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gjuggler's library [233 articles]

Recent papers added to gjuggler's library.
  • Selection shapes malaria genomes and drives divergence between pathogens infecting hominids versus rodents
    BMC Evolutionary Biology, Vol. 8 (30 July 2008), 223.
    by Franck Prugnolle, Kate Mcgee, Jon Keebler, Philip Awadalla
    posted to e-slr by gjuggler on 2008-08-28 20:09:12 as ** along with 1 person hdopazo
  • Relatedness of medically important strains of <I>Saccharomyces cerevisiae</I> as revealed by phylogenetics and metabolomics
    Yeast, Vol. 25, No. 7. (2008), pp. 501-512.
    by Donald A Mackenzie, Marianne Defernez, Warwick B Dunn, Marie Brown, Linda J Fuller, Santiago, Andreas Günther, Steve A James, John Eagles, Mark Philo, Royston Goodacre, Ian N Roberts
    posted to phylogenetics by gjuggler on 2008-08-27 12:34:47 as **
  • Searching the genome for our adaptations
    Evolutionary Anthropology: Issues, News, and Reviews, Vol. 17, No. 3. (2008), pp. 146-157.
    by Eugene E Harris
    posted to e-slr by gjuggler on 2008-08-27 12:34:29 as **
  • Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing.
    Proceedings of the National Academy of Sciences of the United States of America (22 August 2008)
    by Peter J J Campbell, Erin D D Pleasance, Philip J J Stephens, Ed Dicks, Richard Rance, Ian Goodhead, George A A Follows, Anthony R R Green, P Andy A Futreal, Michael R R Stratton
    posted to general by gjuggler on 2008-08-27 11:57:32 as **
  • Tree thinkings for all of biology: the problem with reading phylogenies as ladders of progress
    BioEssays, Vol. 30, No. 9. (2008), pp. 854-867.
    by Kevin E Omland, Lyn G Cook, Michael D Crisp
    posted to phylogenetics by gjuggler on 2008-08-13 08:13:52 as ** along with 1 person bpcusack
  • Mango: multiple alignment with N gapped oligos.
    Journal of bioinformatics and computational biology, Vol. 6, No. 3. (June 2008), pp. 521-541.
    by Z Zhang, H Lin, M Li
    posted to alignment by gjuggler on 2008-08-08 11:00:43 as **
  • ProbCons: Probabilistic consistency-based multiple sequence alignment.
    Genome Res, Vol. 15, No. 2. (February 2005), pp. 330-340.
    by CB Do, MS Mahabhashyam, M Brudno, S Batzoglou
    posted to e-slr by gjuggler on 2008-08-06 15:53:33 as ** along with 6 people and 1 group newton1234 bpb radek balajis stajich olympos Berkeley Mycology
  • Multiple Hypothesis Testing to Detect Lineages Under Positive Selection that Affects Only a Few Sites.
    Mol Biol Evol (5 March 2007)
    by Maria Anisimova, Ziheng Yang
    posted to e-slr by gjuggler on 2008-08-05 13:57:27 as ** along with 3 people and 2 groups stevanspringer operon dpollard EisenLab FAB-lab
  • Recent and ongoing selection in the human genome
    Nat Rev Genet, Vol. 8, No. 11. (November 2007), pp. 857-868.
    by Rasmus Nielsen, Ines Hellmann, Melissa Hubisz, Carlos Bustamante, Andrew G Clark
    posted to e-slr by gjuggler on 2008-08-05 13:51:03 as ** along with 7 people and 1 group bpcusack dchughes ramensky Garamonfok candypmcg ryanraaum lh3 Durbin group
  • Patterns of Positive Selection in Six Mammalian Genomes
    PLoS Genet, Vol. 4, No. 8. (2008), e1000144.
