Tag 31-jul-09 [38 articles] Export

Recent papers classified by the tag 31-jul-09.

	Benchmarking homology detection procedures with low complexity filters [My Copy] Bioinformatics (20 July 2009), btp446. by Kristoffer Forslund, Erik L. L. Sonnhammer posted to 31-jul-09 by ollieredfernwork to the group Orengo Group Journal Picks on 2009-07-31 11:39:40 as
	Upcoming challenges for multiple sequence alignment methods in the high-throughput era [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2455-2465. by Carsten Kemena, Cedric Notredame posted to 31-jul-09 by ollieredfernwork to the group Orengo Group Journal Picks on 2009-07-31 11:39:28 as along with 10 people and 1 group fstrozzi manduca djkt rdiaz sjcockell torfinnnome walshtp nuin natstreet druvus Journal picks
	jClust: a clustering and visualization toolbox [My Copy] Bioinformatics, Vol. 25, No. 15. (1 August 2009), pp. 1994-1996. by Georgios A. Pavlopoulos, Charalampos N. Moschopoulos, Sean D. Hooper, Reinhard Schneider, Sophia Kossida posted to 31-jul-09 by ollieredfernwork to the group Orengo Group Journal Picks on 2009-07-31 11:38:14 as along with 3 people karthikraman jmeppley jxl
	trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 15. (1 August 2009), pp. 1972-1973. by Salvador Capella-Gutiérrez, José M. Silla-Martínez, Toni Gabaldón posted to 31-jul-09 by ollieredfernwork to the group Orengo Group Journal Picks on 2009-07-31 11:38:02 as along with 3 people aprasad gjuggler nuin
	SOAP2: an improved ultrafast tool for short read alignment [My Copy] Bioinformatics, Vol. 25, No. 15. (1 August 2009), pp. 1966-1967. by Ruiqiang Li, Chang Yu, Yingrui Li, et al.Tak-Wah Lam, Siu-Ming Yiu, Karsten Kristiansen, Jun Wang posted to 31-jul-09 by ollieredfernwork to the group Orengo Group Journal Picks on 2009-07-31 11:37:46 as along with 27 people and 5 groups nuin hzoltan agbiotec torfinnnome natstreet cthachuk jforment GustavoLacerda adijr bozdagd stubrown polivares guhjy operon cassj adamjamesreid Stew jamselem dswan idonaldson TRHvidsten humburg djkt farhat n00c jmeppley druvus Bioinformatics Core Service BergmanLab Bioinformatics - CRUK Bioinformatics Journal picks
	InterMap3D: predicting and visualizing co-evolving protein residues [My Copy] Bioinformatics, Vol. 25, No. 15. (1 August 2009), pp. 1963-1965. by Rodrigo Gouveia-Oliveira, Francisco S. Roque, Rasmus Wernersson, et al.Thomas Sicheritz-Ponten, Peter W. Sackett, Anne Molgaard, Anders G. Pedersen posted to 31-jul-09 by ollieredfernwork to the group Orengo Group Journal Picks on 2009-07-31 11:37:33 as along with 4 people sobolevnrm friendpine carlosjavierna phoenixzxl
	Enhancing MEDLINE document clustering by incorporating MeSH semantic similarity [My Copy] Bioinformatics, Vol. 25, No. 15. (1 August 2009), pp. 1944-1951. by Shanfeng Zhu, Jia Zeng, Hiroshi Mamitsuka posted to 31-jul-09 by ollieredfernwork to the group Orengo Group Journal Picks on 2009-07-31 11:36:25 as along with 7 people artaban421 sobolevnrm lmichan dullhunk zimbo1 nuin Gaetan
	Predictor correlation impacts machine learning algorithms: implications for genomic studies [My Copy] Bioinformatics, Vol. 25, No. 15. (1 August 2009), pp. 1884-1890. by Kristin K. Nicodemus, James D. Malley posted to 31-jul-09 by ollieredfernwork to the group Orengo Group Journal Picks on 2009-07-31 11:36:05 as along with 4 people rdiaz TRHvidsten djkt mhamada
	Rapid detection, classification and accurate alignment of up to a million or more related protein sequences [My Copy] Bioinformatics, Vol. 25, No. 15. (1 August 2009), pp. 1869-1875. by Andrew F. Neuwald posted to 31-jul-09 by ollieredfernwork to the group Orengo Group Journal Picks on 2009-07-31 11:35:36 as along with 3 people and 2 groups davidmam robfsouza carlosjavierna Journal picks iSEEM
	CORAL: aligning conserved core regions across domain families [My Copy] Bioinformatics, Vol. 25, No. 15. (1 August 2009), pp. 1862-1868. by Jessica H. Fong, Aron Marchler-Bauer posted to 31-jul-09 by ollieredfernwork to the group Orengo Group Journal Picks on 2009-07-31 11:35:23 as along with 3 people and 2 groups AlexBateman natstreet druvus Journal picks iSEEM
	Seeing the forest for the trees: using the Gene Ontology to restructure hierarchical clustering [My Copy] Bioinformatics, Vol. 25, No. 14. (15 July 2009), pp. 1789-1795. by Dikla Dotan-Cohen, Simon Kasif, Avraham A. Melkman posted to 31-jul-09 by ollieredfernwork to the group Orengo Group Journal Picks on 2009-07-31 11:34:20 as along with 2 people inesdesantiago phoenixzxl
	pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination [My Copy] Bioinformatics, Vol. 25, No. 14. (15 July 2009), pp. 1761-1767. by Anna Lobley, Michael I. Sadowski, David T. Jones posted to 31-jul-09 by ollieredfernwork to the group Orengo Group Journal Picks on 2009-07-31 11:34:04 as along with 1 person carlosjavierna
	ESG: extended similarity group method for automated protein function prediction [My Copy] Bioinformatics, Vol. 25, No. 14. (15 July 2009), pp. 1739-1745. by Meghana Chitale, Troy Hawkins, Changsoon Park, Daisuke Kihara posted to 31-jul-09 by ollieredfernwork to the group Orengo Group Journal Picks on 2009-07-31 11:33:46 as along with 1 person reyez
	Data structures and compression algorithms for genomic sequence data [My Copy] Bioinformatics, Vol. 25, No. 14. (15 July 2009), pp. 1731-1738. by Marty C. Brandon, Douglas C. Wallace, Pierre Baldi posted to 31-jul-09 by ollieredfernwork to the group Orengo Group Journal Picks on 2009-07-31 11:33:34 as along with 4 people jandot reyez dansullivanblk operon
	penalizedSVM: a R-package for feature selection SVM classification [My Copy] Bioinformatics, Vol. 25, No. 13. (1 July 2009), pp. 1711-1712. by Natalia Becker, Wiebke Werft, Grischa Toedt, Peter Lichter, Axel Benner posted to 31-jul-09 by ollieredfernwork to the group Orengo Group Journal Picks on 2009-07-31 11:31:58 as along with 11 people and 1 group jfr sotacam rdiaz anf lwaldron dswan TRHvidsten neils operon phoenixzxl giovanni Bioinformatics
	Domain Interaction Footprint: a multi-classification approach to predict domain-peptide interactions [My Copy] Bioinformatics, Vol. 25, No. 13. (1 July 2009), pp. 1632-1639. by Christian Schillinger, Prisca Boisguerin, Gerd Krause posted to 31-jul-09 by ollieredfernwork to the group Orengo Group Journal Picks on 2009-07-31 11:31:43 as along with 3 people kshameer zwang phoenixzxl
	Flexible structural protein alignment by a sequence of local transformations [My Copy] Bioinformatics, Vol. 25, No. 13. (1 July 2009), pp. 1625-1631. by Jairo Rocha, Joan Segura, Richard C. Wilson, Swagata Dasgupta posted to 31-jul-09 by ollieredfernwork to the group Orengo Group Journal Picks on 2009-07-31 11:31:24 as along with 1 person reyez
	Augmented training of hidden Markov models to recognize remote homologs via simulated evolution [My Copy] Bioinformatics, Vol. 25, No. 13. (1 July 2009), pp. 1602-1608. by Anoop Kumar, Lenore Cowen posted to 31-jul-09 hmms sequence_comparison by ollieredfernwork to the group Orengo Group Journal Picks on 2009-07-31 11:30:27 as along with 2 people and 1 group AlexBateman operon Journal picks
	Visual and statistical comparison of metagenomes [My Copy] Bioinformatics, Vol. 25, No. 15. (1 August 2009), pp. 1849-1855. by Suparna Mitra, Bernhard Klar, Daniel H. Huson posted to 31-jul-09 metagenomics by ollieredfernwork to the group Orengo Group Journal Picks on 2009-07-31 11:24:40 as along with 13 people and 2 groups carlk polivares inesdesantiago taylor73 nuin stajich sriesenfeld idoerg guhjy chrisamiller jmeppley neils druvus Mycology iSEEM
	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 31-jul-09 alignment phylogeny tree by robertrentzsch to the group Orengo Group Journal Picks on 2009-07-30 17:36:18 as along with 26 people and 3 groups gjuggler parnell kinestetika xianjun gdb jbhiatt stajich operon biomcgary kieran101 zwang michaelbarton vingron tatman303 hryk lizbiogen pkonings ppgardne dokky aprasad timflutre inquil TRHvidsten djkt fenghezi phoenixzxl Mycology Journal picks iSEEM
	Missing in action: enzyme functional annotations in biological databases [My Copy] Nature Chemical Biology, Vol. 5, No. 8. (01 August 2009), pp. 521-525. by Nicholas Furnham, John S. Garavelli, Rolf Apweiler, Janet M. Thornton posted to 31-jul-09 annotation enzyme by robertrentzsch to the group Orengo Group Journal Picks on 2009-07-30 17:27:33 as along with 3 people seb1 reyez renatomilani
	Energetics of protein hydrogen bonds [My Copy] Nat Struct Mol Biol, Vol. 16, No. 7. (July 2009), pp. 681-682. by C. Nick Pace posted to 31-jul-09 by AliC to the group Orengo Group Journal Picks on 2009-07-30 17:01:58 as along with 2 people barry aalibes
	A perturbative view of protein structural variation [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 78, No. 1. (2010), pp. 173-180. by Julián Echave, Francisco M. Fernández posted to 31-jul-09 by AliC to the group Orengo Group Journal Picks on 2009-07-30 17:00:07 as along with 1 person dfdong
	Gene ontology functional annotations at the structural domain level [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 76, No. 3. (2009), pp. 598-607. by Daniel Lopez, Florencio Pazos posted to 31-jul-09 by AliC to the group Orengo Group Journal Picks on 2009-07-30 16:58:01 as along with 1 person TRHvidsten
	Evolutionary conservation in multiple faces of protein interaction [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 77, No. 1. (2009), pp. 14-25. by Yoon S. Choi, Jae-Seong Yang, Yonghwan Choi, Sung H. Ryu, Sanguk Kim posted to 31-jul-09 by AliC to the group Orengo Group Journal Picks on 2009-07-30 16:56:23 as along with 2 people paulschlesinger neils
	Prediction of protein-glucose binding sites using support vector machines [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2009), NA. by Houssam Nassif, Hassan Al-Ali, Sawsan Khuri, Walid Keirouz posted to 31-jul-09 by AliC to the group Orengo Group Journal Picks on 2009-07-30 16:55:16 as
	Native secondary structure topology has near minimum contact energy among all possible geometrically constrained topologies [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2009), NA. by Weitao Sun, Jing He posted to 31-jul-09 by AliC to the group Orengo Group Journal Picks on 2009-07-30 16:54:42 as along with 1 person RamuAnandakrishnan
	Beyond the Twilight Zone: Automated prediction of structural properties of proteins by recursive neural networks and remote homology information [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 77, No. 1. (2009), pp. 181-190. by Catherine Mooney, Gianluca Pollastri posted to 31-jul-09 by AliC to the group Orengo Group Journal Picks on 2009-07-30 16:53:50 as
	Predicting structurally conserved contacts for homologous proteins using sequence conservation filters [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 77, No. 2. (20 April 2009), pp. 448-453. by Mayako Michino, Charles L. Brooks posted to 31-jul-09 by AliC to the group Orengo Group Journal Picks on 2009-07-30 16:44:39 as along with 1 person xdeupi
	A complex-centric view of protein network evolution. [My Copy] Nucleic acids research, Vol. 37, No. 12. (1 July 2009), e88. by Nir Yosef, Martin Kupiec, Eytan Ruppin, Roded Sharan posted to 31-jul-09 by davidalee to the group Orengo Group Journal Picks on 2009-07-30 16:27:46 as along with 11 people carlk chica saket dakelley tomhebbron leemond31 druvus kiekyon neils tmmurali grahamc
	Structure is three to ten times more conserved than sequence - A study of structural response in protein cores [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 77, No. 3. (20 April 2009), pp. 499-508. by Kristoffer Illergård, David H. Ardell, Arne Elofsson posted to 31-jul-09 by AliC to the group Orengo Group Journal Picks on 2009-07-30 16:26:38 as along with 4 people TRHvidsten brianb neils reyez
	Fast and accurate automatic structure prediction with HHpred [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 77, No. S9. (0 2009), pp. 128-132. by Andrea Hildebrand, Michael Remmert, Andreas Biegert, Johannes Söding posted to 31-jul-09 by AliC to the group Orengo Group Journal Picks on 2009-07-30 16:24:12 as along with 2 people maria_hauser reyez
	Prediction of ligand binding sites using homologous structures and conservation at CASP8 [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 77, No. S9. (2009), pp. 147-151. by Mark N. Wass, Michael J. E. Sternberg posted to 31-jul-09 by AliC to the group Orengo Group Journal Picks on 2009-07-30 16:21:48 as
	Cancer-associated mutations are preferentially distributed in protein kinase functional sites [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 77, No. 4. (2009), pp. 892-903. by Jose M. G. Izarzugaza, Oliver C. Redfern, Christine A. Orengo, Alfonso Valencia posted to 31-jul-09 by AliC to the group Orengo Group Journal Picks on 2009-07-30 16:18:29 as along with 1 person reyez
	Identification of protein functional surfaces by the concept of a split pocket [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 76, No. 4. (2009), pp. 959-976. by Yan Y. Tseng, Wen-Hsiung Li posted to 31-jul-09 by AliC to the group Orengo Group Journal Picks on 2009-07-30 16:16:30 as along with 1 person nickolay
	Graphical models of protein-protein interaction specificity from correlated mutations and interaction data [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 76, No. 4. (2 February 2009), pp. 911-929. by John Thomas, Naren Ramakrishnan, Chris Bailey-Kellogg posted to 31-jul-09 by AliC to the group Orengo Group Journal Picks on 2009-07-30 16:11:58 as along with 5 people and 1 group dfdong sobolevnrm qluo RebeccaHamer barry baker-group
	Transcriptional programs: Modelling higher order structure in transcriptional control. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (16 July 2009), 218. by John E. Reid, Sascha Ott, Lorenz Wernisch posted to 31-jul-09 by sillitoe to the group Orengo Group Journal Picks on 2009-07-30 15:28:23 as along with 1 person and 1 group TRHvidsten Journal picks
	Enzyme classification with peptide programs: a comparative study. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (24 July 2009), 231. by Daniel Faria, Antonio E. Ferreira, Andre O. Falcao posted to 31-jul-09 by sillitoe to the group Orengo Group Journal Picks on 2009-07-30 15:22:08 as

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alignment	2
annotation	2
enzyme	2
phylogeny	2
tree	2
hmms	1
metagenomics	1
sequence_comparison	1

Tag 31-jul-09 [38 articles] Export

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