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biomcgary's library [109 articles]

Recent papers added to biomcgary's library.
  • Log or Linear? Distinct Intuitions of the Number Scale in Western and Amazonian Indigene Cultures
    Science, Vol. 320, No. 5880. (30 May 2008), pp. 1217-1220.
    by Stanislas Dehaene, Veronique Izard, Elizabeth Spelke, Pierre Pica
    posted to number_systems education by biomcgary on 2008-06-12 15:07:28 as ** along with 6 people and 1 group qwermish cercamon sen_cheng baronka tyrell_turing shivakmr VisionLab
  • Ancestral monogamy shows kin selection is key to the evolution of eusociality.
    Science (New York, N.Y.), Vol. 320, No. 5880. (30 May 2008), pp. 1213-1216.
    by WO Hughes, BP Oldroyd, M Beekman, FL Ratnieks
    posted to selection monogamy kin_selection evolution eusociality by biomcgary on 2008-06-12 15:05:06 as **
  • Massive Horizontal Gene Transfer in Bdelloid Rotifers
    Science, Vol. 320, No. 5880. (30 May 2008), pp. 1210-1213.
    by Eugene A Gladyshev, Matthew Meselson, Irina R Arkhipova
    posted to rotifers metazoan intron_gain intron horizontal_gene_transfer genome_defense fungi dna_repair chromosome_structure bacteria by biomcgary on 2008-06-12 15:03:32 as ** along with 2 people mblwhoi mjoach
  • The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing
    Science (1 May 2008), 1158441.
    by Ugrappa Nagalakshmi, Zhong Wang, Karl Waern, Chong Shou, Debasish Raha, Mark Gerstein, Michael Snyder
    posted to transcription sequencing rna introns by biomcgary on 2008-06-12 14:59:54 as ** along with 7 people and 1 group semrich djkt chad_davis Retchless gjuggler caseybrown stajich Berkeley Mycology
  • Bcl-XL Inhibits Membrane Permeabilization by Competing with Bax
    PLoS Biology, Vol. 6, No. 6. (1 June 2008), e147.
    by Lieven P Billen, Candis L Kokoski, Jonathan F Lovell, Brian Leber, David W Andrews
    posted to protein-protein_interaction oligomerization gene_duplication competitive_interaction competitive_binding apoptosis by biomcgary on 2008-06-10 15:48:18 as ** along with 1 person paulschlesinger
  • Modular Organization and Combinatorial Energetics of Proline–Tyrosine Nuclear Localization Signals
    PLoS Biology, Vol. 6, No. 6. (1 June 2008), e137.
    by Katherine E Süel, Hongmei Gu, Yuh M Chook
    posted to sequence_motif nuclear_import by biomcgary on 2008-06-03 14:59:07 as **
  • Adaptive evolution and functional redesign of core metabolic proteins in snakes.
    PLoS ONE, Vol. 3, No. 5. (2008)
    by TA Castoe, ZJ Jiang, W Gu, ZO Wang, DD Pollock
    posted to snake punctuated_evolution metabolism designed_mutations convergent_evolution by biomcgary on 2008-05-27 15:50:16 as **
  • Darwinian Evolution on a Chip
    PLoS Biology, Vol. 6, No. 4. (1 April 2008), e85.
    by Brian M Paegel, Gerald F Joyce
    posted to rna mutation_rate evolution artificial_selection by biomcgary on 2008-05-20 23:03:55 as ** along with 2 people cjeans mpickett
  • Phosphorylation of Retinoblastoma Protein by Viral Protein with Cyclin-Dependent Kinase Function
    Science, Vol. 320, No. 5877. (9 May 2008), pp. 797-799.
    by Adam J Hume, Jonathan S Finkel, Jeremy P Kamil, Donald M Coen, Michael R Culbertson, Robert F Kalejta
    posted to virus kinase cell_cycle by biomcgary on 2008-05-08 23:01:45 as ** along with 3 people Petersarkies mclarenv neils
  • Regulation of the Cellular Heat Shock Response in Caenorhabditis elegans by Thermosensory Neurons
    Science, Vol. 320, No. 5877. (9 May 2008), pp. 811-814.
    by Veena Prahlad, Tyler Cornelius, Richard I Morimoto
    posted to signal_integration population_density_response neuron heat_shock environmental_sensing dauer c_elegans by biomcgary on 2008-05-08 22:57:18 as ** along with 1 person GX
  • Network-based global inference of human disease genes
    Mol Syst Biol, Vol. 4 (6 May 2008)
    by Xuebing Wu, Rui Jiang, Michael Q Zhang, Shao Li
    posted to predictive_biology network functional_network disease by biomcgary on 2008-05-06 21:37:38 as ** along with 5 people ptrobajo bootsy maralena zwang jyuh
  • Synteny and Collinearity in Plant Genomes
    Science, Vol. 320, No. 5875. (25 April 2008), pp. 486-488.
    by Haibao Tang, John E Bowers, Xiyin Wang, Ray Ming, Maqsudul Alam, Andrew H Paterson
    posted to synteny genome_duplication evolution chromosomal_rearrangement by biomcgary on 2008-04-25 19:16:14 as ** along with 3 people and 1 group natstreet ArtemPankin tanghaibao Khavkin's lab
  • Selection on Major Components of Angiosperm Genomes
    Science, Vol. 320, No. 5875. (25 April 2008), pp. 484-486.
    by Brandon S Gaut, Jeffrey Ross-Ibarra
    posted to selection genome_size genome evolution angiosperm by biomcgary on 2008-04-25 17:48:03 as ** along with 4 people and 1 group echinotrix aprasad ArtemPankin timflutre Khavkin's lab
  • Genomic Plasticity and the Diversity of Polyploid Plants
    Science, Vol. 320, No. 5875. (25 April 2008), pp. 481-483.
    by AR Leitch, IJ Leitch
    posted to polyploid plasticity plant phenotype gene_duplication diversification by biomcgary on 2008-04-25 17:42:38 as ** along with 5 people and 1 group echinotrix natstreet ArtemPankin timflutre imtechnology Khavkin's lab
  • A map of human protein interactions derived from co-expression of human mRNAs and their orthologs
    Mol Syst Biol, Vol. 4 (15 April 2008)
    by Arun K Ramani, Zhihua Li, Traver G Hart, Mark W Carlson, Daniel R Boutz, Edward M Marcotte
    posted to gene_expression mass_spectroscopy network protein-protein_interaction ribosome by biomcgary on 2008-04-15 20:19:27 as ** along with 7 people and 1 group ptrobajo zwang grahamc ardalby giovanni tmmurali phoenixzxl OPIG
  • Convergence of Campylobacter Species: Implications for Bacterial Evolution
    Science, Vol. 320, No. 5873. (11 April 2008), pp. 237-239.
    by Samuel K Sheppard, Noel D Mccarthy, Daniel Falush, Martin C Maiden
    posted to bacteria convergent_evolution de-speciation environmental_niche horizontal_gene_transfer pathogen speciation by biomcgary on 2008-04-11 23:02:23 as ** along with 2 people jmeppley dinnes
  • Perceiving molecular evolution processes in Escherichia coli by comprehensive metabolite and gene expression profiling
    Genome Biology, Vol. 9, No. 4. (2008)
    by Chandran Vijayendran, Aiko Barsch, Karl Friehs, Karsten Niehaus, Anke Becker, Erwin Flaschel
    posted to adaptation convergent_evolution e_coli evolution gene_expression metabolism by biomcgary on 2008-04-10 15:07:38 as ** along with 1 person tonia_schwartz
  • Chromosomal Gene Movements Reflect the Recent Origin and Biology of Therian Sex Chromosomes
    PLoS Biology, Vol. 6, No. 4. (1 April 2008), e80.
    by Lukasz Potrzebowski, Nicolas Vinckenbosch, Ana C Marques, Frédéric Chalmel, Bernard Jégou, Henrik Kaessmann
    posted to chromosomal_rearrangement evolution by biomcgary on 2008-04-01 17:11:12 as **
  • Gene Regulation by Transcription Factors and MicroRNAs
    Science, Vol. 319, No. 5871. (28 March 2008), pp. 1785-1786.
    by Oliver Hobert
    posted to gene_expression microrna transcription_factor by biomcgary on 2008-03-31 21:19:29 as ** along with 6 people and 1 group bootsy ealloza zwang heliopais emptyhb maralena microRNA
  • The Eukaryotic Genome as an RNA Machine
    Science, Vol. 319, No. 5871. (28 March 2008), pp. 1787-1789.
    by Paulo P Amaral, Marcel E Dinger, Tim R Mercer, John S Mattick
    posted to junk_dna mirna ncrna by biomcgary on 2008-03-31 21:13:34 as ** along with 5 people and 1 group dquest operon dullhunk AbnerCYH dlobo GEB
  • Gene Regulation in the Third Dimension
    Science, Vol. 319, No. 5871. (28 March 2008), pp. 1793-1794.
    by Job Dekker
    posted to chromosome_distribution gene_expression by biomcgary on 2008-03-31 21:09:28 as ** along with 8 people and 1 group emptyhb operon AbnerCYH ealloza sunhwan dlobo lambda Haze GEB
  • Transcription Regulation Through Promoter-Proximal Pausing of RNA Polymerase II
    Science, Vol. 319, No. 5871. (28 March 2008), pp. 1791-1792.
    by Leighton J Core, John T Lis
    posted to gene_expression transcription transcription_elongation by biomcgary on 2008-03-31 21:07:58 as ** along with 2 people and 1 group margaritis skoch3 Koch_Lab
  • Complex Riboswitches
    Science, Vol. 319, No. 5871. (28 March 2008), pp. 1795-1797.
    by Ronald R Breaker
    posted to riboswitches by biomcgary on 2008-03-31 20:55:22 as ** along with 2 people austin sunhwan
  • Pleiotropic scaling of gene effects and the ‘cost of complexity’
    Nature, Vol. 452, No. 7186., pp. 470-472.
    by Günter P Wagner, Jane P Kenney-Hunt, Mihaela Pavlicev, Joel R Peck, David Waxman, James M Cheverud
    posted to cost_of_complexity evolution evolutionary_constraint gene_expression mutation pleiotropy qtl skeleton by biomcgary on 2008-03-27 15:16:43 as ** along with 2 people natstreet lusk
  • SIRT6 is a histone H3 lysine 9 deacetylase that modulates telomeric chromatin
    Nature (12 March 2008)
    by Eriko Michishita, Ronald A Mccord, Elisabeth Berber, Mitomu Kioi, Hesed Padilla-Nash, Mara Damian, Peggie Cheung, Rika Kusumoto, Tiara LA Kawahara, Carl J Barrett, Howard Y Chang, Vilhelm A Bohr, Thomas Ried, Or Gozani, Katrin F Chua
    posted to ageing chromatin telomere by biomcgary on 2008-03-27 15:08:32 as ** along with 1 person zhlei
  • Two Seemingly Homologous Noncoding RNAs Act Hierarchically to Activate glmS mRNA Translation
    PLoS Biology, Vol. 6, No. 3. (1 March 2008), e64.
    by Johannes H Urban, Jörg Vogel
    posted to heirarchy ncrna signalling_cascade by biomcgary on 2008-03-25 18:25:11 as **
  • The role of disorder in interaction networks: a structural analysis
    Mol Syst Biol, Vol. 4 (25 March 2008)
    by Philip M Kim, Andrea Sboner, Yu Xia, Mark Gerstein
    posted to disordered_protein evolution_rate hub_protein network protein-protein_interaction protein_structure by biomcgary on 2008-03-25 16:38:11 as ** along with 5 people chad_davis zwang bootsy maralena phoenixzxl
  • Loss of Egg Yolk Genes in Mammals and the Origin of Lactation and Placentation
    PLoS Biology, Vol. 6, No. 3. (1 March 2008), e63.
    by David Brawand, Walter Wahli, Henrik Kaessmann
    posted to comparative_genomics convergent_evolution egg_yolk indel lactation mammalian_evolution marsupial pseudogene by biomcgary on 2008-03-18 16:31:42 as ** along with 1 person sunhwan
  • Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics
    Science, Vol. 319, No. 5869. (14 March 2008), pp. 1539-1543.
    by Caleb J Bashor, Noah C Helman, Shude Yan, Wendell A Lim
    posted to bioengineering feedback_negative feedback_positive kinase mating_pathway protein-protein_interaction scaffold_protein shmoo signalling_cascade systems_biology yeast by biomcgary on 2008-03-13 21:55:36 as ** along with 2 people lisa1 melting
  • Broad phylogenomic sampling improves resolution of the animal tree of life
    Nature (05 March 2008)
    by Casey W Dunn, Andreas Hejnol, David Q Matus, Kevin Pang, William E Browne, Stephen A Smith, Elaine Seaver, Greg W Rouse, Matthias Obst, Gregory D Edgecombe, Martin V Sørensen, Steven HD Haddock, Andreas Schmidt-Rhaesa, Akiko Okusu, Reinhardt M Kristensen, Ward C Wheeler, Mark Q Martindale, Gonzalo Giribet
    posted to ctenophora evolution evolution_rate metazoan_phylogeny model_of_evolution phylogenomics porifera by biomcgary on 2008-03-10 21:08:53 as ** along with 3 people cabbagesofdoom bayesian cmzmasek
  • High-Resolution Mapping of Crossovers Reveals Extensive Variation in Fine-Scale Recombination Patterns Among Humans
    Science (31 January 2008), 1151851.
    by Graham Coop, Xiaoquan Wen, Carole Ober, Jonathan K Pritchard, Molly Przeworski
    posted to biased_recombination gender_differences genetic_variation homologous_recombination linkage_disequilibrium by biomcgary on 2008-03-10 21:00:35 as ** along with 3 people and 1 group djkt stajich lisa1 Berkeley Mycology
  • The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis
    Nature, Vol. 452, No. 7183. (6 March 2008), pp. 88-92.
    by F Martin, A Aerts, D Ahren, A Brun, EGJ Danchin, F Duchaussoy, J Gibon, A Kohler, E Lindquist, V Pereda, A Salamov, HJ Shapiro, J Wuyts, D Blaudez, M Buee, P Brokstein, B Canback, D Cohen, PE Courty, PM Coutinho, C Delaruelle, JC Detter, A Deveau, S Difazio, S Duplessis, L Fraissinet-Tachet, E Lucic, P Frey-Klett, C Fourrey, I Feussner, G Gay, J Grimwood, PJ Hoegger, P Jain, S Kilaru, J Labbe, YC Lin, V Legue, F Le Tacon, R Marmeisse, D Melayah, B Montanini, M Muratet, U Nehls, H Niculita-Hirzel, Oudot-Le MP Secq, M Peter, H Quesneville, B Rajashekar, M Reich, N Rouhier, J Schmutz, T Yin, M Chalot, B Henrissat, U Kues, S Lucas, Y Van de Peer, GK Podila, A Polle, PJ Pukkila, PM Richardson, P Rouze, IR Sanders, JE Stajich, A Tunlid, G Tuskan, IV Grigoriev
    posted to fungi genome mycorrhizal pathogenesis plant symbiosis by biomcgary on 2008-03-06 22:25:07 as ** along with 6 people manzanita jamselem neils alexl cmzmasek urgi
  • eQED: an efficient method for interpreting eQTL associations using protein networks
    Mol Syst Biol, Vol. 4 (4 March 2008)
    by Silpa Suthram, Andreas Beyer, Richard M Karp, Yonina Eldar, Trey Ideker
    posted to eqtl gene_expression network resistance_network by biomcgary on 2008-03-04 20:49:47 as ** along with 6 people ptrobajo jyuh thomaskelder caseybrown zwang jo_davies
  • A systems-level approach to mapping the telomere length maintenance gene circuitry
    Mol Syst Biol, Vol. 4 (4 March 2008)
    by Rafi Shachar, Lior Ungar, Martin Kupiec, Eytan Ruppin, Roded Sharan
    posted to network phenotype_prediction protein-protein_interaction telomere by biomcgary on 2008-03-04 20:47:22 as **
  • Selection to minimise noise in living systems and its implications for the evolution of gene expression
    Mol Syst Biol, Vol. 4 (4 March 2008)
    by Ben Lehner
    posted to evolution evolutionary_constraint gene_expression noise selection stochastic_variation systems_biology variation by biomcgary on 2008-03-04 20:24:43 as ** along with 8 people austin jjray grahamc zwang bootsy wilbur caseybrown michaelbarton
  • Gamete formation without meiosis in Arabidopsis
    Nature (13 February 2008)
    by Maruthachalam Ravi, Mohan PA Marimuthu, Imran Siddiqi
    posted to arabidopsis asexual_reproduction faculative_asexuality heterozygosity hybrid_vigor by biomcgary on 2008-03-03 22:15:00 as **
  • Secondary mutations as a mechanism of cisplatin resistance in BRCA2-mutated cancers
    Nature (10 February 2008)
    by Wataru Sakai, Elizabeth M Swisher, Beth Y Karlan, Mukesh K Agarwal, Jake Higgins, Cynthia Friedman, Emily Villegas, Céline Jacquemont, Daniel J Farrugia, Fergus J Couch, Nicole Urban, Toshiyasu Taniguchi
    posted to biased_mutations cancer crosslinking dna_damage dna_repair selection by biomcgary on 2008-03-03 22:12:44 as **
  • Resistance to therapy caused by intragenic deletion in BRCA2
    Nature (10 February 2008)
    by Stacey L Edwards, Rachel Brough, Christopher J Lord, Rachael Natrajan, Radost Vatcheva, Douglas A Levine, Jeff Boyd, Jorge S Reis-Filho, Alan Ashworth
    posted to biased_mutations breast_cancer dna_damage dna_repair frameshift homologous_recombination indel selection by biomcgary on 2008-03-03 22:11:04 as **
  • Polyglutamine Genes Interact to Modulate the Severity and Progression of Neurodegeneration in Drosophila
    PLoS Biology, Vol. 6, No. 2. (1 February 2008), e29.
    by Derek Lessing, Nancy M Bonini
    posted to aggregation biased_mutation drosophila neurodegeneration polyglutamine repeat_expansion triplet_repeat by biomcgary on 2008-02-28 19:15:55 as ** along with 1 person MartinKreitman
  • The Evolution of Combinatorial Gene Regulation in Fungi
    PLoS Biology, Vol. 6, No. 2. (1 February 2008), e38.
    by Brian B Tuch, David J Galgoczy, Aaron D Hernday, Hao Li, Alexander D Johnson
    posted to comparative_network evolution evolution_rate fungi gene_expression model_of_evolution transcription_factor_binding_site by biomcgary on 2008-02-27 21:36:10 as ** along with 2 people and 1 group stajich cmzmasek Berkeley Mycology
  • Does Mutation Rate Depend on Itself
    PLoS Biology, Vol. 6, No. 2. (1 February 2008), e52.
