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Group: Berkeley Mycology - library [393 articles]

Recent papers posted by members of the Berkeley Mycology group
  • The multiple lives of NMD factors: balancing roles in gene and genome regulation
    Nat Rev Genet, Vol. 9, No. 9. (2008), pp. 699-712.
    by Olaf Isken, Lynne E Maquat
    posted to regulation posttranscriptional nmd gene by stajich to the group Berkeley Mycology on 2008-08-19 17:51:09 as ** along with 1 person bpcusack
  • Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges
    Nat Rev Genet, Vol. 9, No. 9. (2008), pp. 678-688.
    by Lincoln D Stein
    posted to infrastructure informatics genome database bioinformatics by stajich to the group Berkeley Mycology on 2008-08-19 16:25:02 as ** along with 16 people and 3 groups srp33 alaninmcr druvus ilya carolh12 sjcockell thomaskelder fgibson jago GustavoLacerda jandot neils dansullivanblk mrochman tharris dullhunk kpa-resources Knowledge_Economy_Reform Global_health_enterprise_architecture
  • Differential gene expression between the biotrophic-like and saprotrophic mycelia of the witches' broom pathogen Moniliophthora perniciosa.
    Molecular plant-microbe interactions : MPMI, Vol. 21, No. 7. (July 2008), pp. 891-908.
    by J Rincones, LM Scarpari, MF Carazzolle, JM Mondego, EF Formighieri, JG Barau, GG Costa, DM Carraro, HP Brentani, LA Vilas-Boas, BV de Oliveira, M Sabha, R Dias, JM Cascardo, RA Azevedo, LW Meinhardt, GA Pereira
    posted to witchesbroom moniliophthora gene_expression development by stajich to the group Berkeley Mycology on 2008-08-19 02:11:40 as ** along with 1 person GustavoLacerda
  • Annotation of stress-response proteins in the aspergilli.
    Fungal genetics and biology : FG & B (25 July 2008)
    by Márton Miskei, Zsolt Karányi, István Pócsi
    posted to stress_response fungi aspergillus by stajich to the group Berkeley Mycology on 2008-08-17 20:29:32 as ** along with 1 person GustavoLacerda
  • The evolution of 5S ribosomal RNA genes linked to the rDNA units of fungal species.
    Current genetics (15 August 2008)
    by Julie Bergeron, Guy Drouin
    posted to ribosomal rdna fungi 5s by stajich to the group Berkeley Mycology on 2008-08-17 20:29:01 as ** along with 1 person GustavoLacerda
  • Gene Expansion and Retention Leads to a Diverse Tyrosine Kinase Superfamily in Amphioxus
    Mol Biol Evol, Vol. 25, No. 9. (1 September 2008), pp. 1841-1854.
    by Salvatore D'Aniello, Manuel Irimia, Ignacio Maeso, Juan Pascual-Anaya, Senda Jimenez-Delgado, Stephanie Bertrand, Jordi Garcia-Fernandez
    posted to metazoa gene_family expansion evolution chordate animal by stajich to the group Berkeley Mycology on 2008-08-17 19:30:18 as **
  • BranchClust: A phylogenetic algorithm for selecting gene families
    BMC Bioinformatics, Vol. 8 (10 April 2007), 120.
    by Maria S Poptsova, Peter J Gogarten
    posted to phylogenomics phylogenetics paralogs orthology methods gene_tree bioinformatics by stajich to the group Berkeley Mycology on 2008-08-17 18:17:13 as ** along with 1 person and 1 group rvosa FAB-lab
  • ANTHRAX INVESTIGATION: Full-Genome Sequencing Paved the Way From Spores to a Suspect
    Science, Vol. 321, No. 5891. (15 August 2008), pp. 898-899.
    by Martin Enserink
    posted to sequencing news anthrax by stajich to the group Berkeley Mycology on 2008-08-17 18:14:54 as ** along with 2 people druvus MichaelTully
  • Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective.
    PLoS ONE, Vol. 1 (2006)
    by RH Nilsson, M Ryberg, E Kristiansson, K Abarenkov, KH Larsson, U Kõljalg
    posted to taxonomy fungi database by stajich to the group Berkeley Mycology on 2008-08-16 00:55:03 as ** along with 1 person GustavoLacerda
  • A novel regulator couples sporogenesis and trehalose biogenesis in Aspergillus nidulans.
    PLoS ONE, Vol. 2, No. 10. (2007)
    by M Ni, JH Yu
    posted to sugar spore regulation gene fungi aspergillus by stajich to the group Berkeley Mycology on 2008-08-16 00:50:21 as **
  • Comparative genome analysis of filamentous fungi reveals gene family expansions associated with fungal pathogenesis.
    PLoS ONE, Vol. 3, No. 6. (2008)
    by DM Soanes, I Alam, M Cornell, HM Wong, C Hedeler, NW Paton, M Rattray, SJ Hubbard, SG Oliver, NJ Talbot
    posted to phylogenomics genome fungi comparative_genomics analysis by stajich to the group Berkeley Mycology on 2008-08-16 00:49:43 as ** along with 1 person GustavoLacerda
  • Multigene phylogeny of choanozoa and the origin of animals.
    PLoS ONE, Vol. 3, No. 5. (2008)
    by K Shalchian-Tabrizi, MA Minge, M Espelund, R Orr, T Ruden, KS Jakobsen, T Cavalier-Smith
    posted to phylogeny phylogenetics multicellular metazoa animal by stajich to the group Berkeley Mycology on 2008-08-16 00:46:36 as **
  • Ecologic niche modeling of Blastomyces dermatitidis in Wisconsin.
    PLoS ONE, Vol. 3, No. 4. (2008)
    by KD Reed, JK Meece, JR Archer, AT Peterson
    posted to fungi environmental_microbiology ecology blastomyces by stajich to the group Berkeley Mycology on 2008-08-16 00:45:59 as **
  • The Yeast Spore Wall Enables Spores to Survive Passage through the Digestive Tract of Drosophila
    PLoS ONE, Vol. 3, No. 8. (2008), e2873.
    by Alison E Coluccio, Rachael K Rodriguez, Maurice J Kernan, Aaron M Neiman
    posted to yeast spore saccharomyces drosophila cell_wall cell_surface by stajich to the group Berkeley Mycology on 2008-08-07 02:29:11 as **
  • Cell-Cell Adhesion in the Cnidaria: Insights Into the Evolution of Tissue Morphogenesis
    Biol Bull, Vol. 214, No. 3. (1 June 2008), pp. 218-232.
    by Craig R Magie, Mark Q Martindale
    posted to multicellular development cell_wall cell_surface adhesion by stajich to the group Berkeley Mycology on 2008-08-05 23:55:15 as **
  • Estimate of the Mutation Rate per Nucleotide in Humans
    Genetics, Vol. 156, No. 1. (1 September 2000), pp. 297-304.
    by Michael W Nachman, Susan L Crowell
    posted to mutation_rate human cpg by stajich to the group Berkeley Mycology on 2008-08-05 23:53:11 as ** along with 5 people gwenknight skumagai sriram_s nagendraproj ryanraaum
  • Evolutionarily Conserved Substrate Substructures for Automated Annotation of Enzyme Superfamilies
    PLoS Comput Biol, Vol. 4, No. 8. (2008), e1000142.
    by Ranyee A Chiang, Andrej Sali, Patricia C Babbitt
    posted to functional_prediction computational_biology annotation by stajich to the group Berkeley Mycology on 2008-08-05 16:53:15 as **
  • Conserved Secondary Structures in Aspergillus
    PLoS ONE, Vol. 3, No. 7. (30 July 2008), e2812.
    by Abigail M Mcguire, James E Galagan
    posted to rna_gene noncoding_rna genome_evolution aspergillus by stajich to the group Berkeley Mycology on 2008-08-04 23:51:24 as **
  • Impact of whole genome amplification on analysis of copy number variants.
    Nucleic acids research, Vol. 36, No. 13. (August 2008)
    by TJ Pugh, AD Delaney, N Farnoud, S Flibotte, M Griffith, HI Li, H Qian, P Farinha, RD Gascoyne, MA Marra
    posted to genome copy_number_variation amplification by stajich to the group Berkeley Mycology on 2008-07-30 17:56:54 as ** along with 2 people jyuh nuin
  • EVOLUTIONARY SIGNIFICANCE OF IMBALANCED NUCLEAR RATIOS WITHIN HETEROKARYONS OF THE BASIDIOMYCETE FUNGUS HETEROBASIDION PARVIPORUM.
    Evolution; international journal of organic evolution (15 July 2008)
    by Timothy Y Y James, Jan Stenlid, Ake Olson, Hanna Johannesson
    posted to heterokaryon heterobasidion basidiomycota by stajich to the group Berkeley Mycology on 2008-07-28 18:45:21 as **
  • Identification of mating type genes in the bipolar basidiomycetous yeast Rhodosporidium toruloides: first insight into the MAT locus structure of the Sporidiobolales.
    Eukaryotic cell, Vol. 7, No. 6. (June 2008), pp. 1053-1061.
    by MA Coelho, A Rosa, N Rodrigues, A Fonseca, P Gonçalves
    posted to mating_type mating_genes basidiomycota by stajich to the group Berkeley Mycology on 2008-07-28 06:20:08 as **
  • An in silico analysis of cytochrome c from Phanerochaete chrysosporium: its amino acid sequence and characterization of gene structural elements.
    In silico biology, Vol. 8, No. 1. (2008), pp. 1-13.
    by JA Bumpus, M Trax, A Reisdorph, C Boyd, D Gilbert, S Techau, RM Ventullo
    posted to phanerochaete_chrysosporium phanerochaete p450 by stajich to the group Berkeley Mycology on 2008-07-28 06:19:24 as **
  • SCUMBLE: a method for systematic and accurate detection of codon usage bias by maximum likelihood estimation
    Nucl. Acids Res., Vol. 36, No. 11. (1 June 2008), pp. 3819-3827.
    by Morten Kloster, Chao Tang
    posted to methods codon_bias bioinformatics by stajich to the group Berkeley Mycology on 2008-07-28 06:18:17 as ** along with 1 person GustavoLacerda
  • Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes.
    Bioinformatics (Oxford, England), Vol. 24, No. 13. (1 July 2008)
    by C Zheng, Q Zhu, Z Adam, D Sankoff
    posted to simluation saccharomyces genome_evolution genome_duplication duplication by stajich to the group Berkeley Mycology on 2008-07-28 06:18:01 as **
  • The Crystal Structure of [Fe]-Hydrogenase Reveals the Geometry of the Active Site
    Science, Vol. 321, No. 5888. (25 July 2008), pp. 572-575.
    by Seigo Shima, Oliver Pilak, Sonja Vogt, Michael Schick, Marco S Stagni, Wolfram Meyer-Klaucke, Eberhard Warkentin, Rudolf K Thauer, Ulrich Ermler
    posted to hydrogenase crystalstructure by stajich to the group Berkeley Mycology on 2008-07-28 02:32:00 as ** along with 1 person and 1 group kinestetika microbiology_nijmegen
  • Report concludes that a fungal genome database is of "the highest priority".
    Future microbiology, Vol. 3 (August 2008)
    posted to report fungal databases by stajich to the group Berkeley Mycology on 2008-07-27 23:01:13 as **
  • Mating System of the Anther Smut Fungus Microbotryum violaceum: Selfing under Heterothallism
    Eukaryotic Cell, Vol. 7, No. 5. (1 May 2008), pp. 765-775.
    by Tatiana Giraud, Roxana Yockteng, Manuela Lopez-Villavicencio, Guislaine Refregier, Michael E Hood
    posted to smuth selfing microbotryum mating_type mating_systems fungus by stajich to the group Berkeley Mycology on 2008-07-27 08:14:48 as **
  • GBParsy: A GenBank flatfile parser library with high speed
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Tae H Lee, Yeon K Kim, Baek H Nahm
    posted to parser methods bioinformatics by stajich to the group Berkeley Mycology on 2008-07-25 17:03:34 as ** along with 1 person rmk
  • EVOLUTION: Modernizing the Modern Synthesis
    Science, Vol. 321, No. 5886. (11 July 2008), pp. 196-197.
    by Elizabeth Pennisi
    posted to modernsynthesis evolutionary_theory evolution by stajich to the group Berkeley Mycology on 2008-07-25 06:44:15 as ** along with 1 person renatomilani
  • Predicted functional RNAs within coding regions constrain evolutionary rates of yeast proteins.
    PLoS ONE, Vol. 3, No. 2. (2008)
    by CD Warden, SH Kim, SV Yi
    posted to saccharomyces rna noncoding_rna by stajich to the group Berkeley Mycology on 2008-07-21 05:56:32 as **
  • Trait-trait dynamic interaction: 2D-trait eQTL mapping for genetic variation study
    BMC Genomics, Vol. 9, No. 1. (2008)
    by Wei Sun, Shinsheng Yuan, Ker C Li
    posted to quantitative_genetics qtl methods eqtl by stajich to the group Berkeley Mycology on 2008-07-21 05:55:46 as ** along with 4 people jyuh caseybrown ddunbar natstreet
  • An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae.