    by Carolin Kosiol, Tomáš Vinař, Rute R da Fonseca, Melissa J Hubisz, Carlos D Bustamante, Rasmus Nielsen, Adam Siepel
    posted to e-slr by gjuggler on 2008-08-04 12:39:35 as ** along with 4 people hdopazo bpcusack cabbagesofdoom djkt
  • notes Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes
    Genome Res. (7 November 2007), gr.6249707.
    by Andreas Heger, Chris P Ponting
    posted to e-slr by gjuggler on 2008-08-04 10:46:07 as ** along with 5 people and 1 group hdopazo operon indigoviolet balicea nklee EisenLab
  • Rapid Evolution by Positive Darwinian Selection in T-Cell Antigen CD4 in Primates
    Journal of Molecular Evolution, Vol. 66, No. 5. (May 2008), pp. 446-456.
    by Zhang, Zhengdong, Weinstock, George, Gerstein, Mark
    posted to e-slr by gjuggler on 2008-08-04 10:42:25 as **
  • The quest for natural selection in the age of comparative genomics
    Heredity, Vol. aop, No. current.
    by M Anisimova, DA Liberles
    posted to e-slr by gjuggler on 2008-07-30 14:12:43 as ** along with 1 person operon
  • Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level
    Heredity, Vol. aop, No. current.
    by AL Hughes
    posted to e-slr by gjuggler on 2008-07-30 14:08:02 as ** along with 2 people stevanspringer stajich
  • Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection
    Molecular Biology and Evolution, Vol. 22, No. 5. (15 May 2005), pp. 1208-1222.
    by SL Kosakovsky, Simon D Frost
    posted to e-slr by gjuggler on 2008-07-30 14:04:38 as ** along with 4 people marck operon BioNica Garamonfok
  • Determining the movements of the skeleton using well-configured markers
    Journal of biomechanics, Vol. 26, No. 12. (1993), 1473-7.
    by I Soderkvist, PA Wedin
    posted to test by gjuggler on 2008-07-30 10:20:39 as ** along with 1 person devinberg
  • Minimally cationic cell-permeable miniature proteins via alpha-helical arginine display.
    Journal of the American Chemical Society, Vol. 130, No. 10. (12 March 2008), pp. 2948-2949.
    by BA Smith, DS Daniels, AE Coplin, GE Jordan, LM Mcgregor, A Schepartz
    posted to no-tag by gjuggler on 2008-07-24 00:12:22 as **
  • The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci
    Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 732-745.
    by Joel S Rozowsky, Daniel Newburger, Fred Sayward, Jiaqian Wu, Greg Jordan, Jan O Korbel, Ugrappa Nagalakshmi, Jin Yang, Deyou Zheng, Roderic Guigo, Thomas R Gingeras, Sherman Weissman, Perry Miller, Michael Snyder, Mark B Gerstein
    posted to annotation by gjuggler on 2008-07-24 00:04:00 as ** along with 4 people and 1 group jasonflannick djkt olympos ghattem Bioinformatics
  • 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 mutation indels by gjuggler on 2008-07-23 10:47:15 as ***** along with 1 person bpcusack
  • PhyloWidget: web-based visualizations for the tree of life
    Bioinformatics, Vol. 24, No. 14. (15 July 2008), pp. 1641-1642.
    by Gregory E Jordan, William H Piel
    posted to phylowidget by gjuggler on 2008-07-21 14:59:38 as ** along with 2 people papamicd neils
  • Opinion: Re-evaluating prokaryotic species
    Nature Reviews Microbiology, Vol. 3, No. 9. (01 September 2005), pp. 733-739.
    by Dirk Gevers, Frederick M Cohan, Jeffrey G Lawrence, Brian G Spratt, Tom Coenye, Edward J Feil, Erko Stackebrandt, Yves Van de Peer, Peter Vandamme, Fabiano L Thompson, Jean Swings
    posted to mlst by gjuggler on 2008-07-17 13:08:32 as ** along with 2 people and 1 group wenhan kinestetika microbiology_nijmegen
  • Conversation thumbnails for large-scale discussions
    (2003), pp. 742-743.
    by Martin Wattenberg, David Millen
    posted to visualization by gjuggler on 2008-07-16 11:14:05 as ** along with 2 people dingx koles
  • Dynamic complex formation during the yeast cell cycle.
    Science, Vol. 307, No. 5710. (4 February 2005), pp. 724-727.
    by U de Lichtenberg, LJ Jensen, S Brunak, P Bork
    posted to test by gjuggler on 2008-06-24 10:12:35 as ** along with 11 people and 1 group carlk mdimmic chad_davis balajis wnpx koller massivemayhem cjeans arne phoenixzxl larsjuhljensen dIEMoSIRIS
  • The impact of recombination on nucleotide substitutions in the human genome.
    PLoS genetics, Vol. 4, No. 5. (May 2008)
    by L Duret, PF Arndt
    posted to mutation by gjuggler on 2008-06-23 00:08:09 as ** along with 2 people balicea aprasad
  • Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis
    Science, Vol. 320, No. 5883. (20 June 2008), pp. 1632-1635.
    by Ari Loytynoja, Nick Goldman
    posted to goldmanlab by gjuggler on 2008-06-20 13:17:30 as ** along with 22 people and 3 groups marti nuin emptyhb michaelbarton jlgreen AbnerCYH bpcusack bmaust gulsacan Schmidtc bpb zwang aprasad imtechnology marck ArtemPankin djkt hpaces dinnes chad_davis jago phoenixzxl iSEEM Green Lab Khavkin's lab
  • notes Use and misuse of the gene ontology annotations
    Nature reviews. Genetics (13 May 2008)
    by Seung Y Rhee, Valerie Wood, Kara Dolinski, Sorin Draghici
    posted to annotation by gjuggler on 2008-06-19 20:36:54 as ** along with 20 people and 2 groups rvosa bpcusack marck capitall realzhang A_Olympia fpattyn cmzmasek djkt renatomilani giovenko tmmurali cabbagesofdoom ptrobajo RamuAnandakrishnan roys carlk mariakmejia aheilbut jyuh FAB-lab logics of knowledge
  • Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios.
    Science, Vol. 302, No. 5652. (12 December 2003), pp. 1960-1963.
    by AG Clark, S Glanowski, R Nielsen, PD Thomas, A Kejariwal, MA Todd, DM Tanenbaum, D Civello, F Lu, B Murphy, S Ferriera, G Wang, X Zheng, TJ White, JJ Sninsky, MD Adams, M Cargill
    posted to e-slr by gjuggler on 2008-06-17 16:07:59 as ** along with 4 people and 1 group Ema ejeffery hdopazo djkt BioinfoCIPF
  • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.
    Bioinformatics, Vol. 19, No. 2. (22 January 2003), pp. 185-193.
    by BM Bolstad, RA Irizarry, M Astrand, TP Speed
    posted to tss-breadth by gjuggler on 2008-06-17 15:47:40 as ** along with 12 people GeeSharpMinor vertikalist bertelsen cassj Dax42 pcahan1 chad_davis RMGraze filmsternchen qmwwallace joepickrell ghattem
  • Relating tissue specialisation to the differentiation of expression of singleton and duplicate mouse proteins
    Genome Biology, Vol. 7 (09 October 2006), R89.
    by Shiri Freilich, Tim Massingham, Eric Blanc, Leon Goldovsky, Janet M Thornton
    posted to tss-breadth by gjuggler on 2008-06-17 15:47:21 as **
  • A gene atlas of the mouse and human protein-encoding transcriptomes.
    Proc Natl Acad Sci U S A, Vol. 101, No. 16. (20 April 2004), pp. 6062-6067.
    by AI Su, T Wiltshire, S Batalov, H Lapp, KA Ching, D Block, J Zhang, R Soden, M Hayakawa, G Kreiman, MP Cooke, JR Walker, JB Hogenesch
    posted to tss-breadth by gjuggler on 2008-06-17 14:59:45 as ** along with 11 people and 2 groups dragonrez nickluscombe jeremymiller eukfn usagi-kirin cjeans asu shikin jdiezperezj caseybrown maralena EBI-regulation GeschwindLab
  • Assessing the conservation of mammalian gene expression using high-density exon arrays.
