iGDP: An integrated genome decontamination pipeline for wild ciliated microeukaryotes

Absolute quantification of chromosome copy numbers in the polyploid macronucleus of Tetrahymena thermophila at the single‐cell level

(2022) Yuanyuan Zhou et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

An Extremely Streamlined Macronuclear Genome in the Free-Living Protozoan Fabrea salina

(2022) Bing Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Whokaryote: distinguishing eukaryotic and prokaryotic contigs in metagenomes based on gene structure

(2022) Lotte J.U. Pronk et al.   Microbial Genomics

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Bacteria-Derived Hemolysis-Related Genes Widely Exist in Scuticociliates

(2020) Jing Zhang et al.   Microorganisms

Single-Cell Genomic Sequencing of Three Peritrichs (Protista, Ciliophora) Reveals Less Biased Stop Codon Usage and More Prevalent Programmed Ribosomal Frameshifting Than in Other Ciliates

(2020) Xiao Chen et al.   Frontiers in Marine Science

Exploration of Genetic Variations through Single‐cell Whole‐genome Sequencing in the Model Ciliate Tetrahymena thermophila

(2019) Kai Chen et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Hidden genomic evolution in a morphospecies—The landscape of rapidly evolving genes in Tetrahymena

(2019) Jie Xiong et al.   PLOS BIOLOGY

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

ParameciumDB 2019: integrating genomic data across the genus for functional and evolutionary biology

(2019) Olivier Arnaiz et al.   NUCLEIC ACIDS RESEARCH

Comparative Genomics Analysis of Ciliates Provides Insights on the Evolutionary History Within “Nassophorea–Synhymenia–Phyllopharyngea” Assemblage

(2019) Bo Pan et al.   Frontiers in Microbiology

OUP accepted manuscript

(2018)   BIOINFORMATICS

Insights into the origin and evolution of Peritrichia (Oligohymenophorea, Ciliophora) based on analyses of morphology and phylogenomics

(2018) Chuan-Qi Jiang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenomics solves a long-standing evolutionary puzzle in the ciliate world: The subclass Peritrichia is monophyletic

(2017) Eleni Gentekaki et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Distribution and Diversity of Microbial Eukaryotes in Bathypelagic Waters of the South China Sea

(2016) Dapeng Xu et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

The All-Data-Based Evolutionary Hypothesis of Ciliated Protists with a Revised Classification of the Phylum Ciliophora (Eukaryota, Alveolata)

(2016) Feng Gao et al.   Scientific Reports

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

ProDeGe: a computational protocol for fully automated decontamination of genomes

(2015) Kristin Tennessen et al.   ISME Journal

Phylogenomic analyses reveal subclass Scuticociliatia as the sister group of subclass Hymenostomatia within class Oligohymenophorea

(2015) Jin-Mei Feng et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Genome of the facultative scuticociliatosis pathogen Pseudocohnilembus persalinus provides insight into its virulence through horizontal gene transfer

(2015) Jie Xiong et al.   Scientific Reports

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Chromosome Copy Number Variation and Control in the Ciliate Chilodonella uncinata

(2013) Kevin J. Spring et al.   PLoS One

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures

(2012) Marc Strous et al.   Frontiers in Microbiology

Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition

(2011) Isaam Saeed et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS