Bernardo Clavijo

Disentangling the genomic complexity of the Fragilariopsis cylindrus (CCMP1102) genome

This paper presents a novel haplotype-specific assembly method to resolve the complex genome of Fragilariopsis cylindrus, revealing triploidy, aneuploidy, and sexual reproduction.

Sequencing smart: De novo sequencing and assembly approaches for non-model mammals.

The paper evaluates de novo genome assembly methods for a low-quality non-model mammal sample, finding that more data types do not always improve assembly quality.

A genome assembly of the barley 'transformation reference' cultivar Golden Promise

The paper presents a high-quality genome assembly for the barley cultivar Golden Promise, useful for genetic research and CRISPR-Cas9 experiments.

Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency

The paper analyzes recombination patterns in hexaploid wheat, identifies genes controlling recombination and gene conversion, and highlights a novel RecQ helicase gene involved in gene conversion.

The ash dieback invasion of Europe was founded by two individuals from a native population with huge adaptive potential

The paper analyzes the genetic diversity of Hymenoscyphus fraxineus, showing the European population was founded by two divergent haplotypes with adaptive potential.

The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum

The paper presents the first near-complete assembly of the hexaploid bread wheat genome using a combination of short and long-read sequencing technologies.

Skip-mers: increasing entropy and sensitivity to detect conserved genic regions with simple cyclic q-grams

This paper introduces skip-mers as an improved method for detecting conserved genic regions, showing increased entropy and sensitivity compared to traditional k-mers.

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.

W2RAP: a pipeline for high quality, robust assemblies of large complex genomes from short read data

The paper introduces a pipeline for generating high-quality genome assemblies from short read data, demonstrating its effectiveness on plant and human datasets.

A clonally reproducing generalist aphid pest colonises diverse host plants by rapid transcriptional plasticity of duplicated gene clusters

This study shows that the green peach aphid uses rapid transcriptional changes of duplicated genes to colonize diverse host plants without genetic specialization.

KAT: A K-mer Analysis Toolkit to quality control NGS datasets and genome assemblies

KAT assesses quality and contamination in NGS data and assemblies using k-mer frequencies and GC composition without a reference.

Crowdsourced analysis of ash and ash dieback through the Open Ash Dieback project: A year 1 report on datasets and analyses contributed by a self-organising community.

The paper reports on a crowdsourced project analyzing ash dieback fungus data, revealing insights into its genome and biology through community contributions.