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

Shotgun microbial profiling of fossil remains

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

Mitochondrial Diversity and Distribution of African Green Monkeys (ChlorocebusGray, 1870)

(2013) TANJA HAUS et al.   AMERICAN JOURNAL OF PRIMATOLOGY

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

(2013) Hákon Jónsson et al.   BIOINFORMATICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Towards a million-year-old genome

(2013) Craig D. Millar et al.   NATURE

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

(2013) Ludovic Orlando et al.   NATURE

Dietary intervention impact on gut microbial gene richness

(2013) Aurélie Cotillard et al.   NATURE

A mitochondrial genome sequence of a hominin from Sima de los Huesos

(2013) Matthias Meyer et al.   NATURE

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

(2013) Maanasa Raghavan et al.   NATURE

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

Predicting the molecular complexity of sequencing libraries

(2013) Timothy Daley et al.   NATURE METHODS

Mitochondrial Phylogenomics of Modern and Ancient Equids

(2013) Julia T. Vilstrup et al.   PLoS One

DNA analysis of an early modern human from Tianyuan Cave, China

(2013) Q. Fu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments

(2013) J. Dabney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reconstructing genome evolution in historic samples of the Irish potato famine pathogen

(2013) Michael D. Martin et al.   Nature Communications

The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine

(2013) Kentaro Yoshida et al.   eLife

Improving ancient DNA read mapping against modern reference genomes

(2012) Mikkel Schubert et al.   BMC GENOMICS

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   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

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

Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change

(2012) W. Miller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coprolites as a source of information on the genome and diet of the cave hyena

(2012) C. Bon et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe

(2012) P. Skoglund et al.   SCIENCE

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

Next-generation sequencing offers new insights into DNA degradation

(2012) Søren Overballe-Petersen et al.   TRENDS IN BIOTECHNOLOGY

New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing

(2012) Andreas Keller et al.   Nature Communications

Tabix: fast retrieval of sequence features from generic TAB-delimited files

(2011) H. Li   BIOINFORMATICS

mapDamage: testing for damage patterns in ancient DNA sequences

(2011) Aurelien Ginolhac et al.   BIOINFORMATICS

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

The Complete Mitochondrial Genome of an 11,450-year-old Aurochsen (Bos primigenius) from Central Italy

(2011) Martina Lari et al.   BMC EVOLUTIONARY BIOLOGY

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

(2011) Kirsten I. Bos et al.   NATURE

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia

(2011) M. Rasmussen et al.   SCIENCE

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

A Complete mtDNA Genome of an Early Modern Human from Kostenki, Russia

(2010) Johannes Krause et al.   CURRENT BIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

The complete mitochondrial DNA genome of an unknown hominin from southern Siberia

(2010) Johannes Krause et al.   NATURE

Genetic history of an archaic hominin group from Denisova Cave in Siberia

(2010) David Reich et al.   NATURE

Ancient human genome sequence of an extinct Palaeo-Eskimo

(2010) Morten Rasmussen et al.   NATURE

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear

(2010) C. Lindqvist et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture

(2010) H. A. Burbano et al.   SCIENCE

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Methods for comparative metagenomics

(2009) Daniel H Huson et al.   BMC BIOINFORMATICS

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans

(2009) Brian J. Haas et al.   NATURE

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

(2009) Madeleine P Ball et al.   NATURE BIOTECHNOLOGY

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

(2009) Peter J. A. Cock et al.   NUCLEIC ACIDS RESEARCH

Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA

(2009) Adrian W. Briggs et al.   NUCLEIC ACIDS RESEARCH

The complete genome of an individual by massively parallel DNA sequencing

(2008) David A. Wheeler et al.   NATURE

Sequencing the nuclear genome of the extinct woolly mammoth

(2008) Webb Miller 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

Paleo-Eskimo mtDNA Genome Reveals Matrilineal Discontinuity in Greenland

(2008) M. T. P. Gilbert et al.   SCIENCE