    Mol Biol Evol, Vol. 24, No. 6. (June 2007), pp. 1283-1285.
    by Y Xing, Z Ouyang, K Kapur, MP Scott, WH Wong
    posted to tss-breadth by gjuggler on 2008-06-17 12:56:03 as ** along with 1 person jfr
  • Synonymous Codon Usage in Escherichia coli: Selection for Translational Accuracy
    Molecular Biology and Evolution, Vol. 24, No. 2. (February 2007), pp. 374-381.
    by Stoletzki, Nina, Eyre Walker, Adam
    posted to mutation by gjuggler on 2008-06-16 09:28:48 as ** along with 4 people bpcusack smbe2008 operon michaelbarton
  • Transition-Transversion Bias Is Not Universal: A Counter Example from Grasshopper Pseudogenes
    PLoS Genet, Vol. 3, No. 2. (2 February 2007), e22.
    by Irene Keller, Douda Bensasson, Richard A Nichols
    posted to mutation by gjuggler on 2008-06-15 10:37:53 as **
  • The distribution of fitness effects of new mutations
    Nature Reviews Genetics, Vol. 8, No. 8., pp. 610-618.
    by Adam E Walker, Peter D Keightley
    posted to mutation by gjuggler on 2008-06-14 21:17:37 as ** along with 2 people and 1 group joepickrell massivemayhem Bioinformatics
  • The Global Circulation of Seasonal Influenza A (H3N2) Viruses
    Science, Vol. 320, No. 5874. (18 April 2008), pp. 340-346.
    by Colin A Russell, Terry C Jones, Ian G Barr, Nancy J Cox, Rebecca J Garten, Vicky Gregory, Ian D Gust, Alan W Hampson, Alan J Hay, Aeron C Hurt, Jan C de Jong, Anne Kelso, Alexander I Klimov, Tsutomu Kageyama, Naomi Komadina, Alan S Lapedes, Yi P Lin, Ana Mosterin, Masatsugu Obuchi, Takato Odagiri, Albert D Osterhaus, Guus F Rimmelzwaan, Michael W Shaw, Eugene Skepner, Klaus Stohr, Masato Tashiro, Ron A Fouchier, Derek J Smith
    posted to general by gjuggler on 2008-06-13 13:07:45 as ** along with 4 people and 2 groups reyez lshaw wsjames jago Oxford Virology Global_health_enterprise_architecture
  • Uncertainty in homology inferences: Assessing and improving genomic sequence alignment
    Genome Res., Vol. 18, No. 2. (1 February 2008), pp. 298-309.
    by Gerton Lunter, Andrea Rocco, Naila Mimouni, Andreas Heger, Alexandre Caldeira, Jotun Hein
    posted to alignment by gjuggler on 2008-05-29 11:16:00 as ** along with 8 people AaronDarling aprasad brant treangen djkt grahamc dandaman mailund
  • Detecting amino acid sites under positive selection and purifying selection.
    Genetics (16 January 2005)
    by Tim Massingham, Nick Goldman
    posted to goldmanlab e-slr by gjuggler on 2008-05-23 11:14:29 as ** along with 4 people and 1 group stevanspringer operon BioNica Natasha FAB-lab
  • Contrasting evolution of expression differences in the testis between species and subspecies of the house mouse
    Genome Res., Vol. 17, No. 1. (1 January 2007), pp. 42-49.
    by Christian Voolstra, Diethard Tautz, Patrick Farbrother, Ludwig Eichinger, Bettina Harr
    posted to 08-smbe by gjuggler on 2008-05-22 17:20:54 as **
  • Regulatory changes underlying expression differences within and between Drosophila species.
