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gjugglers library [280 articles]

Neue Artikel in gjugglers ordered by to_read.
  • Phylogenetic Inference Using Whole Genomes
    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 3 people druvus aprasad zwang
  • Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes
    Nature (20 July 2008)
    by Dacheng Tian, Qiang Wang, Pengfei Zhang, 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 7 people and 1 group 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.
    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 4 people and 2 groups tharris dchughes stajich GustavoLacerda C. elegans / WormBase Berkeley Mycology
  • On the Origin of Species
    (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.
    Genome Res, Vol. 18, No. 1. (January 2008), pp. 77-87.
    by X Roca, AJ Olson, AR Rao, E Enerly, VN Kristensen, Børresen AL Dale, BS Andresen, AR 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.
    Trends Genet, Vol. 24, No. 1. (January 2008), pp. 5-7.
    by BR 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
    Nature, Vol. 450, No. 7167. (2007), pp. 219-232.
    by Alexander Stark, Michael F Lin, Pouya Kheradpour, 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 19 people and 3 groups kieran101 Neeperando pradiptaray rouault druvus operon tmmurali djkt timflutre stajich lp2 cabbagezs nklee hpaces roys caseybrown shuzhens PetrovLab cisevol csb_journal_club_public Berkeley Mycology Drosophila-Genetics-Genomics-2008
  • HyPhy: Estimating selection pressures on alignments of coding sequences
    (2007)
    by Sergei L Pond, Art F Poon, Simon D Frost
    posted to books by gjuggler on 2008-11-16 23:24:21 as **
  • Whole-genome mutational biases in bacteria.
    Proceedings of the National Academy of Sciences of the United States of America (10 November 2008)
    by Peter A A Lind, Dan I I Andersson
    posted to mutation by gjuggler on 2008-11-13 15:41:05 as **
  • Evaluation of Whether Accelerated Protein Evolution in Chordates Has Occurred before, after, or Simultaneously with Gene Duplication
    Molecular Biology and Evolution, Vol. 24, No. 1. (January 2007), pp. 315-323.
    by Johnston, R Catriona, O'Dushlaine, Colm, Fitzpatrick, A David, Edwards, J Richard, Shields, C Denis
    posted to e-slr by gjuggler on 2008-11-12 16:10:25 as **
  • Comparing Patterns of Natural Selection across Species Using Selective Signatures
    PLoS Genetics, Vol. 4, No. 2. (1 February 2008), e23.
    by Jesse B Shapiro, Eric J Alm
    posted to e-slr by gjuggler on 2008-11-12 13:57:25 as ** along with 4 people operon djkt Garamonfok qwermish
  • Evaluation of whether accelerated protein evolution in chordates has occurred before, after, or simultaneously with gene duplication.
    Molecular biology and evolution, Vol. 24, No. 1. (January 2007), pp. 315-323.
    by CR Johnston, C O'Dushlaine, DA Fitzpatrick, RJ Edwards, DC Shields
    posted to e-slr by gjuggler on 2008-11-12 13:28:10 as **
  • Isochore Evolution in Mammals: A Human-Like Ancestral Structure
    Genetics, Vol. 150, No. 4. (1 December 1998), pp. 1577-1584.
    by Nicolas Galtier, Dominique Mouchiroud
    posted to isochores by gjuggler on 2008-11-11 19:21:37 as **
  • Neutralism and selectionism: a network-based reconciliation.
    Nature reviews. Genetics (29 October 2008)
    by Andreas Wagner
    posted to mutsel by gjuggler on 2008-11-04 10:42:11 as ** along with 2 people renewang pkonings
  • Reconstructing large regions of an ancestral mammalian genome in silico
    Genome Res., Vol. 14, No. 12. (1 December 2004), pp. 2412-2423.
    by Mathieu Blanchette, Eric D Green, Webb Miller, David Haussler
    posted to alngen by gjuggler on 2008-11-02 23:51:08 as ** along with 4 people aprasad balajis gisle Neeperando
  • Positive Natural Selection in the Human Lineage
    Science, Vol. 312, No. 5780. (16 June 2006), pp. 1614-1620.
