Disentangling homeologous contigs in allo-tetraploid assembly: application to durum wheat

FISHIS: Fluorescence In Situ Hybridization in Suspension and Chromosome Flow Sorting Made Easy

(2013) Debora Giorgi et al.   PLoS One

Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars

(2013) C. R. Cavanagh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reference-Free Population Genomics from Next-Generation Transcriptome Data and the Vertebrate–Invertebrate Gap

(2013) Philippe Gayral et al.   PLoS Genetics

High-throughput microbial population genomics using the Cortex variation assembler

(2012) Zamin Iqbal et al.   BIOINFORMATICS

Genomic expression dominance in allopolyploids

(2012) Ryan A Rapp et al.   BMC BIOLOGY

In silico archeogenomics unveils modern plant genome organisation, regulation and evolution

(2012) Jérôme Salse   CURRENT OPINION IN PLANT BIOLOGY

HapCompass: A Fast Cycle Basis Algorithm for Accurate Haplotype Assembly of Sequence Data

(2012) Derek Aguiar et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

De novo assembly and genotyping of variants using colored de Bruijn graphs

(2012) Zamin Iqbal et al.   NATURE GENETICS

Haplotype phasing: existing methods and new developments

(2011) Sharon R. Browning et al.   NATURE REVIEWS GENETICS

Identification, characterization and interpretation of single-nucleotide sequence variation in allopolyploid crop species

(2011) Sukhjiwan Kaur et al.   PLANT BIOTECHNOLOGY JOURNAL

High-throughput SNP discovery and genotyping in durum wheat (Triticum durum Desf.)

(2011) Daniele Trebbi et al.   THEORETICAL AND APPLIED GENETICS

Haplotype Inference by Pure Parsimony: A Survey

(2010) Ana Graça et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

HI: haplotype improver using paired-end short reads

(2009) Q. Long et al.   BIOINFORMATICS

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

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Single nucleotide polymorphism (SNP) discovery in the polyploidBrassica napususing Solexa transcriptome sequencing

(2009) Martin Trick et al.   PLANT BIOTECHNOLOGY JOURNAL

HapCUT: an efficient and accurate algorithm for the haplotype assembly problem

(2008) V. Bansal et al.   BIOINFORMATICS