Exploration of the Germline Genome of the Ciliate Chilodonella uncinata through Single-Cell Omics (Transcriptomics and Genomics)

The evolution of mating-type switching for reproductive assurance

(2016) Bart P. S. Nieuwenhuis et al.   BIOESSAYS

Morphological Identification and Single-Cell Genomics of Marine Diplonemids

(2016) Ryan M.R. Gawryluk et al.   CURRENT BIOLOGY

Nuclear Architecture and Patterns of Molecular Evolution Are Correlated in the CiliateChilodonella uncinata

(2016) Xyrus X. Maurer-Alcalá 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

An epigenetic toolkit allows for diverse genome architectures in eukaryotes

(2015) Xyrus X Maurer-Alcalá et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

DNA Double-Strand Breaks and Telomeres Play Important Roles in Trypanosoma brucei Antigenic Variation

(2015) Bibo Li   EUKARYOTIC CELL

Unexpected selection to retain high GC content and splicing enhancers within exons of multiexonic lncRNA loci

(2015) Wilfried Haerty et al.   RNA

Analyses of Alternatively Processed Genes in Ciliates Provide Insights into the Origins of Scrambled Genomes and May Provide a Mechanism for Speciation

(2015) Feng Gao et al.   mBio

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

(2014) Xiao Chen et al.   CELL

Programmed DNA elimination in multicellular organisms

(2014) Jianbin Wang et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

GENOME STRUCTURE DRIVES PATTERNS OF GENE FAMILY EVOLUTION IN CILIATES, A CASE STUDY USINGCHILODONELLA UNCINATA(PROTISTA, CILIOPHORA, PHYLLOPHARYNGEA)

(2014) Feng Gao et al.   EVOLUTION

The Draft Assembly of the Radically Organized Stylonychia lemnae Macronuclear Genome

(2014) Samuel H. Aeschlimann et al.   Genome Biology and Evolution

Characterization of the Life Cycle and Heteromeric Nature of the Macronucleus of the CiliateChilodonella uncinataUsing Fluorescence Microscopy

(2014) Laure Bellec et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Nanochromosome Copy Number Does not Correlate with RNA Levels Though Patterns are Conserved between Strains of the Ciliate Morphospecies Chilodonella uncinata

(2014) Jie Huang et al.   PROTIST

Single cell genome analysis of an uncultured heterotrophic stramenopile

(2014) Rajat S. Roy et al.   Scientific Reports

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

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

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

Analyses of chromosome copy number and expression level of four genes in the ciliate Chilodonella uncinata reveal a complex pattern that suggests epigenetic regulation

(2012) Laure Bellec et al.   GENE

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Gene family evolution in green plants with emphasis on the origination and evolution ofArabidopsis thalianagenes

(2012) Ya-Long Guo   PLANT JOURNAL

The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences

(2012) Olivier Arnaiz et al.   PLoS Genetics

Evolutionary trends of GC/AT distribution patterns in promoters

(2011) Elisa Calistri et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Estimating the timing of early eukaryotic diversification with multigene molecular clocks

(2011) L. W. Parfrey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell Genomics Reveals Organismal Interactions in Uncultivated Marine Protists

(2011) H. S. Yoon et al.   SCIENCE

The evolution of transcription-associated biases of mutations across vertebrates

(2010) Paz Polak et al.   BMC EVOLUTIONARY BIOLOGY

Alternative processing of scrambled genes generates protein diversity in the ciliate Chilodonella uncinata

(2010) Laura A. Katz et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Triggers for genomic rearrangements: insights into genomic, cellular and environmental influences

(2010) Ram-Shankar Mani et al.   NATURE REVIEWS GENETICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Patterns of exon-intron architecture variation of genes in eukaryotic genomes

(2009) Liucun Zhu et al.   BMC GENOMICS

Programmed loss of millions of base pairs from a vertebrate genome

(2009) J. J. Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Dynamic Nature of Eukaryotic Genomes

(2008) L. W. Parfrey et al.   MOLECULAR BIOLOGY AND EVOLUTION

Enzymes used in molecular biology: a useful guide

(2008) Laure Rittié et al.   Journal of Cell Communication and Signaling