ADFinder: accurate detection of programmed DNA elimination using NGS high-throughput sequencing data

Genome analyses of the new model protist Euplotes vannus focusing on genome rearrangement and resistance to environmental stressors

(2019) Xiao Chen et al.   Molecular Ecology Resources

Insights into an Extensively Fragmented Eukaryotic Genome: De Novo Genome Sequencing of the Multinuclear Ciliate Uroleptopsis citrina

(2018) Weibo Zheng et al.   Genome Biology and Evolution

Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome

(2016) Eileen P Hamilton et al.   eLife

What is next generation sequencing?

(2013) Sam Behjati et al.   Archives of Disease in Childhood-Education and Practice Edition

Genomes on the Edge: Programmed Genome Instability in Ciliates

(2013) John R. Bracht et al.   CELL

Tetrahymena Functional Genomics Database (TetraFGD): an integrated resource for Tetrahymena functional genomics

(2013) Jie Xiong et al.   Database-The Journal of Biological Databases and Curation

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

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

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Genetic Consequences of Programmed Genome Rearrangement

(2012) Jeramiah J. Smith et al.   CURRENT BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

DiffSplice: the genome-wide detection of differential splicing events with RNA-seq

(2012) Yin Hu et al.   NUCLEIC ACIDS RESEARCH

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data

(2012) Shihao Shen et al.   NUCLEIC ACIDS RESEARCH

Genetics, Chromatin Diminution, and Sex Chromosome Evolution in the Parasitic Nematode Genus Strongyloides

(2010) Linda Nemetschke et al.   CURRENT BIOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY