Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners

Cis and trans-regulatory variation in the domestication of the chili pepper fruit

(2020) Erik Díaz-Valenzuela et al.   MOLECULAR BIOLOGY AND EVOLUTION

Considerations in adapting CRISPR/Cas9 in nongenetic model plant systems

(2020) Shengchen Shan et al.   Applications in Plant Sciences

Comparative study of population genomic approaches for mapping colony-level traits

(2020) Shani Inbar et al.   PLoS Computational Biology

Minor allele frequency thresholds strongly affect population structure inference with genomic datasets

(2019) Ethan Linck et al.   Molecular Ecology Resources

A reference-grade wild soybean genome

(2019) Min Xie et al.   Nature Communications

The genetic architecture of teosinte catalyzed and constrained maize domestication

(2019) Chin Jian Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Determining factors, regulation system, and domestication of anthocyanin biosynthesis in rice leaves

(2019) Jie Zheng et al.   NEW PHYTOLOGIST

Origin and evolution of the octoploid strawberry genome

(2019) Patrick P. Edger et al.   NATURE GENETICS

Application and future perspective of CRISPR/Cas9 genome editing in fruit crops

(2019) Junhui Zhou et al.   Journal of Integrative Plant Biology

Plant breeding at the speed of light: the power of CRISPR/Cas to generate directed genetic diversity at multiple sites

(2019) Felix Wolter et al.   BMC PLANT BIOLOGY

De Novo Domestication: An Alternative Route toward New Crops for the Future

(2019) Alisdair R. Fernie et al.   Molecular Plant

Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits

(2019) Rajeev K. Varshney et al.   NATURE GENETICS

The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

(2019) Lei Gao et al.   NATURE GENETICS

Comparative population genomics identified genomic regions and candidate genes associated with fruit domestication traits in peach

(2019) Ke Cao et al.   PLANT BIOTECHNOLOGY JOURNAL

Copy Number Variation in Domestication

(2019) Zoe N. Lye et al.   TRENDS IN PLANT SCIENCE

Comparing Pool‐seq, Rapture, and GBS genotyping for inferring weak population structure: The American lobster ( Homarus americanus ) as a case study

(2019) Yann Dorant et al.   Ecology and Evolution

Deep Genome Resequencing Reveals Artificial and Natural Selection for Visual Deterioration, Plateau Adaptability and High Prolificacy in Chinese Domestic Sheep

(2019) Weimin Wang et al.   Frontiers in Genetics

The presence and impact of reference bias on population genomic studies of prehistoric human populations

(2019) Torsten Günther et al.   PLoS Genetics

A Three-Sample Test for Introgression

(2019) Matthew W Hahn et al.   MOLECULAR BIOLOGY AND EVOLUTION

Optimal sequencing depth design for whole genome re-sequencing in pigs

(2019) Yifan Jiang et al.   BMC BIOINFORMATICS

Latest techniques to study DNA methylation

(2019) Quentin Gouil et al.   Essays in Biochemistry

Genomic architecture and introgression shape a butterfly radiation

(2019) Nathaniel B. Edelman et al.   SCIENCE

Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement

(2019) Aamir W. Khan et al.   TRENDS IN PLANT SCIENCE

Towards the Complete Goat Pan-Genome by Recovering Missing Genomic Segments From the Reference Genome

(2019) Ran Li et al.   Frontiers in Genetics

A practical introduction to sequentially Markovian coalescent methods for estimating demographic history from genomic data

(2019) Niklas Mather et al.   Ecology and Evolution

Comparative analysis of the blood transcriptomes between wolves and dogs

(2018) X. Yang et al.   ANIMAL GENETICS

Population size may shape the accumulation of functional mutations following domestication

(2018) Jianhai Chen et al.   BMC EVOLUTIONARY BIOLOGY

Epigenetic perspectives on the evolution and domestication of polyploid plant and crops

(2018) Mingquan Ding et al.   CURRENT OPINION IN PLANT BIOLOGY

Ancient DNA reveals the timing and persistence of organellar genetic bottlenecks over 3,000 years of sunflower domestication and improvement

(2018) Nathan Wales et al.   Evolutionary Applications

Domestication of cattle: two or three events?

(2018) Daniel Pitt et al.   Evolutionary Applications

A re-evaluation of the domestication bottleneck from archaeogenomic evidence

(2018) Robin G Allaby et al.   Evolutionary Applications

Loter: A Software Package to Infer Local Ancestry for a Wide Range of Species

(2018) Thomas Dias-Alves et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice

(2018) Qiang Zhao et al.   NATURE GENETICS

Targeted resequencing reveals genomic signatures of barley domestication

(2018) Artem Pankin et al.   NEW PHYTOLOGIST

Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus

(2018) Bhavna Hurgobin et al.   PLANT BIOTECHNOLOGY JOURNAL

Differential transcriptome patterns associated with early seedling development in a wild and a domesticated common bean ( Phaseolus vulgaris L.) accession

(2018) Jugpreet Singh et al.   PLANT SCIENCE

Ancient goat genomes reveal mosaic domestication in the Fertile Crescent

(2018) Kevin G. Daly et al.   SCIENCE

Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia

(2018) Ningbo Chen et al.   Nature Communications

Convergent genomic signatures of domestication in sheep and goats

(2018) Florian J. Alberto et al.   Nature Communications

Population genetics and GWAS: A primer

(2018) Greg Gibson   PLOS BIOLOGY

Genome-Wide Association Mapping for Cold Tolerance in a Core Collection of Rice (Oryza sativa L.) Landraces by Using High-Density Single Nucleotide Polymorphism Markers From Specific-Locus Amplified Fragment Sequencing

(2018) Jiayu Song et al.   Frontiers in Plant Science

Pervasive introgression facilitated domestication and adaptation in the Bos species complex

(2018) Dong-Dong Wu et al.   Nature Ecology & Evolution

The axolotl genome and the evolution of key tissue formation regulators

(2018) Sergej Nowoshilow et al.   NATURE

Human influences on the strength of phenotypic selection

(2018) Vincent Fugère et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Whole-Genome Duplication and Plant Macroevolution

(2018) James W. Clark et al.   TRENDS IN PLANT SCIENCE

A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome

(2018) Robert VanBuren et al.   GigaScience

A western Sahara centre of domestication inferred from pearl millet genomes

(2018) Concetta Burgarella et al.   Nature Ecology & Evolution

Characterization of proteome variation during modern maize breeding

(2018) Lu-Guang Jiang et al.   MOLECULAR & CELLULAR PROTEOMICS

The extent of adaptive wild introgression in crops

(2018) Garrett M. Janzen et al.   NEW PHYTOLOGIST

Genome Duplication in Animal Evolution

(2018) K. S. Zadesenets et al.   RUSSIAN JOURNAL OF GENETICS

Comparisons of molecular diversity indices, selective sweeps and population structure of African rice with its wild progenitor and Asian rice

(2018) Marie Noelle Ndjiondjop et al.   THEORETICAL AND APPLIED GENETICS

Genetic Characterization of Dog Personality Traits

(2017) Joanna Ilska et al.   GENETICS

Phylogenomic inferences from reference-mapped and de novo assembled short-read sequence data using RADseq sequencing of California white oaks (Quercus section Quercus)

(2017) Sorel Fitz-Gibbon et al.   GENOME

A novel linkage-disequilibrium corrected genomic relationship matrix for SNP-heritability estimation and genomic prediction

(2017) Boby Mathew et al.   HEREDITY

Genetic Costs of Domestication and Improvement

(2017) Brook T Moyers et al.   JOURNAL OF HEREDITY

DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets

(2017) Julio Rozas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Karyotype Stability and Unbiased Fractionation in the Paleo-Allotetraploid Cucurbita Genomes

(2017) Honghe Sun et al.   Molecular Plant

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

(2017) Hélène Badouin et al.   NATURE

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

(2017) Derek M Bickhart et al.   NATURE GENETICS

Single-stranded DNA library preparation from highly degraded DNA usingT4DNA ligase

(2017) Marie-Theres Gansauge et al.   NUCLEIC ACIDS RESEARCH

The pangenome of hexaploid bread wheat

(2017) Juan D. Montenegro et al.   PLANT JOURNAL

Assessing elements of an extended evolutionary synthesis for plant domestication and agricultural origin research

(2017) Dolores R. Piperno   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Current approaches and methods in plant domestication studies

(2017) Azalea Guerra García et al.   Botanical Sciences

A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors

(2017) Donald M. Bryant et al.   Cell Reports

Current approaches and methods in plant domestication studies

(2017) Azalea Guerra García et al.   Botanical Sciences

A Combined Comparative Transcriptomic, Metabolomic, and Anatomical Analyses of Two Key Domestication Traits: Pod Dehiscence and Seed Dormancy in Pea (Pisum sp.)

(2017) Iveta Hradilová et al.   Frontiers in Plant Science

From Genomes to GENE-omes: Exome Sequencing Concept and Applications in Crop Improvement

(2017) Parampreet Kaur et al.   Frontiers in Plant Science

Domestication Genomics of the Open-Pollinated Scarlet Runner Bean (Phaseolus coccineus L.)

(2017) Azalea Guerra-García et al.   Frontiers in Plant Science

Genetic Characterization of Dog Personality Traits

(2017) Joanna Ilska et al.   GENETICS

A survey of methods and tools to detect recent and strong positive selection

(2017) Pavlos Pavlidis et al.   Journal of Biological Research-Thessaloniki

The palaeogenetics of cat dispersal in the ancient world

(2017) Claudio Ottoni et al.   Nature Ecology & Evolution

Domestication reduces alternative splicing expression variations in sorghum

(2017) Vincent Ranwez et al.   PLoS One

Rapid breeding of parthenocarpic tomato plants using CRISPR/Cas9

(2017) Risa Ueta et al.   Scientific Reports

Detection of selection signatures of population-specific genomic regions selected during domestication process in Jinhua pigs

(2016) Zhengcao Li et al.   ANIMAL GENETICS

Advancements in Next-Generation Sequencing

(2016) Shawn E. Levy et al.   Annual Review of Genomics and Human Genetics

The present and future ofde novowhole-genome assembly

(2016) Jang-il Sohn et al.   BRIEFINGS IN BIOINFORMATICS

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 Evolutionary Origin and Genetic Makeup of Domestic Horses

(2016) P. Librado et al.   GENETICS

The limits and potential of paleogenomic techniques for reconstructing grapevine domestication

(2016) Nathan Wales et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves

(2016) Ilana Janowitz Koch et al.   MOLECULAR ECOLOGY

PSMC analysis of effective population sizes in molecular ecology and its application to black-and-whiteFicedulaflycatchers

(2016) Krystyna Nadachowska-Brzyska et al.   MOLECULAR ECOLOGY

Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation

(2016) David B. Lowry et al.   Molecular Ecology Resources

pcadapt: anRpackage to perform genome scans for selection based on principal component analysis

(2016) Keurcien Luu et al.   Molecular Ecology Resources

Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley

(2016) Martin Mascher et al.   NATURE GENETICS

Domestication history and geographical adaptation inferred from a SNP map of African rice

(2016) Rachel S Meyer et al.   NATURE GENETICS

The origin and evolution of cell types

(2016) Detlev Arendt et al.   NATURE REVIEWS GENETICS

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

Post-transcriptional gene regulation by mRNA modifications

(2016) Boxuan Simen Zhao et al.   NATURE REVIEWS MOLECULAR CELL 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

How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?

(2016) Nicholas J. Schurch et al.   RNA

Integration of omic networks in a developmental atlas of maize

(2016) J. W. Walley et al.   SCIENCE

Genomic and archaeological evidence suggest a dual origin of domestic dogs

(2016) Laurent A. F. Frantz et al.   SCIENCE

Lessons from Domestication: Targeting Cis -Regulatory Elements for Crop Improvement

(2016) Gwen Swinnen et al.   TRENDS IN PLANT SCIENCE

The pangenome of an agronomically important crop plant Brassica oleracea

(2016) Agnieszka A. Golicz et al.   Nature Communications

Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference

(2016) Aaron B. A. Shafer et al.   Methods in Ecology and Evolution

Evolutionary Genomics of Peach and Almond Domestication

(2016) Dianne Velasco et al.   G3-Genes Genomes Genetics

Global epigenomic analysis indicates that Epialleles contribute to Allele-specific expression via Allele-specific histone modifications in hybrid rice

(2015) Zhibin Guo et al.   BMC GENOMICS

N6-Methyldeoxyadenosine Marks Active Transcription Start Sites in Chlamydomonas

(2015) Ye Fu et al.   CELL

Patterns of genomic changes with crop domestication and breeding

(2015) Junpeng Shi et al.   CURRENT OPINION IN PLANT BIOLOGY

Role of transcriptional regulation in the evolution of plant phenotype: A dynamic systems approach

(2015) Emiliano Rodríguez-Mega et al.   DEVELOPMENTAL DYNAMICS

RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping

(2015) O. A. Ali et al.   GENETICS

Comparison of Exome and Genome Sequencing Technologies for the Complete Capture of Protein-Coding Regions

(2015) Stefan H. Lelieveld et al.   HUMAN MUTATION

Adding 'epi-' to behaviour genetics: implications for animal domestication

(2015) P. Jensen   JOURNAL OF EXPERIMENTAL BIOLOGY

The Accumulation of Deleterious Mutations as a Consequence of Domestication and Improvement in Sunflowers and Other Compositae Crops

(2015) Sebastien Renaut et al.   MOLECULAR BIOLOGY AND EVOLUTION

Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR

(2015) Michael Boettcher et al.   MOLECULAR CELL

Seven common mistakes in population genetics and how to avoid them

(2015) Patrick G. Meirmans   MOLECULAR ECOLOGY

The relative power of genome scans to detect local adaptation depends on sampling design and statistical method

(2015) Katie E. Lotterhos et al.   MOLECULAR ECOLOGY

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

(2015) Cristina Gamba et al.   Molecular Ecology Resources

Exploring population size changes using SNP frequency spectra

(2015) Xiaoming Liu et al.   NATURE GENETICS

Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes

(2015) Laurent A F Frantz et al.   NATURE GENETICS

MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing

(2015) Mark A Urich et al.   Nature Protocols

DNA N6-methyladenine: a new epigenetic mark in eukaryotes?

(2015) Guan-Zheng Luo et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Genome scans reveal candidate domestication and improvement genes in cultivated sunflower, as well as post-domestication introgression with wild relatives

(2015) Gregory J. Baute et al.   NEW PHYTOLOGIST

Towards plant pangenomics

(2015) Agnieszka A. Golicz et al.   PLANT BIOTECHNOLOGY JOURNAL

Genomics of crop wild relatives: expanding the gene pool for crop improvement

(2015) Marta Brozynska et al.   PLANT BIOTECHNOLOGY JOURNAL

Demographic inference using genetic data from a single individual: Separating population size variation from population structure

(2015) Olivier Mazet et al.   THEORETICAL POPULATION BIOLOGY

Yak whole-genome resequencing reveals domestication signatures and prehistoric population expansions

(2015) Qiang Qiu et al.   Nature Communications

A new FST-based method to uncover local adaptation using environmental variables

(2015) Pierre de Villemereuil et al.   Methods in Ecology and Evolution

Exome Sequencing: Current and Future Perspectives

(2015) Amanda Warr et al.   G3-Genes Genomes Genetics

Recent Selective Sweeps in North American Drosophila melanogaster Show Signatures of Soft Sweeps

(2015) Nandita R. Garud et al.   PLoS Genetics

Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools

(2015) Janna L. Fierst   Frontiers in Genetics

Fruit Quality Traits Have Played Critical Roles in Domestication of the Apple

(2015) M. Awais Khan et al.   Plant Genome

DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data

(2014) Jean-Marie Cornuet et al.   BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Transgenerational Epigenetic Inheritance: Myths and Mechanisms

(2014) Edith Heard et al.   CELL

Post-Translational Modifications of Histones That Influence Nucleosome Dynamics

(2014) Gregory D. Bowman et al.   CHEMICAL REVIEWS

The contribution of genetic and genomic approaches to plant domestication studies

(2014) Paul Gepts   CURRENT OPINION IN PLANT BIOLOGY

Local and Global Ancestry Inference and Applications to Genetic Association Analysis for Admixed Populations

(2014) Timothy A. Thornton et al.   GENETIC EPIDEMIOLOGY

fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

(2014) Anil Raj et al.   GENETICS

Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci

(2014) Simon H. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evaluation of demographic history and neutral parameterization on the performance ofFSToutlier tests

(2014) Katie E. Lotterhos et al.   MOLECULAR ECOLOGY

Restriction site-associated DNA sequencing, genotyping error estimation andde novoassembly optimization for population genetic inference

(2014) A. Mastretta-Yanes et al.   Molecular Ecology Resources

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

(2014) Ying-hui Li et al.   NATURE BIOTECHNOLOGY

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

A reference genome for common bean and genome-wide analysis of dual domestications

(2014) Jeremy Schmutz et al.   NATURE GENETICS

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

Comparative Analysis of Genome-Wide Chromosomal Histone Modification Patterns in Maize Cultivars and Their Wild Relatives

(2014) Shibin He et al.   PLoS One

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

Storytelling and story testing in domestication

(2014) P. Gerbault et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Current perspectives and the future of domestication studies

(2014) G. Larson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

King penguin demography since the last glaciation inferred from genome-wide data

(2014) E. Trucchi et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Biosynthesis, regulation, and domestication of bitterness in cucumber

(2014) Y. Shang et al.   SCIENCE

Advances and limits of using population genetics to understand local adaptation

(2014) Peter Tiffin et al.   TRENDS IN ECOLOGY & EVOLUTION

Cassava genome from a wild ancestor to cultivated varieties

(2014) Wenquan Wang et al.   Nature Communications

Mapping ecologically relevant social behaviours by gene knockout in wild mice

(2014) Lea Chalfin et al.   Nature Communications

The Role of cis Regulatory Evolution in Maize Domestication

(2014) Zachary H. Lemmon et al.   PLoS Genetics

Epigenetics and transgenerational inheritance in domesticated farm animals

(2014) Amanda Feeney et al.   Journal of Animal Science and Biotechnology

Error estimates for the analysis of differential expression from RNA-seq count data

(2014) Conrad J. Burden et al.   PeerJ

RFMix: A Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference

(2013) Brian K. Maples et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Haplotype Estimation Using Sequencing Reads

(2013) Olivier Delaneau et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Detecting Natural Selection in Genomic Data

(2013) Joseph J. Vitti et al.   Annual Review of Genetics

Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data

(2013) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

RNA-Seq Analysis of Allele-Specific Expression, Hybrid Effects, and Regulatory Divergence in Hybrids Compared with Their Parents from Natural Populations

(2013) Graeme D.M. Bell et al.   Genome Biology and Evolution

Artificial Selection on Brain-Expressed Genes during the Domestication of Dog

(2013) Yan Li et al.   MOLECULAR BIOLOGY AND EVOLUTION

Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations

(2013) Stéphane De Mita et al.   MOLECULAR ECOLOGY

Architecture and evolution of a minute plant genome

(2013) Enrique Ibarra-Laclette et al.   NATURE

Patterns of population epigenomic diversity

(2013) Robert J. Schmitz et al.   NATURE

A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity

(2013) Jianjian Qi et al.   NATURE GENETICS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Evolution of crop species: genetics of domestication and diversification

(2013) Rachel S. Meyer et al.   NATURE REVIEWS GENETICS

Assessing the Effect of Sequencing Depth and Sample Size in Population Genetics Inferences

(2013) Matteo Fumagalli   PLoS One

Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato

(2013) D. Koenig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Genome sequencing and population genomics in non-model organisms

(2013) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

Signatures of Diversifying Selection in European Pig Breeds

(2013) Samantha Wilkinson et al.   PLoS Genetics

Domestication Genomics: Evidence from Animals

(2013) Guo-Dong Wang et al.   Annual Review of Animal Biosciences

OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole-genome datasets

(2012) N. Alachiotis et al.   BIOINFORMATICS

Fast and accurate inference of local ancestry in Latino populations

(2012) Yael Baran et al.   BIOINFORMATICS

Screen for Footprints of Selection during Domestication/Captive Breeding of Atlantic Salmon

(2012) Anti Vasemägi et al.   COMPARATIVE AND FUNCTIONAL GENOMICS

Using identity by descent estimation with dense genotype data to detect positive selection

(2012) Lide Han et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Finalism in Darwinian and Lamarckian Evolution: Lessons from Epigenetics and Developmental Biology

(2012) Carlos Guerrero-Bosagna   Evolutionary Biology

Local Ancestry Corrects for Population Structure in Saccharomyces cerevisiae Genome-Wide Association Studies

(2012) Liyang Diao et al.   GENETICS

The simple fool's guide to population genomics via RNA-Seq: an introduction to high-throughput sequencing data analysis

(2012) Pierre De Wit et al.   Molecular Ecology Resources

A map of rice genome variation reveals the origin of cultivated rice

(2012) Xuehui Huang et al.   NATURE

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

(2012) Yang Dong et al.   NATURE BIOTECHNOLOGY

Comparative population genomics of maize domestication and improvement

(2012) Matthew B Hufford et al.   NATURE GENETICS

Genome-wide genetic changes during modern breeding of maize

(2012) Yinping Jiao et al.   NATURE GENETICS

The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

(2012) Shaogui Guo et al.   NATURE GENETICS

A beginner's guide to eukaryotic genome annotation

(2012) Mark Yandell et al.   NATURE REVIEWS GENETICS

Chromosome rearrangements during domestication of cucumber as revealed by high-density genetic mapping and draft genome assembly

(2012) Luming Yang et al.   PLANT JOURNAL

Genome-wide association study (GWAS) of resistance to head smut in maize

(2012) Ming Wang et al.   PLANT SCIENCE

Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

(2012) Susanna Sawyer et al.   PLoS One

Reshaping of the maize transcriptome by domestication

(2012) R. Swanson-Wagner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Comparison of Brain Gene Expression Levels in Domesticated and Wild Animals

(2012) Frank W. Albert et al.   PLoS Genetics

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

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

Epialleles in plant evolution

(2012) Detlef Weigel et al.   GENOME BIOLOGY

fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios

(2011) Laurent Excoffier et al.   BIOINFORMATICS

Design and validation issues in RNA-seq experiments

(2011) Z. Fang et al.   BRIEFINGS IN BIOINFORMATICS

RADSeq: next-generation population genetics

(2011) J. W. Davey et al.   Briefings in Functional Genomics

Regulation and function of DNA methylation in plants and animals

(2011) Xin-Jian He et al.   CELL RESEARCH

A Regression-Based Approach to Selection Mapping

(2011) Pamela Wiener et al.   JOURNAL OF HEREDITY

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Genetic diversity in farm animals - a review

(2010) L. F. Groeneveld et al.   ANIMAL GENETICS

Discriminant analysis of principal components: a new method for the analysis of genetically structured populations

(2010) Thibaut Jombart et al.   BMC GENETICS

Detecting Selection in Population Trees: The Lewontin and Krakauer Test Extended

(2010) M. Bonhomme et al.   GENETICS

The Next Generation of Molecular Markers From Massively Parallel Sequencing of Pooled DNA Samples

(2010) Andreas Futschik et al.   GENETICS

Population differentiation as a test for selective sweeps

(2010) H. Chen et al.   GENOME RESEARCH

Validation of a Candidate Deoxynivalenol-Inactivating UDP-Glucosyltransferase from Barley by Heterologous Expression in Yeast

(2010) Wolfgang Schweiger et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Environmental epigenetic modifications and reprogramming-recalcitrant genes

(2010) Kazuhiro Sakurada   Stem Cell Research

Fast model-based estimation of ancestry in unrelated individuals

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

Detecting loci under selection in a hierarchically structured population

(2009) L Excoffier et al.   HEREDITY

ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions

(2009) Dominic Schmidt et al.   METHODS

Statistical inferences in phylogeography

(2009) RASMUS NIELSEN et al.   MOLECULAR ECOLOGY

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

Epigenetic responses to environmental change and their evolutionary implications

(2009) B. M. Turner   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

Sensitive Detection of Chromosomal Segments of Distinct Ancestry in Admixed Populations

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