Single-Cell Transcriptomics Reveal a Correlation between Genome Architecture and Gene Family Evolution in Ciliates

PhyloToL: A taxon/gene rich phylogenomic pipeline to explore genome evolution of diverse eukaryotes

(2019) M A Cerón-Romero et al.   MOLECULAR BIOLOGY AND EVOLUTION

“Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell ‘omics”

(2018) Xyrus X Maurer-Alcalá et al.   Genome Biology and Evolution

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

(2018) Xyrus X. Maurer-Alcalá et al.   mBio

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

(2018) Sina M. Adl et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Single-cell transcriptomics of small microbial eukaryotes: limitations and potential

(2017) Zhenfeng Liu et al.   ISME Journal

Nuclear Features of the Heterotrich Ciliate Blepharisma americanum : Genomic Amplification, Life Cycle, and Nuclear Inclusion

(2017) Megan M. Wancura et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Advances in single-cell RNA sequencing and its applications in cancer research

(2017) Sibo Zhu et al.   Oncotarget

Tools for Genomic and Transcriptomic Analysis of Microbes at Single-Cell Level

(2017) Zixi Chen et al.   Frontiers in Microbiology

Reassigning stop codons via translation termination: How a few eukaryotes broke the dogma

(2016) Elena Alkalaeva et al.   BIOESSAYS

Genetic Codes with No Dedicated Stop Codon: Context-Dependent Translation Termination

(2016) Estienne Carl Swart et al.   CELL

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

(2016) Xyrus X. Maurer-Alcalá et al.   Genome Biology and Evolution

Molecular Structures and Coding Genes of the Water-Borne Protein Pheromones ofEuplotes petzi, an Early Diverging Polar Species ofEuplotes

(2016) Bill Pedrini et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Novel Ciliate Genetic Code Variants Including the Reassignment of All Three Stop Codons to Sense Codons inCondylostoma magnum

(2016) Stephen M. Heaphy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Actin evolution in ciliates (Protist, Alveolata) is characterized by high diversity and three duplication events

(2016) Zhenzhen Yi et al.   MOLECULAR PHYLOGENETICS 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

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

Evolution of the Dynein Heavy Chain Family in Ciliates

(2015) Vidyalakshmi Rajagopalan et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection

(2015) Martin D. Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

Single-cell transcriptomics for microbial eukaryotes

(2014) Martin Kolisko et al.   CURRENT BIOLOGY

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

RELAX: Detecting Relaxed Selection in a Phylogenetic Framework

(2014) Joel O. Wertheim et al.   MOLECULAR BIOLOGY AND EVOLUTION

Single-cell RNA-seq: advances and future challenges

(2014) Antoine-Emmanuel Saliba et al.   NUCLEIC ACIDS RESEARCH

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

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

Quantitative biology of single neurons

(2012) J. Eberwine et al.   Journal of the Royal Society Interface

Simulated evolution applied to study the genetic code optimality using a model of codon reassignments

(2011) José Santos et al.   BMC BIOINFORMATICS

Complex phylogenetic distribution of a non-canonical genetic code in green algae

(2010) Ellen Cocquyt 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

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

Genetic Code Supports Targeted Insertion of Two Amino Acids by One Codon

(2009) A. A. Turanov et al.   SCIENCE

Dynamic nuclear reorganization during genome remodeling of Tetrahymena

(2008) Douglas L. Chalker   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Macronuclear genome structure of the ciliate Nyctotherus ovalis: Single-gene chromosomes and tiny introns

(2008) Guénola Ricard et al.   BMC GENOMICS