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Tag 08-smbe [57 articles]

Recent papers classified by the tag 08-smbe.
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  • 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 08-smbe by smbe2008 on 2008-06-02 16:47:22 as ** along with 4 people operon michaelbarton gjuggler bpcusack
  • Whole mtDNA Genome Sequence Analysis of Ancient African Lineages.
    Mol Biol Evol (28 December 2006)
    by Mary Katherine K Gonder, Holly M M Mortensen, Floyd A A Reed, Alexandra de Sousa, Sarah A A Tishkoff
    posted to 08-smbe by smbe2008 on 2008-06-02 16:52:02 as ** along with 2 people and 2 groups Archaeogenetics dchughes G4ID Genetics-of-Gambling
  • Large scale genotype-phenotype correlation analysis based on phylogenetic trees.
    Bioinformatics (31 January 2007)
    by Farhat Habib, Andrew D D Johnson, Ralf Bundschuh, Daniel Janies
    posted to 08-smbe by smbe2008 on 2008-06-02 17:31:41 as ** along with 4 people djkt shigepong balicea farhat
  • Genetics of gene expression and its effect on disease
    Nature (16 March 2008)
    by Valur Emilsson, Gudmar Thorleifsson, Bin Zhang, Amy S Leonardson, Florian Zink, Jun Zhu, Sonia Carlson, Agnar Helgason, Bragi G Walters, Steinunn Gunnarsdottir, Magali Mouy, Valgerdur Steinthorsdottir, Gudrun H Eiriksdottir, Gyda Bjornsdottir, Inga Reynisdottir, Daniel Gudbjartsson, Anna Helgadottir, Aslaug Jonasdottir, Adalbjorg Jonasdottir, Unnur Styrkarsdottir, Solveig Gretarsdottir, Kristinn P Magnusson, Hreinn Stefansson, Ragnheidur Fossdal, Kristleifur Kristjansson, Hjortur G Gislason, Tryggvi Stefansson, Bjorn G Leifsson, Unnur Thorsteinsdottir, John R Lamb, Jeffrey R Gulcher, Marc L Reitman, Augustine Kong, Eric E Schadt, Kari Stefansson
    posted to 08-smbe by smbe2008 on 2008-06-02 17:48:37 as ** along with 14 people and 2 groups druvus brianb djkt lp2 jo_davies shikin caseybrown ptrobajo vplagnol echinotrix natstreet sanchezbuelna guhjy Borelli 4th_floor_JC GeneGo
  • Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization
    BMC Evolutionary Biology, Vol. 8 (08 February 2008), 43.
    by Frederic JJ Chain, Dora Ilieva, Ben J Evans
    posted to 08-smbe by smbe2008 on 2008-06-02 16:43:36 as **
  • Predicting evolutionary patterns of mammalian teeth from development.
    Nature, Vol. 449, No. 7161. (27 September 2007), pp. 427-432.
    by KD Kavanagh, AR Evans, J Jernvall
    posted to 08-smbe by smbe2008 on 2008-06-02 18:08:15 as ** along with 1 person and 1 group dpollard EisenLab
  • Discrimination and scoring using small sets of genes for two-sample microarray data
    Mathematical Biosciences, Vol. 205, No. 2. (February 2007), pp. 195-203.
    by Gilles Guillot, Maja Olsson, Mikael Benson, Mats Rudemo
    posted to 08-smbe by smbe2008 on 2008-06-02 16:22:00 as ** along with 2 people ptrobajo karfunkel
  • Five Drosophila Genomes Reveal Nonneutral Evolution and the Signature of Host Specialization in the Chemoreceptor Superfamily
    Genetics, Vol. 177, No. 3. (1 November 2007), pp. 1395-1416.
    by Carolyn S Mcbride, Roman J Arguello, Brian C O'Meara
    posted to 08-smbe by smbe2008 on 2008-06-02 16:42:51 as ** along with 1 person operon
  • Genomewide Spatial Correspondence Between Nonsynonymous Divergence and Neutral Polymorphism Reveals Extensive Adaptation in Drosophila
    Genetics, Vol. 177, No. 4. (1 December 2007), pp. 2083-2099.
    by Michael J Macpherson, Guy Sella, Jerel C Davis, Dmitri A Petrov
    posted to 08-smbe by smbe2008 on 2008-06-02 17:22:48 as ** along with 3 people brant caseybrown PetrovLab
  • Phylocomposer and phylodirector: analysis and visualization of transducer indel models
    Bioinformatics, Vol. 23, No. 23. (1 December 2007), pp. 3263-3264.
    by Ian Holmes
    posted to 08-smbe by smbe2008 on 2008-06-02 18:00:28 as ** along with 4 people druvus balicea djkt ryanraaum
  • A novel method distinguishes between mutation rates and fixation biases in patterns of single-nucleotide substitution.
    Journal of molecular evolution, Vol. 62, No. 2. (February 2006), pp. 168-175.
    by M Lipatov, PF Arndt, T Hwa, DA Petrov
    posted to 08-smbe by smbe2008 on 2008-06-02 17:22:02 as ** along with 1 person PetrovLab
  • Evidence that strong positive selection drives neofunctionalization in the tandemly duplicated polyhomeotic genes in Drosophila
    Proceedings of the National Academy of Sciences (1 April 2008), 0710892105.
    by Steffen Beisswanger, Wolfgang Stephan
    posted to 08-smbe by smbe2008 on 2008-06-02 17:52:13 as ** along with 3 people maximilianh oelemento gjuggler
  • Genome-wide variation and identification of vaccine targets in the Plasmodium falciparum genome
    Nature Genetics, Vol. 39, No. 1. (10 December 2006), pp. 126-130.
    by Jianbing Mu, Philip Awadalla, Junhui Duan, Kate M Mcgee, Jon Keebler, Karl Seydel, Gilean AT Mcvean, Xin-Zhuan Su
    posted to 08-smbe by smbe2008 on 2008-06-02 16:53:30 as ** along with 5 people fernan becarmson shigepong GeeSharpMinor xingxu
  • Live Hot, Die Young: Transmission Distortion in Recombination Hotspots
    PLoS Genetics, Vol. 3, No. 3. (1 March 2007), e35.
    by Graham Coop, Simon R Myers
    posted to 08-smbe by smbe2008 on 2008-06-02 17:51:31 as ** along with 1 person and 1 group dpollard EisenLab
  • GENETICS: Why Genomes in Pieces?
    Science, Vol. 318, No. 5849. (19 October 2007), pp. 405-407.
    by Laura F Landweber
    posted to 08-smbe by smbe2008 on 2008-06-02 17:24:22 as ** along with 3 people operon gulsacan sharpton
  • Sequence Variants in the RNF212 Gene Associate with Genome-Wide Recombination Rate
    Science, Vol. 319, No. 5868. (7 March 2008), pp. 1398-1401.
    by Augustine Kong, Gudmar Thorleifsson, Hreinn Stefansson, Gisli Masson, Agnar Helgason, Daniel F Gudbjartsson, Gudrun M Jonsdottir, Sigurjon A Gudjonsson, Sverrir Sverrisson, Theodora Thorlacius, Aslaug Jonasdottir, Gudmundur A Hardarson, Stefan T Palsson, Michael L Frigge, Jeffrey R Gulcher, Unnur Thorsteinsdottir, Kari Stefansson
    posted to 08-smbe by smbe2008 on 2008-06-02 17:48:17 as ** along with 2 people and 1 group tharris djkt C. elegans / WormBase
  • Recent Evolutions of Multiple Sequence Alignment Algorithms
    PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e123.
    by Cédric Notredame
    posted to 08-smbe by smbe2008 on 2008-06-02 17:54:16 as read along with 11 people and 2 groups druvus treangen mdimmic rvosa timflutre stajich zwang cabbagezs groepl yoanjacquemin marti Bioinformatics FAB-lab
  • Positional Conservation of Clusters of Overlapping Promoter-Like Sequences in Enterobacterial Genomes
    Molecular Biology and Evolution, Vol. 23, No. 5. (15 May 2006), pp. 997-1010.
    by Araceli M Huerta, Julio Collado-Vides, Pilar M Francino
    posted to 08-smbe by smbe2008 on 2008-06-02 16:40:44 as ** along with 1 person discreteonyxorb
  • Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms.
    J Exp Zoolog B Mol Dev Evol (12 July 2006)
    by Christian Roth, Shruti Rastogi, Lars Arvestad, Katharina Dittmar, Sara Light, Diana Ekman, David A A Liberles
    posted to 08-smbe by smbe2008 on 2008-06-02 16:55:20 as ** along with 6 people zhlei operon bjorns treangen signalduplication LouisKa
  • Parallel evolution of conserved noncoding elements that target a common set of developmental regulatory genes from worms to humans.
    Genome Biology, Vol. 8 (02 February 2007), R15.
    by Tanya Vavouri, Klaudia Walter, Walter R Gilks, Ben Lehner, Greg Elgar
    posted to 08-smbe by smbe2008 on 2008-06-02 18:04:20 as ** along with 7 people and 2 groups indigoviolet dpollard adepace djkt sujaikumar Stew cisevol EisenLab cis-regulatory-evolution
  • Recombination and base composition: the case of the highly self-fertilizing plant Arabidopsis thaliana.
    Genome Biol, Vol. 5, No. 7. (2004)
    by G Marais, B Charlesworth, SI Wright
    posted to 08-smbe by smbe2008 on 2008-06-02 16:20:27 as ** along with 2 people maren timflutre
  • The genomic and epidemiological dynamics of human influenza A virus
    Nature (16 April 2008)
    by Andrew Rambaut, Oliver G Pybus, Martha I Nelson, Cecile Viboud, Jeffery K Taubenberger, Edward C Holmes
    posted to 08-smbe by smbe2008 on 2008-06-02 18:06:55 as ** along with 2 people friendpine emptyhb
  • Strong Variations of Mitochondrial Mutation Rate across Mammals--the Longevity Hypothesis
    Mol Biol Evol, Vol. 25, No. 1. (1 January 2008), pp. 120-130.
    by Benoit Nabholz, Sylvain Glemin, Nicolas Galtier
    posted to 08-smbe by smbe2008 on 2008-06-02 17:15:37 as ** along with 4 people and 1 group aprasad renatomilani stevanspringer rvosa FAB-lab
  • Transposable elements and the evolution of regulatory networks.
    Nat Rev Genet (27 March 2008)
    by Cédric Feschotte
    posted to 08-smbe by smbe2008 on 2008-06-02 17:20:52 as ** along with 11 people and 1 group fhalbrit balicea gwallau djkt bootsy idonaldson cmzmasek eskay roys pradiptaray timflutre BergmanLab
  • Inferring Selection in Partially Sequenced Regions
    Mol Biol Evol (28 December 2007), msm273.
    by Jeffrey D Jensen, Kevin R Thornton, Charles F Aquadro
    posted to 08-smbe by smbe2008 on 2008-06-02 16:48:37 as ** along with 2 people and 1 group djkt dmc Durbin group
  • Long-term evolution of transposable elements
    Proceedings of the National Academy of Sciences (26 November 2007), 0705238104.
    by Arnaud Le Rouzic, Thibaud S Boutin, Pierre Capy
    posted to 08-smbe by smbe2008 on 2008-06-02 17:23:52 as ** along with 5 people operon sebastien_vigneau saru hpaces balicea
  • The Origin and Evolution of tRNA Inferred from Phylogenetic Analysis of Structure
    Journal of Molecular Evolution, Vol. 66, No. 1. (24 January 2008), pp. 21-35.
    by Feng-Jie Sun, Gustavo Caetano-Anollés
    posted to 08-smbe by smbe2008 on 2008-06-02 16:54:16 as ** along with 1 person msierk
  • Genome-wide survey for biologically functional pseudogenes.
    PLoS Comput Biol, Vol. 2, No. 5. (May 2006)
    by O Svensson, L Arvestad, J Lagergren
    posted to 08-smbe by smbe2008 on 2008-06-02 16:58:13 as ** along with 3 people and 2 groups bsmagic cjeans renatomilani Bioinformatics bioinplant
  • Paleontological Evidence to Date the Tree of Life
    Mol Biol Evol, Vol. 24, No. 1. (1 January 2007), pp. 26-53.
    by Michael J Benton, Philip C Donoghue
    posted to 08-smbe by smbe2008 on 2008-06-02 18:06:19 as ** along with 5 people aprasad Archaeogenetics akifumi maximilianh dandaman
  • Insertion/Deletion and Nucleotide Polymorphism Data Reveal Constraints in Drosophila melanogaster Introns and Intergenic Regions
    Genetics, Vol. 169, No. 3. (1 March 2005), pp. 1521-1527.
    by Lino Ometto, Wolfgang Stephan, David De Lorenzo
    posted to 08-smbe by smbe2008 on 2008-06-02 16:45:22 as ** along with 2 people and 1 group penka cisevol Nie
  • Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals.
    Proceedings. Biological sciences / The Royal Society, Vol. 271, No. 1554. (7 November 2004), pp. 2201-2207.
    by VJ Lynch, JJ Roth, K Takahashi, CW Dunn, DF Nonaka, GF Stopper, GP Wagner
    posted to 08-smbe by smbe2008 on 2008-06-02 18:10:16 as **
  • Reduced efficacy of selection in regions of the Drosophila genome that lack crossing over
    Genome Biology, Vol. 8 (06 February 2007), R18.
    by Penelope R Haddrill, Daniel L Halligan, Dimitris Tomaras, Brian Charlesworth
    posted to 08-smbe by smbe2008 on 2008-06-02 17:52:43 as ** along with 3 people and 2 groups dpollard djkt cisevol EisenLab cis-regulatory-evolution
  • Exploring Variation in the d N /d S Ratio Among Sites and Lineages Using Mutational Mappings: Applications to the Influenza Virus
    Journal of Molecular Evolution, Vol. 65, No. 3. (2007), pp. 340-348.
    by Weiwei Zhai, Montgomery Slatkin, Rasmus Nielsen
    posted to 08-smbe by smbe2008 on 2008-06-02 17:27:29 as ** along with 1 person stevanspringer
  • Selection against spurious promoter motifs correlates with translational efficiency across bacteria.
    PLoS ONE, Vol. 2, No. 1. (2007)
    by JL Froula, MP Francino
    posted to 08-smbe by smbe2008 on 2008-06-02 16:19:20 as **
  • Do mosquitoes filter the access of Plasmodium cytochrome b lineages to an avian host?
    Molecular Ecology, Vol. 17, No. 10. (May 2008), pp. 2552-2561.
    by Andrea B Gager, Rosario DEL Loaiza, E Jos, Donald C Dearborn, Eldredge Bermingham
    posted to 08-smbe by smbe2008 on 2008-06-02 16:50:11 as **
  • Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence
    Nucl. Acids Res., Vol. 36, No. 6. (1 April 2008), pp. 1913-1927.
    by Gilly Padalon-Brauch, Ruth Hershberg, Maya Elgrably-Weiss, Kobi Baruch, Ilan Rosenshine, Hanah Margalit, Shoshy Altuvia
    posted to 08-smbe by smbe2008 on 2008-06-02 17:30:53 as ** along with 1 person eskay
  • Structural polymorphism and diversifying selection on the pregnancy malaria vaccine candidate VAR2CSA
    Molecular and Biochemical Parasitology, Vol. 155, No. 2. (October 2007), pp. 103-112.
    by Joseph Bockhorst, Fangli Lu, Joel H Janes, Jon Keebler, Benoit Gamain, Philip Awadalla, Xin-Zhuan Su, Ram Samudrala, Nebojsa Jojic, Joseph D Smith
    posted to 08-smbe by smbe2008 on 2008-06-02 16:53:03 as **
  • MATLIGN: a motif clustering, comparison and matching tool
    BMC Bioinformatics, Vol. 8 (08 June 2007), 189.
    by Matti Kankainen, Ari Loytynoja
    posted to 08-smbe by smbe2008 on 2008-06-02 17:55:23 as ** along with 3 people and 1 group idonaldson isimpson xili03 BergmanLab
  • Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome
    Nature Genetics, Vol. 39, No. 4. (04 March 2007), pp. 457-466.
    by Michael Weber, Ines Hellmann, Michael B Stadler, Liliana Ramos, Svante Pääbo, Michael Rebhan, Dirk Schübeler
    posted to 08-smbe by gjuggler on 2008-05-22 16:22:55 as ** along with 7 people aprickett myrtilus epigenetics bioyang vmsr bpcusack rschulz
  • Deciphering Human Immunodeficiency Virus Type 1 Transmission and Early Envelope Diversification by Single-Genome Amplification and Sequencing
    J. Virol., Vol. 82, No. 8. (15 April 2008), pp. 3952-3970.
    by Jesus, Elizabeth Bailes, Kimmy T Pham, Maria G Salazar, Brad M Guffey, Brandon F Keele, Cynthia A Derdeyn, Paul Farmer, Eric Hunter, Susan Allen, Olivier Manigart, Joseph Mulenga, Jeffrey A Anderson, Ronald Swanstrom, Barton F Haynes, Gayathri S Athreya, Bette T Korber, Paul M Sharp, George M Shaw, Beatrice H Hahn
    posted to 08-smbe by gjuggler on 2008-05-22 16:55:37 as ** along with 1 person kieran101
  • 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 5 people and 2 groups jbsaltz dpollard djkt cisevol emptyhb EisenLab cis-regulatory-evolution
  • PhylomeDB: a database for genome-wide collections of gene phylogenies.
    Nucleic acids research, Vol. 36, No. Database issue. (January 2008)
    by Huerta J Cepas, A Bueno, J Dopazo, T Gabaldón
    posted to 08-smbe by gjuggler on 2008-05-22 16:59:35 as ** along with 1 person treangen
  • GENOMICS: Lining Up to Avoid Bias
    Science, Vol. 319, No. 5862. (25 January 2008), pp. 416-417.
    by Antonis Rokas
    posted to 08-smbe by gjuggler on 2008-05-22 17:04:19 as ** along with 8 people treangen operon dayjm cjeans lilou dandaman renatomilani bpcusack
  • 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 **
  • A genome-wide approach to identifying novel-imprinted genes.
    Hum Genet, Vol. 122, No. 6. (January 2008), pp. 625-634.
    by KS Pollard, D Serre, X Wang, H Tao, E Grundberg, TJ Hudson, AG Clark, K Frazer
    posted to 08-smbe by gjuggler on 2008-05-22 16:58:08 as ** along with 2 people and 1 group nolodie dpollard RockmanLab
  • 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 **
  • 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
  • The Inverse Relationship Between Evolutionary Rate and Age of Mammalian Genes Is an Artifact of Increased Genetic Distance with Rate of Evolution and Time of Divergence
    Molecular Biology and Evolution, Vol. 23, No. 1. (January 2006), pp. 1-3.
    by Eran Elhaik, Niv Sabath
    posted to 08-smbe by gjuggler on 2008-05-22 17:02:47 as ** along with 1 person akifumi
  • Global analysis of alternative splicing differences between humans and chimpanzees
    Genes Dev. (31 October 2007), gad.1606907.
    by John A Calarco, Yi Xing, Mario Caceres, Joseph P Calarco, Xinshu Xiao, Qun Pan, Christopher Lee, Todd M Preuss, Benjamin J Blencowe
    posted to 08-smbe by gjuggler on 2008-05-22 17:01:29 as ** along with 2 people saru bpcusack
  • 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 **
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