metaBIT, an integrative and automated metagenomic pipeline for analysing microbial profiles from high-throughput sequencing shotgun data

InteMAP: Integrated metagenomic assembly pipeline for NGS short reads

(2015) Binbin Lai et al.   BMC BIOINFORMATICS

The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies

(2015) J Paul Brooks et al.   BMC MICROBIOLOGY

Evolutionary Genomics and Conservation of the Endangered Przewalski’s Horse

(2015) Clio Der Sarkissian et al.   CURRENT BIOLOGY

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Reconstructing ancient genomes and epigenomes

(2015) Ludovic Orlando et al.   NATURE REVIEWS GENETICS

Molecular cartography of the human skin surface in 3D

(2015) Amina Bouslimani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments

(2015) Pablo Librado et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe

(2015) Gemma L. Kay et al.   Nature Communications

Pros and cons of methylation-based enrichment methods for ancient DNA

(2015) Andaine Seguin-Orlando et al.   Scientific Reports

Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

(2015) Kirsten A. Ziesemer et al.   Scientific Reports

The Earth Microbiome project: successes and aspirations

(2014) Jack A Gilbert et al.   BMC BIOLOGY

Comparison of seven methods for extraction of bacterial DNA from fecal and cecal samples of mice

(2014) Janina Ferrand et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Shotgun microbial profiling of fossil remains

(2014) C. Der Sarkissian et al.   MOLECULAR ECOLOGY

Genomics of schizophrenia: time to consider the gut microbiome?

(2014) T G Dinan et al.   MOLECULAR PSYCHIATRY

Pathogens and host immunity in the ancient human oral cavity

(2014) Christina Warinner et al.   NATURE GENETICS

Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX

(2014) Mikkel Schubert et al.   Nature Protocols

Parallel detection of ancient pathogens via array-based DNA capture

(2014) K. I. Bos et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ancient and modern environmental DNA

(2014) Mikkel Winther Pedersen et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Prehistoric genomes reveal the genetic foundation and cost of horse domestication

(2014) Mikkel Schubert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array

(2014) Alison M. Devault et al.   Scientific Reports

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

(2013) Hákon Jónsson et al.   BIOINFORMATICS

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

(2013) Pascal Hingamp et al.   ISME Journal

Computational meta'omics for microbial community studies

(2013) N. Segata et al.   Molecular Systems Biology

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

(2013) Ludovic Orlando et al.   NATURE

Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions

(2013) Christina J Adler et al.   NATURE GENETICS

Ligation Bias in Illumina Next-Generation DNA Libraries: Implications for Sequencing Ancient Genomes

(2013) Andaine Seguin-Orlando et al.   PLoS One

Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries

(2012) Jesse Dabney et al.   BIOTECHNIQUES

A framework for human microbiome research

(2012)   NATURE

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Functional interactions between the gut microbiota and host metabolism

(2012) Valentina Tremaroli et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

(2012) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

A draft genome of Yersinia pestis from victims of the Black Death

(2011) Kirsten I. Bos et al.   NATURE

The skin microbiome

(2011) Elizabeth A. Grice et al.   NATURE REVIEWS MICROBIOLOGY

An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia

(2011) M. Rasmussen et al.   SCIENCE

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Ancient human genome sequence of an extinct Palaeo-Eskimo

(2010) Morten Rasmussen et al.   NATURE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

(2009) C. L. Lauber et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

Sequencing the nuclear genome of the extinct woolly mammoth

(2008) Webb Miller et al.   NATURE

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes

(2008) M. T. P. Gilbert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA