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

Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin

(2016) Matthew W. Snyder et al.   CELL

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

(2016) Matthias Meyer et al.   NATURE

Genomic insights into the origin of farming in the ancient Near East

(2016) Iosif Lazaridis et al.   NATURE

Early farmers from across Europe directly descended from Neolithic Aegeans

(2016) Zuzana Hofmanová et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenetics: It's Getting Old. Past Meets Future in Paleoepigenetics

(2016) David Gokhman et al.   TRENDS IN ECOLOGY & EVOLUTION

Joint Estimation of Contamination, Error and Demography for Nuclear DNA from Ancient Humans

(2016) Fernando Racimo et al.   PLoS Genetics

Evolutionary analysis of selective constraints identifies ameloblastin (AMBN) as a potential candidate for amelogenesis imperfecta

(2015) Frédéric Delsuc et al.   BMC EVOLUTIONARY BIOLOGY

Complete Genomes Reveal Signatures of Demographic and Genetic Declines in the Woolly Mammoth

(2015) Eleftheria Palkopoulou et al.   CURRENT BIOLOGY

Evolutionary Genomics and Conservation of the Endangered Przewalski’s Horse

(2015) Clio Der Sarkissian et al.   CURRENT BIOLOGY

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

(2015) Cristina Gamba et al.   Molecular Ecology Resources

Population genomics of Bronze Age Eurasia

(2015) Morten E. Allentoft et al.   NATURE

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

Reconstructing ancient genomes and epigenomes

(2015) Ludovic Orlando et al.   NATURE REVIEWS GENETICS

Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques

(2015) Torsten Günther et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome

(2015) Lara M. Cassidy 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

Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa

(2015) M. Gallego Llorente et al.   SCIENCE

The epigenomic landscape of African rainforest hunter-gatherers and farmers

(2015) Maud Fagny et al.   Nature Communications

Upper Palaeolithic genomes reveal deep roots of modern Eurasians

(2015) Eppie R. Jones et al.   Nature Communications

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

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

Detection of Cytosine Methylation in Ancient DNA from Five Native American Populations Using Bisulfite Sequencing

(2015) Rick W. A. Smith et al.   PLoS One

Altered promoter nucleosome positioning is an early event in gene silencing

(2014) Luke B Hesson et al.   Epigenetics

Selective enrichment of damaged DNA molecules for ancient genome sequencing

(2014) Marie-Theres Gansauge et al.   GENOME RESEARCH

Ancient human genomes suggest three ancestral populations for present-day Europeans

(2014) Iosif Lazaridis et al.   NATURE

The genome of a Late Pleistocene human from a Clovis burial site in western Montana

(2014) Morten Rasmussen et al.   NATURE

Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European

(2014) Iñigo Olalde et al.   NATURE

Genome sequence of a 45,000-year-old modern human from western Siberia

(2014) Qiaomei Fu et al.   NATURE

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

(2014) Mikkel Schubert et al.   Nature Protocols

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

Speciation with gene flow in equids despite extensive chromosomal plasticity

(2014) Hákon Jónsson 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

Genomic structure in Europeans dating back at least 36,200 years

(2014) A. Seguin-Orlando 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

A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes

(2013) Qiaomei Fu et al.   CURRENT BIOLOGY

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

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

DNA methylation contributes to natural human variation

(2013) H. Heyn et al.   GENOME RESEARCH

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

(2013) Ludovic Orlando et al.   NATURE

Charting a dynamic DNA methylation landscape of the human genome

(2013) Michael J. Ziller et al.   NATURE

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

(2013) Matthias Meyer et al.   NATURE

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA

(2013) Marie-Theres Gansauge et al.   Nature Protocols

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

Bridging the transgenerational gap with epigenetic memory

(2013) Jana P. Lim et al.   TRENDS IN GENETICS

Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array

(2013) Roderick C Slieker et al.   Epigenetics & Chromatin

DNA methylation age of human tissues and cell types

(2013) Steve Horvath   GENOME BIOLOGY

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

Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules

(2012) T. K. Kelly et al.   GENOME RESEARCH

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

High-Resolution Analysis of Cytosine Methylation in Ancient DNA

(2012) Bastien Llamas et al.   PLoS One

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

Controls of Nucleosome Positioning in the Human Genome

(2012) Daniel J. Gaffney et al.   PLoS Genetics

Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome

(2011) Juan Sandoval et al.   Epigenetics

CpG islands and the regulation of transcription

(2011) A. M. Deaton et al.   GENES & DEVELOPMENT

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

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

(2010) Johannes Krause et al.   CURRENT BIOLOGY

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

Ancient human genome sequence of an extinct Palaeo-Eskimo

(2010) Morten Rasmussen et al.   NATURE

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

DNA methylation differences after exposure to prenatal famine are common and timing- and sex-specific

(2009) Elmar W. Tobi et al.   HUMAN MOLECULAR GENETICS

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

(2009) Madeleine P Ball et al.   NATURE BIOTECHNOLOGY

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Nucleosome positioning and gene regulation: advances through genomics

(2009) Cizhong Jiang et al.   NATURE REVIEWS GENETICS

In vivo methylation of mtDNA reveals the dynamics of protein–mtDNA interactions

(2009) Adriana P. Rebelo 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

Genome-scale DNA methylation maps of pluripotent and differentiated cells

(2008) Alexander Meissner et al.   NATURE

Preferentially Quantized Linker DNA Lengths in Saccharomyces cerevisiae

(2008) Ji-Ping Wang et al.   PLoS Computational Biology

The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome

(2008) Yutao Fu et al.   PLoS Genetics