High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads

Benchmarking of next and third generation sequencing technologies and their associated algorithms for de novo genome assembly

(2021) Marios Gavrielatos et al.   Molecular Medicine Reports

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

(2021) Haoyu Cheng et al.   NATURE METHODS

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

(2021) Glennis A. Logsdon et al.   NATURE

Two gap-free reference genomes and a global view of the centromere architecture in rice

(2021) Jia-Ming Song et al.   Molecular Plant

The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types

(2021) Tingting Chen et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Genome Warehouse: A Public Repository Housing Genome-scale Data

(2021) Meili Chen et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Methplotlib: analysis of modified nucleotides from nanopore sequencing

(2020) Wouter De Coster et al.   BIOINFORMATICS

Conservation of CENH3 Interaction Partners in Plants

(2020) Burcu Nur Keçeli et al.   JOURNAL OF EXPERIMENTAL BOTANY

TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats

(2020) Alla Mikheenko et al.   BIOINFORMATICS

Weighted minimizer sampling improves long read mapping

(2020) Chirag Jain et al.   BIOINFORMATICS

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data

(2020) Chengjie Chen et al.   Molecular Plant

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

(2020) Karen H. Miga et al.   NATURE

Centromere studies in the era of ‘telomere-to-telomere’ genomics

(2020) Karen H. Miga   EXPERIMENTAL CELL RESEARCH

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

(2020) Sergey Nurk et al.   GENOME RESEARCH

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

(2019) Aaron M. Wenger et al.   NATURE BIOTECHNOLOGY

NextPolish: a fast and efficient genome polishing tool for long-read assembly

(2019) Jiang Hu et al.   BIOINFORMATICS

Versatile genome assembly evaluation with QUAST-LG

(2018) Alla Mikheenko et al.   BIOINFORMATICS

Genetic and epigenetic variation in 5S ribosomal RNA genes reveals genome dynamics in Arabidopsis thaliana

(2018) Lauriane Simon et al.   NUCLEIC ACIDS RESEARCH

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

(2018) Todd P. Michael et al.   Nature Communications

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

D-GENIES: dot plot large genomes in an interactive, efficient and simple way

(2018) Floréal Cabanettes et al.   PeerJ

Plant centromeres: genetics, epigenetics and evolution

(2018) Ludmila Cristina Oliveira et al.   MOLECULAR BIOLOGY REPORTS

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

(2017) Shamoni Maheshwari et al.   GENOME RESEARCH

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer

(2017) Benjamin Istace et al.   GigaScience

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

(2016) Taiji Kawakatsu et al.   CELL

A high resolution map of theArabidopsis thalianadevelopmental transcriptome based on RNA-seq profiling

(2016) Anna V. Klepikova et al.   PLANT JOURNAL

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden

(2013) Quan Long et al.   NATURE GENETICS

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

(2013) Daniël P Melters et al.   GENOME BIOLOGY

Holocentric chromosomes: convergent evolution, meiotic adaptations, and genomic analysis

(2012) Daniël P. Melters et al.   CHROMOSOME RESEARCH

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Tabix: fast retrieval of sequence features from generic TAB-delimited files

(2011) H. Li   BIOINFORMATICS

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell 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

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Epigenetic Modification of Centromeric Chromatin: Hypomethylation of DNA Sequences in the CENH3-Associated Chromatin in Arabidopsis thaliana and Maize

(2008) W. Zhang et al.   PLANT CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY