Pop group meeting: Difference between revisions
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# James Robert White [http://www.pnas.org/content/104/21/8918.full Artificial selection of simulated microbial ecosystems.] PNAS | # James Robert White [http://www.pnas.org/content/104/21/8918.full Artificial selection of simulated microbial ecosystems.] PNAS | ||
# MohammadReza Ghodsi [http://aem.asm.org/cgi/content/abstract/74/5/1453 Metagenomics: Read Length Matters] Applied Environmental Microbiology | # MohammadReza 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 = | = 10/13/2008 = | ||
| Line 33: | Line 34: | ||
# Daniela Puiu [http://genomebiology.com/content/pdf/gb-2008-9-10-r151.pdf A simple, fast, and accurate method of phylogenomic inference] Genome Biology | # 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 | # 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 | |||
= 10/27/2008 = | = 10/27/2008 = | ||
Revision as of 14:31, 27 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
- Sergey Koren Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads PLoS Computational Biology
10/13/2008
- Daniela Puiu, Daniel Sommer MetaSim—A Sequencing Simulator for Genomics and Metagenomics PLoS ONE
- 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)
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
- Bo Liu Accelerated evolution of resistance in multidrug environments PNAS
Drug interactions modulate the potential for evolution of resistance PNAS - 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
- Sergey Koren Scientific software: seeing the SNPs between us Nature Methods
10/27/2008
- Sergey Koren Aggressive Assembly of Pyrosequencing Reads with Mates Bioinformatics
- Daniela Puiu ZOOM! Zillions of oligos mapped Bioinformatics