sriesenfeld's library 41 articles Export

	Analysis of Rare Genomic Changes Does Not Support the Unikont-Bikont Phylogeny and Suggests Cyanobacterial Symbiosis as the Point of Primary Radiation of Eukaryotes [My Copy] Genome Biol Evol, Vol. 2009, No. 0. (22 June 2009), pp. 99-113. by Igor B. Rogozin, Malay K. Basu, Miklos Csuros, Eugene V. Koonin posted to deep divergence eukaryote phylogeny by sriesenfeld on 2009-07-16 20:00:36 as
	Adaptive prediction of environmental changes by microorganisms [My Copy] Nature, Vol. 460, No. 7252. (17 June 2009), pp. 220-224. by Amir Mitchell, Gal H. Romano, Bella Groisman, et al.Avihu Yona, Erez Dekel, Martin Kupiec, Orna Dahan, Yitzhak Pilpel posted to adaptation change environmental microbial by sriesenfeld on 2009-07-14 00:34:16 as along with 8 people and 1 group yyfwuhan kinestetika biomcgary timotay izuleta djkt jjray michaelbarton iSEEM
	Large-Scale Assessment of the Effect of Popularity on the Reliability of Research [My Copy] PLoS ONE, Vol. 4, No. 6. (24 June 2009), e5996. by Thomas Pfeiffer, Robert Hoffmann posted to misc research by sriesenfeld on 2009-07-03 01:47:25 as along with 5 people radagabriel nellapower bpcusack rdiaz dullhunk
	A pattern-based nearest neighbor search approach for promoter prediction using DNA structural profiles [My Copy] Bioinformatics, Vol. 25, No. 16. (15 August 2009), pp. 2006-2012. by Yanglan Gan, Jihong Guan, Shuigeng Zhou posted to algorithm nearest neighbor prediction promoter search by sriesenfeld on 2009-07-02 20:25:09 as along with 2 people junehlee TRHvidsten
	Clustered sequence representation for fast homology search. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 14, No. 5. (June 2007), pp. 594-614. by M. Cameron, Y. Bernstein, H. E. Williams posted to algorithm blast clustering open-source software by sriesenfeld on 2009-07-02 20:20:35 as along with 1 person dgront
	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 data metagenomics simulations by sriesenfeld on 2009-07-02 20:17:54 as along with 16 people and 5 groups dakelley taylor73 Thaverkamp skembel druvus Yanno oamg jmeppley bluto azazello GustavoLacerda carlk alexl mjetten jlgreen djkt Glimcher_Lab Bioinformatics microbiology_nijmegen Green Lab iSEEM
	Binning sequences using very sparse labels within a metagenome [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (28 April 2008), 215. by Chon K. Chan, Arthur Hsu, Saman Halgamuge, Sen L. Tang posted to algorithm binning metagenomics by sriesenfeld on 2009-07-02 20:16:30 as along with 13 people and 3 groups skembel esyoun jmeppley dakelley Thaverkamp idoerg azazello druvus alexl mjetten werwiesel jlgreen djkt Bioinformatics microbiology_nijmegen iSEEM
	SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences [My Copy] Bioinformatics, Vol. 25, No. 14. (15 July 2009), pp. 1722-1730. by M. Monzoorul Haque, Tarini S. Ghosh, Dinakar Komanduri, Sharmila S. Mande posted to binning metagenomics software taxonomy by sriesenfeld on 2009-07-02 20:10:23 as along with 5 people and 1 group dakelley sharpton djkt guhjy operon iSEEM
	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 metagenomics software statistical visual by sriesenfeld on 2009-07-02 20:02:47 as along with 13 people and 3 groups carlk polivares inesdesantiago taylor73 ollieredfernwork nuin stajich idoerg guhjy chrisamiller jmeppley neils druvus Orengo Group Journal Picks Mycology iSEEM
