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stajich's library [497 articles]

Recent papers added to stajich's library.
  • Enhanced Production of Trichoderma reesei Endoglucanases and Use of the New Cellulase Preparations in Producing the Stonewashed Effect on Denim Fabric
    Appl. Environ. Microbiol., Vol. 68, No. 8. (1 August 2002), pp. 3956-3964.
    by Arja Miettinen-Oinonen, Pirkko Suominen
    posted to trichoderma stonewashed cellulase by stajich on 2008-05-12 02:31:06 as ** along with 1 group Berkeley Mycology
  • DNA sequence of the excision sites of a mitochondrial plasmid from senescent Podospora anserina.
    Nucleic acids research, Vol. 11, No. 7. (11 April 1983), pp. 2111-2119.
    by DJ Cummings, RM Wright
    posted to senescence podospora by stajich on 2008-05-12 02:11:03 as ** along with 1 group Berkeley Mycology
  • The genome sequence of the model ascomycete fungus Podospora anserina
    Genome Biology, Vol. 9 (06 May 2008), R77.
    by Eric Espagne, Olivier Lespinet, Fabienne Malagnac, Corinne Da Silva, Olivier Jaillon, Betina M Porcel, Arnaud Couloux, Jean-Marc Aury, Béatrice Ségurens, Julie Poulain, Véronique Anthouard, Sandrine Grossetete, Hamid Khalili, Evelyne Coppin, Michelle Déquard-Chablat, Marguerite Picard, Véronique Contamine, Sylvie Arnaise, Anne Bourdais, Véronique Berteaux-Lecellier, Daniel Gautheret, Ronald P de Vries, Evy Battaglia, Pedro M Coutinho, Etienne GJ Danchin, Bernard Henrissat, Riyad EL Khoury, Annie Sainsard-Chanet, Antoine Boivin, Bérangère Pinan-Lucarré, Carole H Sellem, Robert Debuchy, Patrick Wincker, Jean Weissenbach, Philippe Silar
    posted to podospora genome_paper genome by stajich on 2008-05-12 00:48:27 as ** along with 1 group Berkeley Mycology
  • Complete mitochondrial genome sequence of the wine yeast Candida zemplinina: intraspecies distribution of a novel group-IIB1 intron with eubacterial affiliations.
    FEMS yeast research, Vol. 8, No. 2. (March 2008), pp. 311-327.
    by PV Pramateftaki, VN Kouvelis, P Lanaridis, MA Typas
    posted to yeast intron evolution candida by stajich on 2008-05-11 23:44:29 as ** along with 1 group Berkeley Mycology
  • Histoplasma requires SID1, a member of an iron-regulated siderophore gene cluster, for host colonization.
    PLoS pathogens, Vol. 4, No. 4. (2008)
    by LH Hwang, JA Mayfield, J Rine, A Sil
    posted to regulation iron histoplasma gene_expression by stajich on 2008-05-11 23:42:35 as ** along with 1 group Berkeley Mycology
  • 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 Eyre-Walker
    posted to population_genomics population_genetics molecular_evolution methods adaptation by stajich on 2008-05-10 01:44:49 as ** along with 1 person and 1 group stevanspringer Berkeley Mycology
  • The Parasexual Cycle in Candida albicans Provides an Alternative Pathway to Meiosis for the Formation of Recombinant Strains
    PLoS Biology, Vol. 6, No. 5. (1 May 2008), e110.
    by Anja Forche, Kevin Alby, Dana Schaefer, Alexander D Johnson, Judith Berman, Richard J Bennett
    posted to recombination parasexual meiosis candida by stajich on 2008-05-06 20:14:20 as ** along with 1 group Berkeley Mycology
  • The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes
    Science, Vol. 320, No. 5874. (18 April 2008), pp. 362-365.
    by Maureen E Hillenmeyer, Eula Fung, Jan Wildenhain, Sarah E Pierce, Shawn Hoon, William Lee, Michael Proctor, St, Mike Tyers, Daphne Koller, Russ B Altman, Ronald W Davis, Corey Nislow, Guri Giaever
    posted to yeast phenotypic chemical_genomics by stajich on 2008-05-05 19:08:07 as ** along with 3 people and 1 group bala tmmurali nfreed Berkeley Mycology
  • Gene prediction in metagenomic fragments: a large scale machine learning approach
    BMC Bioinformatics, Vol. 9 (28 April 2008), 217.
    by Katharina J Hoff, Maike Tech, Thomas Lingner, Rolf Daniel, Burkhard Morgenstern, Peter Meinicke
    posted to metagenomics gene_prediction gene_finding by stajich on 2008-05-05 04:33:17 as ** along with 1 group Berkeley Mycology
  • Transcription Factor Substitution during the Evolution of Fungal Ribosome Regulation
    Molecular Cell, Vol. 29, No. 5. (14 March 2008), pp. 552-562.
    by Herve Hogues, Hugo Lavoie, Adnane Sellam, Maria Mangos, Terry Roemer, Enrico Purisima, Andre Nantel, Malcolm Whiteway
    posted to transcription_factor ribosomes fungi evolution by stajich on 2008-05-05 02:58:13 as ** along with 1 person and 1 group zwang Berkeley Mycology
  • Adaptive Evolution of Recently Duplicated Accessory Gland Protein Genes in Desert Drosophila
    Genetics, Vol. 177, No. 2. (1 October 2007), pp. 1023-1030.
    by Bradley J Wagstaff, David J Begun
    posted to sexual_selection gene_duplication drosophila by stajich on 2008-05-05 02:57:51 as ** along with 2 people and 2 groups breden signalduplication Berkeley Mycology signal-duplication
  • Long-distance dispersal and recombination in environmental populations of Cryptococcus neoformans var. grubii from India
    Microbiology, Vol. 154, No. 5. (1 May 2008), pp. 1513-1524.
    by Sanjay S Hiremath, Anuradha Chowdhary, Tusharantak Kowshik, Harbans S Randhawa, Sheng Sun, Jianping Xu
    posted to population_genetics cryptococcus by stajich on 2008-05-05 02:54:59 as ** along with 1 group Berkeley Mycology
  • The Neutral Coalescent Process for Recent Gene Duplications and Copy-Number Variants
    Genetics, Vol. 177, No. 2. (1 October 2007), pp. 987-1000.
    by Kevin R Thornton
    posted to population_genetics gene_duplication copy_number_variation coalescent by stajich on 2008-05-05 02:48:34 as ** along with 1 group Berkeley Mycology
  • Towards a molecular understanding of symbiont function: Identification of a fungal gene for the degradation of xylan in the fungus gardens of leaf-cutting ants
    BMC Microbiology, Vol. 8 (28 February 2008), 40.
    by Morten Schioett, Henrik, Lene Lange, Jacobus J Boomsma
    posted to rotting mutalism fungi ant by stajich on 2008-05-05 02:40:00 as ** along with 1 group Berkeley Mycology
  • 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 solexa rnaseq by stajich on 2008-05-02 06:49:25 as ** along with 2 people and 1 group gjuggler caseybrown Berkeley Mycology
  • Rapid large-scale evolutionary divergence in morphology and performance associated with exploitation of a different dietary resource.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 105, No. 12. (25 March 2008), pp. 4792-4795.
    by A Herrel, K Huyghe, B Vanhooydonck, T Backeljau, K Breugelmans, I Grbac, R Van Damme, DJ Irschick
    posted to evolution by stajich on 2008-05-02 02:05:55 as ** along with 2 people and 1 group iBartomeus operon Berkeley Mycology
  • Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
    Genome Res. (7 February 2008), gr.7080508.
    by David S Johnson, Wei Li, Benjamin D Gordon, Arindam Bhattacharjee, Bo Curry, Jayati Ghosh, Leonardo Brizuela, Jason S Carroll, Myles Brown, Paul Flicek, Christopher M Koch, Ian Dunham, Mark Bieda, Xiaoqin Xu, Peggy J Farnham, Philipp Kapranov, David A Nix, Thomas R Gingeras, Xinmin Zhang, Heather Holster, Nan Jiang, Roland Green, Jun S Song, Scott A Mccuine, Elizabeth Anton, Loan Nguyen, Nathan D Trinklein, Zhen Ye, Keith Ching, David Hawkins, Bing Ren, Peter C Scacheri, Joel Rozowsky, Alexander Karpikov, Ghia Euskirchen, Sherman Weissman, Mark Gerstein, Michael Snyder, Annie Yang, Zarmik Moqtaderi, Heather Hirsch, Hennady P Shulha, Yutao Fu, Zhiping Weng, Kevin Struhl, Richard M Myers, Jason D Lieb, Shirley X Liu
    posted to solexa sequencing chipseq by stajich on 2008-05-02 02:05:43 as ** along with 10 people and 2 groups gracio lp2 magusina jfr kengg djkt xiaobeizhao cabbagezs idonaldson caseybrown Berkeley Mycology BergmanLab
  • Life without RNase P
    Nature, Vol. 453, No. 7191., pp. 120-123.
    by Lennart Randau, Imke Schröder, Dieter Söll
    posted to rnasep noncoding_rna archea by stajich on 2008-05-01 02:25:51 as ** along with 3 people and 2 groups kinestetika zwang neils microbiology_nijmegen Berkeley Mycology
  • GENOMEPOP: A program to simulate genomes in populations
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Antonio C Rodriguez
    posted to simulation population_genomics methods bioinformatics by stajich on 2008-04-30 19:51:50 as ** along with 1 person and 1 group tonia_schwartz Berkeley Mycology
  • Temperature-induced switch to the pathogenic yeast form of Histoplasma capsulatum requires Ryp1, a conserved transcriptional regulator
    Proceedings of the National Academy of Sciences, Vol. 105, No. 12. (25 March 2008), pp. 4880-4885.
    by Van Q Nguyen, Anita Sil
    posted to transcriptional_regulation histoplasma dimorphism by stajich on 2008-04-27 21:41:52 as ** along with 1 group Berkeley Mycology
  • Discovering microRNAs from deep sequencing data using miRDeep
    Nature Biotechnology, Vol. 26, No. 4., pp. 407-415.
    by Marc R Friedländer, Wei Chen, Catherine Adamidi, Jonas Maaskola, Ralf Einspanier, Signe Knespel, Nikolaus Rajewsky
    posted to smallrna mirna methods evolution by stajich on 2008-04-25 23:40:15 as ** along with 2 people and 1 group tmmurali giovanni Berkeley Mycology
  • Adaptive Evolution of Newly Emerged Micro-RNA Genes in Drosophila
    Mol Biol Evol, Vol. 25, No. 5. (1 May 2008), pp. 929-938.
    by Jian Lu, Yonggui Fu, Supriya Kumar, Yang Shen, Kai Zeng, Anlong Xu, Richard Carthew, Chung-I Wu
    posted to smallrna mirna evolution drosophila by stajich on 2008-04-25 23:38:17 as ** along with 1 person and 1 group lp2 Berkeley Mycology
  • The birth and death of microRNA genes in Drosophila.
    Nat Genet (17 February 2008)
    by Jian Lu, Yang Shen, Qingfa Wu, Supriya Kumar, Bin He, Suhua Shi, Richard W W Carthew, San Ming M Wang, Chung-I I Wu
    posted to smallrna mirna methods evolution drosophila by stajich on 2008-04-25 23:38:05 as ** along with 5 people and 1 group djkt bootsy emptyhb cellison megraw Berkeley Mycology
  • Conservation of divergent transcription in fungi
    Trends in Genetics, Vol. 24, No. 5. (May 2008), pp. 207-211.
    by Philip R Kensche, Martin Oti, Bas E Dutilh, Martijn A Huynen
    posted to transcription fungi evolution divergent_genes by stajich on 2008-04-25 23:37:16 as ** along with 1 group Berkeley Mycology
  • Statistical issues in the analysis of Illumina data
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Mark Dunning, Nuno B Morais, Andy Lynch, Simon Tavare, Matthew Ritchie
    posted to statistics shortread methods illumina array by stajich on 2008-04-25 16:11:11 as ** along with 3 people and 1 group neveaire RockHI thomaskelder Berkeley Mycology
  • DNA from herbarium specimens settles a controversy about origins of the European potato
    Am. J. Bot., Vol. 95, No. 2. (1 February 2008), pp. 252-257.
    by Mercedes Ames, David M Spooner
    posted to plant hybridization herbarium evolution by stajich on 2008-04-24 18:28:18 as ** along with 1 group Berkeley Mycology
  • A nuclear receptor-like pathway regulating multidrug resistance in fungi
    Nature, Vol. 452, No. 7187., pp. 604-609.
    by Jitendra K Thakur, Haribabu Arthanari, Fajun Yang, Shih-Jung Pan, Xiaochun Fan, Julia Breger, Dominique P Frueh, Kailash Gulshan, Darrick K Li, Eleftherios Mylonakis, Kevin Struhl, Scott W Moye-Rowley, Brendan P Cormack, Gerhard Wagner, Anders M Näär
    posted to receptor nuclear fungi drug_resistance by stajich on 2008-04-24 18:24:33 as ** along with 1 group Berkeley Mycology
  • Identifying selected regions from heterozygosity and divergence using a light-coverage genomic dataset from two human populations.
    PLoS ONE, Vol. 3, No. 3. (2008)
    by TK Oleksyk, K Zhao, FM De La Vega, DA Gilbert, SJ O'Brien, MW Smith
    posted to population_genomics human by stajich on 2008-04-23 20:13:04 as ** along with 1 group Berkeley Mycology
  • Evolution of microRNAs and their targets: Are all microRNAs biologically relevant?
    Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Vol. In Press, Uncorrected Proof
    by Michael J Axtell
    posted to smallrna mirna evolution by stajich on 2008-04-23 20:09:56 as ** along with 2 people and 1 group maralena eckart_bindewald Berkeley Mycology
  • Multigene analysis suggests ecological speciation in the fungal pathogen Claviceps purpurea
    Molecular Ecology, Vol. 17, No. 9. (2008), pp. 2276-2286.
    by GW Douhan, ME Smith, KL Huyrn, A Westbrook, P Beerli, AJ Fisher
    posted to claviceps ecological_speciation fungi by stajich on 2008-04-22 07:11:47 as ** along with 1 group Berkeley Mycology
  • Soil as natural reservoir for human pathogenic fungi.
    Science (New York, N.Y.), Vol. 123, No. 3203. (18 May 1956), pp. 876-879.
    by L AJELLO
    posted to coccidioides coccipaper keritinophilic pathogen by stajich on 2008-04-21 06:16:44 as ** along with 1 group Berkeley Mycology
  • The use of bait in isolating coccidioides immitis from soil: A preliminary study
    Mycopathologia, Vol. 36, No. 1. (31 December 1975), pp. 28-32.
    by GF Orr
    posted to bait coccidioides coccipaper by stajich on 2008-04-21 06:00:45 as ** along with 1 group Berkeley Mycology
  • Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.
    Mol Biol Evol, Vol. 17, No. 4. (April 2000), pp. 540-552.
    by J Castresana
    posted to alignment coccipaper methods phylogenetics by stajich on 2008-04-21 01:28:35 as ** along with 4 people and 1 group cmzmasek aprasad treangen ArtemPankin Berkeley Mycology
  • 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 alignment coccipaper methods multiple_sequence_alignment by stajich on 2008-04-21 01:26:08 as ** along with 4 people and 1 group bpb radek balajis olympos Berkeley Mycology
  • Gene prediction with a hidden Markov model and a new intron submodel.
    Bioinformatics, Vol. 19 Suppl 2 (October 2003)
    by M Stanke, S Waack
    posted to coccipaper gene_prediction genome_annotation by stajich on 2008-04-21 01:19:32 as ** along with 3 people and 2 groups indigoviolet alexl wenhan EisenLab Berkeley Mycology
  • Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion
    PLoS Computational Biology, Vol. 4, No. 1. (1 January 2008), e13.
    by Guo-Cheng Yuan, Jun S Liu
    posted to computational_biology nucleosome prediction whole_genome by stajich on 2008-04-20 02:12:19 as ** along with 1 person and 1 group aalibes Berkeley Mycology
  • A multi-locus phylogeny for Phytophthora utilizing markers derived from complete genome sequences.
    Fungal genetics and biology : FG & B, Vol. 45, No. 3. (March 2008), pp. 266-277.
    by JE Blair, MD Coffey, SY Park, DM Geiser, S Kang
    posted to oomycete phylogenetic_marker_selection phylogenetics phylogeny phytophthora by stajich on 2008-04-19 21:42:49 as ** along with 1 group Berkeley Mycology
  • A test for concordance between the multilocus genealogies of genes and microsatellites in the pathogenic fungus Coccidioides immitis.
    Molecular biology and evolution, Vol. 17, No. 8. (August 2000), pp. 1164-1174.
    by MC Fisher, G Koenig, TJ White, JW Taylor
    posted to coccidioides coccipaper cryptic_species gene_tree speciation species_tree by stajich on 2008-04-19 21:41:17 as ** along with 1 group Berkeley Mycology
  • Disease surveillance in recombining pathogens: multilocus genotypes identify sources of human Coccidioides infections.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 13. (25 June 2002), pp. 9067-9071.
    by MC Fisher, B Rannala, V Chaturvedi, JW Taylor
    posted to coccidioides coccipaper cryptic_species recombination speciation by stajich on 2008-04-19 21:40:12 as ** along with 1 group Berkeley Mycology
  • Biogeographic range expansion into South America by Coccidioides immitis mirrors New World patterns of human migration.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 98, No. 8. (10 April 2001), pp. 4558-4562.
    by MC Fisher, GL Koenig, TJ White, G San-Blas, R Negroni, IG Alvarez, B Wanke, JW Taylor
    posted to coccidioides coccipaper cryptic_species speciation by stajich on 2008-04-19 21:39:31 as ** along with 1 group Berkeley Mycology
  • A parasitic phase-specific adhesin of Coccidioides immitis contributes to the virulence of this respiratory Fungal pathogen.
    Infection and immunity, Vol. 70, No. 7. (July 2002), pp. 3443-3456.
    by CY Hung, JJ Yu, KR Seshan, U Reichard, GT Cole
    posted to coccidioides coccipaper virulence virulence_factor by stajich on 2008-04-19 21:38:38 as ** along with 1 group Berkeley Mycology
  • Positive directional selection in the proline-rich antigen (PRA) gene among the human pathogenic fungi Coccidioides immitis, C. posadasii and their closest relatives.
    Molecular biology and evolution, Vol. 21, No. 6. (June 2004), pp. 1134-1145.
    by H Johannesson, P Vidal, J Guarro, RA Herr, GT Cole, JW Taylor
    posted to coccidioides coccipaper positive_selection virulence_factor by stajich on 2008-04-19 21:37:31 as ** along with 1 group Berkeley Mycology
  • A metalloproteinase of Coccidioides posadasii contributes to evasion of host detection.
    Infection and immunity, Vol. 73, No. 10. (October 2005), pp. 6689-6703.
    by CY Hung, KR Seshan, JJ Yu, R Schaller, J Xue, V Basrur, MJ Gardner, GT Cole
    posted to coccidioides coccipaper virulence virulence_factor by stajich on 2008-04-19 21:36:13 as ** along with 1 group Berkeley Mycology
  • PAML: a program package for phylogenetic analysis by maximum likelihood.
    Comput Appl Biosci, Vol. 13, No. 5. (October 1997), pp. 555-556.
    by Z Yang
    posted to coccipaper codon_model methods molecular_evolution paml phylogenetics by stajich on 2008-04-19 21:34:23 as ** along with 9 people and 3 groups bjorns chrn chad_davis indigoviolet penka BioNica pv usagi-kirin jmjimenez EisenLab Nie Berkeley Mycology
  • Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages.
    Mol Biol Evol, Vol. 19, No. 6. (June 2002), pp. 908-917.
    by Z Yang, R Nielsen
    posted to coccipaper codon_model molecular_evolution paml selection selection_test by stajich on 2008-04-19 21:31:03 as ** along with 3 people and 2 groups stevanspringer operon Garamonfok FAB-lab Berkeley Mycology
  • Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection
    Molecular Biology and Evolution, Vol. 22, No. 4. (April 2005), pp. 1107-1118.
    by Ziheng Yang, Wendy S Wong, Rasmus Nielsen
    posted to coccipaper codon_model molecular_evolution paml positive_selecion selection selection_test by stajich on 2008-04-19 21:29:42 as ** along with 4 people and 1 group rabu BioNica Natasha Garamonfok Berkeley Mycology
  • PAML 4: Phylogenetic Analysis by Maximum Likelihood
    Mol Biol Evol (4 May 2007), msm088.
    by Ziheng Yang
    posted to coccipaper codon_model molecular_evolution paml selection selection_test by stajich on 2008-04-19 21:29:02 as ** along with 6 people and 1 group RamuAnandakrishnan operon akifumi hdopazo BioNica ryanraaum Berkeley Mycology
  • Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage.
    Mol Biol Evol (3 January 2008)
    by Ziheng Yang, Rasmus Nielsen
    posted to codon_model molecular_evolution paml selection selection_test by stajich on 2008-04-19 21:28:47 as ** along with 2 people and 1 group cjeans gjuggler Berkeley Mycology
  • Genome sequences of the honey bee pathogens Paenibacillus larvae and Ascosphaera apis
    Insect Molecular Biology, Vol. 15, No. 5. (October 2006), pp. 715-718.
    by X Qin, JD Evans, KA Aronstein, KD Murray, GM Weinstock
    posted to ascosphaera coccipaper genome paenibacillus by stajich on 2008-04-19 21:26:14 as read along with 1 group Berkeley Mycology
  • Host Factors That Control Long Terminal Repeat Retrotransposons in Saccharomyces cerevisiae: Implications for Regulation of Mammalian Retroviruses
    Eukaryotic Cell, Vol. 6, No. 7. (1 July 2007), pp. 1069-1080.
    by Patrick H Maxwell, Joan M Curcio
    posted to ltr repeats retrotransposon saccharomyces transposable_elements transposon by stajich on 2008-04-19 17:34:03 as ** along with 1 group Berkeley Mycology
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