    Nat Genet (17 February 2008)
    by Patricia JJ Wittkopp, Belinda KK Haerum, Andrew GG Clark
    posted to 08-smbe by gjuggler on 2008-05-22 17:19:55 as ** along with 3 people brant djkt mimulus_99
  • Evaluating the role of natural selection in the evolution of gene regulation
    Heredity, Vol. aop, No. current.
    by JC Fay, PJ Wittkopp
    posted to 08-smbe by gjuggler on 2008-05-22 17:19:37 as ** along with 4 people and 2 groups dpollard djkt cisevol emptyhb EisenLab cis-regulatory-evolution
  • Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.
    Genome Biology, Vol. 8 (22 February 2007), R23.
    by Alan M Moses, Jean K Heriche, Richard Durbin
    posted to 08-smbe by gjuggler on 2008-05-22 17:18:02 as ** along with 1 person and 1 group dpollard EisenLab
  • The McDonald-Kreitman Test and Slightly Deleterious Mutations
    Mol Biol Evol, Vol. 25, No. 6. (1 June 2008), pp. 1007-1015.
    by Jane Charlesworth, Adam E Walker
    posted to mutation by gjuggler on 2008-05-22 17:15:58 as ** along with 5 people and 1 group bpcusack Stew cabbagesofdoom stajich stevanspringer Berkeley Mycology
  • Differentiated evolutionary rates in alternative exons and the implications for splicing regulation
    BMC Evolutionary Biology, Vol. 6 (22 June 2006), 50.
    by Mireya Plass, Eduardo Eyras
    posted to 08-smbe by gjuggler on 2008-05-22 17:13:15 as **
  • Widespread Evolutionary Conservation of Alternatively Spliced Exons in Caenorhabditis
    Mol Biol Evol, Vol. 25, No. 2. (1 February 2008), pp. 375-382.
    by Manuel Irimia, Jakob L Rukov, David Penny, Jordi G Fernandez, Jeppe Vinther, Scott W Roy
    posted to 08-smbe by gjuggler on 2008-05-22 17:12:13 as **
  • Spliceosomal introns as tools for genomic and evolutionary analysis
    Nucl. Acids Res., Vol. 36, No. 5. (1 March 2008), pp. 1703-1712.
    by Manuel Irimia, Scott W Roy
    posted to 08-smbe by gjuggler on 2008-05-22 17:10:14 as **
  • Intron mis-splicing: no alternative?
    Genome Biology, Vol. 9 (19 February 2008), 208.
    by Scott W Roy, Manuel Irimia
    posted to 08-smbe by gjuggler on 2008-05-22 17:09:44 as **
  • Refined analysis of genetic variability parameters in hepatitis C virus and the ability to predict antiviral treatment response
    Journal of Viral Hepatitis, Vol. 0, No. 0. (0), pp. ???-???.
    by JM Cuevas, Torres M Puente, Jimenez N Hernandez, MA Bracho, Garcia I Robles, F Carnicer, JD Olmo, E Ortega, A Moya, Gonzalez F Candelas
    posted to 08-smbe by gjuggler on 2008-05-22 17:07:35 as **
  • Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila
    Nature, Vol. 445, No. 7123. (4 January 2007), pp. 82-85.
    by Cathy H Liautard, Mark Dorris, Xulio Maside, Steven Macaskill, Daniel L Halligan, Brian Charlesworth, Peter D Keightley
    posted to mutation by gjuggler on 2008-05-22 17:06:28 as ** along with 6 people and 1 group operon dpollard jri stajich ramensky lusk EisenLab
  • Mutation Accumulation Studies in Evolutionary Genetics
    Annual Review of Ecology, Evolution, and Systematics, Vol. 39, No. 1. (2008)
    by Peter D Keightley
    posted to 08-smbe by gjuggler on 2008-05-22 17:05:57 as **
  • Evolution of Multicellularity (Choanflagelates)
    Annual Review of Genetics, Vol. 42, No. 1. (2008)
    by Antonis Rokas
    posted to 08-smbe by gjuggler on 2008-05-22 17:04:56 as **
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