	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 communities metagenomics method statistical by sriesenfeld on 2009-04-15 21:54:17 as along with 11 people and 2 groups CorinYeats dayjm taylor73 Thaverkamp hpaces APRegier dswan druvus djkt skembel idoerg Orengo Group Journal Picks iSEEM
	The effect of the guide tree on multiple sequence alignments and subsequent phylogenetic analyses. [My Copy] Pac Symp Biocomput (2008), pp. 25-36. by S. Nelesen, K. Liu, D. Zhao, C. R. Linder, T. Warnow posted to alignment guide phylogeny tree by sriesenfeld on 2009-04-06 20:55:33 as along with 2 people and 1 group treangen dpollard EisenLab
	Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment? [My Copy] BMC Evolutionary Biology, Vol. 8 (26 March 2008), 95. by Stefanie Hartmann, Todd J. Vision posted to ests phylogenomics phylogeny by sriesenfeld on 2009-02-17 20:01:42 as along with 7 people and 2 groups skembel treangen natstreet druvus stajich Patola aprasad iSEEM Mycology
	RAMI, a tool for identification and characterization of phylogenetic clusters in microbial communities [My Copy] Bioinformatics (17 February 2009), btp051. by Thomas Pommier, Bjorn Canback, Per Lundberg, Ake Hagstrom, Anders Tunlid posted to cluster communities metagenomics phylogeny software by sriesenfeld on 2009-02-17 18:45:51 as along with 4 people and 2 groups elbrodie hpaces skembel djkt phylocom iSEEM
	Detecting selective sweeps: a new approach based on hidden markov models. [My Copy] Genetics, Vol. 181, No. 4. (9 April 2009), pp. 1567-1578. by Simon Boitard, Christian Schlötterer, Andreas Futschik posted to hmm linkage popgen selective sweeps by sriesenfeld on 2009-02-11 18:56:54 as along with 4 people sameersoi ilyashl druvus djkt
	A structural EM algorithm for phylogenetic inference. [My Copy] J Comput Biol, Vol. 9, No. 2. (2002), pp. 331-353. by N. Friedman, M. Ninio, I. Pe'er, T. Pupko posted to algorithm em phylogeny by sriesenfeld on 2009-02-09 20:26:39 as along with 3 people Garamonfok tale wenhan
	Experimental evolution reveals natural selection on standing genetic variation [My Copy] Nat Genet, Vol. 41, No. 2. (February 2009), pp. 251-257. by Henrique Teotonio, Ivo M. Chelo, Martina Bradic, Michael R. Rose, Anthony D. Long posted to evolution experimental genetics population by sriesenfeld on 2009-01-28 19:13:58 as along with 3 people tomhebbron emptyhb djkt
	A hierarchical model for incomplete alignments in phylogenetic inference [My Copy] Bioinformatics, Vol. 25, No. 5. (1 March 2009), pp. 592-598. by Fuxia Cheng, Stefanie Hartmann, Mayetri Gupta, Joseph G. Ibrahim, Todd J. Vision posted to alignment est incomplete phylogeny by sriesenfeld on 2009-01-16 20:09:03 as along with 7 people and 1 group nuin druvus skembel djkt mhamada jmeppley jameswasmuth iSEEM
	Taxonomic distribution of large DNA viruses in the sea [My Copy] Genome Biology, Vol. 9, No. 7. (2008) by Adam Monier, Jean M. Claverie, Hiroyuki Ogata posted to metagenomics phylogeny taxonomy virus by sriesenfeld on 2009-01-15 01:19:16 as along with 4 people and 1 group idoerg skembel neils djkt 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 phylogeny taxonomy by sriesenfeld on 2009-01-15 01:18:15 as along with 7 people esyoun ematsen dakelley idoerg skembel hpaces vrich
	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 simulations by sriesenfeld on 2009-01-15 01:16:59 as along with 10 people and 2 groups jonilaserson polivares michaelbarton idoerg skembel guhjy azazello hpaces druvus nuin BergmanLab iSEEM
	The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. [My Copy] PLoS Biol, Vol. 3, No. 10. (October 2005) by F. Ge, L. S. Wang, J. Kim posted to hgt microbial phylogenomics by sriesenfeld on 2009-01-07 00:16:41 as along with 4 people and 2 groups operon ana jmeppley AaronDarling structural_bioinformatics Bioinformatics
	Fast-evolving non-coding sequences in the human genome [My Copy] Genome Biology, Vol. 8 (19 June 2007), R118. by Christine P. Bird, Barbara E. Stranger, Maureen Liu, et al.Daryl J. Thomas, Catherine E. Ingle, Claude Beazley, Webb Miller, Matthew E. Hurles, Emmanouil T. Dermitzakis posted to evolution genomics human noncoding variation by sriesenfeld on 2008-12-13 01:45:21 as along with 8 people and 2 groups balicea xianjun djkt Stew jlangdon cisevol iris42 bpcusack EisenLab cis-regulatory-evolution
	Adaptive Evolution of Conserved Noncoding Elements in Mammals [My Copy] PLoS Genetics, Vol. 3, No. 9. (1 September 2007), e147. by Su Y. Kim, Jonathan K. Pritchard posted to conserved evolution method noncoding statistical variation by sriesenfeld on 2008-12-13 01:43:57 as along with 11 people and 5 groups sujaikumar mattjb livingthingdan djkt stajich Garamonfok cabbagezs Stew cisevol rrhudson bpcusack EisenLab ComplexAdaptiveSystems DSTO-CAS livingthing cis-regulatory-evolution
	An RNA gene expressed during cortical development evolved rapidly in humans [My Copy] Nature, Vol. 443, No. 7108. (16 August 2006), pp. 167-172. by Katherine S. Pollard, Sofie R. Salama, Nelle Lambert, et al.Marie-Alexandra Lambot, Sandra Coppens, Jakob S. Pedersen, Sol Katzman, Bryan King, Courtney Onodera, Adam Siepel, Andrew D. Kern, Colette Dehay, Haller Igel, Manuel Ares, Pierre Vanderhaeghen, David Haussler posted to evolution human rate by sriesenfeld on 2008-12-13 01:39:25 as along with 15 people and 3 groups galka8_diploma brewbooks Ema brian bpb marcius nickluscombe larios joshuashen ealloza ce2benna lusk bpcusack nolodie rrhudson EBI-regulation BioinfoCIPF SGU-CIPF
	Forces Shaping the Fastest Evolving Regions in the Human Genome [My Copy] PLoS Genetics, Vol. 2, No. 10. (1 October 2006), e168. by Katherine S. Pollard, Sofie R. Salama, Bryan King, et al.Andrew D. Kern, Tim Dreszer, Sol Katzman, Adam Siepel, Jakob S. Pedersen, Gill Bejerano, Robert Baertsch, Kate R. Rosenbloom, Jim Kent, David Haussler posted to evolution genome human rate variation by sriesenfeld on 2008-12-13 01:34:41 as along with 6 people and 2 groups balicea skembel eskay nickluscombe iris42 rvosa EBI-regulation FAB-lab
	New methods for detecting lineage-specific selection [My Copy] Lect. Notes Comput. Sci., Vol. 3909 LNBI, pp. 190-205. by A. Siepel, K. S. Pollard, D. Haussler posted to algorithm evolution phylogenomics selection by sriesenfeld on 2008-12-13 01:29:03 as along with 2 people bpb pradiptaray
	Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. [My Copy] Mol Biol Evol, Vol. 21, No. 3. (March 2004), pp. 468-488. by A. Siepel, D. Haussler posted to evolution likelihood maximum phylogenomics rates substitution by sriesenfeld on 2008-12-13 01:26:26 as along with 6 people mgledi mdimmic penka djkt tale uwe
	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 alignment phylogeny rrna software taxonomy by sriesenfeld on 2008-12-13 01:23:00 as along with 6 people and 3 groups AaronDarling skembel druvus vaulot skato_toyaku djkt Papers recommended by the Roscoff Plankton Group Microbial-Ecology iSEEM
	Unexpected dynamic gene family evolution in algal actins [My Copy] Mol Biol Evol (13 November 2008), msn263. by Min Wu, Josep M. Comeron, Hwan S. Yoon, Debashish Bhattacharya posted to evolution family gene rate variation by sriesenfeld on 2008-12-13 01:18:59 as
	The importance of stupidity in scientific research [My Copy] J Cell Sci, Vol. 121, No. 11. (1 June 2008), 1771. by Martin A. Schwartz posted to misc by sriesenfeld on 2008-12-13 01:15:22 as along with 36 people and 2 groups tomhebbron Sergey_gerbek sarelfa DLLP mmborges CarlosMorais Anita13 soniapereira vigneshjvn munzmarci CulCog jxl mutesa brembs operon yangjustinc coela silberbauer eyliu Publicase Thermaneutist spl michaelbanks bayesian alexgeorgiou chemistmd susz idoerg cerca aramata dullhunk arindrartow barry ibuch casutton jporternj McCammon structural_bioinformatics
	Progress and challenges in genome-wide association studies in humans [My Copy] Nature, Vol. 456, No. 7223. (10 December 2008), pp. 728-731. by Peter Donnelly posted to association genome human review by sriesenfeld on 2008-12-13 01:08:15 as along with 17 people and 1 group alweber daforerog sameersoi jfr guhjy gruberjd psique raiyar Zephyrus Hans45 sg45653 lp2 jo_davies pkonings allysonlister neils djkt Roswell Cancer Crosstalk
	Reverse engineering the genotype\|[ndash]\|phenotype map with natural genetic variation [My Copy] Nature, Vol. 456, No. 7223. (10 December 2008), pp. 738-744. by Matthew V. Rockman posted to association genotype phenotype popgen variation by sriesenfeld on 2008-12-12 19:38:45 as along with 15 people and 1 group gdb carlk Keywan TRHvidsten jfr roys Zephyrus mjoach sg45653 natstreet druvus lp2 pkonings stringertheory djkt Roswell Cancer Crosstalk
	Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 105, No. 30. (29 July 2008), pp. 10583-10588. by Jennifer F. Biddle, Sorel Fitz-Gibbon, Stephan C. Schuster, Jean E. Brenchley, Christopher H. House posted to community evolution metagenomics by sriesenfeld on 2008-12-03 20:00:54 as along with 5 people and 2 groups michaelbarton jmeppley Thaverkamp skembel skato_toyaku Microbial-Ecology iSEEM
	Quantitative phylogenetic assessment of microbial communities in diverse environments. [My Copy] Science (New York, N.Y.), Vol. 315, No. 5815. (23 February 2007), pp. 1126-1130. by C. von Mering, P. Hugenholtz, J. Raes, et al.S. G. Tringe, T. Doerks, L. J. Jensen, N. Ward, P. Bork posted to evolution metagenomics microbial phylogeny by sriesenfeld on 2008-12-03 17:53:05 as along with 18 people and 7 groups pkm michaelbarton idoerg skembel kozo-ni ana nickluscombe michC bluto agg19954 TaqSys azazello Thaverkamp larsjuhljensen rvgomes mjetten jlgreen djkt structural_bioinformatics Bioinformatics EBI-regulation Microbial-Ecology microbiology_nijmegen Green Lab iSEEM
	Signature Genes as a Phylogenomic Tool. [My Copy] Molecular biology and evolution (19 May 2008) by Bas E E. Dutilh, Berend Snel, Thijs J G J. Ettema, Martijn A A. Huynen posted to gene microbial phylogenomics by sriesenfeld on 2008-12-02 02:16:16 as along with 2 people and 3 groups skembel mjetten iSEEM anammox microbiology_nijmegen
	Phylogenetic Approaches for Describing and Comparing the Diversity of Microbial Communities [My Copy] Appl. Environ. Microbiol., Vol. 68, No. 8. (1 August 2002), pp. 3673-3682. by Andrew P. Martin posted to communities diversity by sriesenfeld on 2008-11-26 03:36:55 as along with 7 people and 2 groups sharpton skembel jmeppley Thaverkamp mcox Olaf_Ilzins djkt Microbial-Ecology iSEEM
	High-resolution metagenomics targets specific functional types in complex microbial communities [My Copy] Nature Biotechnology, Vol. 26, No. 9. (17 August 2008), pp. 1029-1034. by Marina G. Kalyuzhnaya, Alla Lapidus, Natalia Ivanova, et al.Alex C. Copeland, Alice C. Mchardy, Ernest Szeto, Asaf Salamov, Igor V. Grigoriev, Dominic Suciu, Samuel R. Levine, Victor M. Markowitz, Isidore Rigoutsos, Susannah G. Tringe, David C. Bruce, Paul M. Richardson, Mary E. Lidstrom, Ludmila Chistoserdova posted to communities ecology function metagenomics microbial by sriesenfeld on 2008-11-19 04:06:05 as along with 10 people and 2 groups sameersoi Thaverkamp EKotlarska jbhiatt jmeppley skembel apostola Katje Huub_odc zwang Microbial-Ecology microbiology_nijmegen
	An exact algorithm for the geodesic distance between phylogenetic trees. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 15, No. 6. (g 2008), pp. 577-591. by A. Kupczok, A. V. Haeseler, S. Klaere posted to algorithm metric phylogeny by sriesenfeld on 2008-11-19 03:53:39 as along with 1 person nuin
	Variational Upper and Lower Bounds for Probabilistic Graphical Models [My Copy] Journal of Computational Biology, Vol. 15, No. 7. (2008), pp. 721-735. by Ydo Wexler, Dan Geiger posted to dna evolution phylogeny by sriesenfeld on 2008-11-19 03:45:48 as
	Gene Family Evolution by Duplication, Speciation, and Loss [My Copy] Journal of Computational Biology, Vol. 15, No. 8. (October 2008), pp. 1043-1062. by Cedric Chauve, Jean-Philippe Doyon, Nadia El-Mabrouk posted to duplication evolution family gene phylogeny by sriesenfeld on 2008-11-19 03:42:32 as along with 3 people gdv druvus nuin
	Multiple sequence alignment based on profile alignment of intermediate sequences. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 15, No. 7. (September 2008), pp. 767-777. by Y. Lu, S. H. Sze posted to alignment hmm multiple profile sequence by sriesenfeld on 2008-11-19 03:41:16 as along with 2 people nuin timflutre

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phylogeny	13
evolution	12
metagenomics	12
algorithm	6
microbial	5
phylogenomics	5
software	5
variation	5
alignment	4
communities	4
human	4
taxonomy	4
gene	3
rate	3
statistical	3
association	2
binning	2
family	2
genome	2
hmm	2
method	2
misc	2
noncoding	2
popgen	2
simulations	2
adaptation	1
blast	1
change	1
cluster	1
clustering	1
community	1
conserved	1
data	1
deep	1
divergence	1
diversity	1
dna	1
duplication	1
ecology	1
em	1
environmental	1
est	1
ests	1
eukaryote	1
experimental	1
function	1
genetics	1
genomics	1
genotype	1
guide	1
hgt	1
incomplete	1
likelihood	1
linkage	1
maximum	1
metric	1
multiple	1
nearest	1
neighbor	1
open-source	1
phenotype	1
population	1
prediction	1
profile	1
promoter	1
rates	1
research	1
review	1
rrna	1
search	1
selection	1
selective	1
sequence	1
substitution	1
sweeps	1
tree	1
virus	1
visual	1

sriesenfeld's library 41 articles Export

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