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  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)


  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


  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


  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


  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


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


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


  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


  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


  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