Search filters

List of works by Carlos D. Bustamante

A Markov chain Monte Carlo approach for joint inference of population structure and inbreeding rates from multilocus genotype data

scientific article

A Maximum Likelihood Method for Analyzing Pseudogene Evolution: Implications for Silent Site Evolution in Humans and Rodents ⬇️

scientific article published on January 1, 2002

A composite-likelihood approach for detecting directional selection from DNA sequence data

scientific article

A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome

scientific article published on 11 October 2016

A genetic counseling needs assessment of Mexico

scientific article published on 01 April 2019

A genome-wide association study identifies only two ancestry specific variants associated with spontaneous preterm birth

scientific article published on 9 January 2018

A genome-wide association study of bronchodilator response in Latinos implicates rare variants

scientific article published on 29 August 2013

A genome-wide linkage scan in German shepherd dogs localizes canine platelet procoagulant deficiency (Scott syndrome) to canine chromosome 27.

scientific article

A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids

scientific article

A mutation in the myostatin gene increases muscle mass and enhances racing performance in heterozygote dogs

scientific article published on 25 May 2007

A novel splice mutation within equine KIT and the W15 allele in the homozygous state lead to all white coat color phenotypes.

scientific article published on 5 April 2017

A population genetic approach to mapping neurological disorder genes using deep resequencing

scientific article

A research roadmap for next-generation sequencing informatics

scientific article published on April 2016

A scan for positively selected genes in the genomes of humans and chimpanzees

scientific article

A simple genetic architecture underlies morphological variation in dogs

scientific article

A single IGF1 allele is a major determinant of small size in dogs

scientific article

A statistical characterization of consistent patterns of human immunodeficiency virus evolution within infected patients

scientific article published on 27 October 2004

A tale of two haplotypes: the EDA2R/AR Intergenic region is the most divergent genomic segment between Africans and East Asians in the human genome.

scientific article

ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations

scientific article

Achieving high-sensitivity for clinical applications using augmented exome sequencing

scientific article

Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks

scientific article published on 20 February 2017

An ADAM9 mutation in canine cone-rod dystrophy 3 establishes homology with human cone-rod dystrophy 9

scientific article

An Aboriginal Australian genome reveals separate human dispersals into Asia

scientific article (publication date: 7 October 2011)

An Efficient Multiple-Testing Adjustment for eQTL Studies that Accounts for Linkage Disequilibrium between Variants.

scientific article published on 30 December 2015

An expressed fgf4 retrogene is associated with breed-defining chondrodysplasia in domestic dogs

scientific article

Analysis of the genetic basis of disease in the context of worldwide human relationships and migration

scientific article

Ancient DNA reveals five streams of migration into Micronesia and matrilocality in early Pacific seafarers

scientific article published on 30 June 2022

Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe

Ascertainment bias in studies of human genome-wide polymorphism.

scientific article

Assessing the evolutionary impact of amino acid mutations in the human genome

scientific article

Author Correction: Comparative and demographic analysis of orang-utan genomes

correction of a scholarly article

Balancing selection maintains a form of ERAP2 that undergoes nonsense-mediated decay and affects antigen presentation

scientific article

Bayesian analysis suggests that most amino acid replacements in Drosophila are driven by positive selection

scientific article

Bayesian linkage analysis of categorical traits for arbitrary pedigree designs

scientific article (publication date: 26 August 2010)

Beyond the reference genome

scientific article

Caring without sharing: Meta-analysis 2.0 for massive genome-wide association studies

ClinGen--the Clinical Genome Resource

scientific article

Coat variation in the domestic dog is governed by variants in three genes

scientific article

Colloquium paper: genome-wide patterns of population structure and admixture among Hispanic/Latino populations

scientific article

Compact genome of the Antarctic midge is likely an adaptation to an extreme environment

scientific article (publication date: 12 August 2014)

Comparative and demographic analysis of orang-utan genomes

scientific article

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

scientific article published in 2015

Complex population structure in African village dogs and its implications for inferring dog domestication history

scientific article

Complexities of gene expression patterns in natural populations of an extremophile fish (Poecilia mexicana, Poeciliidae).

scientific article published on 09 June 2017

Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events

scientific article published on 18 May 2015

Context dependence, ancestral misidentification, and spurious signatures of natural selection

scientific article published in June 2007

Context-dependent mutation rates may cause spurious signatures of a fixation bias favoring higher GC-content in humans

scientific article published on 26 July 2007

Copy number variation of CCL3-like genes affects rate of progression to simian-AIDS in Rhesus Macaques (Macaca mulatta)

scientific article (publication date: 2009)

Darwinian and demographic forces affecting human protein coding genes

scientific article published on 11 March 2009

Data mining of digitized health records in a resource-constrained setting reveals that timely immunophenotyping is associated with improved breast cancer outcomes

scientific article published on 27 September 2018

Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques

scientific article

Demographic history and rare allele sharing among human populations

scientific article

Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs

scientific article

Detecting and annotating genetic variations using the HugeSeq pipeline

scientific article

Detecting coevolving amino acid sites using Bayesian mutational mapping

scientific article published in June 2005

Detecting directional selection in the presence of recent admixture in African-Americans

scientific article

Detection of heterozygous mutations in the genome of mismatch repair defective diploid yeast using a Bayesian approach

scientific article

Development of a Panel of Genome-Wide Ancestry Informative Markers to Study Admixture Throughout the Americas

scientific article (publication date: 8 March 2012)

Development of a Research Platform for Dissecting Phenotype–Genotype Associations in Rice (Oryza spp.)

article

Direct measure of the de novo mutation rate in autism and schizophrenia cohorts

scientific article

Directional Selection and the Site-Frequency Spectrum ⬇️

scientific article published on December 1, 2001

Discovery and functional characterization of a neomorphic PTEN mutation.

scientific article

Distance from sub-Saharan Africa predicts mutational load in diverse human genomes

scientific article published on 28 December 2015

Distinguishing between selective sweeps and demography using DNA polymorphism data

scientific article

Efficient analysis of large datasets and sex bias with ADMIXTURE.

scientific article

Erratum: Genes mirror geography within Europe

scientific article published in Nature

Estimating the mutation load in human genomes

scientific article published on 12 May 2015

Evaluating signatures of sex-specific processes in the human genome

scientific article published on January 2009

Evolution and functional impact of rare coding variation from deep sequencing of human exomes

scientific article (publication date: 6 July 2012)

Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

scientific article

Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans ⬇️

scientific article published on 10 December 2012

Evolutionary history of GS3, a gene conferring grain length in rice

scientific article published on 08 June 2009

Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence

scientific article

Exclusion of ABCA-1 as a candidate gene for canine Scott syndrome

scientific article published on September 2008

Exome capture from saliva produces high quality genomic and metagenomic data

scientific article

Exploring population genetic models with recombination using efficient forward-time simulations

scientific article published on April 2008

FIRE: functional inference of genetic variants that regulate gene expression

scientific article published on 24 August 2017

Factors associated with degree of atopy in Latino children in a nationwide pediatric sample: the Genes-environments and Admixture in Latino Asthmatics (GALA II) study

scientific article published on 16 May 2013

Fast and cost-effective genetic mapping in apple using next-generation sequencing

scientific article

Fast, exact linkage analysis for categorical traits on arbitrary pedigree designs

scientific article published on 25 April 2011

Fine-scale population structure and the era of next-generation sequencing.

scientific article published on 28 September 2010

GBStools: A Statistical Method for Estimating Allelic Dropout in Reduced Representation Sequencing Data

scientific article

GENOME-WIDE ASSOCIATION MAPPING AND RARE ALLELES: FROM POPULATION GENOMICS TO PERSONALIZED MEDICINE – Session Introduction ⬇️

scientific article published on January 1, 2011

Gene expression imputation identifies candidate genes and susceptibility loci associated with cutaneous squamous cell carcinoma

scientific article published in Nature Communications

Gene flow from North Africa contributes to differential human genetic diversity in southern Europe

scientific article

Genes mirror geography within Europe

scientific article

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

scientific article

Genetic Diversity Turns a New PAGE in Our Understanding of Complex Traits

Genetic Mapping and Biochemical Basis of Yellow Feather Pigmentation in Budgerigars

scientific article

Genetic ancestry influences asthma susceptibility and lung function among Latinos.

scientific article

Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping

scientific article

Genetic recombination is targeted towards gene promoter regions in dogs.

scientific article

Genetic structure and domestication history of the grape

scientific article

Genetic structure in village dogs reveals a Central Asian domestication origin

scientific article (publication date: 19 October 2015)

Genetic variant in folate homeostasis is associated with lower warfarin dose in African Americans.

scientific article

Genome sequencing and analysis of admixed genomes of African and Mexican ancestry: implications for personal ancestry reconstruction and multi-ethnic medical genomics.

scientific article

Genome sequencing highlights the dynamic early history of dogs

scientific article published in January 2014

Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication

scientific article

Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean

scientific article

Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa

scientific article

Genome-wide association study and admixture mapping identify different asthma-associated loci in Latinos: the Genes-environments & Admixture in Latino Americans study

scientific article

Genome-wide association study and admixture mapping reveal new loci associated with total IgE levels in Latinos

scientific article published on 6 December 2014

Genome-wide patterns of nucleotide polymorphism in domesticated rice

scientific article

Genome-wide patterns of population structure and admixture in West Africans and African Americans

scientific article

Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds

scientific article

Genomewide SNP variation reveals relationships among landraces and modern varieties of rice

scholarly article

Genomic Insights into the Ancestry and Demographic History of South America

scientific article (publication date: 4 December 2015)

Genomic ancestry of North Africans supports back-to-Africa migrations

scientific article

Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome

scientific article

Genomic evidence for the Pleistocene and recent population history of Native Americans

scientific article

Genomic insights into the origin and diversification of late maritime hunter-gatherers from the Chilean Patagonia

article published in the Proceedings of the National Academy of Sciences of the United States of America

Genomic scans for selective sweeps using SNP data

scientific article

Genomics for the world

scientific article published on 13 July 2011

Germline determinants of the somatic mutation landscape in 2,642 cancer genomes

article

Global dissemination of a single mutation conferring white pericarp in rice

scientific article

Global distribution of genomic diversity underscores rich complex history of continental human populations

scientific article

Great ape genetic diversity and population history

scientific article published on 03 July 2013

Gut microbiome transition across a lifestyle gradient in Himalaya

High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform

article by Michael J. Thomson et al published 20 November 2011 in Molecular Breeding

High-throughput two-dimensional root system phenotyping platform facilitates genetic analysis of root growth and development

scientific article published on 03 September 2012

Human Demographic History Impacts Genetic Risk Prediction across Diverse Populations

scientific article published on 28 March 2017

Human Genome Variation 2006: emerging views on structural variation and large-scale SNP analysis

scientific article published in February 2007

Human demographic history impacts genetic risk prediction across diverse populations

Human genetics. The genetics of Mexico recapitulates Native American substructure and affects biomedical traits.

scientific article

Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome

scientific article

Human origins: Shadows of early migrations

scientific article published in December 2010

Hunter-gatherer genomic diversity suggests a southern African origin for modern humans

scientific article

IQCB1 and PDE6B mutations cause similar early onset retinal degenerations in two closely related terrier dog breeds

scientific article published on 25 October 2013

Identification of a Novel Somatic Mutation Leading to Allele Dropout for EGFR L858R Genotyping in Non-Small Cell Lung Cancer

scientific article published on 29 March 2017

Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome

scientific article

Improving the fitness of high-dimensional biomechanical models via data-driven stochastic exploration

scientific article

Imputation-Aware Tag SNP Selection To Improve Power for Large-Scale, Multi-ethnic Association Studies

scholarly article by Genevieve L Wojcik published in October 2018

Imputation-based assessment of next generation rare exome variant arrays

scientific article published on January 2014

In-solution Y-chromosome capture-enrichment on ancient DNA libraries

article published in 2018

In-solution Y-chromosome capture-enrichment on ancient DNA libraries

Inexpensive and Highly Reproducible Cloud-Based Variant Calling of 2,535 Human Genomes

scientific article published on 25 June 2015

Inference of gorilla demographic and selective history from whole-genome sequence data.

scientific article

Inferring SNP function using evolutionary, structural, and computational methods

scientific article published on 01 January 2005

Inferring genome-wide patterns of admixture in Qataris using fifty-five ancestral populations.

scientific article

Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data

scientific article

Levels and Patterns of Nucleotide Variation in Domestication QTL Regions on Rice Chromosome 3 Suggest Lineage-Specific Selection ⬇️

scientific article published on June 6, 2011

Limited evidence for classic selective sweeps in African populations

scientific article

Linkage disequilibrium and demographic history of wild and domestic canids

scientific article published on 02 February 2009

Localizing recent adaptive evolution in the human genome

scientific article

Maximum likelihood and Bayesian methods for estimating the distribution of selective effects among classes of mutations using DNA polymorphism data.

scientific article published in March 2003

Mechanisms Underlying Adaptation to Life in Hydrogen Sulfide-Rich Environments

scientific article published on 9 February 2016

Medical relevance of protein-truncating variants across 337,205 individuals in the UK Biobank study.

scientific article published on 24 April 2018

Melanesian blond hair is caused by an amino acid change in TYRP1

scientific article

Methods for human demographic inference using haplotype patterns from genomewide single-nucleotide polymorphism data

scientific article

Molecular and evolutionary history of melanism in North American gray wolves

scientific article

Molecular evidence for a single evolutionary origin of domesticated rice

scientific article (publication date: 17 May 2011)

Multidimensional structure-function relationships in human β-cardiac myosin from population-scale genetic variation

scientific article

Mutation Hot Spots in Yeast Caused by Long-Range Clustering of Homopolymeric Sequences ⬇️

scientific article published on January 26, 2012

Natural selection on genes that underlie human disease susceptibility

scientific article (publication date: 24 June 2008)

Natural selection on protein-coding genes in the human genome

scientific article (publication date: 20 October 2005)

Natural selection on the olfactory receptor gene family in humans and chimpanzees

scientific article

Network enhancement as a general method to denoise weighted biological networks

scientific article published in Nature Communications

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

scientific article

Next-Generation Sequencing of the Complete Mitochondrial Genome of the Endangered Species Black Lion Tamarin Leontopithecus chrysopygus (Primates) and Mitogenomic Phylogeny Focusing on the Callitrichidae Family

scientific article published on 12 April 2018

North African Jewish and non-Jewish populations form distinctive, orthogonal clusters

scientific article

North African populations carry the signature of admixture with Neandertals

scientific article published in 2012

On Identifying the Optimal Number of Population Clusters via the Deviance Information Criterion ⬇️

scientific article published on June 28, 2011

On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in nonequilibrium populations

scientific article

PATH-SCAN: a reporting tool for identifying clinically actionable variants

scientific article

PCAdmix: Principal Components-Based Assignment of Ancestry Along Each Chromosome in Individuals with Admixed Ancestry from Two or More Populations ⬇️

scientific article published on August 1, 2012

Patterns of genomic and phenomic diversity in wine and table grapes

scientific article published on 02 August 2017

Patterns of positive selection in six Mammalian genomes

scientific article

Phased whole-genome genetic risk in a family quartet using a major allele reference sequence

scientific article

Phylogenetic applications of whole Y-chromosome sequences and the Near Eastern origin of Ashkenazi Levites

scientific article

Polygenic risk scores: a biased prediction?

article

Population Genetic Analysis of the DARC Locus (Duffy) Reveals Adaptation from Standing Variation Associated with Malaria Resistance in Humans

scholarly article published 25 April 2016

Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation

scientific article

Population genetics of polymorphism and divergence for diploid selection models with arbitrary dominance

scientific article

Population genetics of polymorphism and divergence under fluctuating selection

scientific article published on 18 October 2007

Population genomic analyses of the chocolate tree, Theobroma cacao L., provide insights into its domestication process

Population genomic analysis of ancient and modern genomes yields new insights into the genetic ancestry of the Tyrolean Iceman and the genetic structure of Europe

scientific article (publication date: May 2014)

Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii)

scientific article (publication date: 2013)

Population structure in Argentina.

scientific article published in May 2018

Population-specific single-nucleotide polymorphism confers increased risk of venous thromboembolism in African Americans

scientific article published on 21 June 2016

Privacy Risks from Genomic Data-Sharing Beacons

scientific article

Proportionally more deleterious genetic variation in European than in African populations.

scientific article

Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries

scientific article (publication date: 7 November 2013)

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences

scientific article

RETRACTED: Darwinian selection on a selfing locus

retracted scientific article published on December 2004

REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants

scientific article published on 21 September 2016

RFMix: a discriminative modeling approach for rapid and robust local-ancestry inference

scientific article published on August 2013

Randomized trial of personal genomics for preventive cardiology: design and challenges

scientific article

Recent and ongoing selection in the human genome

scientific article

Reconstructing Native American migrations from whole-genome and whole-exome data

scientific article (publication date: 2013)

Reconstructing the population genetic history of the Caribbean.

scientific article

Reply to Ge and Sang: A single origin of domesticated rice.

scientific article published on 7 September 2011

Reply to Hublin and Klein: Locating a geographic point of dispersion in Africa for contemporary humans.

scientific article

Reply to Wang et al.: Sequencing datasets do not refute Central Asian domestication origin of dogs

scientific article published on 20 April 2016

Response—How the Gray Wolf Got Its Color

scientific article published in Science

Retraction: Darwinian selection on a selfing locus

SNP identification, verification, and utility for population genetics in a non-model genus

scientific article

Selection on rapidly evolving proteins in the Arabidopsis genome

scientific article

Selective sweep mapping of genes with large phenotypic effects

scientific article

Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females

scientific article

Simultaneous inference of selection and population growth from patterns of variation in the human genome

scientific article

Single nucleotide polymorphisms for DNA typing in the domestic horse

scientific article

SnIPRE: Selection Inference Using a Poisson Random Effects Model ⬇️

scientific article published on December 6, 2012

SnapShot: Human biomedical genomics

scientific article published on 01 September 2011

Spectrum and prevalence of genetic predisposition in medulloblastoma: a retrospective genetic study and prospective validation in a clinical trial cohort.

scientific article

Standardized Biogeographic Grouping System for Annotating Populations in Pharmacogenetic Research

scholarly article by Rachel Huddart et al published May 2019 in Clinical Pharmacology & Therapeutics

Strategies for Enriching Variant Coverage in Candidate Disease Loci on a Multiethnic Genotyping Array

scientific article

Successful computational prediction of novel imprinted genes from epigenomic features.

scientific article

Targets of balancing selection in the human genome

scientific article published on 27 August 2009

The Divergence of Neandertal and Modern Human Y Chromosomes

scientific article

The Genome of the Self-Fertilizing Mangrove Rivulus Fish, Kryptolebias marmoratus: A Model for Studying Phenotypic Plasticity and Adaptations to Extreme Environments

scientific article published on 19 June 2016

The Population Reference Sample, POPRES: a resource for population, disease, and pharmacological genetics research

scientific article published on 28 August 2008

The Time Scale of Recombination Rate Evolution in Great Apes

scientific article published on 15 December 2015

The ancestry and affiliations of Kennewick Man

scientific article

The baker's yeast diploid genome is remarkably stable in vegetative growth and meiosis

scientific article

The cost of inbreeding in Arabidopsis

scientific article published in April 2002

The effect of recent admixture on inference of ancient human population history

scientific article

The functional spectrum of low-frequency coding variation ⬇️

scientific article published on September 14, 2011

The genetic prehistory of southern Africa

scientific article

The genetic prehistory of the New World Arctic

scientific article

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

scientific article

The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color

scientific article

The phylogenetic and geographic structure of Y-chromosome haplogroup R1a

scientific article

The possibility of de novo assembly of the genome and population genomics of the mangrove rivulus, Kryptolebias marmoratus

scientific article published on 21 June 2012

Tracking genes and finding mutations: finding genes for complex traits in the domestic dog (Canis familiaris).

scientific article

Transcriptome sequencing from diverse human populations reveals differentiated regulatory architecture

scientific article

Type 2 diabetes risk alleles demonstrate extreme directional differentiation among human populations, compared to other diseases

scientific article

Using genotype array data to compare multi- and single-sample variant calls and improve variant call sets from deep coverage whole-genome sequencing data

scientific article

Variation of BMP3 contributes to dog breed skull diversity

scientific article (publication date: 2012)

Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia

scientific article published on 22 March 2018

Whole-genome sequencing reveals the extent of heterozygosity in a preferentially self-fertilizing hermaphroditic vertebrate

scientific article published on 21 December 2017

Paulina is supported by:

About Paulina

Help