU-CIPF
	Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening. [My Copy] Current protein & peptide science, Vol. 7, No. 5. (October 2006), pp. 395-406. by Alasdair T. Laurie, Richard M. Jackson posted to drug-design minor-proposal by caporaso on 2006-12-06 19:26:00 as along with 2 people and 1 group mkotlyar jinghu_fandm biomedical-nlp
	BioCreAtIvE task 1A: gene mention finding evaluation. [My Copy] BMC Bioinformatics, Vol. 6 Suppl 1 (2005) by A. Yeh, A. Morgan, M. Colosimo, L. Hirschman posted to biomedical nlp by caporaso on 2006-12-04 05:35:49 as along with 4 people and 2 groups yas helliontroy zlu johnkork T_lab 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 29 people and 5 groups 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
	Residue coevolution: Modeling and interpretation [My Copy] (August 2006) by Zhengyuan Wang posted to coevolution compensatory comps major-proposal by caporaso on 2006-11-11 00:44:42 as along with 1 group biomedical-nlp
	Sarcomeric Proteins and Familial Hypertrophic Cardiomyopathy: Linking Mutations in Structural Proteins to Complex Cardiovascular Phenotypes [My Copy] Heart Failure Reviews, Vol. 10, No. 3. (September 2005), pp. 237-248. by Jil Tardiff posted to comps major-proposal myosin by caporaso on 2006-11-11 00:39:35 as along with 1 group biomedical-nlp
	Context dependence and coevolution among amino acid residues in proteins. [My Copy] Methods Enzymol, Vol. 395 (2005), pp. 779-790. by Z. O. Wang, D. D. Pollock posted to coevolution major-proposal protein by caporaso on 2006-11-08 15:08:49 as along with 1 group biomedical-nlp
	Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution [My Copy] Protein Eng., Vol. 10, No. 6. (1 June 1997), pp. 647-657. by D. D. Pollock, W. R. Taylor posted to coevolution compensatory major-proposal mutation by caporaso on 2006-11-08 01:01:53 as along with 2 people and 1 group janani137 friendpine biomedical-nlp
	The Role of Compensatory Mutations in the Emergence of Drug Resistance. [My Copy] PLoS Comput Biol, Vol. 2, No. 10. (13 October 2006) by Andreas Handel, Roland R R. Regoes, Rustom Antia posted to compensatory major-proposal mutation by caporaso on 2006-10-29 22:56:02 as along with 1 person and 1 group ramensky biomedical-nlp
	Characterization of Compensated Mutations in Terms of Structural and Physico-Chemical Properties. [My Copy] J Mol Biol (26 September 2006) by Carles Ferrer-Costa, Modesto Orozco, Xavier de la D. Cruz posted to compensatory major-proposal mutation by caporaso on 2006-10-29 22:54:53 as along with 3 people and 2 groups ramensky cat_worth cjeans structural_bioinformatics 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
	Coupled two-way clustering analysis of gene microarray data. [My Copy] Proc Natl Acad Sci U S A, Vol. 97, No. 22. (24 October 2000), pp. 12079-12084. by G. Getz, E. Levine, E. Domany posted to clustering major-proposal by caporaso on 2006-10-06 17:23:09 as along with 5 people and 1 group zufar ihpark wnpx shikin tvdbulck biomedical-nlp
	Structural interpretation of the mutations in the beta-cardiac myosin that have been implicated in familial hypertrophic cardiomyopathy [My Copy] Proc Natl Acad Sci U S A, Vol. 92, No. 9. (Apr 1995), pp. 3864-3868. by I. Rayment, H. M. Holden, J. R. Sellers, L. Fananapazir, N. D. Epstein posted to major-proposal mutation myosin protein by caporaso on 2006-10-05 17:08:57 as along with 1 group biomedical-nlp
	[Familial hypertrophic cardiomyopathy: genes, mutations and animal models. A review] [My Copy] Invest Clin, Vol. 45, No. 1. (Mar 2004), pp. 69-99. by C. D. Ramírez, R. Padrón posted to major-proposal mutation myosin protein by caporaso on 2006-10-05 17:08:57 as along with 1 group biomedical-nlp
	One third of Danish hypertrophic cardiomyopathy patients with MYH7 mutations have mutations [corrected] in MYH7 rod region [My Copy] Eur J Hum Genet, Vol. 13, No. 2. (Feb 2005), pp. 161-165. by L. Hougs, O. Havndrup, H. Bundgaard, et al.L. Kober, J. Vuust, L. A. Larsen, M. Christiansen, P. S. Andersen posted to major-proposal mutation myosin protein by caporaso on 2006-10-05 17:08:57 as along with 1 group biomedical-nlp
	Myopathies associated with myosin heavy chain mutations [My Copy] Acta Myol, Vol. 23, No. 2. (Sep 2004), pp. 90-96. by A. Oldfors, H. Tajsharghi, N. Darin, C. Lindberg posted to major-proposal mutation myosin protein by caporaso on 2006-10-05 17:08:56 as along with 1 group biomedical-nlp
	Horizontal gene transfer in prokaryotes: quantification and classification. [My Copy] Annu Rev Microbiol, Vol. 55 (2001), pp. 709-742. by E. V. Koonin, K. S. Makarova, L. Aravind posted to major-proposal by caporaso on 2006-09-30 01:54:28 as along with 4 people and 4 groups ana jmeppley madhadron vwchan structural_bioinformatics Bioinformatics biomedical-nlp beta
	Divergent evolution within protein superfolds inferred from profile-based phylogenetics. [My Copy] Journal of molecular biology, Vol. 354, No. 3. (2 December 2005), pp. 722-737. by Douglas L. Theobald, Deborah S. Wuttke posted to major-proposal by caporaso on 2006-09-30 01:52:12 as along with 6 people and 4 groups martainn cmura yuslinaz ana barry dlr structural_bioinformatics Bioinformatics biomedical-nlp McCammon
	A gold standard set of mechanistically diverse enzyme superfamilies. [My Copy] Genome Biol, Vol. 7, No. 1. (2006) by S. D. Brown, J. A. Gerlt, J. L. Seffernick, P. C. Babbitt posted to major-proposal by caporaso on 2006-09-30 01:42:02 as along with 3 people and 1 group kuhn robert JeremyZucker biomedical-nlp
	Evolution of enzyme superfamilies. [My Copy] Current opinion in chemical biology In Analytical techniques / Mechanisms, Vol. 10, No. 5. (October 2006), pp. 492-497. by Margaret E. Glasner, John A. Gerlt, Patricia C. Babbitt posted to major-proposal by caporaso on 2006-09-30 01:40:56 as along with 6 people and 1 group NickFurnham yuslinaz kuhn tny robert ucbcjbm biomedical-nlp
	Divergence of function in the thioredoxin fold suprafamily: evidence for evolution of peroxiredoxins from a thioredoxin-like ancestor. [My Copy] Biochemistry, Vol. 43, No. 44. (9 November 2004), pp. 13981-13995. by S. D. Copley, W. R. Novak, P. C. Babbitt posted to major-proposal by caporaso on 2006-09-30 01:38:41 as along with 1 group biomedical-nlp
	Evolutionary information for specifying a protein fold [My Copy] Nature, Vol. 437, No. 7058., pp. 512-518. by Michael Socolich, Steve W. Lockless, William P. Russ, Heather Lee, Kevin H. Gardner, Rama Ranganathan posted to major-proposal sca by caporaso on 2006-09-29 23:11:51 as along with 15 people and 5 groups ucbcjbm ana barry lna bpb Einat balajis marcius gbart analogAI nirfriedman massivemayhem mingzhi bethbromley ca3295 structural_bioinformatics Bioinformatics biomedical-nlp BioinfoCIPF SGU-CIPF
	Finding the fittest fold: using the evolutionary record to design new proteins. [My Copy] Cell, Vol. 122, No. 6. (23 September 2005), pp. 832-834. by R. G. Smock, L. M. Gierasch posted to major-proposal sca by caporaso on 2006-09-29 23:11:06 as along with 2 people and 3 groups marcius analogAI biomedical-nlp BioinfoCIPF SGU-CIPF
	Natural-like function in artificial WW domains [My Copy] Nature, Vol. 437, No. 7058., pp. 579-583. by William P. Russ, Drew M. Lowery, Prashant Mishra, Michael B. Yaffe, Rama Ranganathan posted to major-proposal sca by caporaso on 2006-09-29 23:09:08 as along with 6 people and 5 groups ana barry balajis marcius bethbromley ca3295 structural_bioinformatics Bioinformatics biomedical-nlp BioinfoCIPF SGU-CIPF
	5' cleavage site in eukaryotic pre-mRNA splicing is determined by the overall 5' splice region, not by the conserved 5' GU. [My Copy] Cell, Vol. 50, No. 2. (17 July 1987), pp. 237-246. by M. Aebi, H. Hornig, C. Weissmann posted to compensatory major-proposal mutation by caporaso on 2006-09-29 00:56:39 as along with 1 group biomedical-nlp
