rvosa's methods [at least 200 articles] Export

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

	The Neandertal genome and ancient DNA authenticity [My Copy] The EMBO Journal, Vol. 28, No. 17. (06 August 2009), pp. 2494-2502. by Richard E. Green, Adrian W. Briggs, Johannes Krause, et al.Kay Prufer, Hernan A. Burbano, Michael Siebauer, Michael Lachmann, Svante Paabo posted to primates phylogenomics nuclear mitochondrial methods humans hominidae genome genetics fossils divergence data-mining anthropology by rvosa on 2009-10-06 09:58:04 as along with 1 group FAB-lab
	Life sciences on the Semantic Web: the Neurocommons and beyond. [My Copy] Briefings in bioinformatics, Vol. 10, No. 2. (1 March 2009), pp. 193-204. by Alan Ruttenberg, Jonathan A. Rees, Matthias Samwald, M. Scott Marshall posted to data-mining databases dbhack1 methods nexml ontology phyloinformatics programming software xml by rvosa on 2009-07-30 21:06:03 as along with 10 people and 2 groups jfr Effie guhjy druvus mikel_egana ehealthgr cassj dullhunk allysonlister fgibson FAB-lab NaCTeM
	Advancing translational research with the Semantic Web [My Copy] BMC Bioinformatics, Vol. 8, No. Suppl 3. (2007), S2. by Alan Ruttenberg, Tim Clark, William Bug, et al.Matthias Samwald, Olivier Bodenreider, Helen Chen, Donald Doherty, Kerstin Forsberg, Yong Gao, Vipul Kashyap, June Kinoshita, Joanne Luciano, M. Scott Marshall, Chimezie Ogbuji, Jonathan Rees, Susie Stephens, Gwendolyn Wong, Elizabeth Wu, Davide Zaccagnini, Tonya Hongsermeier, Eric Neumann, Ivan Herman, Kei H. Cheung posted to data-mining databases dbhack1 methods nexml ontology programming software xml by rvosa on 2009-07-30 21:04:48 as along with 26 people and 4 groups beanformer artaban421 nicklynch vkwn eesruiz Effie simonmcbride druvus gmcmahon fgibson nuin daforerog guhjy Cortel wnpx dullhunk hpiwowar egonw suizan jasonbobe ibuch PredictER bmaust benfqt Gaetan dansullivanblk FAB-lab ImagCom - Biomedical Text Computing NaCTeM Evidence-based-medicine
	PhyloExplorer: a web server to validate, explore and query phylogenetic trees [My Copy] BMC Evolutionary Biology, Vol. 9, No. 1. (18 May 2009), 108. by Vincent Ranwez, Nicolas Clairon, Frederic Delsuc, et al.Saeed Pourali, Nicolas Auberval, Sorel Diser, Vincent Berry posted to algorithms biodiversity classification data-mining databases graph graphics methods phyloinformatics programming software taxonomy by rvosa on 2009-06-27 09:11:43 as along with 1 person and 1 group djkt FAB-lab
	BEAST: Bayesian evolutionary analysis by sampling trees. [My Copy] BMC evolutionary biology, Vol. 7, No. 1. (08 November 2007), 214. by Alexei J. Drummond, Andrew Rambaut posted to algorithms bayesian markov-chains methods nexml phylogeny phyloinformatics software xml by rvosa on 2009-05-22 07:02:10 as along with 5 people and 1 group usagi-kirin lizbiogen operon druvus treangen FAB-lab
	The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages [My Copy] Proceedings of the National Academy of Sciences (7 April 2009) by Yuri I. Wolf, Pavel S. Novichkov, Georgy P. Karev, Eugene V. Koonin, David J. Lipman posted to adaptation amino-acid divergence estimation genetics genome methods models protein rates selection sequence-evolution statistics by rvosa on 2009-04-24 09:19:23 as along with 4 people and 1 group RamuAnandakrishnan deanmalmgren jjray gjuggler FAB-lab
	Reliabilities of identifying positive selection by the branch-site and the site-prediction methods [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 16. (21 April 2009), pp. 6700-6705. by Masafumi Nozawa, Yoshiyuki Suzuki, Masatoshi Nei posted to adaptation amino-acid likelihood methods protein selection substitution-models vertebrates by rvosa on 2009-04-24 09:15:52 as along with 8 people and 1 group ckenaley sameersoi djkt ramiro2k gjuggler bpcusack atphan gulsacan FAB-lab
	A Linear-Time Majority Tree Algorithm [My Copy] Algorithms in Bioinformatics (2003), pp. 216-227. by Nina Amenta, Frederick Clarke, Katherine St. John posted to algorithms graph methods phylogeny phyloinformatics software topology by rvosa on 2008-12-18 02:35:27 as along with 1 group FAB-lab
	A Randomized Linear-time Majority Tree Algorithm [My Copy] European Conference on Computational Biology (27-30 September 2003) by Nina Amenta, Frederick Clarke, Katherine St. John posted to algorithms data-mining methods phylogeny phyloinformatics software by rvosa on 2008-12-18 02:26:42 as along with 1 group FAB-lab
	MAXIMUM LIKELIHOOD FRAMEWORK FOR GENETIC SEQUENCE ANALYSIS [My Copy] by Sergei L. Pond posted to algorithms dna estimation inference likelihood methods models phylogeny phyloinformatics sequence-evolution substitution-models by rvosa on 2008-12-18 02:20:47 as along with 1 group FAB-lab
	Pandit: a database of protein and associated nucleotide domains with inferred trees. [My Copy] Bioinformatics (Oxford, England), Vol. 19, No. 12. (12 August 2003), pp. 1556-1563. by S. Whelan, P. I. de Bakker, N. Goldman posted to alignment amino-acid databases dbhack1 dna evolution homology likelihood methods models phylogenomics phylogeny phyloinformatics protein sequence by rvosa on 2008-12-18 02:07:33 as along with 1 person and 1 group mcox FAB-lab
	PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. [My Copy] Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006) by S. Whelan, P. I. de Bakker, E. Quevillon, N. Rodriguez, N. Goldman posted to alignment amino-acid data-mining databases dbhack1 dna evolution homology methods phylogeny protein sequence by rvosa on 2008-12-18 02:00:54 as along with 1 person and 1 group Schmidtc FAB-lab
	Mixture models in phylogenetic inference [My Copy] In Statistical and computational challenges in molecular phylogenetics and evolution (28 April 2008) by Mark Pagel posted to bayesian markov-chains methods monte-carlo phylogeny rates substitution-models by rvosa on 2008-08-18 02:27:00 as along with 1 group FAB-lab
	Modelling Heterotachy in Phylogenetic Inference by Reversible-Jump Markov chain Monte Carlo [My Copy] Philosophical Transactions of the Royal Society of London Series B: Biological Sciences, Vol. In review by Mark Pagel, Andrew Meade posted to bayesian markov-chains methods monte-carlo rates substitution-models by rvosa on 2008-08-18 01:50:23 as along with 1 group FAB-lab
	Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data. [My Copy] Computer Appl. Biosciences, Vol. 11 (1995), pp. 247-251. by Andy Purvis, Andrew Rambaut posted to comparative methods software by rvosa on 2008-08-14 03:02:20 as along with 1 group FAB-lab
	Use and misuse of the gene ontology annotations [My Copy] Nature Reviews Genetics, Vol. 9, No. 7. (13 May 2008), pp. 509-515. by Seung Yon Rhee, Valerie Wood, Kara Dolinski, Sorin Draghici posted to genetics genome methods ontology programming by rvosa on 2008-08-12 07:52:51 as along with 40 people and 3 groups singhsh epigenetics davidmam Thaverkamp druvus dullhunk suizan dolchan Borelli Zephyrus VGreiff klo thomaskelder ilyashl phoenixzxl MarcoAlvarez isakemal bertelsen daforerog jfr djkt guhjy aheilbut mariakmejia cmzmasek A_Olympia realzhang carlk roys gjuggler fpattyn RamuAnandakrishnan ptrobajo giovenko cabbagesofdoom tmmurali renatomilani capitall marck bpcusack 8_01 logics of knowledge FAB-lab