    by Charles F Baer
    posted to environmental_effects genetic_load genetic_meltdown mutation_rate by biomcgary on 2008-02-27 21:32:48 as **
  • Sequence Context affects the rate of short insertions and deletions in flies and primates
    Genome Biology, Vol. 9 (21 February 2008), R37.
    by Amos Tanay, Eric D Siggia
    posted to biased_mutation indel introns mutation_rate by biomcgary on 2008-02-21 15:57:44 as ** along with 5 people aprasad brant djkt lusk gjuggler
  • Functional protein divergence in the evolution of Homo sapiens
    Genome Biology, Vol. 9 (15 February 2008), R33.
    by Nuria Lopez-Bigas, Subhajyoti De, Sarah A Teichmann
    posted to evolution evolution_rate gene_duplication human protein_function sequence_divergence by biomcgary on 2008-02-15 16:00:14 as ** along with 4 people aalibes djkt grahamc zhanglab
  • Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method
    Mol Syst Biol, Vol. 4 (12 February 2008)
    by Lukas Burger, Erik van Nimwegen
    posted to bayesian_methods kinase predictive_biology protein-protein_interaction sequence_alignment signalling_cascade two-component_signalling by biomcgary on 2008-02-14 20:30:19 as ** along with 10 people pansapiens kengg grahamc laughcry zwang cabbagezs roys cdeane gjuggler phoenixzxl
  • Morphological and Molecular Evidence for a Stepwise Evolutionary Transition from Teeth to Baleen in Mysticete Whales
    Systematic Biology, Vol. 57, No. 1. (2008), pp. 15-37.
    by Thomas A Deméré, Michael R Mcgowen, Annalisa Berta, John Gatesy
    posted to baleen evolution whale by biomcgary on 2008-02-13 22:42:02 as **
  • Predicting synthetic rescues in metabolic networks
    Mol Syst Biol, Vol. 4 (12 February 2008)
    by Adilson E Motter, Natali Gulbahce, Eivind Almaas, Albert-Laszlo Barabasi
    posted to compensatory_mutations fault_tolerance gene_deletion graceful_degradation metabolism network synthetic_rescue by biomcgary on 2008-02-13 21:14:07 as ** along with 9 people tmmurali debasis kentsis zwang bootsy cabbagezs westoll shikin shung
  • Genomes evolve, but how?
    Nature, Vol. 451, No. 7180. (14 February 2008), pp. 771-772.
    by Axel Meyer
    posted to book_review evolution genome population_genetics theodosius_dobzhansky usefulness_of_evolutionary_theory by biomcgary on 2008-02-13 20:34:21 as ** along with 1 person blick
  • Finding exonic islands in a sea of non-coding sequence: splicing related constraints on protein composition and evolution are common in intron-rich genomes
    Genome Biology, Vol. 9, No. 2. (2008)
    by Tobias Warnecke, Joanna Parmley, Laurence Hurst
    posted to biased_mutations convergent_evolution evolution intron protein splicing by biomcgary on 2008-02-07 19:57:53 as ** along with 1 person GustavoLacerda
  • Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication.
    Genome Biology, Vol. 9, No. 2. (2008)
    by Maria F Cardone, Zhaoshi Jiang, Pietro D'Addabbo, Nicoletta Archidiacono, Mariano Rocchi, Evan Eichler, Mario Ventura
    posted to biased_mutations chromosomal_rearrangement evolution primate repetitive_sequence segmental_duplication by biomcgary on 2008-02-07 19:56:21 as **
  • Evolution of insect proteomes: Insights into synapse organization and synaptic vesicle life cycle
    Genome Biology, Vol. 9, No. 2. (2008)
    by Chava Yanay, Noa Morpurgo, Michal Linial
    posted to comparative_network evolution insect network neuron protein-protein_interaction synapse vesicle by biomcgary on 2008-02-07 19:52:23 as **
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