Pop group meeting: Difference between revisions
Jump to navigation
Jump to search
| Line 18: | Line 18: | ||
= 10/13/2008 = | = 10/13/2008 = | ||
# Daniela Puiu | # Daniela Puiu [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0003373 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: [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 | # 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) | # MohammadReza Ghodsi [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2557142 Probing Metagenomics by Rapid Cluster Analysis of Very Large Datasets] (PLoS one) | ||
Revision as of 20:28, 13 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 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)
- Niranjan Nagarajan Metagenomics: questions to answer (Nature)
- 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 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)