Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past

Non-Cholera Vibrios: The Microbial Barometer of Climate Change

(2017) Craig Baker-Austin et al.   TRENDS IN MICROBIOLOGY

Taming the Past: Ancient DNA and the Study of Animal Domestication

(2017) David E. MacHugh et al.   Annual Review of Animal Biosciences

The Egyptian Red Sea coastal microbiome: A study revealing differential microbial responses to diverse anthropogenic pollutants

(2016) Ghada A. Mustafa et al.   ENVIRONMENTAL POLLUTION

De novo assembly and annotation of the European abalone Haliotis tuberculata transcriptome

(2016) Ewan Harney et al.   Marine Genomics

Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX

(2016) Kristian Hanghøj et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2016) Guillaume Louvel et al.   Molecular Ecology Resources

Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins

(2016) Matthias Meyer et al.   NATURE

A First Insight into the Genome of the Filter-Feeder Mussel Mytilus galloprovincialis

(2016) Maria Murgarella et al.   PLoS One

Climate influence onVibrioand associated human diseases during the past half-century in the coastal North Atlantic

(2016) Luigi Vezzulli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ancient DNA and human history

(2016) Montgomery Slatkin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary Patterns and Processes: Lessons from Ancient DNA

(2016) Michela Leonardi et al.   SYSTEMATIC BIOLOGY

Annually resolved North Atlantic marine climate over the last millennium

(2016) D. J. Reynolds et al.   Nature Communications

Deciphering the molecular adaptation of the king scallop (Pecten maximus) to heat stress using transcriptomics and proteomics

(2015) Sébastien Artigaud et al.   BMC GENOMICS

RNA-Seq in Mytilus galloprovincialis: comparative transcriptomics and expression profiles among different tissues

(2015) Rebeca Moreira et al.   BMC GENOMICS

Evolutionary Genomics and Conservation of the Endangered Przewalski’s Horse

(2015) Clio Der Sarkissian et al.   CURRENT BIOLOGY

Major transitions in human evolution revisited: A tribute to ancient DNA

(2015) Luca Ermini et al.   JOURNAL OF HUMAN EVOLUTION

Structure of Manila Clam (Ruditapes philippinarum) Microbiota at the Organ Scale in Contrasting Sets of Individuals

(2015) Guillaume Meisterhans et al.   MICROBIAL ECOLOGY

Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing

(2015) Cristina Gamba et al.   Molecular Ecology Resources

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

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Comparative performance of two whole-genome capture methodologies on ancient DNA Illumina libraries

(2015) María C. Ávila-Arcos et al.   Methods in Ecology and Evolution

Development of a Taqman real-time PCR assay for rapid detection and quantification ofVibrio tapetisin extrapallial fluids of clams

(2015) Adeline Bidault et al.   PeerJ

Transcriptional changes in Manila clam (Ruditapes philippinarum) in response to Brown Ring Disease

(2014) Bassem Allam et al.   FISH & SHELLFISH IMMUNOLOGY

Deep transcriptome sequencing of Pecten maximus hemocytes: A genomic resource for bivalve immunology

(2014) Marianna Pauletto et al.   FISH & SHELLFISH IMMUNOLOGY

Hemolymph microbiome of Pacific oysters in response to temperature, temperature stress and infection

(2014) Ana Lokmer et al.   ISME Journal

Deep sequencing of the mantle transcriptome of the great scallop Pecten maximus

(2014) Sébastien Artigaud et al.   Marine Genomics

Mitogenomics of recombinant mitochondrial genomes of Baltic Sea Mytilus mussels

(2014) Małgorzata Zbawicka et al.   MOLECULAR GENETICS AND GENOMICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Spatially resolved transcriptomics and beyond

(2014) Nicola Crosetto et al.   NATURE REVIEWS GENETICS

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

An epigenetic window into the past?

(2014) L. Orlando et al.   SCIENCE

Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan

(2014) D. Gokhman et al.   SCIENCE

Genome flux and stasis in a five millennium transect of European prehistory

(2014) Cristina Gamba et al.   Nature Communications

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

(2013) Hákon Jónsson et al.   BIOINFORMATICS

Exploring the hologenome concept in marine bivalvia: haemolymph microbiota as a pertinent source of probiotics for aquaculture

(2013) Florie Desriac et al.   FEMS MICROBIOLOGY LETTERS

Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

(2013) J. S. Pedersen et al.   GENOME RESEARCH

Differential expression of genes involved in immunity and biomineralization during Brown Ring Disease development and shell repair in the Manila clam, Ruditapes philippinarum

(2013) Fanny Jeffroy et al.   JOURNAL OF INVERTEBRATE PATHOLOGY

Impacts of ocean acidification on marine shelled molluscs

(2013) Frédéric Gazeau et al.   MARINE BIOLOGY

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

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

(2013) Matthias Meyer et al.   NATURE

Mitochondrial Phylogenomics of Modern and Ancient Equids

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

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

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

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

IntCal13 and Marine13 Radiocarbon Age Calibration Curves 0–50,000 Years cal BP

(2013) Paula J Reimer et al.   RADIOCARBON

Ancient DNA Damage

(2013) J. Dabney et al.   Cold Spring Harbor Perspectives in Biology

Improving ancient DNA read mapping against modern reference genomes

(2012) Mikkel Schubert et al.   BMC GENOMICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang 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

Variability of marine climate on the North Icelandic Shelf in a 1357-year proxy archive based on growth increments in the bivalve Arctica islandica

(2012) Paul G. Butler et al.   PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY

Transcriptomics of In Vitro Immune-Stimulated Hemocytes from the Manila Clam Ruditapes philippinarum Using High-Throughput Sequencing

(2012) Rebeca Moreira et al.   PLoS One

Variation in Size and Growth of the Great Scallop Pecten maximus along a Latitudinal Gradient

(2012) Laurent Chauvaud et al.   PLoS One

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 effects of temperature and salinity on shell formation and general condition in Baltic Sea Mytilus edulis and Arctica islandica

(2011) C Hiebenthal et al.   Aquatic Biology

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Transcriptome sequencing and microarray development for the Manila clam, Ruditapes philippinarum: genomic tools for environmental monitoring

(2011) Massimo Milan et al.   BMC GENOMICS

Gene expression analysis of clams Ruditapes philippinarum and Ruditapes decussatus following bacterial infection yields molecular insights into pathogen resistance and immunity

(2011) R. Moreira et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Genome Sequence of Vibrio rotiferianus Strain DAT722

(2011) P. R. Chowdhury et al.   JOURNAL OF BACTERIOLOGY

Barium and molybdenum records in bivalve shells: Geochemical proxies for phytoplankton dynamics in coastal environments?

(2011) Julien ThÉbault et al.   LIMNOLOGY AND OCEANOGRAPHY

De Novo Assembly of the Manila Clam Ruditapes philippinarum Transcriptome Provides New Insights into Expression Bias, Mitochondrial Doubly Uniparental Inheritance and Sex Determination

(2011) F. Ghiselli et al.   MOLECULAR BIOLOGY AND EVOLUTION

A chronological framework for the British Quaternary based on Bithynia opercula

(2011) Kirsty E. H. Penkman et al.   NATURE

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

(2011) Kirsten I. Bos et al.   NATURE

Mineral phase in shell repair of Manila clam Venerupis philippinarum affected by brown ring disease

(2010) N Trinkler et al.   DISEASES OF AQUATIC ORGANISMS

Variability of shell repair in the Manila clam Ruditapes philippinarum affected by the Brown Ring Disease: A microstructural and biochemical study

(2010) Nolwenn Trinkler et al.   JOURNAL OF INVERTEBRATE PATHOLOGY

Fossil avian eggshell preserves ancient DNA

(2010) C. L. Oskam et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Climate oscillations of the Holsteinian (Mazovian) Interglacial recorded in shell morphometry of Viviparus diluvianus (Kunth, 1865) from eastern Poland

(2010) Marcin Szymanek   QUATERNARY INTERNATIONAL

Clam shell repair from the brown ring disease: a study of the organic matrix using Confocal Raman micro-spectrometry and WDS microprobe

(2009) Nowenn Trinkler et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Influence of food supply on the δ13C signature of mollusc shells: implications for palaeoenvironmental reconstitutions

(2009) Franck Lartaud et al.   GEO-MARINE LETTERS

Resistance to Brown Ring Disease in the Manila clam, Ruditapes philippinarum: A study of selected stocks showing a recovery process by shell repair

(2009) Nolwenn Trinkler et al.   JOURNAL OF INVERTEBRATE PATHOLOGY

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Vibrio tapetis-like strain isolated from introduced Manila clams Ruditapes philippinarum showing symptoms of brown ring disease in Norway

(2008) C Paillard et al.   DISEASES OF AQUATIC ORGANISMS

Advances in mollusc sclerochronology and sclerochemistry: tools for understanding climate and environment

(2008) Darren R. Gröcke et al.   GEO-MARINE LETTERS

Use of mollusc shells for DNA-based molecular analyses

(2008) J. Geist et al.   JOURNAL OF MOLLUSCAN STUDIES