    PLoS ONE, Vol. 2, No. 10. (2007)
    by I Lee, Z Li, EM Marcotte
    posted to saccharomyces gene_network bioinformatics by stajich to the group Berkeley Mycology on 2008-07-21 05:00:25 as **
  • Sexual attraction: on the role of fungal pheromone/receptor systems (A review).
    Acta microbiologica et immunologica Hungarica, Vol. 55, No. 2. (June 2008), pp. 125-143.
    by E Kothe
    posted to signaling receptor pheremone fungi fungal by stajich to the group Berkeley Mycology on 2008-07-21 04:20:07 as **
  • The asexual yeast Candida glabrata maintains distinct a and alpha haploid mating types.
    Eukaryotic cell, Vol. 7, No. 5. (May 2008), pp. 848-858.
    by H Muller, C Hennequin, J Gallaud, B Dujon, C Fairhead
    posted to saccharomyces mating_type mating_genes genome fungi candida by stajich to the group Berkeley Mycology on 2008-07-21 04:14:00 as **
  • Evolution and phylogenetic relationships of APSES proteins from Hemiascomycetes.
    FEMS yeast research, Vol. 8, No. 4. (June 2008), pp. 511-519.
    by B Ramírez-Zavala, A Domínguez
    posted to saccharomyces phylogenetics fungi evolution by stajich to the group Berkeley Mycology on 2008-07-21 04:13:26 as **
  • Exploring contradictory phylogenetic relationships in yeasts.
    FEMS yeast research, Vol. 8, No. 4. (June 2008), pp. 641-650.
    by Q Wu, SA James, IN Roberts, V Moulton, KT Huber
    posted to yeast systematics saccharomyces phylogeny fungi by stajich to the group Berkeley Mycology on 2008-07-21 04:12:58 as **
  • A genomic approach for the identification and classification of genes involved in cell wall formation and its regulation in Saccharomyces cerevisiae.
    Comparative and functional genomics, Vol. 2, No. 3. (2001), pp. 124-142.
    by PW de Groot, C Ruiz, CR Vázquez de Aldana, E Duenas, VJ Cid, F Del Rey, JM Rodríquez-Peña, P Pérez, A Andel, J Caubín, J Arroyo, JC García, C Gil, M Molina, LJ García, C Nombela, FM Klis
    posted to saccharomyces fungal cell_wall by stajich to the group Berkeley Mycology on 2008-07-21 04:08:17 as **
  • GENOMICS: Billion-Dollar Cancer Mapping Project Steps Forward
    Science, Vol. 321, No. 5885. (4 July 2008), pp. 26a-27.
    by Jocelyn Kaiser
    posted to news genomics funding cancer by stajich to the group Berkeley Mycology on 2008-07-16 17:55:26 as ** along with 1 person reyez
  • Unraveling Protein Networks with Power Graph Analysis
    PLoS Comput Biol, Vol. 4, No. 7. (11 July 2008), e1000108.
    by Loïc Royer, Matthias Reimann, Bill Andreopoulos, Michael Schroeder
    posted to visualization protein_interactions protein methods graphics bioinformatics by stajich to the group Berkeley Mycology on 2008-07-16 17:12:31 as ** along with 17 people and 1 group rsantana sebk roys lptolik MatthiasReimann jmuhlich AbnerCYH royerloic tmmurali chad_davis renatomilani askrajiv Borelli nuin reyez kengg Ema OPIG
  • Conditional Variable Importance for Random Forests
    BMC Bioinformatics, Vol. 9 (11 July 2008), 307.
    by Carolin Strobl, Anne-Laure Boulesteix, Thomas Kneib, Thomas Augustin, Achim Zeileis
    posted to randomforest methods bioinformatics by stajich to the group Berkeley Mycology on 2008-07-16 12:29:30 as ** along with 1 person jyuh
  • How Well Does the HoT Score Reflect Sequence Alignment Accuracy?
