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= Meetings =
= 09/29/2008 =


== 09/29/2008 ==
=== Papers ===
# Benjamin Langmead [http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0003263 Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression] (PLoS one)
# Benjamin Langmead [http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0003263 Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression] (PLoS one)
# Bo Liu
# Bo Liu [http://genomebiology.com/2008/9/9/R139 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)
# Daniela Puiu [http://genome.cshlp.org/cgi/reprint/gr.080200.108v1 Sequencing of natural strains of Arabidopsis thaliana with short reads] (Genome Research)
# Daniela Puiu [http://genome.cshlp.org/cgi/reprint/gr.080200.108v1 Sequencing of natural strains of Arabidopsis thaliana with short reads] (Genome Research)
# Dan Sommer [http://www.nature.com/nature/journal/v455/n7212/edsumm/e080925-04.html Metagenomics: questions to answer] (Nature)
# Dan Sommer, Niranjan Nagarajan [http://www.nature.com/nature/journal/v455/n7212/edsumm/e080925-04.html Metagenomics: questions to answer] (Nature)
# James Robert White [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V73-4SHVST0-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=961305&md5=4115e7b8186a36db60f6b11a217a8798 Microbial population dynamics during aerobic sludge granulation at different organic loading rates] (ScienceDirect)
# James Robert White [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V73-4SHVST0-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=961305&md5=4115e7b8186a36db60f6b11a217a8798 Microbial population dynamics during aerobic sludge granulation at different organic loading rates] (ScienceDirect)
# Mohammad Reza Ghodsi [http://nar.oxfordjournals.org/cgi/content/short/36/16/5180 A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library] (NAR)
# Mohammad Reza Ghodsi [http://nar.oxfordjournals.org/cgi/content/short/36/16/5180 A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library] (NAR)
# Niranjan Nagarajan [http://www.nature.com/nature/journal/v455/n7212/edsumm/e080925-04.html Metagenomics: questions to answer] (Nature)
# Sergey Koren [http://www.biomedcentral.com/1471-2105/9/390 R/parallel - speeding up bioinformatics analysis with R] (BMC Bioinformatics)
# Sergey Koren [http://www.biomedcentral.com/1471-2105/9/390 R/parallel - speeding up bioinformatics analysis with R] (BMC Bioinformatics)
# Ted Gibbons [http://www.ncbi.nlm.nih.gov/pubmed/18711340 High-resolution metagenomics targets specific functional types in complex microbial communities] (Nature Biotechnology) <BR> [http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function] (Systems Microbiology)
= 10/06/2008 =
# Bo Liu [http://www.pnas.org/content/105/39/15076.short The convergence of carbohydrate active gene repertoires in human gut microbes.] PNAS
# Daniela Puiu [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/20/2395 SeqMap: mapping massive amount of oligonucleotides to the genome] Bioinformatics
# James Robert White [http://www.pnas.org/content/104/21/8918.full Artificial selection of simulated microbial ecosystems.] PNAS
# Mohammad Reza Ghodsi [http://aem.asm.org/cgi/content/abstract/74/5/1453 Metagenomics: Read Length Matters] Applied Environmental Microbiology
# Sergey Koren [http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.1000186 Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads] PLoS Computational Biology
= 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
# 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/
      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: [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]
= 10/20/2008 =
# Bo Liu [http://www.pnas.org/content/105/37/13977.short?rss=1 Accelerated evolution of resistance in multidrug environments] PNAS <br> [http://www.pnas.org/content/105/39/14918.short?rss=1 Drug interactions modulate the potential for evolution of resistance] PNAS
# Daniel Sommer [http://www.ncbi.nlm.nih.gov/pubmed/18927115?dopt=Abstract NCBI Reference Sequences: current status, policy and new initiatives] NAR
# Daniela Puiu [http://genomebiology.com/content/pdf/gb-2008-9-10-r151.pdf A simple, fast, and accurate method of phylogenomic inference] Genome Biology
# Niranjan Nagarajan [http://www.springerlink.com/content/cn3551154w232l73/fulltext.pdf The Stastical Power of Phylogenetic Motif Models] RECOMB 2008
# Sergey Koren [http://www.nature.com/nmeth/journal/v5/n10/full/nmeth1008-903.html Scientific software: seeing the SNPs between us] Nature Methods
# Mohammadreza Ghodsi [http://www.biomedcentral.com/1471-2105/9/386 The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes] BMC Bioinformatics
= 10/27/2008 =
# Bo Liu [http://www.pnas.org/content/105/37/14130.short?rss=1 Frequent emergence and limited geographic dispersal of methicillin-resistant Staphylococcus aureus] PNAS
# Sergey Koren [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn548 Aggressive Assembly of Pyrosequencing Reads with Mates] Bioinformatics
# Daniela Puiu [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/21/2431 ZOOM! Zillions of oligos mapped] Bioinformatics
# Mohammadreza Ghodsi [http://www.ncbi.nlm.nih.gov/pubmed/18692931 Biodiversity of the microbial community in a Spanish farmhouse cheese as revealed by culture-dependent and culture-independent methods]
= 11/03/2008 =
# Daniela Puiu [http://genome.cshlp.org/cgi/content/abstract/gr.7088808v1 Short read fragment assembly of bacterial genomes] (Genome Research)
= 11/10/2008 =
# Bo Liu [http://www.pnas.org/content/early/2008/11/04/0802782105.abstract Metagenome analysis of an extreme microbial symbiosis reveals eurythermal adaptation and metabolic flexibility] PNAS
= 11/17/2008 =
# Bo Liu [http://bioinformatics.oxfordjournals.org/cgi/content/short/24/22/2579?rss=1 Phylogenetic distances are encoded in networks of interacting pathways] Bioinformatics
# Daniela Puiu [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn582 Human genomes as email attachments] Bioinformatics
# Mohammad Ghodsi [http://nar.oxfordjournals.org/cgi/content/short/36/18/e120 Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers] Nucleic Acids Research
# Sergey Koren [http://www.biomedcentral.com/1471-2105/9/420/abstract XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data] (BMC Bioinformatics)
# James Robert White [http://www.pnas.org/content/early/2008/08/08/0801925105.abstract?etoc Resistance, resilience, and redundancy in microbial communities] PNAS
= 11/24/2008 =
# Ted Gibbons [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pbio.0060295 Gut Reaction: Pyrosequencing Provides the Poop on Distal Gut Bacteria (summary)] PLoS <br> [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pbio.0060280 The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing] PLoS <br> [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000255 Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing] PLoS Genetics
= 12/1/2008 =
# Mohammad Ghodsi [http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0002836 Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing] PLoS ONE
# Ben Langmead [http://www.sciencemag.org/cgi/rapidpdf/1162986v1.pdf Real-Time DNA Sequencing from Single Polymerase Molecules], Science