	A second-site mutation at phenylalanine-137 that increases catalytic efficiency in the mutant aspartate-27----serine Escherichia coli dihydrofolate reductase. [My Copy] Biochemistry, Vol. 29, No. 37. (18 September 1990), pp. 8561-8569. by E. E. Howell, C. Booth, M. Farnum, J. Kraut, M. S. Warren posted to compensatory major-proposal mutation by caporaso on 2006-09-29 00:55:39 as along with 1 group biomedical-nlp
	Long-Range Structural Effects in a Second-Site Revertant of a Mutant Dihydrofolate Reductase [My Copy] PNAS, Vol. 90, No. 24. (15 December 1993), pp. 11753-11756. by Ka Brown, Ee Howell, J. Kraut posted to bioi7712 compensatory major-proposal mutation structure by caporaso on 2006-09-29 00:53:59 as along with 1 group biomedical-nlp
	Combinatorial exploration of the catalytic site of a drug-resistant dihydrofolate reductase: creating alternative functional configurations [My Copy] Protein Engineering, Design and Selection, Vol. 17, No. 11. (November 2004), pp. 809-819. by Andreea R. Schmitzer, Francois Lepine, Joelle N. Pelletier posted to compensatory major-proposal mutation protein by caporaso on 2006-09-28 23:50:40 as along with 1 group biomedical-nlp
	Comparing genomes in terms of protein structure: surveys of a finite parts list. [My Copy] FEMS Microbiol Rev, Vol. 22, No. 4. (October 1998), pp. 277-304. by M. Gerstein, H. Hegyi posted to comps evolution major-proposal protein by caporaso on 2006-09-23 01:40:45 as along with 1 group biomedical-nlp
	Global mapping of pharmacological space [My Copy] Nature Biotechnology, Vol. 24, No. 7. (13 July 2006), pp. 805-815. by Gaia V. Paolini, Richard H. B. Shapland, Willem P. van Hoorn, Jonathan S. Mason, Andrew L. Hopkins posted to comps drug-design minor-proposal by caporaso on 2006-09-22 21:13:18 as along with 12 people and 1 group bertelsen sameersoi superpyrin richardbickerton ramensky Yanno BragilMassoud guhjy kuhn bicko allmensch jerome_ucsf_slb biomedical-nlp
	Evolutionarily conserved networks of residues mediate allosteric communication in proteins [My Copy] Nature Structural & Molecular Biology, Vol. 10, No. 1. (16 December 2002), pp. 59-69. by Gurol M. Suel, Steve W. Lockless, Mark A. Wall, Rama Ranganathan posted to compensatory evolution major-proposal protein sca structural-biology by caporaso on 2006-09-20 00:43:16 as along with 20 people and 3 groups mgomes qluo arjun_citeulike RebeccaHamer ynaito lna dimka marcius eckart_bindewald gbart analogAI nirfriedman dgront choonpeng efge carlescorbi mingzhi yalexeev weisblum ca3295 biomedical-nlp BioinfoCIPF SGU-CIPF
	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 Robert C. Edgar, Serafim 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
	Structural determinants of allosteric ligand activation in RXR heterodimers. [My Copy] Cell, Vol. 116, No. 3. (6 February 2004), pp. 417-429. by A. I. Shulman, C. Larson, D. J. Mangelsdorf, R. Ranganathan posted to comps evolution protein by caporaso on 2006-09-14 22:35:47 as along with 3 people and 3 groups lna marcius gbart biomedical-nlp BioinfoCIPF SGU-CIPF
	Allosteric determinants in guanine nucleotide-binding proteins. [My Copy] Proc Natl Acad Sci U S A, Vol. 100, No. 24. (25 November 2003), pp. 14445-14450. by M. E. Hatley, S. W. Lockless, S. K. Gibson, A. G. Gilman, R. Ranganathan posted to comps evolution major-proposal by caporaso on 2006-09-14 22:34:07 as along with 5 people and 5 groups qluo barry lna Einat marcius structural_bioinformatics Bioinformatics biomedical-nlp BioinfoCIPF SGU-CIPF

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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

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