    Mol Biol Evol, Vol. 25, No. 8. (1 August 2008), pp. 1576-1580.
    by Barry G Hall
    posted to statistics molecular_evolution methods bioinformatics alignment by stajich to the group Berkeley Mycology on 2008-07-15 16:36:43 as ** along with 2 people bpcusack cabbagesofdoom
  • A genome-wide 20K citrus microarray for gene expression analysis
    BMC Genomics, Vol. 9 (03 July 2008), 318.
    by Angeles M Martinez-Godoy, Nuria Mauri, Jose Juarez, Carmen M Marques, Julia Santiago, Javier Forment, Jose Gadea
    posted to plant microarray citrus by stajich to the group Berkeley Mycology on 2008-07-09 05:44:15 as ** along with 1 person JavierTerol
  • Evolution of SET-domain protein families in the unicellular and multicellular Ascomycota fungi
    BMC Evolutionary Biology, Vol. 8 (01 July 2008), 190.
    by Chendhore S Veerappan, Zoya Avramova, Etsuko N Moriyama
    posted to yeast multicellular fungi filamentous by stajich to the group Berkeley Mycology on 2008-07-09 00:20:23 as **
  • The ins and outs of plant cell walls.
    Current opinion in plant biology, Vol. 9, No. 6. (December 2006), pp. 616-620.
    by JN Johansen, S Vernhettes, H Höfte
    posted to plant cell_wall cellulose_synthase by stajich to the group Berkeley Mycology on 2008-07-08 22:45:31 as **
  • Growth of the plant cell wall
    Nature Reviews Molecular Cell Biology, Vol. 6, No. 11. (01 November 2005), pp. 850-861.
    by Daniel J Cosgrove
    posted to plant cellulose_synthase by stajich to the group Berkeley Mycology on 2008-07-08 22:08:53 as **
  • Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes
    Genome Res., Vol. 18, No. 7. (1 July 2008), pp. 1133-1142.
    by Nitin Gupta, Jamal Benhamida, Vipul Bhargava, Daniel Goodman, Elisabeth Kain, Ian Kerman, Ngan Nguyen, Noah Ollikainen, Jesse Rodriguez, Jian Wang, Mary S Lipton, Margaret Romine, Vineet Bafna, Richard D Smith, Pavel A Pevzner
    posted to undergraduate_research proteomics by stajich to the group Berkeley Mycology on 2008-07-08 18:20:05 as ** along with 2 people Neeperando biehl
  • A Gene Wiki for Community Annotation of Gene Function
    PLoS Biology, Vol. 6, No. 7. (1 July 2008), e175.
    by Jon W Huss, Camilo Orozco, James Goodale, Chunlei Wu, Serge Batalov, Tim J Vickers, Faramarz Valafar, Andrew I Su
    posted to wiki gene annotation by stajich to the group Berkeley Mycology on 2008-07-08 16:23:50 as ** along with 13 people and 1 group jyuh inesdesantiago thomaskelder GMTurner ChrisEvelo barriot kristina reyez zwang kintoki sjc tharris dullhunk VisionLab
  • Cloning of cellulose synthesis related genes from Acetobacter xylinum ATCC23769 and ATCC53582: comparison of cellulose synthetic ability between strains.
    DNA Res, Vol. 9, No. 5. (31 October 2002), pp. 149-156.
    by S Kawano, K Tajima, Y Uemori, H Yamashita, T Erata, M Munekata, M Takai
    posted to cellulose_synthase bacteria by stajich to the group Berkeley Mycology on 2008-07-08 06:59:27 as ** along with 1 person orenoCiteULike
  • Genes required for cellulose synthesis in Agrobacterium tumefaciens
    J. Bacteriol., Vol. 177, No. 4. (1 February 1995), pp. 1069-1075.
    by AG Matthysse, S White, R Lightfoot
    posted to cellulose_synthase bacteria by stajich to the group Berkeley Mycology on 2008-07-08 06:59:19 as **
  • Cellulose Synthesis in Phytophthora infestans Is Required for Normal Appressorium Formation and Successful Infection of Potato
    Plant Cell, Vol. 20, No. 3. (1 March 2008), pp. 720-738.
    by Laura J Grenville-Briggs, Victoria L Anderson, Johanna Fugelstad, Anna O Avrova, Jamel Bouzenzana, Alison Williams, Stephan Wawra, Stephen C Whisson, Paul R Birch, Vincent Bulone, Pieter van West
    posted to phytophthora cell_wall cellulose_synthase by stajich to the group Berkeley Mycology on 2008-07-08 01:51:23 as **
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