Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions

Reconstruction and analysis of a carbon-core metabolic network for Dunaliella salina

(2020) Melanie Fachet et al.   BMC BIOINFORMATICS

Development of decreased-gluten wheat enabled by determination of the genetic basis of lys3a barley

(2019) Charles Paul Moehs et al.   PLANT PHYSIOLOGY

Worldwide phylogeography and history of wheat genetic diversity

(2019) François Balfourier et al.   Science Advances

Fragmentation of Pooled PCR Products for Highly Multiplexed TILLING

(2019) Andrea Tramontano et al.   G3-Genes Genomes Genetics

Comparison and Characterization of Mutations Induced by Gamma-Ray and Carbon-Ion Irradiation in Rice (Oryza sativa L.) Using Whole-Genome Resequencing

(2019) Feng Li et al.   G3-Genes Genomes Genetics

Characterization, genetic diversity, phylogenetic relationships, and expression of the aluminum tolerance MATE1 gene in Secale species

(2018) E. Santos et al.   BIOLOGIA PLANTARUM

Comparison of normalization methods for the analysis of metagenomic gene abundance data

(2018) Mariana Buongermino Pereira et al.   BMC GENOMICS

Functional analysis of a pathogenesis-related thaumatin-like protein gene TaLr35PR5 from wheat induced by leaf rust fungus

(2018) Jiarui Zhang et al.   BMC PLANT BIOLOGY

Genetic diversity and relationship between domesticated rye and its wild relatives as revealed through genotyping-by-sequencing

(2018) Mona Schreiber et al.   Evolutionary Applications

Decreasing fructose-1,6-bisphosphate aldolase activity reduces plant growth and tolerance to chilling stress in tomato seedlings

(2018) Bingbing Cai et al.   PHYSIOLOGIA PLANTARUM

Detecting Somatic Mutations in Normal Cells

(2018) Yanmei Dou et al.   TRENDS IN GENETICS

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

(2018) Wensheng Wang et al.   NATURE

Identification of induced mutations in hexaploid wheat genome using exome capture assay

(2018) Momina Hussain et al.   PLoS One

Phylogeny and genetic structure in the genus Secale

(2018) Öncü Maraci et al.   PLoS One

Next-Generation Sequencing Accelerates Crop Gene Discovery

(2018) Khanh Le Nguyen et al.   TRENDS IN PLANT SCIENCE

The Gsp-1 genes encode the wheat arabinogalactan peptide

(2017) Mark D. Wilkinson et al.   JOURNAL OF CEREAL SCIENCE

Next-generation sequencing (NGS)-based identification of induced mutations in a doubly mutagenized tomato (Solanum lycopersicum ) population

(2017) Prateek Gupta et al.   PLANT JOURNAL

Towards a whole-genome sequence for rye (Secale cerealeL.)

(2017) Eva Bauer et al.   PLANT JOURNAL

Genetic Diversity, Population Structure and Ancestral Origin of Australian Wheat

(2017) Reem Joukhadar et al.   Frontiers in Plant Science

Deep Assessment of Genomic Diversity in Cassava for Herbicide Tolerance and Starch Biosynthesis

(2017) Jorge Duitama et al.   Computational and Structural Biotechnology Journal

A systematic review of rye (Secale cereale L.) as a source of resistance to pathogens and pests in wheat (Triticum aestivum L.)

(2017) Leonardo A. Crespo-Herrera et al.   HEREDITAS

vcfr: a package to manipulate and visualize variant call format data in R

(2016) Brian J. Knaus et al.   Molecular Ecology Resources

Evolutionary relationships in the genus Secale revealed by DArTseq DNA polymorphism

(2016) Maja Al-Beyroutiová et al.   PLANT SYSTEMATICS AND EVOLUTION

Maize endosperm-specific transcription factors O2 and PBF network the regulation of protein and starch synthesis

(2016) Zhiyong Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DArT Markers Effectively Target Gene Space in the Rye Genome

(2016) Piotr Gawroński et al.   Frontiers in Plant Science

Harnessing Diversity in Wheat to Enhance Grain Yield, Climate Resilience, Disease and Insect Pest Resistance and Nutrition Through Conventional and Modern Breeding Approaches

(2016) Suchismita Mondal et al.   Frontiers in Plant Science

Genetic Distinctiveness of Rye In situ Accessions from Portugal Unveils a New Hotspot of Unexplored Genetic Resources

(2016) Filipa Monteiro et al.   Frontiers in Plant Science

Two-group comparisons of zero-inflated intensity values: the choice of test statistic matters

(2015) Andreas Gleiss et al.   BIOINFORMATICS

Rapid identification and recovery of ENU-induced mutations with next-generation sequencing and Paired-End Low-Error analysis

(2015) Luyuan Pan et al.   BMC GENOMICS

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

(2015) Zhengkui Zhou et al.   NATURE BIOTECHNOLOGY

SIFT missense predictions for genomes

(2015) Robert Vaser et al.   Nature Protocols

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

(2015) Melanie Schirmer et al.   NUCLEIC ACIDS RESEARCH

Assessment of Genetic Diversity in Secale cereale Based on SSR Markers

(2015) M. Targońska et al.   PLANT MOLECULAR BIOLOGY REPORTER

Genome-wide DNA polymorphisms in low Phosphate tolerant and sensitive rice genotypes

(2015) Poonam Mehra et al.   Scientific Reports

VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants

(2014) V. Obenchain et al.   BIOINFORMATICS

Genome-wide characterization of genetic diversity and population structure in Secale

(2014) Hanna Bolibok-Brągoszewska et al.   BMC PLANT BIOLOGY

POPTREEW: Web Version of POPTREE for Constructing Population Trees from Allele Frequency Data and Computing Some Other Quantities

(2014) Naoko Takezaki et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP genotyping method based on custom amplicon sequencing

(2014) Nathan R. Campbell et al.   Molecular Ecology Resources

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

Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing

(2013) Ying-hui Li et al.   BMC GENOMICS

Feeding the future

(2013) Susan McCouch et al.   NATURE

Aluminum tolerance in maize is associated with higher MATE1 gene copy number

(2013) L. G. Maron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Qualimap: evaluating next-generation sequencing alignment data

(2012) Fernando García-Alcalde et al.   BIOINFORMATICS

GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update

(2012) R. Peakall et al.   BIOINFORMATICS

Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

(2012) Jian Ye et al.   BMC BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency

(2012) Rico Gamuyao et al.   NATURE

Cultivar development of allogamous crops

(2012) Cláudio Lopes de Souza Jr.   Crop Breeding and Applied Biotechnology

High levels of nucleotide diversity and fast decline of linkage disequilibrium in rye (Secale cereale L.) genes involved in frost response

(2011) Yongle Li et al.   BMC PLANT BIOLOGY

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data

(2011) Zhi Wei et al.   NUCLEIC ACIDS RESEARCH

Discovery of polymorphisms in starch-related genes in rice germplasm by amplification of pooled DNA and deeply parallel sequencing†

(2011) Ardashir Kharabian-Masouleh et al.   PLANT BIOTECHNOLOGY JOURNAL

Large-scale detection of rare variants via pooled multiplexed next-generation sequencing: towards next-generation Ecotilling

(2011) Fabio Marroni et al.   PLANT JOURNAL

Discovery of Rare Mutations in Populations: TILLING by Sequencing

(2011) H. Tsai et al.   PLANT PHYSIOLOGY

A statistical method for the detection of variants from next-generation resequencing of DNA pools

(2010) V. Bansal   BIOINFORMATICS

DNA polymorphisms and haplotype patterns of transcription factors involved in barley endosperm development are associated with key agronomic traits

(2010) Grit Haseneyer et al.   BMC PLANT BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The nature of selection during plant domestication

(2009) Michael D. Purugganan et al.   NATURE

A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R

(2008) Jan Bartoš et al.   BMC PLANT BIOLOGY

Establishment of introgression libraries in hybrid rye (Secale cereale L.) from an Iranian primitive accession as a new tool for rye breeding and genomics

(2008) K. C. Falke et al.   THEORETICAL AND APPLIED GENETICS