Latest revision as of 21:04, 8 December 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. Ted 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. Mohammad Reza Ghodsi Metagenomics: Read Length Matters Applied Environmental Microbiology
  5. Sergey Koren Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads PLoS Computational Biology

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. Bo Liu Accelerated evolution of resistance in multidrug environments PNAS
    Drug interactions modulate the potential for evolution of resistance PNAS
  2. Daniel Sommer NCBI Reference Sequences: current status, policy and new initiatives NAR
  3. Daniela Puiu A simple, fast, and accurate method of phylogenomic inference Genome Biology
  4. Niranjan Nagarajan The Stastical Power of Phylogenetic Motif Models RECOMB 2008
  5. Sergey Koren Scientific software: seeing the SNPs between us Nature Methods
  6. Mohammadreza Ghodsi The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes BMC Bioinformatics

10/27/2008

  1. Bo Liu Frequent emergence and limited geographic dispersal of methicillin-resistant Staphylococcus aureus PNAS
  2. Sergey Koren Aggressive Assembly of Pyrosequencing Reads with Mates Bioinformatics
  3. Daniela Puiu ZOOM! Zillions of oligos mapped Bioinformatics
  4. Mohammadreza Ghodsi Biodiversity of the microbial community in a Spanish farmhouse cheese as revealed by culture-dependent and culture-independent methods

11/03/2008

  1. Daniela Puiu Short read fragment assembly of bacterial genomes (Genome Research)

11/10/2008

  1. Bo Liu Metagenome analysis of an extreme microbial symbiosis reveals eurythermal adaptation and metabolic flexibility PNAS

11/17/2008

  1. Bo Liu Phylogenetic distances are encoded in networks of interacting pathways Bioinformatics
  2. Daniela Puiu Human genomes as email attachments Bioinformatics
  3. Mohammad Ghodsi Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers Nucleic Acids Research
  4. Sergey Koren XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data (BMC Bioinformatics)
  5. James Robert White Resistance, resilience, and redundancy in microbial communities PNAS

11/24/2008

  1. Ted Gibbons Gut Reaction: Pyrosequencing Provides the Poop on Distal Gut Bacteria (summary) PLoS
    The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing PLoS
    Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing PLoS Genetics

12/1/2008

  1. Mohammad Ghodsi Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing PLoS ONE
  2. Ben Langmead Real-Time DNA Sequencing from Single Polymerase Molecules, Science