	Cases in which Parsimony or Compatibility Methods Will be Positively Misleading [My Copy] Systematic Zoology, Vol. 27, No. 4. (1978), pp. 401-410. by Joseph Felsenstein posted to characters inference methods parsimony phylogeny by rvosa on 2008-08-12 05:17:15 as along with 1 group FAB-lab
	Frequent False Detection of Positive Selection by the Likelihood Method with Branch-Site Models [My Copy] Mol Biol Evol, Vol. 21, No. 7. (1 July 2004), pp. 1332-1339. by Jianzhi Zhang posted to genetics likelihood methods selection sequence-evolution substitution-models by rvosa on 2008-08-12 04:02:24 as along with 1 person and 1 group Garamonfok FAB-lab
	Calculating independent contrasts for the comparative study of substitution rates. [My Copy] Journal of theoretical biology, Vol. 251, No. 4. (21 April 2008), pp. 667-678. by J. J. Welch, D. Waxman posted to comparative contrasts likelihood methods rates substitution-models by rvosa on 2008-08-09 21:42:43 as along with 1 person and 1 group druvus FAB-lab
	Phylogenetic Mixture Models Can Reduce Node-Density Artifacts [My Copy] Systematic Biology, Vol. 57, No. 2. (2008), pp. 286-293. by Chris Venditti, Andrew Meade, Mark Pagel posted to inference methods models phylogeny sequence-evolution substitution-models by rvosa on 2008-08-09 10:43:22 as along with 1 person and 1 group aprasad FAB-lab
	A Phylogenetic Mixture Model for Detecting Pattern-Heterogeneity in Gene Sequence or Character-State Data [My Copy] Syst Biol, Vol. 53, No. 4. (1 August 2004), pp. 571-581. by Mark Pagel, Andrew Meade posted to characters genetics methods models phylogeny sequence substitution-models by rvosa on 2008-08-09 10:21:04 as along with 1 person and 1 group djohnson FAB-lab
	Bayesian Analysis of Correlated Evolution of Discrete Characters by Reversible-Jump Markov Chain Monte Carlo. [My Copy] The American naturalist, Vol. 167, No. 6. (9 May 2006), pp. 808-825. by Mark Pagel, Andrew Meade posted to bayesian characters comparative evolution markov-chains methods monte-carlo statistics by rvosa on 2008-08-09 09:41:27 as along with 1 person and 1 group yonatanf FAB-lab
	The 2006 NESCent Phyloinformatics Hackathon: A Field Report [My Copy] Evolutionary Bioinformatics, Vol. 3 (2007), pp. 287-296. by Hilmar Lapp, Sendu Bala, James P. Balhoff, et al.Amy Bouck, Naohisa Goto, Mark Holder, Richard Holland, Alisha Holloway, Toshiaki Katayama, Paul O. Lewis, Aaron J. Mackey, Brian I. Osborne, William H. Piel, Sergei, Art F. Y. Poon, Wei-Gang Qiu, Jason E. Stajich, Arlin Stoltzfus, Tobias Thierer, Albert J. Vilella, Rutger A. Vos, Christian M. Zmasek, Derrick J. Zwickl, Todd J. Vision posted to algorithms methods programming by rvosa on 2008-08-08 07:37:01 as
	Detecting putative orthologs. [My Copy] Bioinformatics, Vol. 19, No. 13. (1 September 2003), pp. 1710-1711. by D. P. Wall, H. B. Fraser, A. E. Hirsh posted to algorithms alignment databases data-mining genome likelihood methods phylogenomics phyloinformatics by rvosa on 2008-08-08 07:27:51 as along with 7 people and 3 groups cgaugain operon ana indigoviolet dquest ninch cerca structural_bioinformatics Bioinformatics EisenLab
	Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases [My Copy] Bioinformatics, Vol. 21, No. 11. (1 June 2005), pp. 2596-2603. by Jean-Francois Dufayard, Laurent Duret, Simon Penel, Manolo Gouy, Francois Rechenmann, Guy Perriere posted to algorithms alignment databases data-mining genome methods phylogenomics phyloinformatics by rvosa on 2008-08-08 07:21:45 as along with 2 people and 2 groups ana stajich structural_bioinformatics Bioinformatics
	Improving the specificity of high-throughput ortholog prediction. [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (28 May 2006) by Debra L. Fulton, Yvonne Y. Li, Matthew R. Laird, Benjamin G. Horsman, Fiona M. Roche, Fiona S. Brinkman posted to algorithms alignment data-mining genome homology methods phylogenomics phyloinformatics by rvosa on 2008-08-08 07:17:36 as along with 4 people and 2 groups operon indigoviolet kaspermunch cerca Bioinformatics EisenLab
	BranchClust: A phylogenetic algorithm for selecting gene families [My Copy] BMC Bioinformatics, Vol. 8 (10 April 2007), 120. by Maria S. Poptsova, Peter J. Gogarten posted to algorithms alignment data-mining genome homology methods phylogenomics phyloinformatics programming by rvosa on 2008-08-08 07:02:46 as along with 4 people and 2 groups GustavoLacerda cgaugain dandaman stajich FAB-lab Mycology
	Detecting the historical signature of key innovations using stochastic models of character evolution and cladogenesis. [My Copy] Evolution; international journal of organic evolution, Vol. 59, No. 2. (February 2005), pp. 257-265. by R. H. Ree posted to adaptation characters comparative diversification evolution methods radiation rates speciation by rvosa on 2008-07-11 19:33:14 as
	Accelerated molecular evolution as a consequence of transitions to mutualism [My Copy] Proceedings of the national academy of sciences, Vol. 94, No. 21. (1997), pp. 11422-11427. by Francois Lutzoni, Mark Pagel posted to bacteria comparative divergence fungi methods rates ratio-test substitution-models by rvosa on 2008-07-11 18:54:57 as along with 1 group FAB-lab
	Understanding the Metropolis-Hastings Algorithm [My Copy] The American Statistician, Vol. 49, No. 4. (1995), pp. 327-335. by Siddhartha Chib, Edward Greenberg posted to algorithms bayesian markov-chains methods monte-carlo statistics by rvosa on 2008-05-13 01:30:09 as along with 15 people and 2 groups fordela ashleygeorge Borelli okouma ldietz pcarbo icosma adriandefroment leonnovelo i-stevenson jrw quianominorleo ansobol markusd nojhan FAB-lab Metaheuristics
	What is principal component analysis? [My Copy] Nature Biotechnology, Vol. 26, No. 3. (01 March 2008), pp. 303-304. by Markus Ringnér posted to data-mining methods statistics by rvosa on 2008-05-13 01:28:59 as along with 69 people and 3 groups singhsh Jporci tnhh ruvido ucbcjbm daforerog Diego_Prada abellogin nguizard thegoose2 arsyed Zephyrus flips svozil VGreiff kaniko ssgong Yanno guhjy operon barry baaic dullhunk Bevan_Weir zeji gareth massivemayhem zwang GustavoLacerda GeeSharpMinor bmaust zambujo mingzhi starz1010101 maralena wchannels sunhwan jennifermbui kdelavega zhouyu rsantana sobolevnrm fryanpan kengg dekay23 adacier hpaces waghsk rchauhan pavanghatty kristgy jfr bibay2004 xingxu quianominorleo craigwilson06 ashko markusd dayjm dimka i-stevenson chrissp100 tharris ale mjoach HugoMarcelo jdiezperezj rrbarb Nici baker-group FAB-lab Bioinformatics
	Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). [My Copy] Omics : a journal of integrative biology, Vol. 10, No. 2. (2006), pp. 231-237. by J. Leebens-Mack, T. Vision, E. Brenner, et al.J. E. Bowers, S. Cannon, M. J. Clement, C. W. Cunningham, C. dePamphilis, R. deSalle, J. J. Doyle, J. A. Eisen, X. Gu, J. Harshman, R. K. Jansen, E. A. Kellogg, E. V. Koonin, B. D. Mishler, H. Philippe, J. C. Pires, Y. L. Qiu, S. Y. Rhee, K. Sjölander, D. E. Soltis, P. S. Soltis, D. W. Stevenson, K. Wall, T. Warnow, C. Zmasek posted to methods nexml by rvosa on 2008-04-22 20:26:55 as along with 3 people and 1 group AaronDarling cmzmasek jandot FAB-lab
	Using Perl for Statistics: Data Processing and Statistical Computing [My Copy] Journal of Statistical Software, Vol. 11, No. 1. (May 2004) by Giovanni Baiocchi posted to algorithms data-mining methods programming software by rvosa on 2008-02-08 03:21:56 as
	Estimating Evolutionary Rates in the Primate epsilon-globin Pseudogene [My Copy] (12 August 2004) by Toby Johnson posted to animals likelihood mammals methods primates rates ratio-test software substitution-models vertebrates by rvosa on 2008-02-08 03:13:21 as along with 1 group FAB-lab
	Missing data, incomplete taxa, and phylogenetic accuracy [My Copy] Systematic Biology, Vol. 52, No. 4. (2003), pp. 528-538. by J. J. Wiens posted to characters data-mining fossils methods parsimony phylogeny phyloinformatics simulation by rvosa on 2008-02-07 00:05:51 as
	A novel method for economical diagnosis of cladograms under Sankoff optimization [My Copy] Cladistics, Vol. 10 (1994), pp. 207-213. by Ward C. Wheeler, Kevin Nixon posted to algorithms methods parsimony phylogeny by rvosa on 2008-02-07 00:05:51 as
	Iterative pass optimization of sequence data [My Copy] Cladistics-the International Journal of the Willi Hennig Society, Vol. 19, No. 3. (2003), pp. 254-260. by W. C. Wheeler posted to algorithms alignment methods phylogeny sequence by rvosa on 2008-02-07 00:05:51 as
	Search-based optimization [My Copy] Cladistics-the International Journal of the Willi Hennig Society, Vol. 19, No. 4. (2003), pp. 348-355. by W. C. Wheeler posted to alignment methods parsimony by rvosa on 2008-02-07 00:05:51 as
	Combinatorial weights in phylogenetic analysis: a statistical parsimony procedure [My Copy] Cladistics, Vol. 6 (1990), pp. 269-275. by Ward C. Wheeler posted to algorithms methods parsimony phylogeny weighting by rvosa on 2008-02-07 00:05:51 as
	Noise [My Copy] Cladistics, Vol. 15 (1999), pp. 51-64. by John W. Wenzel, Mark E. Siddall posted to methods parsimony phylogeny by rvosa on 2008-02-07 00:05:51 as
	IQPNNI: Moving Fast Through Tree Space and Stopping in Time [My Copy] Molecular Biology and Evolution, Vol. 21, No. 8. (2004), pp. 1565-1571. by Le S. Vinh, Arndt von Haeseler posted to algorithms likelihood methods by rvosa on 2008-02-07 00:05:51 as
	Inching toward Reality: An Improved Likelihood Model of Sequence Evolution [My Copy] Journal of Molecular Evolution, Vol. 34 (1992), pp. 3-16. by Jeffrey L. Thorne, Hirohisa Kishino, Joseph Felsenstein posted to algorithms alignment evolution likelihood methods programming substitution-models by rvosa on 2008-02-07 00:05:50 as
	Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used [My Copy] Molecular Biology and Evolution, Vol. 17, No. 8. (2000), pp. 1251-1258. by K. Takahashi, M. Nei posted to algorithms likelihood methods parsimony by rvosa on 2008-02-07 00:05:49 as
	Global lability, regional resolution, and majority-rule consensus bias [My Copy] Paleobiology, Vol. 27, No. 2. (2001), pp. 254-261. by C. D. Sumrall, C. A. Brochu, J. W. Merck posted to fossils methods by rvosa on 2008-02-07 00:05:48 as
	Distributions of Tree Comparison Metrics - Some New Results [My Copy] Systematic Biology, Vol. 42, No. 2. (1993), pp. 126-141. by M. A. Steel, D. Penny posted to algorithms evolution methods phylogeny topology by rvosa on 2008-02-07 00:05:48 as
	The maximum likelihood point for a phylogenetic tree is not unique [My Copy] Systematic Biology, Vol. 43 (1994), pp. 560-564. by M. A. Steel posted to likelihood methods phylogeny by rvosa on 2008-02-07 00:05:48 as
	Numerical taxonomy: The principles and practice of numerical classification. [My Copy] (1973) by P. H. A. Sneath, R. R. Sokal posted to classification methods phylogeny taxonomy by rvosa on 2008-02-07 00:05:48 as
	Amino acid vs. nucleotide characters: challenging preconceived notions [My Copy] Molecular Phylogenetics and Evolution, Vol. 24 (2002), pp. 78-90. by M. P. Simmons, H. Ochoterena, J. V. Freudenstein posted to amino-acid characters dna methods phylogeny by rvosa on 2008-02-07 00:05:47 as
	PAUPRat: PAUP* implementation of the parsimony ratchet. [My Copy] (2001) by D. S. Sikes, Paul O. Lewis posted to algorithms methods parsimony software by rvosa on 2008-02-07 00:05:47 as
	Brooks parsimony analysis: a valiant failure [My Copy] Cladistics-the International Journal of the Willi Hennig Society, Vol. 19, No. 6. (2003), pp. 554-564. by M. E. Siddall, S. L. Perkins posted to methods parsimony by rvosa on 2008-02-07 00:05:47 as

Note: You may cite this page as: http://www.citeulike.org/user/rvosa/tag/methods

Result page: 1 2 3 4 5 Next

animals	606
vertebrates	463
mammals	447
phylogeny	432
primates	420
evolution	233
methods	230
source-trees	125
dna	123
genetics	117
algorithms	114
mitochondrial	104
comparative	102
likelihood	91
rates	90
speciation	89
substitution-models	88
invertebrates	85
data-mining	84
divergence	83
morphology	82
behaviour	80
classification	79
biodiversity	77
phyloinformatics	77
diversification	76
software	74
sequence-evolution	73
humans	72
clock-like	68
insects	68
encephalization	62
reconstruction	62
programming	62
ecology	58
taxonomy	57
sequence	57
hominidae	56
fossils	55
genome	54
models	52
selection	52
adaptation	51
parsimony	51
bayesian	50
topology	49
parasitism	49
nuclear	49
biogeography	49
dbhack1	48
databases	47
supertree	45
protein	44
characters	42
sociality	40
phylogenomics	36
plants	36
sexual	36
xml	32
amino-acid	32
morphometrics	31
inference	31
markov-chains	31
monte-carlo	30
anthropology	30
extinction	29
mrp	28
bacteria	28
life-history	28
nexml	27
population-genetics	27
alignment	25
contrasts	25
ratio-test	24
population	20
radiation	20
karyotyping	20
lemuridae	19
simulation	19
ontology	18
rodents	18
conservation	17
strepsirrhines	17
birds	16
statistics	15
specialization	14
viruses	13
hybridization	13
predation	12
weighting	12
rna	12
homology	11
colobinae	11
fungi	11
vision	11
carnivora	11
networks	11
polymorphism	10
restriction	10
fishes	9
cebidae	9
phenetics	9
graph	9
recombination	9
chiroptera	8
platyrrhines	8
polymerase-chain-reaction	8
proteomics	7
mice	7
lexicostatistics	7
competition	7
estimation	6
regions	6
lizards	6
alcids	5
metabolomics	5
cercopithecidae	5
graphics	4
rats	4
cells	4
cercopithecinae	4
sine	3
variability	3
cheirogaleidae	3
catarrhines	3
cetartiodactyla	2
haplorhini	2
shrews	1
philosophy	1
fingerprinting	1
songbirds	1
microarray	1
cattle	1
line	1
hylobates	1
tarsiidae	1
nucleic	1
dogs	1

rvosa's methods [at least 200 articles] Export

rvosa's tags