Transposon activity, local duplications and propagation of structural variants across haplotypes drive the evolution of the Drosophila S2 cell line

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits

(2021) Doruk Beyter et al.   NATURE GENETICS

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

(2021) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Transposable element profiles reveal cell line identity and loss of heterozygosity in Drosophila cell culture

(2021) Shunhua Han et al.   GENETICS

Pan-cancer analysis of whole genomes

(2020)   NATURE

Long-read DNA sequencing fully characterized chromothripsis in a patient with Langer–Giedion syndrome and Cornelia de Lange syndrome-4

(2020) Ming Lei et al.   JOURNAL OF HUMAN GENETICS

Linked‐read sequencing enables haplotype‐resolved resequencing at population scale

(2020) Dave Lutgen et al.   Molecular Ecology Resources

pyGenomeTracks: reproducible plots for multivariate genomic data sets

(2020) Lucille Lopez-Delisle et al.   BIOINFORMATICS

Long-read sequencing for non-small-cell lung cancer genomes

(2020) Yoshitaka Sakamoto et al.   GENOME RESEARCH

A genome engineering resource to uncover principles of cellular organization and tissue architecture by lipid signaling

(2020) Deepti Trivedi et al.   eLife

Resolving the full spectrum of human genome variation using Linked-Reads

(2019) Patrick Marks et al.   GENOME RESEARCH

Fast and accurate long-read assembly with wtdbg2

(2019) Jue Ruan et al.   NATURE METHODS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line

(2018) Maria Nattestad et al.   GENOME RESEARCH

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

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Generating and working with Drosophila cell cultures: Current challenges and opportunities

(2018) Arthur Luhur et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Genome-Wide Estimates of Transposable Element Insertion and Deletion Rates in Drosophila Melanogaster

(2017) Jeffrey R. Adrion et al.   Genome Biology and Evolution

Icarus: visualizer for de novo assembly evaluation

(2016) Alla Mikheenko et al.   BIOINFORMATICS

Asexual Amoebae Escape Muller's Ratchet through Polyploidy

(2016) Sutherland K. Maciver   TRENDS IN PARASITOLOGY

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations

(2014) G. dos Santos et al.   NUCLEIC ACIDS RESEARCH

Transposition-mediated DNA re-replication in maize

(2014) Jianbo Zhang et al.   eLife

DNA copy number evolution in Drosophila cell lines

(2014) Hangnoh Lee et al.   GENOME BIOLOGY

Single-Stranded Annealing Induced by Re-Initiation of Replication Origins Provides a Novel and Efficient Mechanism for Generating Copy Number Expansion via Non-Allelic Homologous Recombination

(2013) Kenneth J. Finn et al.   PLoS Genetics

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

(2012) Haibin Xu et al.   PLoS One

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

(2011) Valentina Boeva et al.   BIOINFORMATICS

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The transcriptional diversity of 25 Drosophila cell lines

(2010) L. Cherbas et al.   GENOME RESEARCH

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Unlocking the secrets of the genome

(2009) Susan E. Celniker et al.   NATURE

Quantifying the threat of extinction from Muller's ratchet in the diploid Amazon molly (Poecilia formosa)

(2008) Laurence Loewe et al.   BMC EVOLUTIONARY BIOLOGY