skembel's methods [28 articles] Export

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

	Distributions of Tree Comparison Metrics--Some New Results [My Copy] Syst Biol, Vol. 42, No. 2. (1 June 1993), pp. 126-141. by Mike A. Steel, David Penny posted to phylogenetics methods by skembel on 2009-11-04 19:13:32 as along with 1 group iSEEM
	The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference [My Copy] Syst Biol, Vol. 58, No. 1. (1 February 2009), pp. 130-145. by Alan R. Lemmon, Jeremy M. Brown, Kathrin Stanger-Hall, Emily M. Lemmon posted to phylogenetics ml methods bayesian by skembel on 2009-09-10 19:45:19 as along with 2 people gjuggler ematsen
	Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous [My Copy] Nature, Vol. 431, No. 7011. (21 October 2004), pp. 980-984. by Bryan Kolaczkowski, Joseph W. Thornton posted to phylogenetics mp ml methods by skembel on 2009-09-10 19:42:46 as along with 2 people aprasad tale
	Wrinkles in the rare biosphere: pyrosequencing errors lead to artificial inflation of diversity estimates [My Copy] Environmental Microbiology, Vol. 9999, No. 9999. (2009) by Victor Kunin, Anna Engelbrektson, Howard Ochman, Philip Hugenholtz posted to pyrosequencing methods diversity by skembel on 2009-09-03 20:05:56 as along with 2 people and 1 group jgill jmeppley iSEEM
	Accurate phylogenetic classification of variable-length DNA fragments [My Copy] Nature Methods, Vol. 4, No. 1. (10 December 2006), pp. 63-72. by Alice C. Mchardy, Héctor G. Martín, Aristotelis Tsirigos, Philip Hugenholtz, Isidore Rigoutsos posted to metagenomics methods by skembel on 2009-04-28 23:21:58 as along with 10 people and 4 groups esyoun dakelley Thaverkamp idoerg jmeppley bluto azazello wenhan jlgreen djkt Bioinformatics MBLAB Green Lab iSEEM
	Annotation of metagenome short reads using proxygenes [My Copy] Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i7-13. by Daniel Dalevi, Natalia N. Ivanova, Konstantinos Mavromatis, et al.Sean D. Hooper, Ernest Szeto, Philip Hugenholtz, Nikos C. Kyrpides, Victor M. Markowitz posted to metagenomics methods by skembel on 2009-04-13 22:05:24 as along with 4 people and 1 group Thaverkamp druvus hpaces neils iSEEM
	Ultrafast and memory-efficient alignment of short DNA sequences to the human genome [My Copy] Genome Biology, Vol. 10, No. 3. (2009), R25. by Ben Langmead, Cole Trapnell, Mihai Pop, Steven Salzberg posted to alignment genomics methods by skembel on 2009-04-13 19:31:54 as along with 36 people and 4 groups jfr hzoltan cthachuk darshan fstrozzi adijr debasis bozdagd polivares torfinnnome n00c talponer jmcq rschulz ghattem operon humburg idonaldson mmartin dquest heliopais djkt GeeSharpMinor bertelsen darian semrich dakelley idoerg vmsr hpaces admash pdexheimer mhamada fpattyn natstreet druvus BergmanLab SIMR bioinformatics iSEEM Notre Dame Bioinformatics
	Evaluation of next generation sequencing platforms for population targeted sequencing studies [My Copy] Genome Biology, Vol. 10, No. 3. (2009), R32. by Olivier Harismendy, Pauline Ng, Robert Strausberg, et al.Xiaoyun Wang, Timothy Stockwell, Karen Beeson, Nicholas Schork, Sarah Murray, Eric Topol, Samuel Levy, Kelly Frazer posted to 454 methods nextgensequencing by skembel on 2009-04-13 19:28:32 as along with 25 people and 2 groups heliopais jfr hzoltan dbensasson GustavoLacerda adijr agbiotec jgill darian jandot n00c jonilaserson maren inesdesantiago mlog ppgardne kiekyon michaelbarton idoerg stajich giovanni druvus lwaldron djkt natstreet Journal picks Mycology
	Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples [My Copy] PLoS Comput Biol, Vol. 5, No. 4. (10 April 2009), e1000352. by James R. White, Niranjan Nagarajan, Mihai Pop posted to metagenomics methods simulation by skembel on 2009-04-10 23:07:29 as along with 12 people and 2 groups jfr CorinYeats dayjm taylor73 Thaverkamp hpaces sriesenfeld APRegier dswan druvus djkt idoerg Orengo Group Journal Picks iSEEM
	Phyutility: a phyloinformatics tool for trees, alignments, and molecular data [My Copy] Bioinformatics (28 January 2008), btm619. by Smith, Dunn posted to methods phylogenetics by skembel on 2009-02-11 00:42:22 as along with 3 people druvus guhjy renatomilani
	An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP) [My Copy] PLoS ONE, Vol. 3, No. 7. (2 July 2008), e2566. by Dongying Wu, Amber Hartman, Naomi Ward, Jonathan A. Eisen posted to methods phylogenetics phylotyping by skembel on 2009-01-23 21:37:10 as along with 7 people and 4 groups Katje AaronDarling sriesenfeld druvus vaulot skato_toyaku djkt microbiology_nijmegen Papers recommended by the Roscoff Plankton Group Microbial-Ecology iSEEM
	GST and its relatives do not measure differentiation [My Copy] Molecular Ecology, Vol. 17, No. 18. (September 2008), pp. 4015-4026. by L. O. U. Jost posted to diversity methods by skembel on 2009-01-22 00:20:01 as along with 3 people jsatkosk rs heinokonrad
	MetaSim—A Sequencing Simulator for Genomics and Metagenomics [My Copy] PLoS ONE, Vol. 3, No. 10. (8 October 2008), e3373. by Daniel C. Richter, Felix Ott, Alexander F. Auch, Ramona Schmid, Daniel H. Huson posted to metagenomics methods simulation by skembel on 2008-12-11 22:07:45 as along with 10 people and 2 groups jonilaserson polivares michaelbarton idoerg sriesenfeld guhjy azazello hpaces druvus nuin BergmanLab iSEEM
	Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. [My Copy] Nature methods, Vol. 4, No. 6. (29 June 2007), pp. 495-500. by Konstantinos Mavromatis, Natalia Ivanova, Kerrie Barry, et al.Harris Shapiro, Eugene Goltsman, Alice C. McHardy, Isidore Rigoutsos, Asaf Salamov, Frank Korzeniewski, Miriam Land, Alla Lapidus, Igor Grigoriev, Paul Richardson, Philip Hugenholtz, Nikos C. Kyrpides posted to metagenomics methods by skembel on 2008-12-11 18:57:56 as along with 16 people and 5 groups dakelley taylor73 sriesenfeld Thaverkamp druvus Yanno oamg jmeppley bluto azazello GustavoLacerda carlk alexl mjetten jlgreen djkt Glimcher_Lab Bioinformatics microbiology_nijmegen Green Lab iSEEM
	Emerging patterns in the comparative analysis of phylogenetic community structure [My Copy] Molecular Ecology, Vol. 9999, No. 9999. (2008) by S. M. Vamosi, S. B. Heard, J. C. Vamosi, C. O. Webb posted to methods phylodiversity by skembel on 2008-12-05 22:01:48 as along with 2 people and 1 group jlgreen anphony iSEEM
	Artifacts and Artifictions in Biodiversity Research [My Copy] Folia Geobotanica, Vol. 43, No. 3. (2008), pp. 245-257. by Michael Palmer, Daniel Mcglinn, Jason Fridley posted to diversity methods by skembel on 2008-12-05 21:54:51 as along with 1 person liucun
	Quantitative assessment of protein function prediction from metagenomics shotgun sequences [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 35. (28 August 2007), pp. 13913-13918. by E. D. Harrington, A. H. Singh, T. Doerks, et al.I. Letunic, C. von Mering, L. J. Jensen, J. Raes, P. Bork posted to annotation metagenomics methods phylotyping by skembel on 2008-11-30 23:01:22 as along with 3 people and 1 group michC bluto larsjuhljensen iSEEM
	Signature, a web server for taxonomic characterization of sequence samples using signature genes. [My Copy] Nucleic acids research (23 May 2008) by Bas E E. Dutilh, Ying He, Maarten L L. Hekkelman, Martijn A A. Huynen posted to metagenomics methods phylotyping by skembel on 2008-11-30 22:59:47 as along with 1 person and 2 groups mjetten anammox microbiology_nijmegen
	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 bayesian mcmc methods by skembel on 2008-11-21 21:32:43 as along with 3 people druvus ryanraaum Xavier
	A STANDARDIZED GENETIC DIFFERENTIATION MEASURE [My Copy] Evolution, Vol. 59, No. 8. (2005), pp. 1633-1638. by Philip W. Hedrick posted to betadiversity diversity methods by skembel on 2008-11-21 21:16:48 as
	A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library [My Copy] Nucl. Acids Res. (5 August 2008), gkn496. by Chaysavanh Manichanh, Charles E. Chapple, Lionel Frangeul, Karine Gloux, Roderic Guigo, Joel Dore posted to diversity metagenomics methods by skembel on 2008-11-19 19:17:16 as along with 3 people and 1 group bluto sconlan druvus iSEEM
	Phylogenetic classification of short environmental DNA fragments [My Copy] Nucl. Acids Res., Vol. 36, No. 7. (19 February 2008), pp. gkn038-2239. by Lutz Krause, Naryttza N. Diaz, Alexander Goesmann, et al.Scott Kelley, Tim W. Nattkemper, Forest Rohwer, Robert A. Edwards, Jens Stoye posted to metagenomics methods pyrosequencing by skembel on 2008-11-19 19:15:18 as along with 7 people esyoun ematsen dakelley idoerg sriesenfeld hpaces vrich
	A statistical toolbox for metagenomics: assessing functional diversity in microbial communities [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (23 January 2008), 34. by Patrick Schloss, Jo Handelsman posted to communityecology methods microbial by skembel on 2008-11-14 22:37:44 as along with 13 people and 4 groups ajsferreira hwright orzenil taylor73 idoerg jonathaneisen druvus jmeppley Thaverkamp alexisfjdufresne mjetten bluto djkt Microbial-Ecology anammox microbiology_nijmegen iSEEM
	Predicting Functional Gene Links from Phylogenetic-Statistical Analyses of Whole Genomes [My Copy] PLoS Comput Biol, Vol. 1, No. 1. (24 June 2005), e3. by Daniel Barker, Mark Pagel posted to comparativemethods methods phylogenetics by skembel on 2008-11-14 22:35:57 as along with 10 people and 1 group jperkins biomcgary Robinder rw294 balajis maryee arunyan bartleby pradiptaray rvosa iSEEM
	$My PDF lozupone_06_unifrac.pdf$ UniFrac - An online tool for comparing microbial community diversity in a phylogenetic context [My Copy] BMC Bioinformatics, Vol. 7 (07 August 2006), 371. by Catherine Lozupone, Micah Hamady, Rob Knight posted to betadiversity methods by skembel on 2008-11-13 23:37:57 as along with 3 people and 1 group esyoun mcox djkt iSEEM
	Testing for Differentiation of Microbial Communities Using Phylogenetic Methods: Accounting for Uncertainty of Phylogenetic Inference and Character State Mapping [My Copy] Microbial Ecology, Vol. 52, No. 3. (October 2006), pp. 408-417. by Jones, Ryan, Martin, Andrew posted to betadiversity comparativemethods methods by skembel on 2008-11-13 23:37:19 as along with 1 person and 1 group djkt iSEEM
	Testing for Neutrality in Samples With Sequencing Errors [My Copy] Genetics, Vol. 179, No. 3. (1 July 2008), pp. 1409-1424. by Guillaume Achaz posted to methods by skembel on 2008-11-07 19:19:24 as along with 3 people druvus treangen BioNica
	Short pyrosequencing reads suffice for accurate microbial community analysis [My Copy] Nucl. Acids Res., Vol. 35, No. 18. (25 September 2007), e120. by Zongzhi Liu, Catherine Lozupone, Micah Hamady, Frederic D. Bushman, Rob Knight posted to diversity methods microbial by skembel on 2008-11-07 00:17:26 as along with 4 people and 2 groups niallhaslam vrich jlgreen djkt Green Lab iSEEM

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diversity	46
phylogenetics	42
metagenomics	40
microbial	32
methods	28
phylodiversity	20
communityecology	15
genomics	14
microbiome	13
pyrosequencing	12
comparativemethods	10
microbes	8
454	7
neutral	7
16s	6
alignment	6
betadiversity	6
diversification	6
entropy	6
roots	6
selection	6
software	6
functionaldiversity	5
ocean	5
phylogenomics	5
phylotyping	5
ecology	4
gos	4
phylogeny	4
supermatrix	4
supertrees	4
traits	4
viral	4
adaptation	3
bacteria	3
bayesian	3
biogeography	3
foraging	3
fungi	3
leaves	3
niche	3
r	3
roc	3
abundance	2
air	2
ants	2
cf	2
coalescent	2
community	2
competition	2
endophytes	2
evolution	2
genetics	2
genomes	2
gut	2
ml	2
nextgensequencing	2
otu	2
profiling	2
simulation	2
species	2
angiosperms	1
annotation	1
archaea	1
bacterial	1
barcode	1
bats	1
bci	1
belowground	1
binning	1
bioinformatics	1
bootstrap	1
climatechange	1
clustering	1
coevolution	1
cogs	1
community_ecology	1
community_structure	1
copy_number	1
cystic_fibrosis	1
data	1
depth	1
diatoms	1
dispersal	1
drift	1
ess	1
ffp	1
functional_characterization	1
funding	1
gene_prediction	1
grants	1
greedyalgorithm	1
hpc	1
incongruence	1
kmer	1
ltt	1
marine	1
mcmc	1
megatree	1
metabolic	1
metacommunity	1
metatranscriptomics	1
missingdata	1
mp	1
mutualisms	1
nserc	1
operon	1
orthologs	1
otus	1
outofafrica	1
partitioning	1
pd	1
ph	1
phenology	1
phyllosphere	1
phylochip	1
plants	1
popgen	1
profiles	1
proteomics	1
pseudomonas	1
rarity	1
rna	1
sampling	1
sanger	1
schizophrenia	1
sequencing	1
shannon	1
shewanella	1
shotgun_sequencing	1
spatial	1
speciation	1
symbioses	1
systems_biology	1
tag	1
teaching	1
transcriptome	1
treeoflife	1
underground	1
wow	1

skembel's methods [28 articles] Export

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