    by PC Sabeti, SF Schaffner, B Fry, J Lohmueller, P Varilly, O Shamovsky, A Palma, TS Mikkelsen, D Altshuler, ES Lander
    posted to e-slr by gjuggler on 2008-11-02 23:46:21 as ** along with 9 people and 4 groups kndiaye dchughes cmm larios hdopazo djkt ramensky iris42 jasonflannick FAB-lab G4ID BioinfoCIPF Genetics-of-Gambling
  • More genes underwent positive selection in chimpanzee evolution than in human evolution.
    Proc Natl Acad Sci U S A, Vol. 104, No. 18. (1 May 2007), pp. 7489-7494.
    by MA Bakewell, P Shi, J Zhang
    posted to e-slr by gjuggler on 2008-11-02 23:42:23 as ** along with 5 people and 1 group bpb usagi-kirin pradiptaray Garamonfok rvosa FAB-lab
  • Using multiple alignment methods to assess the quality of genomic data analysis
    (2001)
    by Cedric Notredame, Chantal Abergel
    posted to no-tag by gjuggler on 2008-10-26 11:05:49 as **
  • Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs.
    Genome research (10 October 2008)
    by Benedict Paten, Javier Herrero, Kathryn Beal, Stephen Fitzgerald, Ewan Birney
    posted to alignment by gjuggler on 2008-10-25 22:49:32 as ** along with 1 person Neeperando
  • On the nature of human housekeeping genes
    Trends in Genetics, Vol. 24, No. 10. (October 2008), pp. 481-484.
    by J Zhu, F He, S Hu, J Yu
    posted to tss-breadth by gjuggler on 2008-10-20 15:27:03 as ** along with 1 person Zephyrus
  • Phylogenomic analysis of natural selection pressure in Streptococcus genomes
    BMC Evolutionary Biology, Vol. 7 (30 August 2007), 154.
    by Maria Anisimova, Joseph Bielawski, Katherine Dunn, Ziheng Yang
    posted to e-slr by gjuggler on 2008-10-20 13:59:50 as ** along with 1 person operon
  • Empirical and structural models for insertions and deletions in the divergent evolution of proteins.
    J Mol Biol, Vol. 229, No. 4. (20 February 1993), pp. 1065-1082.
    by SA Benner, MA Cohen, GH Gonnet
    posted to alngen by gjuggler on 2008-10-16 14:24:51 as ** along with 4 people and 4 groups ana barry mattjb martainn structural_bioinformatics Bioinformatics ComplexAdaptiveSystems DSTO-CAS
  • notes Exploring the Relationship between Sequence Similarity and Accurate Phylogenetic Trees
    Molecular Biology and Evolution, Vol. 23, No. 11. (November 2006), pp. 2090-2100.
    by Cantarel, L Brandi, Morrison, G Hilary, Pearson, William
    posted to alngen by gjuggler on 2008-10-16 14:22:17 as ** along with 2 people mblwhoi ArtemPankin
  • Genome-wide nucleotide-level mammalian ancestor reconstruction.
    Genome research (10 October 2008)
    by Benedict Paten, Javier Herrero, Stephen Fitzgerald, Kathryn Beal, Paul Flicek, Ian Holmes, Ewan Birney
    posted to alngen alignment by gjuggler on 2008-10-16 13:29:18 as ** along with 2 people Neeperando bpcusack
  • The accuracy of several multiple sequence alignment programs for proteins
    BMC Bioinformatics, Vol. 7 (24 October 2006), 471.
    by Paulo AS Nuin, Zhuozhi Wang, Elisabeth RM Tillier
    posted to alngen by gjuggler on 2008-10-16 13:06:42 as ** along with 6 people winterschlaefer viktor21614 carlfulp tny plofje rabio
  • Exact and heuristic algorithms for the Indel Maximum Likelihood Problem.
    J Comput Biol, Vol. 14, No. 4. (May 2007), pp. 446-461.
    by AB Diallo, V Makarenkov, M Blanchette
    posted to alngen by gjuggler on 2008-10-16 11:54:38 as ** along with 2 people timflutre aprasad
  • MCALIGN2: Faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution
    BMC Bioinformatics, Vol. 7 (08 June 2006), 292.
    by Jun Wang, Peter D Keightley, Toby Johnson
    posted to alngen by gjuggler on 2008-10-16 11:26:12 as ** along with 4 people and 1 group Ayest dpollard papamicd bozdagd EisenLab
  • Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment
    Bioinformatics, Vol. 23, No. 3. (1 February 2007), pp. 289-297.
    by Jaebum Kim, Saurabh Sinha
    posted to alngen by gjuggler on 2008-10-16 11:25:53 as ** along with 4 people and 1 group timflutre druvus aprasad indigoviolet EisenLab
  • Noisy: identification of problematic columns in multiple sequence alignments
    Algorithms for Molecular Biology, Vol. 3 (24 June 2008), 7.
    by Andreas WM Dress, Christoph Flamm, Guido Fritzsch, Stefan Grunewald, Matthias Kruspe, Sonja J Prohaska, Peter F Stadler
    posted to phylogenetics by gjuggler on 2008-10-16 11:16:23 as **
  • Statistical methods for detecting molecular adaptation.
    TRENDS IN ECOLOGY AND EVOLUTION, Vol. 15, No. 12. (1 December 2000), pp. 496-503.
    by Z Yang, JP Bielawski
    posted to e-slr by gjuggler on 2008-10-16 10:18:23 as ** along with 3 people and 3 groups stevanspringer hdopazo clearbluespring Bioinformatics FAB-lab BioinfoCIPF
  • PAML FAQs
    (October 2008)
    by Ziheng Yang
    posted to docs by gjuggler on 2008-10-16 10:10:11 as **
  • Accuracy and Power of Bayes Prediction of Amino Acid Sites Under Positive Selection
    Mol Biol Evol, Vol. 19, No. 6. (1 June 2002), pp. 950-958.
    by Maria Anisimova, Joseph P Bielawski, Ziheng Yang
    posted to e-slr by gjuggler on 2008-10-16 10:08:18 as ** along with 2 people rabu CharlesM
  • Malaria research in the post-genomic era
    Nature, Vol. 455, No. 7214., pp. 751-756.
    by Elizabeth A Winzeler
    posted to general by gjuggler on 2008-10-09 15:12:46 as ** along with 3 people zwang shung GeeSharpMinor
  • Synonymous and Nonsynonymous Rate Variation in Nuclear Genes of Mammals
    Journal of Molecular Evolution, Vol. 46, No. 4. (24 April 1998), pp. 409-418.
    by Ziheng Yang, Rasmus Nielsen
    posted to e-slr by gjuggler on 2008-10-05 18:40:07 as **
  • Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution.
    Mol Biol Evol, Vol. 18, No. 8. (August 2001), pp. 1585-1592.
    by M Anisimova, JP Bielawski, Z Yang
    posted to e-slr by gjuggler on 2008-10-05 18:22:01 as ** along with 3 people and 1 group stevanspringer ankur_iitg CharlesM FAB-lab
  • An evolutionary model for maximum likelihood alignment of DNA sequences.
    Journal of molecular evolution, Vol. 33, No. 2. (August 1991), pp. 114-124.
    by JL Thorne, H Kishino, J Felsenstein
    posted to alignment by gjuggler on 2008-10-03 17:06:25 as ** along with 1 person timflutre
  • Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution.
    Mol Biol Evol, Vol. 15, No. 5. (May 1998), pp. 568-573.
    by Z Yang
    posted to tac-1 by gjuggler on 2008-10-03 17:00:48 as ** along with 3 people AaronDarling usagi-kirin Garamonfok
  • Computational Molecular Evolution (Oxford Series in Ecology and Evolution)
    (07 December 2006)
    by Ziheng Yang
    posted to books by gjuggler on 2008-10-03 16:58:04 as ** along with 2 people druvus CharlesM
  • Evolutionary diversification of multigene families: allelic selection of toxins in predatory cone snails.
    Molecular biology and evolution, Vol. 17, No. 9. (September 2000), pp. 1286-1293.
    by TF Duda, SR Palumbi
    posted to tac-1 by gjuggler on 2008-10-03 16:57:11 as **
  • Non-Darwinian evolution.
    Science (New York, N.Y.), Vol. 164, No. 881. (16 May 1969), pp. 788-798.
    by JL King, TH Jukes
    posted to tac-1 by gjuggler on 2008-10-02 23:37:43 as **
  • Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection
    Nature, Vol. 335, No. 6186. (1988), pp. 167-170.
    by Austin L Hughes, Masatoshi Nei
    posted to tac-1 by gjuggler on 2008-10-02 23:03:43 as ** along with 1 person cjeans
  • Evolutionary rate at the molecular level.
    Nature, Vol. 217, No. 5129. (17 February 1968), pp. 624-626.
    by M Kimura
    posted to tac-1 by gjuggler on 2008-10-02 23:00:34 as ** along with 3 people renewang timflutre elfar
  • Mutually exclusive var gene expression in the malaria parasite: multiple layers of regulation.
    Trends in parasitology (2 September 2008)
    by Thanat Chookajorn, Patrath Ponsuwanna, Liwang Cui
    posted to epidemiology by gjuggler on 2008-10-02 11:21:50 as **
  • Inferring Phylogenies
    (04 September 2003)
    by Joseph Felsenstein
    posted to tac-1 phylogenetics by gjuggler on 2008-10-01 10:27:26 as ** along with 6 people and 2 groups rw294 bayesian dpollard cmm farhat dlizcano EisenLab FAB-lab
  • DNA assembly with gaps (Dawg): simulating sequence evolution.
    Bioinformatics, Vol. 21 Suppl 3 (1 November 2005)
    by RA Cartwright
    posted to tac-1 alngen by gjuggler on 2008-09-26 16:34:17 as ** along with 2 people timflutre aprasad
  • Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
    Nature, Vol. 428, No. 6982. (1 April 2004), pp. 493-521.
    by Rat
    posted to general by gjuggler on 2008-09-26 09:54:44 as ** along with 6 people and 4 groups aprasad ccots rvosa dchughes djkt stajich FAB-lab G4ID Genetics-of-Gambling Berkeley Mycology
  • THE LOCUS OF EVOLUTION: EVO DEVO AND THE GENETICS OF ADAPTATION
    Evolution, Vol. 61, No. 5. (2007), pp. 995-1016.
    by Hopi E Hoekstra, Jerry A Coyne
    posted to general by gjuggler on 2008-09-25 14:40:53 as ** along with 12 people and 2 groups stevanspringer mcphee dpollard balicea bpcusack TaqSys epigenetics jayster4 mimulus_99 mjoach kndiaye rvosa EisenLab FAB-lab
  • SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution
    BMC Bioinformatics, Vol. 6, No. 1. (2005)
    by Andy Pang, Andrew Smith, Paulo Nuin, Elisabeth Tillier
    posted to indels alngen by gjuggler on 2008-09-22 14:46:44 as ** along with 2 people pansapiens martainn
  • Probabilistic Phylogenetic Inference with Insertions and Deletions
    PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000172.
    by Elena Rivas, Sean R Eddy
    posted to phylogenetics by gjuggler on 2008-09-22 14:19:40 as ** along with 8 people and 1 group pradiptaray zwang nuin timflutre druvus djkt aprasad emptyhb iSEEM
  • Inference of selection from multiple species alignments.
    Curr Opin Genet Dev, Vol. 12, No. 6. (December 2002), pp. 688-694.
    by Z Yang
    posted to e-slr by gjuggler on 2008-09-19 13:04:30 as ** along with 5 people natstreet druvus operon mingzhi friendpine
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