Capture of complete ciliate chromosomes in single sequencing reads reveals widespread chromosome isoforms

Identification of a DNA N6-Adenine Methyltransferase Complex and Its Impact on Chromatin Organization

(2019) Leslie Y. Beh et al.   CELL

Multi-platform discovery of haplotype-resolved structural variation in human genomes

(2019) Mark J. P. Chaisson et al.   Nature Communications

PANNZER2: a rapid functional annotation web server

(2018) Petri Törönen et al.   NUCLEIC ACIDS RESEARCH

Russian Doll Genes and Complex Chromosome Rearrangements in Oxytricha trifallax

(2018) Jasper Braun et al.   G3-Genes Genomes Genetics

Isoform Sequencing and State-of-Art Applications for Unravelling Complexity of Plant Transcriptomes

(2018) Dong An et al.   Genes

Young genes have distinct gene structure, epigenetic profiles, and transcriptional regulation

(2018) Michael S Werner et al.   GENOME RESEARCH

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Preferential expression of scores of functionally and evolutionarily diverse DNA and RNA-binding proteins during Oxytricha trifallax macronuclear development

(2017) Zachary T. Neeb et al.   PLoS One

De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species

(2017) Wirulda Pootakham et al.   Scientific Reports

Recurring patterns among scrambled genes in the encrypted genome of the ciliate Oxytricha trifallax

(2016) Jonathan Burns et al.   JOURNAL OF THEORETICAL BIOLOGY

Chromosome fusions triggered by noncoding RNA

(2016) John R. Bracht et al.   RNA Biology

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction

(2015) David Laehnemann et al.   BRIEFINGS IN BIOINFORMATICS

One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly

(2015) Sergey Koren et al.   CURRENT OPINION IN MICROBIOLOGY

Combinatorial DNA rearrangement facilitates the origin of new genes in ciliates

(2015) Xiao Chen et al.   Genome Biology and Evolution

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Molecular organization and comparative analysis of chromosome 5B of the wild wheat ancestor Triticum dicoccoides

(2015) Bala Ani Akpinar et al.   Scientific Reports

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

The Architecture of a Scrambled Genome Reveals Massive Levels of Genomic Rearrangement during Development

(2014) Xiao Chen et al.   CELL

Resolving the complexity of the human genome using single-molecule sequencing

(2014) Mark J. P. Chaisson et al.   NATURE

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Analysing complex Triticeae genomes – concepts and strategies

(2013) Manuel Spannagl et al.   Plant Methods

The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes

(2013) Estienne C. Swart et al.   PLOS BIOLOGY

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

Piwi-Interacting RNAs Protect DNA against Loss during Oxytricha Genome Rearrangement

(2012) Wenwen Fang et al.   CELL

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS