Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history

Commensal Rats and Humans: Integrating Rodent Phylogeography and Zooarchaeology to Highlight Connections between Human Societies

(2020) Emily E. Puckett et al.   BIOESSAYS

Modeling the Justinianic Plague: Comparing hypothesized transmission routes

(2020) Lauren A. White et al.   PLoS One

Tracking the Near Eastern origins and European dispersal of the western house mouse

(2020) Thomas Cucchi et al.   Scientific Reports

Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA

(2020) Marie-Theres Gansauge et al.   Nature Protocols

THE INTCAL20 NORTHERN HEMISPHERE RADIOCARBON AGE CALIBRATION CURVE (0–55 CAL kBP)

(2020) Paula J Reimer et al.   RADIOCARBON

MARINE20—THE MARINE RADIOCARBON AGE CALIBRATION CURVE (0–55,000 CAL BP)

(2020) Timothy J Heaton et al.   RADIOCARBON

Ancient pathogen genomics as an emerging tool for infectious disease research

(2019) Maria A. Spyrou et al.   NATURE REVIEWS GENETICS

Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541–750)

(2019) Marcel Keller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Barn Owls and Black Rats from a Rural Roman Villa at Gatehampton, South Oxfordshire

(2019) Thomas Walker et al.   ENVIRONMENTAL ARCHAEOLOGY

Human ectoparasites and the spread of plague in Europe during the Second Pandemic

(2018) Katharine R. Dean et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rethinking ruralization in terms of resilience: Subsistence strategies in sixth-century Caričin Grad in the light of plant and animal bone finds

(2018) Henriette Baron et al.   QUATERNARY INTERNATIONAL

The transition from late antiquity to early Middle Ages in Italy. A zooarchaeological perspective

(2018) Frank Salvadori   QUATERNARY INTERNATIONAL

Phylogeography of the black rat Rattus rattus in India and the implications for its dispersal history in Eurasia

(2018) Mumtaz Baig et al.   BIOLOGICAL INVASIONS

Urban rats have less variable, higher protein diets

(2018) E. Guiry et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Population Genomics Reveals Speciation and Introgression between Brown Norway Rats and Their Sibling Species

(2017) Huajing Teng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reconstructing Asian faunal introductions to eastern Africa from multi-proxy biomolecular and archaeological datasets

(2017) Mary E. Prendergast et al.   PLoS One

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

A High-CoverageYersinia pestisGenome from a Sixth-Century Justinianic Plague Victim

(2016) Michal Feldman et al.   MOLECULAR BIOLOGY AND EVOLUTION

Cooling and societal change during the Late Antique Little Ice Age from 536 to around 660 AD

(2016) Ulf Büntgen et al.   Nature Geoscience

Ecological consequences of human niche construction: Examining long-term anthropogenic shaping of global species distributions

(2016) Nicole L. Boivin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Ecological and Evolutionary Framework for Commensalism in Anthropogenic Environments

(2016) Ardern Hulme-Beaman et al.   TRENDS IN ECOLOGY & EVOLUTION

Bayesian Analysis of Radiocarbon Dates

(2016) Christopher Bronk Ramsey   RADIOCARBON

Approaches to Estimating Marine Protein in Human Collagen for Radiocarbon Date Calibration

(2016) Genevieve Dewar et al.   RADIOCARBON

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Mitochondrial phylogeography of the black rat supports a single invasion of the western Mediterranean basin

(2015) P. Colangelo et al.   BIOLOGICAL INVASIONS

An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data

(2015) Goo Jun et al.   GENOME RESEARCH

Recent Evolution inRattus norvegicusIs Shaped by Declining Effective Population Size

(2015) Eva E. Deinum et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improving access to endogenous DNA in ancient bones and teeth

(2015) Peter B. Damgaard et al.   Scientific Reports

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Yersinia pestis and the Plague of Justinian 541–543 AD: a genomic analysis

(2014) David M Wagner et al.   LANCET INFECTIOUS DISEASES

Rating the rat: global patterns and research priorities in impacts and management of rodent pests

(2014) Dario Capizzi et al.   MAMMAL REVIEW

Partial uracil-DNA-glycosylase treatment for screening of ancient DNA

(2014) N. Rohland et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2013) Hákon Jónsson et al.   BIOINFORMATICS

On the trail of Neolithic mice and men towards Transcaucasia: zooarchaeological clues from Nakhchivan (Azerbaijan)

(2013) Thomas Cucchi et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

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

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

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

Genetic tracking of mice and other bioproxies to infer human history

(2013) Eleanor P. Jones et al.   TRENDS IN GENETICS

Cryptic genetic diversity in Rattus of the San Francisco Bay region, California

(2012) Chris J. Conroy et al.   BIOLOGICAL INVASIONS

Fellow travellers: a concordance of colonization patterns between mice and men in the North Atlantic region

(2012) EP Jones et al.   BMC EVOLUTIONARY BIOLOGY

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

Rats cannot have been intermediate hosts for Yersinia pestis during medieval plague epidemics in Northern Europe

(2012) Anne Karin Hufthammer et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Invasion facilitates hybridization with introgression in theRattus rattusspecies complex

(2012) JUSTIN B. LACK et al.   MOLECULAR ECOLOGY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

Improving SNP discovery by base alignment quality

(2011) H. Li   BIOINFORMATICS

On the history of the spread of the black rat (Rattus rattus L., 1758) in northwestern Russia

(2011) A. B. Savinetsky et al.   BIOLOGY BULLETIN

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Bayesian inference of ancient human demography from individual genome sequences

(2011) Ilan Gronau et al.   NATURE GENETICS

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Meraculous: De Novo Genome Assembly with Short Paired-End Reads

(2011) Jarrod A. Chapman et al.   PLoS One

Multiple Geographic Origins of Commensalism and Complex Dispersal History of Black Rats

(2011) Ken P. Aplin et al.   PLoS One

Early colonization of Mediterranean islands by Rattus rattus: a review of zooarcheological data

(2010) Lise Ruffino et al.   BIOLOGICAL INVASIONS

Revisiting the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries

(2010) Marie Pagès et al.   BMC EVOLUTIONARY BIOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

Ancient mitochondrial DNA analysis reveals complexity of indigenous North American turkey domestication

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

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

Rodent-borne diseases and their risks for public health

(2009) Bastiaan G Meerburg et al.   CRITICAL REVIEWS IN MICROBIOLOGY

Phylogeography of the introduced speciesRattus rattusin the western Indian Ocean, with special emphasis on the colonization history of Madagascar

(2009) Charlotte Tollenaere et al.   JOURNAL OF BIOGEOGRAPHY

Mitochondrial DNA evidence for the spread of Pacific rats through Oceania

(2008) Elizabeth Matisoo-Smith et al.   BIOLOGICAL INVASIONS

Uluburun shipwreck stowaway house mouse: molar shape analysis and indirect clues about the vessel's last journey

(2008) T. Cucchi   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Dating of divergences within the Rattus genus phylogeny using whole mitochondrial genomes

(2008) Judith H. Robins et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION