gjuggler's library 483 articles Export

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	Phylogenetic inference using whole genomes. [My Copy] Annual review of genomics and human genetics, Vol. 9, No. 1. (2008), pp. 217-231. by Bruce Rannala, Ziheng Yang posted to phylogenetics by gjuggler on 2008-09-04 11:51:46 as along with 9 people and 1 group katholt friendpine inquil gwallau operon treangen druvus aprasad zwang LabDros
	Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes. [My Copy] Nature, Vol. 455, No. 7209. (4 July 2008), pp. 105-108. by Dacheng Tian, Qiang Wang, Pengfei Zhang, et al.Hitoshi Araki, Sihai Yang, Martin Kreitman, Thomas Nagylaki, Richard Hudson, Joy Bergelson, Jian Q. Chen posted to indels mutation by gjuggler on 2008-07-23 10:47:15 as along with 9 people and 1 group biomcgary Annab aprasad dakelley zwang psique djkt caseybrown bpcusack parkinson's disease references
	Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes. [My Copy] Genome Res, Vol. 18, No. 1. (January 2008), pp. 88-103. by S. Schwartz, J. Silva, D. Burstein, T. Pupko, E. Eyras, G. Ast posted to splicing by gjuggler on 2008-01-04 13:15:53 as along with 5 people and 2 groups thegoose2 tharris dchughes stajich GustavoLacerda C. elegans / WormBase Mycology
	On the Origin of Species [My Copy] (1859) by Charles Darwin posted to nopdf phylowidget by gjuggler on 2007-12-21 03:35:35 as
	Features of 5'-splice-site efficiency derived from disease-causing mutations and comparative genomics. [My Copy] Genome Res, Vol. 18, No. 1. (January 2008), pp. 77-87. by X. Roca, A. J. Olson, A. R. Rao, et al.E. Enerly, V. N. Kristensen, Borresen A. L. Dale, B. S. Andresen, A. R. Krainer, R. Sachidanandam posted to splicing by gjuggler on 2008-01-04 12:27:18 as along with 2 people dchughes ohara
	The haplo-spliceo-transcriptome: common variations in alternative splicing in the human population. [My Copy] Trends Genet, Vol. 24, No. 1. (January 2008), pp. 5-7. by B. R. Graveley posted to splicing by gjuggler on 2008-01-04 11:39:40 as
	Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. [My Copy] Nature, Vol. 450, No. 7167. (8 November 2007), pp. 219-232. by Alexander Stark, Michael F. Lin, Pouya Kheradpour, et al.Jakob S. Pedersen, Leopold Parts, Joseph W. Carlson, Madeline A. Crosby, Matthew D. Rasmussen, Sushmita Roy, Ameya N. Deoras, Graham J. Ruby, Julius Brennecke, Harvard F. Curators, Berkeley, Emily Hodges, Angie S. Hinrichs, Anat Caspi, Benedict Paten, Seung W. Park, Mira V. Han, Morgan L. Maeder, Benjamin J. Polansky, Bryanne E. Robson, Stein Aerts, Jacques van Helden, Bassem Hassan, Donald G. Gilbert, Deborah A. Eastman, Michael Rice, Michael Weir, Matthew W. Hahn, Yongkyu Park, Colin N. Dewey, Lior Pachter, James W. Kent, David Haussler, Eric C. Lai, David P. Bartel, Gregory J. Hannon, Thomas C. Kaufman, Michael B. Eisen, Andrew G. Clark, Douglas Smith, Susan E. Celniker, William M. Gelbart, Manolis Kellis posted to annotation by gjuggler on 2007-11-21 12:40:27 as along with 21 people and 3 groups heliopais anphony kieran101 Neeperando pradiptaray rouault druvus operon tmmurali djkt timflutre stajich lp2 cabbagezs nklee hpaces roys caseybrown shuzhens PetrovLab cisevol microRNA Mycology Drosophila-Genetics-Genomics-2008
	Seasonal variation in satellite-derived effects of aerosols on clouds in the Arabian Sea [My Copy] Journal of Geophysical Research - Atmospheres, Vol. 113, No. D9. (15 May 2008), D09207. by Thomas A. Jones, Sundar A. Christopher posted to sync-test by gjuggler on 2009-11-13 13:31:10 as along with 4 people ravikiranv arragi harish cermak
	Top-Down Identification of Protein Biomarkers in Bacteria with Unsequenced Genomes [My Copy] Analytical Chemistry, Vol. 0, No. 0. (0000) by Colin Wynne, Catherine Fenselau, Plamen A. Demirev, Nathan Edwards posted to sync-test by gjuggler on 2009-11-13 13:29:29 as along with 2 people brianb nedwards
	Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes. [My Copy] Nature reviews. Genetics, Vol. 9, No. 4. (April 2008), pp. 303-313. by Elliott H. Margulies, Ewan Birney posted to general by gjuggler on 2009-11-13 12:54:15 as along with 8 people akundaje timflutre guhjy zwang mingzhi phoenixzxl ptrobajo natstreet
	False Discovery Rates of Protein Identifications: A Strike against the Two-Peptide Rule [My Copy] Journal of Proteome Research, Vol. 8, No. 9. (4 September 2009), pp. 4173-4181. by Nitin Gupta, Pavel A. Pevzner posted to sync-test by gjuggler on 2009-11-13 11:05:54 as along with 3 people nedwards carlosjavierna brianb
	High mitogenomic evolutionary rates and time dependency. [My Copy] Trends in genetics : TIG, Vol. 25, No. 11. (14 November 2009), pp. 482-486. by Sankar Subramanian, Dee R. Denver, Craig D. Millar, et al.Tim Heupink, Angelique Aschrafi, Steven D. Emslie, Carlo Baroni, David M. Lambert posted to evo-rate by gjuggler on 2009-11-13 10:43:59 as along with 1 person and 1 group ppgardne Journal picks
	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
	TOPD/FMTS: a new software to compare phylogenetic trees [My Copy] Bioinformatics, Vol. 23, No. 12. (25 April 2007), pp. btm135-1558. by Pere Puigbo, Santiago Garcia-Vallve, James O. McInerney posted to phylogenetics by gjuggler on 2009-11-09 10:02:54 as along with 6 people vallve sharpton BioNica druvus dparks tny
	Gene regulation in primates evolves under tissue-specific selection pressures. [My Copy] PLoS genetics, Vol. 4, No. 11. (21 November 2008), e1000271. by Ran Blekhman, Alicia Oshlack, Adrien E. Chabot, Gordon K. Smyth, Yoav Gilad posted to tss-breadth by gjuggler on 2009-11-06 14:21:28 as along with 12 people and 2 groups gderwin JustinCrocker Zephyrus bpcusack bertrandservin cisevol operon emptyhb shoshin djkt gdb caseybrown R.E.A.D cis-regulatory-evolution
	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
	Gene duplication and the adaptive evolution of a classic genetic switch [My Copy] Nature, Vol. 449, No. 7163. (11 October 2007), pp. 677-681. by Chris T. Hittinger, Sean B. Carroll posted to dupldiv by gjuggler on 2009-11-06 14:13:10 as along with 16 people and 2 groups sameersoi gipsoma wangbo dakelley druvus treangen mcphee dpollard dchughes djkt biomcgary blobbybirdman kjlipin skumagai clearbluespring bpcusack EisenLab cis-regulatory-evolution
	Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees [My Copy] Science, Vol. 324, No. 5934. (19 June 2009), pp. 1561-1564. by Kevin Liu, Sindhu Raghavan, Serita Nelesen, C. Randal Linder, Tandy Warnow posted to general by gjuggler on 2009-11-06 14:12:57 as along with 26 people and 4 groups parnell kinestetika robertrentzsch xianjun gdb jbhiatt stajich operon biomcgary kieran101 zwang michaelbarton vingron tatman303 hryk lizbiogen pkonings ppgardne dokky aprasad timflutre inquil TRHvidsten djkt fenghezi phoenixzxl Orengo Group Journal Picks Mycology Journal picks iSEEM
	Genetic and molecular insights into the development and evolution of sexual dimorphism [My Copy] Nature Reviews Genetics, Vol. 10, No. 11. (01 November 2009), pp. 797-804. by Thomas M. Williams, Sean B. Carroll posted to general by gjuggler on 2009-10-31 00:23:21 as along with 4 people and 1 group psique qayub reyez bpcusack Journal picks
	Spatial patterns of variation due to natural selection in humans [My Copy] Nat Rev Genet, Vol. 10, No. 11. (13 October 2009), pp. 745-755. by John Novembre, Anna Di Rienzo posted to general by gjuggler on 2009-10-31 00:20:33 as along with 5 people and 1 group psique emptyhb qayub merpublic daforerog Journal picks
	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
	Functional Enhancers at the Gene-Poor 8q24 Cancer-Linked Locus [My Copy] PLoS Genet, Vol. 5, No. 8. (14 August 2009), e1000597. by Li Jia, Gilad Landan, Mark Pomerantz, et al.Rami Jaschek, Paula Herman, David Reich, Chunli Yan, Omar Khalid, Phil Kantoff, William Oh, J. Robert Manak, Benjamin P. Berman, Brian E. Henderson, Baruch Frenkel, Christopher A. Haiman, Matthew Freedman, Amos Tanay, Gerhard A. Coetzee posted to general by gjuggler on 2009-10-20 20:07:24 as along with 2 people djkt xingxu
	Macroevolution of Complex Retroviruses [My Copy] Science, Vol. 325, No. 5947. (18 September 2009), 1512. by Aris Katzourakis, Robert J. Gifford, Michael Tristem, Gilbert, Oliver G. Pybus posted to general by gjuggler on 2009-10-13 21:55:14 as along with 1 person maren
	Evolution of genome architecture. [My Copy] The international journal of biochemistry & cell biology, Vol. 41, No. 2. (February 2009), pp. 298-306. by Eugene V. Koonin posted to general by gjuggler on 2009-10-12 03:19:22 as along with 7 people and 2 groups daveGerrard natstreet Zephyrus polivares druvus gwallau operon R.E.A.D BergmanLab
	Recent de novo origin of human protein-coding genes. [My Copy] Genome research, Vol. 19, No. 10. (2 October 2009), pp. 1752-1759. by David G. Knowles, Aoife McLysaght posted to general by gjuggler on 2009-10-09 16:03:04 as along with 8 people and 2 groups psique xianjun biomcgary megraw fenghezi avilella bpcusack djkt Journal picks Ensembl Compara citations
	Darwinian alchemy: Human genes from noncoding DNA [My Copy] Genome Research, Vol. 19, No. 10. (October 2009), pp. 1693-1695. by Adam Siepel posted to general by gjuggler on 2009-10-09 16:02:54 as along with 4 people and 1 group xianjun owhitney ppgardne inesdesantiago Journal picks
	Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome [My Copy] Science, Vol. 326, No. 5950. (9 October 2009), pp. 289-293. by Erez Lieberman-Aiden, Nynke L. van Berkum, Louise Williams, et al.Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, Bryan R. Lajoie, Peter J. Sabo, Michael O. Dorschner, Richard Sandstrom, Bradley Bernstein, M. A. Bender, Mark Groudine, Andreas Gnirke, John Stamatoyannopoulos, Leonid A. Mirny, Eric S. Lander, Job Dekker posted to general by gjuggler on 2009-10-09 16:02:12 as along with 31 people and 3 groups pmcarlton alhufton psique qayub chvlyl TorstenWaldminghaus kintoki Garamonfok inesdesantiago NickFurnham DrRichardBadge roys rdiaz daveGerrard colinveal frohike nrk891 zwang timflutre afenley kshameer polivares mgatmedsci diamantis flbarroso jdoconnell fenghezi daforerog bpcusack gdb gbloeb JLab BergmanLab Journal picks
	A General Tendency for Conservation of Protein Length Across Eukaryotic Kingdoms [My Copy] Mol Biol Evol, Vol. 22, No. 1. (1 January 2005), pp. 142-147. by Daryi Wang, Mufen Hsieh, Wen-Hsiung Li posted to indels by gjuggler on 2009-10-08 16:27:38 as
	Variation in the Ratio of Nucleotide Substitution and Indel Rates across Genomes in Mammals and Bacteria [My Copy] Mol Biol Evol, Vol. 26, No. 7. (1 July 2009), pp. 1523-1531. by Jian-Qun Chen, Ying Wu, Haiwang Yang, Joy Bergelson, Martin Kreitman, Dacheng Tian posted to indels by gjuggler on 2009-10-08 16:26:34 as along with 3 people djkt bmajoros nuin
	Insertion–deletion biases and the evolution of genome size [My Copy] Gene, Vol. 324 (07 January 2004), pp. 15-34. by Gregory posted to indels by gjuggler on 2009-10-08 16:20:15 as
	Genomic DNA k-mer spectra: models and modalities [My Copy] Genome Biology, Vol. 10, No. 10. (2009), R108. by Benny Chor, David Horn, Yaron Levy, Nick Goldman, Tim Massingham posted to goldmanlab by gjuggler on 2009-10-08 11:05:49 as along with 3 people and 1 group djkt TRHvidsten medic0747 iSEEM
	Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes. [My Copy] Philosophical transactions of the Royal Society of London. Series B, Biological sciences, Vol. 363, No. 1512. (27 December 2008), pp. 4013-4021. by Mark T. Holder, Derrick J. Zwickl, Christophe Dessimoz posted to phylogenetics by gjuggler on 2009-10-02 10:30:19 as along with 1 person operon
	The Microbe browser for comparative genomics. [My Copy] Nucleic acids research, Vol. 37, No. Web Server issue. (1 July 2009), gkp268. by Alexandre Gattiker, Christophe Dessimoz, Adrian Schneider, Ioannis Xenarios, Marco Pagni, Jacques Rougemont posted to visualization by gjuggler on 2009-10-02 10:29:24 as along with 1 person neils
	Structural and functional constraints in the evolution of protein families [My Copy] Nature Reviews Molecular Cell Biology, Vol. 10, No. 10. (16 September 2009), pp. 709-720. by Catherine L. Worth, Sungsam Gong, Tom L. Blundell posted to proteins by gjuggler on 2009-09-23 23:13:23 as along with 6 people and 1 group aaltenburger kshameer dchughes reyez leliavski ppgardne Journal picks
	Local DNA topography correlates with functional noncoding regions of the human genome. [My Copy] Science (New York, N.Y.), Vol. 324, No. 5925. (17 April 2009), pp. 389-392. by Stephen C. Parker, Loren Hansen, Hatice Ozel O. Abaan, Thomas D. Tullius, Elliott H. Margulies posted to general by gjuggler on 2009-09-23 15:10:14 as along with 38 people and 6 groups daveGerrard operon sujaikumar antonkratz pradiptaray roys benjaminsb gdb hagechouchin443 tomtullius scjparker psique orzenil emptyhb ilyashl coela VGreiff APRegier myzhang pkonings akundaje athma absterga rpatward timflutre stajich bpcusack jbhiatt djkt dhlbh friendpine dpollard inesdesantiago JustinCrocker aprasad maximilianh idonaldson kshundyak BergmanLab Mycology structural_bioinformatics RockmanLab EisenLab cis-regulatory-evolution
	Evolutionary trees from DNA sequences: a maximum likelihood approach. [My Copy] Journal of molecular evolution, Vol. 17, No. 6. (1981), pp. 368-376. by J. Felsenstein posted to phylogenetics by gjuggler on 2009-09-21 20:07:04 as along with 10 people and 1 group BioNica alexeid bpb chrn kaspermunch dquest djkt timflutre dmc elfar Bioinformatics
	Structural biology and phylogenetic estimation [My Copy] Nature, Vol. 388, No. 6642. (07 August 1997), pp. 527-528. by Gavin J. P. Naylor, Wesley M. Brown posted to proteins phylogenetics by gjuggler on 2009-09-21 19:40:31 as
	Coevolving protein residues: maximum likelihood identification and relationship to structure. [My Copy] Journal of molecular biology, Vol. 287, No. 1. (19 March 1999), pp. 187-198. by D. D. Pollock, W. R. Taylor, N. Goldman posted to proteins by gjuggler on 2009-09-21 19:31:12 as along with 3 people mgomes nirfriedman pradiptaray
	Structural Constraints and Emergence of Sequence Patterns in Protein Evolution [My Copy] Mol Biol Evol, Vol. 18, No. 5. (1 May 2001), pp. 750-756. by Gustavo Parisi, Julian Echave posted to proteins by gjuggler on 2009-09-21 19:30:09 as
	Protein Evolution with Dependence Among Codons Due to Tertiary Structure [My Copy] Mol Biol Evol, Vol. 20, No. 10. (1 October 2003), pp. 1692-1704. by Douglas M. Robinson, David T. Jones, Hirohisa Kishino, Nick Goldman, Jeffrey L. Thorne posted to phylogenetics by gjuggler on 2009-09-21 19:24:48 as along with 3 people penka redelings tale
	A stochastic model for the evolution of autocorrelated DNA sequences. [My Copy] Molecular phylogenetics and evolution, Vol. 3, No. 3. (September 1994), pp. 240-247. by M. Schöniger, A. von Haeseler posted to phylogenetics by gjuggler on 2009-09-21 19:02:28 as
	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 by gjuggler on 2009-09-16 15:34:32 as along with 2 people skembel ematsen
	Effect of nonindependent substitution on phylogenetic accuracy. [My Copy] Systematic biology, Vol. 48, No. 2. (June 1999), pp. 317-328. by J. P. Huelsenbeck, R. Nielsen posted to phylogenetics by gjuggler on 2009-09-16 12:10:54 as
	Species Tree Inference by Minimizing Deep Coalescences [My Copy] PLoS Comput Biol, Vol. 5, No. 9. (11 September 2009), e1000501. by Cuong Than, Luay Nakhleh posted to phylogenetics by gjuggler on 2009-09-11 15:59:17 as along with 6 people and 2 groups parnell qcjones gdb djkt ppgardne druvus iSEEM Journal picks
	Interrogating 11 Fast-Evolving Genes for Signatures of Recent Positive Selection in Worldwide Human Populations [My Copy] Mol Biol Evol, Vol. 26, No. 10. (1 October 2009), pp. 2285-2297. by Andres Moreno-Estrada, Kun Tang, Martin Sikora, et al.Tomas Marques-Bonet, Ferran Casals, Arcadi Navarro, Francesc Calafell, Jaume Bertranpetit, Mark Stoneking, Elena Bosch posted to general by gjuggler on 2009-09-11 15:59:01 as along with 3 people and 1 group operon djkt ppgardne Journal picks
	Genomic views of distant-acting enhancers [My Copy] Nature, Vol. 461, No. 7261. (09 September 2009), pp. 199-205. by Axel Visel, Edward M. Rubin, Len A. Pennacchio posted to general by gjuggler on 2009-09-11 15:58:27 as along with 7 people and 1 group cmzmasek bpcusack inesdesantiago greg polivares daforerog djkt Journal picks
	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
	A Simple Statistical Method for Estimating Type-II (Cluster-Specific) Functional Divergence of Protein Sequences [My Copy] Mol Biol Evol, Vol. 23, No. 10. (1 October 2006), pp. 1937-1945. by Xun Gu posted to dupldiv by gjuggler on 2009-08-12 15:02:41 as along with 2 people ramiro2k barry

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