gjuggler's e-slr [109 articles] Export

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	Accumulation of slightly deleterious mutations in mitochondrial protein-coding genes of large versus small mammals. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 33. (14 August 2007), pp. 13390-13395. by Konstantin Popadin, Leonard V. Polishchuk, Leila Mamirova, Dmitry Knorre, Konstantin Gunbin posted to e-slr by gjuggler on 2009-11-27 11:48:59 as
	The rates of molecular evolution in rodent and primate mitochondrial DNA. [My Copy] Journal of molecular evolution, Vol. 52, No. 1. (January 2001), pp. 40-50. by D. M. Weinreich posted to e-slr by gjuggler on 2009-11-27 11:47:55 as
	Gene conversion among paralogs results in moderate false detection of positive selection using likelihood methods. [My Copy] Journal of molecular evolution, Vol. 68, No. 6. (June 2009), pp. 679-687. by Claudio Casola, Matthew W. Hahn posted to e-slr by gjuggler on 2009-11-11 21:42:04 as
	The Population Genetics of dN/dS [My Copy] PLoS Genet, Vol. 4, No. 12. (12 December 2008), e1000304. by Sergey Kryazhimskiy, Joshua B. Plotkin posted to e-slr by gjuggler on 2009-11-06 14:13:41 as along with 17 people and 2 groups operon seb1 dposada gwallau ilyashl skembel proulx zwang nuin bpcusack Zephyrus balicea renewang stajich michaelbarton druvus djkt R.E.A.D Mycology
	Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G. [My Copy] PLoS biology, Vol. 2, No. 9. (September 2004) by Sara L. Sawyer, Michael Emerman, Harmit S. Malik posted to e-slr by gjuggler on 2009-10-24 15:04:58 as along with 3 people memerman madhadron kieran101
	Episodic adaptive evolution of primate lysozymes. [My Copy] Nature, Vol. 385, No. 6612. (9 January 1997), pp. 151-154. by W. Messier, C. B. Stewart posted to e-slr by gjuggler on 2009-10-22 22:28:54 as along with 1 person and 1 group stevanspringer FAB-lab
	Comparisons of dN/dS are time dependent for closely related bacterial genomes. [My Copy] Journal of theoretical biology, Vol. 239, No. 2. (21 March 2006), pp. 226-235. by Eduardo P. Rocha, John Maynard M. Smith, Laurence D. Hurst, et al.Matthew T. Holden, Jessica E. Cooper, Noel H. Smith, Edward J. Feil posted to e-slr by gjuggler on 2009-08-18 19:18:17 as along with 4 people GustavoLacerda treangen druvus bjorns
	Nonlinear Dynamics of Nonsynonymous (dN) and Synonymous (dS) Substitution Rates Affects Inference of Selection [My Copy] Genome Biol Evol, Vol. 2009, No. 0. (4 September 2009), pp. 308-319. by Jochen B. W. Wolf, Axel Kunstner, Kiwoong Nam, Mattias Jakobsson, Hans Ellegren posted to e-slr by gjuggler on 2009-08-17 19:44:25 as along with 5 people and 3 groups avilella operon stajich sharpton gwallau Ensembl Compara citations Mycology iSEEM
	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 e-slr by gjuggler on 2009-08-07 11:06:46 as along with 3 people and 1 group aprasad ollieredfernwork nuin Orengo Group Journal Picks
	Ensembl 2007. [My Copy] Nucleic acids research, Vol. 35, No. Database issue. (January 2007) by T. J. Hubbard, B. L. Aken, K. Beal, et al.B. Ballester, M. Caccamo, Y. Chen, L. Clarke, G. Coates, F. Cunningham, T. Cutts, T. Down, S. C. Dyer, S. Fitzgerald, J. Fernandez-Banet, S. Graf, S. Haider, M. Hammond, J. Herrero, R. Holland, K. Howe, K. Howe, N. Johnson, A. Kahari, D. Keefe, F. Kokocinski, E. Kulesha, D. Lawson, I. Longden, C. Melsopp, K. Megy, P. Meidl, B. Ouverdin, A. Parker, A. Prlic, S. Rice, D. Rios, M. Schuster, I. Sealy, J. Severin, G. Slater, D. Smedley, G. Spudich, S. Trevanion, A. Vilella, J. Vogel, S. White, M. Wood, T. Cox, V. Curwen, R. Durbin, X. M. Fernandez-Suarez, P. Flicek, A. Kasprzyk, G. Proctor, S. Searle, J. Smith, A. Ureta-Vidal, E. Birney posted to e-slr by gjuggler on 2009-08-07 11:03:55 as along with 12 people and 2 groups timhubbard ilyashl kuhn dullhunk massivemayhem incovoma Garamonfok asddd loopback007 flexer skumagai kcrawlik References for 3DSim paper Cancer_Stem_Cells
	Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. [My Copy] Bioinformatics (Oxford, England), Vol. 22, No. 13. (1 July 2006), pp. 1600-1607. by Adrian Alexa, Jörg Rahnenführer, Thomas Lengauer posted to e-slr by gjuggler on 2009-08-05 06:46:21 as along with 5 people and 2 groups cmzmasek yas ealloza sgoetz marck T_lab BioinfoCIPF
	Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes [My Copy] Annual Review of Genomics and Human Genetics, Vol. 10, No. 1. (16 July 2009), pp. 285-311. by Laurent Duret, Nicolas Galtier posted to e-slr by gjuggler on 2009-08-02 21:45:12 as along with 3 people lindaodenthalhesse scmelton aprasad
	Identification of deleterious mutations within three human genomes [My Copy] Genome Research, Vol. 19, No. 9. (3 September 2009), pp. 1553-1561. by Sung Chun, Justin C. Fay posted to e-slr by gjuggler on 2009-08-02 20:39:41 as along with 9 people xingxu operon bpcusack djkt aprasad jessopher fenghezi jbhiatt daforerog
	DNA indels in coding regions reveal selective constraints on protein evolution in the human lineage. [My Copy] BMC evolutionary biology, Vol. 7, No. 1. (12 October 2007), 191. by N. de la Chaux, P. W. Messer, P. F. Arndt posted to e-slr by gjuggler on 2009-07-11 00:46:22 as along with 2 people djkt PetrovLab
	Inverse relationship between longevity and evolutionary rate of mitochondrial proteins in mammals and birds [My Copy] Mitochondrion, Vol. 9, No. 1. (February 2009), pp. 51-57. by Nicolas Galtier, Pierre U. Blier, Benoit Nabholz posted to e-slr by gjuggler on 2009-07-06 10:00:56 as along with 1 person aprasad
	Cytochrome b evolution in birds and mammals: an evaluation of the avian constraint hypothesis. [My Copy] Molecular biology and evolution, Vol. 16, No. 11. (November 1999), pp. 1575-1585. by S. E. Stanley, R. G. Harrison posted to e-slr by gjuggler on 2009-07-06 09:56:00 as
	Estimates of Positive Darwinian Selection Are Inflated by Errors in Sequencing, Annotation, and Alignment [My Copy] Genome Biol Evol, Vol. 2009, No. 0. (22 June 2009), pp. 114-118. by Adrian Schneider, Alexander Souvorov, Niv Sabath, Giddy Landan, Gaston H. Gonnet, Dan Graur posted to e-slr by gjuggler on 2009-07-06 05:59:19 as along with 4 people BioNica druvus natstreet aprasad
	Potential impact of recombination on sitewise approaches for detecting positive natural selection. [My Copy] Genet Res, Vol. 81, No. 2. (April 2003), pp. 115-121. by D. Shriner, D. C. Nickle, M. A. Jensen, J. I. Mullins posted to e-slr by gjuggler on 2009-06-18 14:52:34 as along with 1 person Natasha
	Solvent Exposure Imparts Similar Selective Pressures across a Range of Yeast Proteins [My Copy] Molecular Biology and Evolution, Vol. 26, No. 5., pp. 1155-1161. by Gavin C. Conant, Peter F. Stadler posted to e-slr by gjuggler on 2009-06-17 10:50:36 as
	Positive and Negative Selection on the Human Genome [My Copy] Genetics, Vol. 158, No. 3. (1 July 2001), pp. 1227-1234. by Justin C. Fay, Gerald J. Wyckoff, Chung-I Wu posted to e-slr by gjuggler on 2009-06-09 11:40:35 as along with 8 people and 1 group emptyhb provero stevanspringer ramensky ankur_iitg shoshin friendpine skumagai FAB-lab
	Positive Darwinian selection after gene duplication in primate ribonuclease genes [My Copy] Proceedings of the National Academy of Sciences, Vol. 95, No. 7. (31 March 1998), pp. 3708-3713. by Jianzhi Zhang, Helene F. Rosenberg, Masatoshi Nei posted to e-slr by gjuggler on 2009-06-09 11:40:07 as along with 2 people atphan BioNica
	Protein Coding Gene Nucleotide Substitution Pattern in the Apicomplexan Protozoa Cryptosporidium parvum and Cryptosporidium hominis. [My Copy] Comparative and functional genomics (2008) by G. Ge, L. Cowen, X. Feng, G. Widmer posted to e-slr by gjuggler on 2009-06-08 15:09:36 as
	Comparative analysis of protein coding sequences from human, mouse and the domesticated pig. [My Copy] BMC biology, Vol. 3 (2005) by F. G. Jørgensen, A. Hobolth, H. Hornshøj, C. Bendixen, M. Fredholm, M. H. Schierup posted to e-slr by gjuggler on 2009-06-08 15:07:11 as
	Identifying sites under positive selection with uncertain parameter estimates. [My Copy] Genome / National Research Council Canada = Génome / Conseil national de recherches Canada, Vol. 49, No. 7. (July 2006), pp. 767-776. by S. Aris-Brosou posted to e-slr by gjuggler on 2009-06-08 15:00:58 as
	Rapid Detection of Positive Selection in Genes and Genomes Through Variation Clusters [My Copy] Genetics, Vol. 176, No. 4. (1 August 2007), pp. 2451-2463. by Andreas Wagner posted to e-slr by gjuggler on 2009-06-05 11:58:02 as along with 2 people operon bpcusack
	Quantification of Adaptive Evolution of Genes Expressed in Avian Brain and the Population Size Effect on the Efficacy of Selection [My Copy] Mol Biol Evol, Vol. 26, No. 5. (1 May 2009), pp. 1073-1079. by Erik Axelsson, Hans Ellegren posted to e-slr by gjuggler on 2009-06-05 11:46:29 as along with 1 person and 1 group rvosa FAB-lab
	Phylogenetics by likelihood: Evolutionary modeling as a tool for understanding the genome [My Copy] Journal of Biomedical Informatics In Phylogenetic Inferencing: Beyond Biology, Vol. 39, No. 1. (February 2006), pp. 51-61. by C. Kosiol, L. Bofkin, S. Whelan posted to e-slr goldmanlab by gjuggler on 2009-06-05 11:34:43 as along with 4 people katholt aprasad akifumi BioNica
	Selectionism and Neutralism in Molecular Evolution [My Copy] Mol Biol Evol, Vol. 22, No. 12. (1 December 2005), pp. 2318-2342. by Masatoshi Nei posted to e-slr by gjuggler on 2009-06-05 11:26:02 as along with 11 people and 2 groups codonusage aprasad stevanspringer operon akifumi penka BioNica timflutre ankur_iitg ArtemPankin druvus Nie FAB-lab
	The complexity of selection at the major primate beta-defensin locus [My Copy] BMC Evolutionary Biology, Vol. 5, No. 1. (2005), 32. by Colin Semple, Alison Maxwell, Philippe Gautier, et al.Fiona Kilanowski, Hayden Eastwood, Perdita Barran, Julia Dorin posted to e-slr by gjuggler on 2009-06-05 11:02:16 as
	Constructing genomic maps of positive selection in humans: Where do we go from here? [My Copy] Genome Research, Vol. 19, No. 5. (May 2009), pp. 711-722. by Joshua M. Akey posted to e-slr by gjuggler on 2009-05-16 13:51:02 as along with 6 people sharpton aprasad VGreiff Zephyrus djkt ilyashl
	Detecting the presence and location of selection in proteins. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 452 (2008), pp. 311-329. by T. Massingham posted to e-slr by gjuggler on 2009-05-15 14:41:22 as
	How confident can we be that orthologs are similar, but paralogs differ? [My Copy] Trends in Genetics, Vol. 25, No. 5. (13 May 2009), pp. 210-216. by Romain A. Studer, Marc Robinson-Rechavi posted to e-slr by gjuggler on 2009-05-11 10:01:18 as along with 8 people and 1 group idoerg dchughes natstreet druvus kshameer GustavoLacerda kiekyon stajich Mycology
	The role of positive selection in determining the molecular cause of species differences in disease. [My Copy] BMC evolutionary biology, Vol. 8 (06 October 2008), 273. by Jessica J. Vamathevan, Samiul Hasan, Richard D. Emes, et al.Heather Amrine-Madsen, Dilip Rajagopalan, Simon D. Topp, Vinod Kumar, Michael Word, Mark D. Simmons, Steven M. Foord, Philippe Sanseau, Ziheng Yang, Joanna D. Holbrook posted to e-slr by gjuggler on 2009-05-11 09:54:16 as
	Adaptive evolution of young gene duplicates in mammals. [My Copy] Genome research, Vol. 19, No. 5. (May 2009), pp. 859-867. by Mira V. Han, Jeffery P. Demuth, Casey L. McGrath, Claudio Casola, Matthew W. Hahn posted to e-slr by gjuggler on 2009-05-07 05:55:48 as along with 4 people cmzmasek clearbluespring maximilianh djkt
	The difficulty of avoiding false positives in genome scans for natural selection [My Copy] Genome Research, Vol. 19, No. 5. (May 2009), pp. 922-933. by Swapan Mallick, Sante Gnerre, Paul Muller, David Reich posted to e-slr by gjuggler on 2009-05-07 05:54:53 as along with 4 people operon dakelley djkt jbhiatt
	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 e-slr by gjuggler on 2009-04-07 18:02:40 as along with 8 people and 1 group ckenaley sameersoi djkt rvosa ramiro2k bpcusack atphan gulsacan FAB-lab
	Darwinian evolution in the light of genomics [My Copy] Nucl. Acids Res., Vol. 37, No. 4. (1 March 2009), pp. 1011-1034. by Eugene V. Koonin posted to e-slr general by gjuggler on 2009-03-06 10:48:26 as along with 23 people and 2 groups jasontsai vvoorr qayub michaelbarton polivares pawelsobko Zephyrus gwallau dayjm nurban natstreet druvus biomcgary mlog tomhebbron haloin VGreiff lizbiogen inquil lp2 guhjy sebastien_vigneau sjcockell Journal picks LabDros
	Natural selection on protein-coding genes in the human genome [My Copy] Nature, Vol. 437, No. 7062. (20 October 2005), pp. 1153-1157. by Carlos D. Bustamante, Adi Fledel-Alon, Scott Williamson, et al.Rasmus Nielsen, Melissa Todd Hubisz, Stephen Glanowski, David M. Tanenbaum, Thomas J. White, John J. Sninsky, Ryan D. Hernandez, Daniel Civello, Mark D. Adams, Michele Cargill, Andrew G. Clark posted to e-slr by gjuggler on 2009-02-10 09:14:40 as along with 25 people and 5 groups JAShapiro tomhebbron VGreiff ilyashl athma provero jimithystok renewang jo_davies stevanspringer operon jwortman aprasad dayjm balajis marcius dpollard hdopazo djkt JBEgwa01 ramensky Garamonfok iris42 dmc shoshin EisenLab FAB-lab BioinfoCIPF SGU-CIPF Durbin group
	The power of phylogenetic comparison in revealing protein function. [My Copy] Proc Natl Acad Sci U S A (22 February 2005) by Ziheng Yang posted to e-slr by gjuggler on 2009-02-10 09:06:41 as along with 6 people and 1 group mdimmic stevanspringer bpb BioNica tale bpcusack FAB-lab
	Family specific rates of protein evolution [My Copy] Bioinformatics, Vol. 22, No. 10. (15 May 2006), pp. 1166-1171. by Hannes Luz, Martin Vingron posted to e-slr by gjuggler on 2009-02-09 13:31:29 as along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
	Bayesian estimation of positively selected sites. [My Copy] Journal of molecular evolution, Vol. 58, No. 6. (June 2004), pp. 661-672. by J. P. Huelsenbeck, K. A. Dyer posted to e-slr by gjuggler on 2009-02-06 13:00:07 as
	Modeling the site-specific variation of selection patterns along lineages. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 35. (31 August 2004), pp. 12957-12962. by S. Guindon, A. G. Rodrigo, K. A. Dyer, J. P. Huelsenbeck posted to e-slr by gjuggler on 2009-02-06 12:54:40 as
	FUNC: a package for detecting significant associations between gene sets and ontological annotations [My Copy] BMC Bioinformatics, Vol. 8 (06 February 2007), 41. by Kay Prufer, Bjoern Muetzel, Hong-Hai Do, et al.Gunter Weiss, Philipp Khaitovich, Erhard Rahm, Svante Paabo, Michael Lachmann, Wolfgang Enard posted to e-slr by gjuggler on 2009-01-28 21:26:45 as along with 6 people and 1 group renewang leechuck cap1 ealloza heliopais ndiaz BioinfoCIPF
	A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. [My Copy] J Mol Evol, Vol. 59, No. 1. (July 2004), pp. 121-132. by J. P. Bielawski, Z. Yang posted to e-slr by gjuggler on 2009-01-23 10:25:40 as along with 2 people and 1 group stevanspringer skumagai FAB-lab
	The Pfam protein families database. [My Copy] Nucleic acids research, Vol. 36, No. Database issue. (11 January 2008), pp. D281-288. by R. D. Finn, J. Tate, J. Mistry, et al.P. C. Coggill, S. J. Sammut, H. R. Hotz, G. Ceric, K. Forslund, S. R. Eddy, E. L. Sonnhammer, A. Bateman posted to e-slr by gjuggler on 2009-01-23 07:19:05 as along with 13 people sjcockell badi MarcoAlvarez calderonv katholt urgi guhjy idoerg BioNica paszkows bicko niallhaslam coela
	Detecting amino acid sites under positive selection and purifying selection. [My Copy] Genetics, Vol. 169, No. 3. (16 January 2005), pp. 1753-1762. by Tim Massingham, Nick Goldman posted to e-slr by gjuggler on 2009-01-22 17:29:09 as along with 6 people and 1 group MRCBIRD gwallau stevanspringer operon BioNica Natasha FAB-lab
	Announcing the worldwide Protein Data Bank [My Copy] Nat Struct Mol Biol, Vol. 10, No. 12. (December 2003), pp. 980-980. by Helen Berman, Kim Henrick, Haruki Nakamura posted to e-slr by gjuggler on 2009-01-22 13:44:56 as along with 5 people hadesnumb kumar_physics massivemayhem allmensch reyez
	The Universal Protein Resource (UniProt) 2009. [My Copy] Nucleic acids research, Vol. 37, No. Database issue. (1 January 2009), pp. D169-174. by UniProt Consortium posted to e-slr by gjuggler on 2009-01-22 13:42:37 as along with 12 people saunders barmak7282 azazello badi MarcoAlvarez tfuji nedwards niallhaslam bicko lptolik coela sjcockell
	M-Coffee: combining multiple sequence alignment methods with T-Coffee [My Copy] Nucleic Acids Research, Vol. 34, No. 6. (2006), pp. 1692-1699. by Iain M. Wallace, Orla O'Sullivan, Desmond G. Higgins, Cedric Notredame posted to e-slr by gjuggler on 2009-01-22 13:40:40 as along with 2 people and 2 groups BioNica marcius BioinfoCIPF SGU-CIPF
	MUSCLE: multiple sequence alignment with high accuracy and high throughput [My Copy] Nucl. Acids Res., Vol. 32, No. 5. (19 March 2004), pp. 1792-1797. by Robert C. Edgar posted to e-slr by gjuggler on 2009-01-22 13:35:49 as along with 29 people and 2 groups mgomes jeargle tomjad foxpowa esyoun natstreet dquest BioNica edvin yylin treangen sebk agustinarce fhsantanna nachtalp bpb chrn jwm Haggan sanchezbuelna timflutre olympos martainn newton1234 skumagai bmaust sconlan dmp kcrawlik Radiation_Damage Stressosome

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e-slr	109
general	44
phylogenetics	29
goldmanlab	23
phylowidget	23
palindromes	22
isochores	21
nopdf	21
08-smbe	19
test	19
tss-breadth	19
tss	18
alignment	17
alngen	15
dupldiv	15
mutation	14
splicing	12
ultraconserved	11
indels	10
annotation	9
mutsel	9
tac-1	8
proteins	7
evo-rate	6
pseudogenes	5
books	4
bp2009	4
visualization	4
cyt-b	3
edu	3
mol-clocks	3
sync-test	3
docs	2
epidemiology	2
gersteinlab	2
hzygo	2
tss-gauss	2
go	1
language	1
mlst	1
open-access	1

gjuggler's e-slr [109 articles] Export

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