Pop group meeting: Difference between revisions
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# 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) | # 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) | ||
# 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) | ||
# Theodore 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) | # Theodore 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) | ||
Revision as of 20:57, 20 October 2008
09/29/2008
- Benjamin Langmead Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression (PLoS one)
- 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)
- Daniela Puiu Sequencing of natural strains of Arabidopsis thaliana with short reads (Genome Research)
- Dan Sommer, Niranjan Nagarajan Metagenomics: questions to answer (Nature)
- James Robert White Microbial population dynamics during aerobic sludge granulation at different organic loading rates (ScienceDirect)
- Mohammad Reza Ghodsi A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library (NAR)
- Sergey Koren R/parallel - speeding up bioinformatics analysis with R (BMC Bioinformatics)
- 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
- Bo Liu The convergence of carbohydrate active gene repertoires in human gut microbes. PNAS
- Daniela Puiu SeqMap: mapping massive amount of oligonucleotides to the genome Bioinformatics
- James Robert White Artificial selection of simulated microbial ecosystems. PNAS
- MohammadReza Ghodsi Metagenomics: Read Length Matters Applied Environmental Microbiology
10/13/2008
- Daniela Puiu (Daniel Sommer, same paper) MetaSim—A Sequencing Simulator for Genomics and Metagenomics 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
- Bo Liu & James Robert White Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth. Science
- MohammadReza Ghodsi Probing Metagenomics by Rapid Cluster Analysis of Very Large Datasets (PLoS one)
10/20/2008
- Daniel Sommer NCBI Reference Sequences: current status, policy and new initiatives NAR
- Daniela Puiu A simple, fast, and accurate method of phylogenomic inference Genome Biology
- Niranjan Nagarajan The Stastical Power of Phylogenetic Motif Models RECOMB 2008