Multiproxy evidence highlights a complex evolutionary legacy of maize in South America

Pre-Columbian earth-builders settled along the entire southern rim of the Amazon

(2018) Jonas Gregorio de Souza et al.   Nature Communications

Direct archaeological evidence for Southwestern Amazonia as an early plant domestication and food production centre

(2018) Jennifer Watling et al.   PLoS One

Improved maize reference genome with single-molecule technologies

(2017) Yinping Jiao et al.   NATURE

A new model for ancient DNA decay based on paleogenomic meta-analysis

(2017) Logan Kistler et al.   NUCLEIC ACIDS RESEARCH

SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data

(2017) Yuxin Chen et al.   GigaScience

Genome Sequence of a 5,310-Year-Old Maize Cob Provides Insights into the Early Stages of Maize Domestication

(2016) Jazmín Ramos-Madrigal et al.   CURRENT BIOLOGY

The earliest maize from San Marcos Tehuacán is a partial domesticate with genomic evidence of inbreeding

(2016) Miguel Vallebueno-Estrada et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A 6900-year history of landscape modification by humans in lowland Amazonia

(2016) M.B. Bush et al.   QUATERNARY SCIENCE REVIEWS

Long-term man–environment interactions in the Bolivian Amazon: 8000 years of vegetation dynamics

(2016) Sandra O. Brugger et al.   QUATERNARY SCIENCE REVIEWS

Bayesian Analysis of Radiocarbon Dates

(2016) Christopher Bronk Ramsey   RADIOCARBON

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

MCMCpack: Markov Chain Monte Carlo inR

(2015) Andrew D. Martin et al.   Journal of Statistical Software

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Optimization of DNA Recovery and Amplification from Non-Carbonized Archaeobotanical Remains

(2014) Nathan Wales et al.   PLoS One

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

(2013) Hákon Jónsson et al.   BIOINFORMATICS

Archaic period settlement and subsistence in the Maya lowlands: new starch grain and lithic data from Freshwater Creek, Belize

(2013) Robert M. Rosenswig et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

SHCal13 Southern Hemisphere Calibration, 0–50,000 Years cal BP

(2013) Alan G Hogg et al.   RADIOCARBON

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

Comparative population genomics of maize domestication and improvement

(2012) Matthew B Hufford et al.   NATURE GENETICS

Maize HapMap2 identifies extant variation from a genome in flux

(2012) Jer-Ming Chia et al.   NATURE GENETICS

Preceramic maize from Paredones and Huaca Prieta, Peru

(2012) A. Grobman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) P. Skoglund et al.   SCIENCE

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Bayesian phylogeography of the Arawak expansion in lowland South America

(2011) R. S. Walker et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2010) A. McKenna et al.   GENOME RESEARCH

Pre-pottery farmers on the Pacific coast of southern Mexico

(2010) Douglas J. Kennett et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Genetic signals of origin, spread, and introgression in a large sample of maize landraces

(2010) J. van Heerwaarden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

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

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

The diffusion of maize to the southwestern United States and its impact

(2009) William L. Merrill et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Starch grain and phytolith evidence for early ninth millennium B.P. maize from the Central Balsas River Valley, Mexico

(2009) D. R. Piperno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Pre-Columbian Urbanism, Anthropogenic Landscapes, and the Future of the Amazon

(2008) M. J. Heckenberger et al.   SCIENCE

Identifying crop plants with phytoliths (and starch grains) in Central and South America: A review and an update of the evidence

(2007) Dolores R. Piperno   QUATERNARY INTERNATIONAL