druvus's algorithm [60 articles] Export

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

	Significant speedup of database searches with HMMs by search space reduction with PSSM family models. [My Copy] Bioinformatics (Oxford, England) (14 October 2009), btp593. by Michael Beckstette, Robert Homann, Robert Giegerich, Stefan Kurtz posted to hmm algorithm by druvus on 2009-10-15 11:15:06 as along with 2 people operon kshameer
	BLASTO: a tool for searching orthologous groups [My Copy] Nucl. Acids Res., Vol. 35, No. suppl_2. (13 July 2007), pp. W678-682. by Yi Zhou, Laura F. Landweber posted to ortholog blast algorithm by druvus on 2009-08-12 11:54:41 as along with 4 people Keywan guhjy bpb cerca
	Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2613-2614. by Takehiro Hashimoto, Michiel J. L. de Hoon, Sean M. Grimmond, Carsten O. Daub, Yoshihide Hayashizaki, Geoffrey J. Faulkner posted to algorithm next_generation software by druvus on 2009-07-16 08:43:12 as along with 3 people and 1 group guhjy mkiyer natstreet Chinnaiyan Lab
	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 algorithm alignment by druvus on 2009-05-29 08:45:28 as along with 18 people and 1 group seb1 rdowell timflutre natstreet n00c yylin aprasad Gorzomagnificent guhjy dakelley reyez rec3141 farhat operon bmduggan nuin AlexBateman djkt Journal picks
	Displaying the relatedness among isolates of bacterial species - the eBURST approach [My Copy] FEMS Microbiology Letters, Vol. 241, No. 2. (2004), pp. 129-134. by Brian G. Spratt, William P. Hanage, Bao Li, David M. Aanensen, Edward J. Feil posted to algorithm phylogeny software by druvus on 2009-05-27 14:52:40 as along with 1 person Xavier
	eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. [My Copy] Journal of bacteriology, Vol. 186, No. 5. (March 2004), pp. 1518-1530. by E. J. Feil, B. C. Li, D. M. Aanensen, W. P. Hanage, B. G. Spratt posted to algorithm phylogeny software by druvus on 2009-05-27 14:28:38 as along with 6 people katholt pkm vplagnol Xavier CharlesM bakakaj
	Analyses of clonality and the evolution of bacterial pathogens [My Copy] Current Opinion in Microbiology, Vol. 7, No. 3. (June 2004), pp. 308-313. by E. Feil, M. Enright posted to algorithm phylogeny software by druvus on 2009-05-27 14:25:59 as
	Word correlation matrices for protein sequence analysis and remote homology detection [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Thomas Lingner, Peter Meinicke posted to algorithm homology by druvus on 2009-03-30 09:33:49 as along with 1 person Tingting
	Fast model-based protein homology detection without alignment [My Copy] Bioinformatics, Vol. 23, No. 14. (15 July 2007), pp. 1728-1736. by Sepp Hochreiter, Martin Heusel, Klaus Obermayer posted to algorithm homology by druvus on 2009-03-30 09:32:30 as along with 2 people cjeans niallhaslam
	Remote homology detection based on oligomer distances [My Copy] Bioinformatics, Vol. 22, No. 18. (15 September 2006), pp. 2224-2231. by Lingner, Thomas, Meinicke, Peter posted to algorithm homology by druvus on 2009-03-30 09:31:57 as
	Application of Nonnegative Matrix Factorization to Improve Profile-Profile Alignment Features for Fold Recognition and Remote Homolog Detection [My Copy] BMC Bioinformatics, Vol. 9 (01 July 2008), 298. by Inkyung Jung, Jaehyung Lee, Soo-Young Lee, Dongsup Kim posted to algorithm homology by druvus on 2009-03-30 09:30:38 as
	Dual multiple change-point model leads to more accurate recombination detection [My Copy] Bioinformatics, Vol. 21, No. 13. (1 July 2005), pp. 3034-3042. by Vladimir N. Minin, Karin S. Dorman, Fang Fang, Marc A. Suchard posted to algorithm model recombination by druvus on 2009-03-27 09:28:46 as along with 2 people aprasad treangen
	Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm [My Copy] Mol Biol Evol, Vol. 23, No. 10. (1 October 2006), pp. 1891-1901. by Sergei L. Kosakovsky Pond, David Posada, Michael B. Gravenor, Christopher H. Woelk, Simon D. W. Frost posted to algorithm phylogeny recombination by druvus on 2009-03-27 09:24:00 as along with 5 people calderonv operon Natasha Garamonfok larbiza
	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 Sacomoto, Alair D. Lago, Nadia Pisanti, Marie F. Sagot posted to algorithm repeat by druvus on 2009-03-18 07:48:47 as along with 4 people renatocarmo gwallau timflutre svenrahmann
	SIMPRO: simple protein homology detection method by using indirect signals [My Copy] Bioinformatics (22 January 2009), btp048. by Inkyung Jung, Dongsup Kim posted to algorithm classification proteome by druvus on 2009-03-13 08:08:30 as along with 1 person Neeperando
	The multiple gene duplication problem revisited [My Copy] Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. i132-138. by Mukul S. Bansal, Oliver Eulenstein posted to algorithm duplication phylogeny by druvus on 2009-03-06 09:30:24 as along with 6 people and 1 group wiedenhoeft anazhu86 thegoose2 bpcusack tharris stajich Mycology
	Empirical profile mixture models for phylogenetic reconstruction. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 20. (15 October 2008), pp. 2317-2323. by l. e. . S. Quang, O. Gascuel, N. Lartillot posted to algorithm alignment likelihood by druvus on 2009-03-04 12:40:11 as along with 1 person nuin
	An improved general amino acid replacement matrix. [My Copy] Molecular biology and evolution, Vol. 25, No. 7. (1 July 2008), pp. 1307-1320. by Si Quang Q. Le, Olivier Gascuel posted to algorithm alignment likelihood by druvus on 2009-03-04 12:34:54 as along with 5 people and 1 group BioNica lizbiogen stajich friendpine dmp Mycology
	A topological transformation in evolutionary tree search methods based on maximum likelihood combining p-ECR and neighbor joining [My Copy] BMC Bioinformatics, Vol. 9, No. Suppl 6. (2008) by Mao Z. Guo, Jian F. Li, Yang Liu posted to algorithm alignment likelihood by druvus on 2009-03-04 12:29:53 as
	Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood [My Copy] Bioinformatics, Vol. 21, No. 24. (15 December 2005), pp. 4338-4347. by Wim Hordijk, Olivier Gascuel posted to algorithm alignment likelihood software by druvus on 2009-03-04 12:27:39 as
	Edge Detection in Microscopy Images using Curvelets [My Copy] BMC Bioinformatics, Vol. 10 (03 March 2009), 75. by Tobias Gebaeck, Petros Koumoutsakos posted to algorithm image microscope by druvus on 2009-03-04 07:44:18 as
	MOM: maximum oligonucleotide mapping [My Copy] Bioinformatics, Vol. 25, No. 7. (1 April 2009), pp. 969-970. by Hugh L. Eaves, Yuan Gao posted to 454 algorithm mapping by druvus on 2009-02-23 09:03:37 as along with 7 people seb1 jfr n00c cassj rschulz mmartin guhjy
	Single-Locus Tests of Microsatellite Evolution: Multi-Step Mutations and Constraints on Allele Size [My Copy] Molecular Phylogenetics and Evolution, Vol. 11, No. 3. (April 1999), pp. 477-484. by R. Nielsen posted to algorithm repeat software ssr tandem by druvus on 2009-01-30 09:21:01 as
	An algorithm for detecting directional and non-directional positive selection, neutrality and negative selection in protein coding DNA sequences. [My Copy] Gene, Vol. 300, No. 1-2. (30 October 2002), pp. 43-51. by C. J. Creevey, J. O. McInerney posted to algorithm evolution proteome selection by druvus on 2009-01-29 11:46:42 as
	A Novel Approach to the Detection of Genomic Approximate Tandem Repeats in the Levenshtein Metric [My Copy] Journal of Computational Biology, Vol. 14, No. 7. (2007), pp. 873-891. by Nevzat O. Domaniç, Franco P. Preparata posted to algorithm repeat software tandem by druvus on 2009-01-26 10:35:47 as
	Finding Approximate Tandem Repeats in Genomic Sequences [My Copy] Journal of Computational Biology, Vol. 12, No. 7. (2005), pp. 928-942. by Ydo Wexler, Zohar Yakhini, Yechezkel Kashi, Dan Geiger posted to algorithm repeat software tandem by druvus on 2009-01-26 10:34:15 as
	A new systematic computational approach to predicting target genes of transcription factors [My Copy] Nucl. Acids Res. (18 June 2007), gkm454. by Xinbin Dai, Ji He, Xuechun Zhao posted to algorithm target tf by druvus on 2008-12-19 16:56:41 as along with 3 people lptolik GustavoLacerda cabbagezs
	PocketMatch: A new algorithm to compare binding sites in protein structures [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008), 543. by Kalidas Yeturu, Nagasuma Chandra posted to algorithm binding predictions proteome target by druvus on 2008-12-17 14:14:12 as along with 9 people and 1 group cdsouthan nanonan pauldobson sobolevnrm jteyra kshameer reyez tny higueruelo baker-group
	Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. [My Copy] Genetics, Vol. 161, No. 3. (July 2002), pp. 1307-1320. by A. J. Drummond, G. K. Nicholls, A. G. Rodrigo, W. Solomon posted to algorithm mutation population software by druvus on 2008-12-16 08:59:34 as along with 3 people and 1 group alexeid kaspermunch AaronDarling Bioinformatics
	UPSEC: An Algorithm for Classifying Unaligned Protein Sequences into Functional Families [My Copy] Journal of Computational Biology, Vol. 15, No. 4. (2008), pp. 431-443. by Patrick C. H. Ma, Keith C. C. Chan posted to algorithm classification proteome by druvus on 2008-12-15 13:43:39 as along with 1 person eskay
	Discovering relationships among dispersed repeats using spatial association rule mining [My Copy] BMC Bioinformatics, Vol. 9, No. Suppl 10. (2008) by Surya Saha, Susan Bridges, Zenaida Magbanua, Daniel Peterson posted to algorithm repeat software by druvus on 2008-12-15 13:19:06 as
	Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences [My Copy] Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. i165-171. by Lucas D. Ward, Harmen J. Bussemaker posted to algorithm binding predictions tf by druvus on 2008-12-12 08:00:45 as along with 6 people mox kittipat emptyhb hplatero xili03 maximilianh
	Predicting transcription factor affinities to DNA from a biophysical model [My Copy] Bioinformatics, Vol. 23, No. 2. (15 January 2007), pp. 134-141. by Helge G. Roider, Aditi Kanhere, Thomas Manke, Martin Vingron posted to algorithm predictions tf by druvus on 2008-12-12 07:59:38 as along with 5 people and 1 group Baschl malcook indigoviolet dpollard xili03 EisenLab
	PASTAA: identifying transcription factors associated with sets of co-regulated genes [My Copy] Bioinformatics (9 December 2008), btn627. by Helge G. Roider, Thomas Manke, Sean O'Keeffe, Martin Vingron, Stefan A. Haas posted to algorithm software tf by druvus on 2008-12-12 07:35:57 as along with 10 people and 1 group TRHvidsten maximilianh jimineep cassj idonaldson dswan djkt dolchan nuin natstreet Bioinformatics
	OMWSA: detection of DNA repeats using moving window spectral analysis. [My Copy] Bioinformatics (31 January 2007) by Liping Du, Hongxia Zhou, Hong Yan posted to algorithm repeat software by druvus on 2008-12-05 09:07:17 as along with 1 person mtagaya
	Algorithm of OMA for large-scale orthology inference [My Copy] BMC Bioinformatics, Vol. 9 (04 December 2008), 518. by Alexander, Christophe Dessimoz posted to algorithm ortholog by druvus on 2008-12-04 16:32:32 as along with 5 people AaronDarling alpae cgaugain grahamc barriot
	Indexing strategies for rapid searches of short words in genome sequences. [My Copy] PLoS ONE, Vol. 2, No. 6. (2007) by C. Iseli, G. Ambrosini, P. Bucher, C. V. Jongeneel posted to algorithm alignment genome sequence by druvus on 2008-12-03 14:18:44 as along with 2 people maximilianh natstreet
	GapCoder automates the use of indel characters in phylogenetic analysis. [My Copy] BMC Bioinformatics, Vol. 4 (19 February 2003) by N. D. Young, J. Healy posted to algorithm indel software by druvus on 2008-12-02 14:23:41 as along with 1 person echinotrix
	Splign: algorithms for computing spliced alignments with identification of paralogs [My Copy] Biology Direct, Vol. 3 (21 May 2008), 20. by Yuri Kapustin, Alexander Souvorov, Tatiana Tatusova, David Lipman posted to algorithm alignment genome paralog software by druvus on 2008-11-17 09:47:46 as along with 1 person natstreet
	Homology search for genes [My Copy] Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. i97-103. by Xuefeng Cui, Tomas Vinar, Brona Brejova, Dennis Shasha, Ming Li posted to algorithm blast gene homology mapping software by druvus on 2008-11-17 09:28:55 as along with 2 people guhjy GustavoLacerda
	Stability of Multiple Alignments and Phylogenetic Trees: An Analysis of ABC-Transporter Proteins [My Copy] Algorithms for Molecular Biology, Vol. 3 (06 November 2008), 15. by Andreas W. M. Dress, Burkhard Morgenstern, Holger Wagner posted to algorithm alignment phylogeny software by druvus on 2008-11-07 13:11:47 as along with 2 people treangen nuin
	FastBLAST: Homology Relationships for Millions of Proteins [My Copy] PLoS ONE, Vol. 3, No. 10. (31 October 2008), e3589. by Morgan N. Price, Paramvir S. Dehal, Adam P. Arkin posted to algorithm blast proteome by druvus on 2008-11-03 09:25:09 as along with 4 people AaronDarling treangen natstreet reyez
	Recent Evolutions of Multiple Sequence Alignment Algorithms [My Copy] PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e123. by Cédric Notredame posted to algorithm alignment assembly review by druvus on 2008-11-03 08:47:40 as along with 9 people and 1 group BioNica treangen natstreet giovenko agustinarce skhadar sobolevnrm hpaces mingzhi baker-group
	ESTIMATING SPECIES TREES USING MULTIPLE-ALLELE DNA SEQUENCE DATA [My Copy] Evolution, Vol. 62, No. 8. (August 2008), pp. 2080-2091. by Liang Liu, Dennis K. Pearl, Robb T. Brumfield, Scott V. Edwards posted to algorithm phylogeny sequence by druvus on 2008-10-27 11:41:23 as along with 2 people lizbiogen AaronDarling
	A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence [My Copy] Nucl. Acids Res., Vol. 36, No. 8. (1 May 2008), pp. 2630-2638. by Osamu Gotoh posted to algorithm alignment genome by druvus on 2008-10-27 09:37:35 as along with 7 people kittipat natstreet zhouyu guhjy wisdom_love GenEglob inesdesantiago
	Supervised Principal Component Analysis for Gene Set Enrichment of Microarray Data with Continuous or Survival Outcomes [My Copy] Bioinformatics (27 August 2008), btn458. by Xi Chen, Lily Wang, Jonathan D. Smith, Bing Zhang posted to algorithm enrichment multivariate r by druvus on 2008-10-27 09:17:26 as along with 5 people guhjy jfr ptrobajo aconesa paszkows
	Species Trees from Gene Trees: Reconstructing Bayesian Posterior Distributions of a Species Phylogeny Using Estimated Gene Tree Distributions [My Copy] Syst Biol, Vol. 56, No. 3. (1 June 2007), pp. 504-514. by Liang Liu, Dennis K. Pearl posted to algorithm bayesian coalescent phylogeny by druvus on 2008-10-27 09:07:48 as along with 3 people lizbiogen aprasad akifumi
	High-resolution species trees without concatenation [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 14. (3 April 2007), pp. 5936-5941. by Scott V. Edwards, Liang Liu, Dennis K. Pearl posted to algorithm coalescent phylogeny by druvus on 2008-10-27 09:05:58 as along with 8 people and 1 group lizbiogen robfsouza treangen alexeid stevanspringer operon aprasad zwang FAB-lab
	A review of estimation of distribution algorithms in bioinformatics. [My Copy] BioData mining, Vol. 1, No. 1. (11 September 2008) by Ruben Armananzas, Inaki Inza, Roberto Santana, et al.Yvan Saeys, Jose L. Flores, Jose A. Lozano, Yves Van de Peer, Rosa Blanco, Victor Robles, Concha Bielza, Pedro Larranaga posted to algorithm bioinformatics statistics by druvus on 2008-10-20 08:36:03 as along with 2 people ptrobajo guhjy
	Approximate Bayesian Computation in Population Genetics [My Copy] Genetics, Vol. 162, No. 4. (1 December 2002), pp. 2025-2035. by Mark A. Beaumont, Wenyang Zhang, David J. Balding posted to algorithm genetics population by druvus on 2008-10-13 13:59:04 as along with 3 people skembel ryanraaum Xavier

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genome	390
software	375
evolution	279
phylogeny	270
statistics	221
review	211
bacteria	188
database	173
francisella	162
proteome	160
repeat	158
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plant	140
tandem	124
alignment	119
marker	106
network	104
annotation	99
semantic	97
wms	95
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population	89
comperative_genomics	82
tf	81
sequence	79
populus	71
mirna	69
gene	66
genetics	66
algorithm	60
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snp	57
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r	51
web_20	51
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pcr	39
synthetic_biology	38
indel	37
model	36
distance	35
ecoli	35
mutation	35
454	34
likelihood	33
ortholog	33
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motif	32
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ontology	30
references	30
wiki	30
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rice	27
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browser	25
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ssr	25
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domain	21
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tom	21
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blast	13
comment	13
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vntr	13
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hmm	12
ricinus	12
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solexa	12
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binding	11
datasharing	11
development	11
human	11
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anthrax	10
cis	10
drosophila	10
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parallel	10
pubmed	10
repeats	10
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das	9
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uorf	3
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base_calling	2
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blog	2
chado	2
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codeigniter	2
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cotton	2
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drupal	2
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full-length	2
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kegg	2
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regulon	2
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rnai	2
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viewer	1
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wgcna	1
wheat	1
wolbachia	1

druvus's algorithm [60 articles] Export

druvus's tags