Pop group meeting: Difference between revisions

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= 10/13/2008 =
= 10/13/2008 =
# Daniela Puiu, Daniel Sommer [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0003373 MetaSim—A Sequencing Simulator for Genomics and Metagenomics] PLoS ONE
# Daniela Puiu, Daniel Sommer [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0003373 MetaSim—A Sequencing Simulator for Genomics and Metagenomics] PLoS ONE
    MetaSim software:
# Bo Liu, James Robert White [http://www.sciencemag.org/cgi/content/full/322/5899/275 Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth.] Science
# MohammadReza Ghodsi [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2557142 Probing Metagenomics by Rapid Cluster Analysis of Very Large Datasets] (PLoS one)
 
MetaSim software:
       Location:        /fs/sz-user-supported/common/packages/MetaSim/  
       Location:        /fs/sz-user-supported/common/packages/MetaSim/  
       Executable(Java): /fs/sz-user-supported/common/packages/MetaSim/metasim/MetaSim  
       Executable(Java): /fs/sz-user-supported/common/packages/MetaSim/metasim/MetaSim  
       Database:        /fs/sz-user-supported/common/packages/MetaSim/database             # create a symlink to it from your working directory, otherwise you have to import it  
       Database:        /fs/sz-user-supported/common/packages/MetaSim/database          
    NCBI databases: [ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/all.fna.tar.gz Complete bacteria]; [ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz Taxonomy]
      create a symlink to it from your working directory, otherwise you have to import it  
 
      NCBI databases: [ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/all.fna.tar.gz Complete bacteria];   [ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz Taxonomy]
# Bo Liu & James Robert White [http://www.sciencemag.org/cgi/content/full/322/5899/275 Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth.] Science
# MohammadReza Ghodsi [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2557142 Probing Metagenomics by Rapid Cluster Analysis of Very Large Datasets] (PLoS one)


= 10/20/2008 =
= 10/20/2008 =

Revision as of 20:59, 20 October 2008

09/29/2008

  1. Benjamin Langmead Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression (PLoS one)
  2. Bo Liu Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues (Genome Biology)
  3. Daniela Puiu Sequencing of natural strains of Arabidopsis thaliana with short reads (Genome Research)
  4. Dan Sommer, Niranjan Nagarajan Metagenomics: questions to answer (Nature)
  5. James Robert White Microbial population dynamics during aerobic sludge granulation at different organic loading rates (ScienceDirect)
  6. Mohammad Reza Ghodsi A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library (NAR)
  7. Sergey Koren R/parallel - speeding up bioinformatics analysis with R (BMC Bioinformatics)
  8. Theodore Gibbons High-resolution metagenomics targets specific functional types in complex microbial communities (Nature Biotechnology)
    Molecular eco-systems biology: towards an understanding of community function (Systems Microbiology)

10/06/2008

  1. Bo Liu The convergence of carbohydrate active gene repertoires in human gut microbes. PNAS
  2. Daniela Puiu SeqMap: mapping massive amount of oligonucleotides to the genome Bioinformatics
  3. James Robert White Artificial selection of simulated microbial ecosystems. PNAS
  4. MohammadReza Ghodsi Metagenomics: Read Length Matters Applied Environmental Microbiology

10/13/2008

  1. Daniela Puiu, Daniel Sommer MetaSim—A Sequencing Simulator for Genomics and Metagenomics PLoS ONE
  2. Bo Liu, James Robert White Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth. Science
  3. MohammadReza Ghodsi Probing Metagenomics by Rapid Cluster Analysis of Very Large Datasets (PLoS one)

MetaSim software: 

     Location:         /fs/sz-user-supported/common/packages/MetaSim/ 
     Executable(Java): /fs/sz-user-supported/common/packages/MetaSim/metasim/MetaSim 
     Database:         /fs/sz-user-supported/common/packages/MetaSim/database           
     create a symlink to it from your working directory, otherwise you have to import it 
     NCBI databases: Complete bacteria;   Taxonomy

10/20/2008

  1. Daniel Sommer NCBI Reference Sequences: current status, policy and new initiatives NAR
  2. Daniela Puiu A simple, fast, and accurate method of phylogenomic inference Genome Biology
  3. Niranjan Nagarajan The Stastical Power of Phylogenetic Motif Models RECOMB 2008
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