The genetic and epigenetic landscape of the Arabidopsis centromeres

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

The structure, function and evolution of a complete human chromosome 8

(2021) Glennis A. Logsdon et al.   NATURE

Towards complete and error-free genome assemblies of all vertebrate species

(2021) Arang Rhie et al.   NATURE

Identifying and removing haplotypic duplication in primary genome assemblies

(2020) Dengfeng Guan et al.   BIOINFORMATICS

Interacting genomic landscapes of REC8-cohesin, chromatin and meiotic recombination in Arabidopsis thaliana

(2020) Christophe Lambing et al.   PLANT CELL

GenMap: ultra-fast computation of genome mappability

(2020) Christopher Pockrandt et al.   BIOINFORMATICS

Arabidopsis retrotransposon virus-like particles and their regulation by epigenetically activated small RNA

(2020) Seung Cho Lee et al.   GENOME RESEARCH

Weighted minimizer sampling improves long read mapping

(2020) Chirag Jain et al.   BIOINFORMATICS

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

(2020) Michael Alonge et al.   CELL

Telomere-to-telomere assembly of a complete human X chromosome

(2020) Karen H. Miga et al.   NATURE

ASY1 acts as a dosage-dependent antagonist of telomere-led recombination and mediates crossover interference inArabidopsis

(2020) Christophe Lambing et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Liftoff: accurate mapping of gene annotations

(2020) Alaina Shumate et al.   BIOINFORMATICS

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Cooler: scalable storage for Hi-C data and other genomically labeled arrays

(2019) Nezar Abdennur et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Transposable elements: genome innovation, chromosome diversity, and centromere conflict

(2018) Savannah J. Klein et al.   CHROMOSOME RESEARCH

Nucleosomes and DNA methylation shape meiotic DSB frequency inArabidopsis thalianatransposons and gene regulatory regions

(2018) Kyuha Choi et al.   GENOME RESEARCH

Epigenetic activation of meiotic recombination nearArabidopsis thalianacentromeres via loss of H3K9me2 and non-CG DNA methylation

(2018) Charles J. Underwood et al.   GENOME RESEARCH

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

Correction of Persistent Errors in Arabidopsis Reference Mitochondrial Genomes

(2018) Daniel B. Sloan et al.   PLANT CELL

Massive crossover elevation via combination ofHEI10andrecq4a recq4bduringArabidopsismeiosis

(2018) Heïdi Serra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A universal SNP and small-indel variant caller using deep neural networks

(2018) Ryan Poplin et al.   NATURE BIOTECHNOLOGY

Centromere location in Arabidopsis is unaltered by extreme divergence in CENH3 protein sequence

(2017) Shamoni Maheshwari et al.   GENOME RESEARCH

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees

(2016) Kazunori D. Yamada et al.   BIOINFORMATICS

Epigenome confrontation triggers immediate reprogramming of DNA methylation and transposon silencing inArabidopsis thalianaF1 epihybrids

(2016) Mélanie Rigal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The molecular basis for centromere identity and function

(2015) Kara L. McKinley et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Genome-Wide Prediction and Validation of Intergenic Enhancers in Arabidopsis Using Open Chromatin Signatures

(2015) Bo Zhu et al.   PLANT CELL

Rapid and Inexpensive Whole-Genome Genotyping-by-Sequencing for Crossover Localization and Fine-Scale Genetic Mapping

(2015) Beth A. Rowan et al.   G3-Genes Genomes Genetics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The Histone Variant H2A.W Defines Heterochromatin and Promotes Chromatin Condensation in Arabidopsis

(2014) Ramesh Yelagandula et al.   CELL

Genome-wide Hi-C Analyses in Wild-Type and Mutants Reveal High-Resolution Chromatin Interactions in Arabidopsis

(2014) Suhua Feng et al.   MOLECULAR CELL

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Comprehensive Analysis of Silencing Mutants Reveals Complex Regulation of the Arabidopsis Methylome

(2013) Hume Stroud et al.   CELL

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

(2013) Hume Stroud et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana

(2013) Erik Wijnker et al.   eLife

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

(2013) Daniël P Melters et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Centromere-targeted de novo integrations of an LTR retrotransposon of Arabidopsis lyrata

(2012) S. Tsukahara et al.   GENES & DEVELOPMENT

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

RAxML and FastTree: Comparing Two Methods for Large-Scale Maximum Likelihood Phylogeny Estimation

(2011) Kevin Liu et al.   PLoS One

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Haploid plants produced by centromere-mediated genome elimination

(2010) Maruthachalam Ravi et al.   NATURE

Widespread Gene Conversion in Centromere Cores

(2010) Jinghua Shi et al.   PLOS 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

Major Evolutionary Transitions in Centromere Complexity

(2009) Harmit S. Malik et al.   CELL

ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing

(2009) Yannick Jacob et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Database indexing for production MegaBLAST searches

(2008) Aleksandr Morgulis et al.   BIOINFORMATICS

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets

(2008) Nicolas Buisine et al.   GENOMICS