4.6 Article

The Role of cis Regulatory Evolution in Maize Domestication

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors

Jinpu Jin et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Mathematical & Computational Biology

A novel multi-alignment pipeline for high-throughput sequencing data

Shunping Huang et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2014)

Review Plant Sciences

A Bountiful Harvest: Genomic Insights into Crop Domestication Phenotypes

Kenneth M. Olsen et al.

ANNUAL REVIEW OF PLANT BIOLOGY, VOL 64 (2013)

Article Biochemistry & Molecular Biology

Inheritance of Gene Expression Level and Selective Constraints on Trans- and Cis-Regulatory Changes in Yeast

Bernhard Schaefke et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Biochemistry & Molecular Biology

Epigenetic and Genetic Influences on DNA Methylation Variation in Maize Populations

Steven R. Eichten et al.

PLANT CELL (2013)

Article Multidisciplinary Sciences

Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato

Daniel Koenig et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Multidisciplinary Sciences

CACTA-like transposable element in ZmCCT attenuated photoperiod sensitivity and accelerated the postdomestication spread of maize

Qin Yang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Genetics & Heredity

From Many, One: Genetic Control of Prolificacy during Maize Domestication

David M. Wills et al.

PLOS GENETICS (2013)

Article Biochemistry & Molecular Biology

Genome-wide Analysis of Cis-regulatory Divergence between Species in the Arabidopsis Genus

Fei He et al.

MOLECULAR BIOLOGY AND EVOLUTION (2012)

Article Genetics & Heredity

Comparative population genomics of maize domestication and improvement

Matthew B. Hufford et al.

NATURE GENETICS (2012)

Article Genetics & Heredity

Parallel domestication of the Shattering1 genes in cereals

Zhongwei Lin et al.

NATURE GENETICS (2012)

Article Biochemistry & Molecular Biology

KEGG for integration and interpretation of large-scale molecular data sets

Minoru Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemistry & Molecular Biology

A new strategy to reduce allelic bias in RNA-Seq readmapping

Ravi Vijaya Satya et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Multidisciplinary Sciences

Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing

Candice N. Hansey et al.

PLOS ONE (2012)

Review Biology

What can patterns of differentiation across plant genomes tell us about adaptation and speciation?

Jared L. Strasburg et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2012)

Article Multidisciplinary Sciences

Reshaping of the maize transcriptome by domestication

Ruth Swanson-Wagner et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Genetics & Heredity

A Survey for Novel Imprinted Genes in the Mouse Placenta by mRNA-seq

Xu Wang et al.

GENETICS (2011)

Article Biotechnology & Applied Microbiology

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Manfred G. Grabherr et al.

NATURE BIOTECHNOLOGY (2011)

Article Genetics & Heredity

A framework for variation discovery and genotyping using next-generation DNA sequencing data

Mark A. DePristo et al.

NATURE GENETICS (2011)

Article Genetics & Heredity

Identification of a functional transposon insertion in the maize domestication gene tb1

Anthony Studer et al.

NATURE GENETICS (2011)

Article Biochemistry & Molecular Biology

Regulatory divergence in Drosophila revealed by mRNA-seq

C. Joel McManus et al.

GENOME RESEARCH (2010)

Article Biochemistry & Molecular Biology

Natural selection on cis and trans regulation in yeasts

J. J. Emerson et al.

GENOME RESEARCH (2010)

Article Biochemistry & Molecular Biology

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

Aaron McKenna et al.

GENOME RESEARCH (2010)

Review Plant Sciences

Genetic perspectives on crop domestication

Briana L. Gross et al.

TRENDS IN PLANT SCIENCE (2010)

Article Biotechnology & Applied Microbiology

Gene ontology analysis for RNA-seq: accounting for selection bias

Matthew D. Young et al.

GENOME BIOLOGY (2010)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Article Genetics & Heredity

Global Analysis of Allele-Specific Expression in Arabidopsis thaliana

Xu Zhang et al.

GENETICS (2009)

Article Biochemistry & Molecular Biology

Estimating the Rate of Adaptive Molecular Evolution in the Presence of Slightly Deleterious Mutations and Population Size Change

Adam Eyre-Walker et al.

MOLECULAR BIOLOGY AND EVOLUTION (2009)

Review Multidisciplinary Sciences

The nature of selection during plant domestication

Michael D. Purugganan et al.

NATURE (2009)

Article Multidisciplinary Sciences

A Yeast Hybrid Provides Insight into the Evolution of Gene Expression Regulation

Itay Tirosh et al.

SCIENCE (2009)

Article Biotechnology & Applied Microbiology

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Ben Langmead et al.

GENOME BIOLOGY (2009)

Review Plant Sciences

Molecular insights into the evolution of crop plants

Jutta C. Burger et al.

AMERICAN JOURNAL OF BOTANY (2008)

Article Biochemistry & Molecular Biology

Allele-specific expression patterns reveal biases and embryo-specific parent-of-origin effects in hybrid maize

Nathan M. Springer et al.

PLANT CELL (2007)

Review Biochemistry & Molecular Biology

The molecular genetics of crop domestication

John F. Doebley et al.

Article Multidisciplinary Sciences

An SNP caused loss of seed shattering during rice domestication

Saeko Konishi et al.

SCIENCE (2006)

Article Multidisciplinary Sciences

The origin of the naked grains of maize

H Wang et al.

NATURE (2005)

Article Biochemistry & Molecular Biology

Evolution at two levels: On genes and form

SB Carroll

PLOS BIOLOGY (2005)

Article Multidisciplinary Sciences

The role of barren stalk1 in the architecture of maize

A Gallavotti et al.

NATURE (2004)

Article Biochemistry & Molecular Biology

Selection versus demography: A multilocus investigation of the domestication process in maize

MI Tenaillon et al.

MOLECULAR BIOLOGY AND EVOLUTION (2004)

Article Statistics & Probability

A direct approach to false discovery rates

JD Storey

JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY (2002)

Article Multidisciplinary Sciences

fw2.2:: A quantitative trait locus key to the evolution of tomato fruit size

A Frary et al.

SCIENCE (2000)

Article Biochemistry & Molecular Biology

KEGG: Kyoto Encyclopedia of Genes and Genomes

M Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2000)