Rearrangement of macronucleus chromosomes correspond to TAD-like structures of micronucleus chromosomes in Tetrahymena thermophila

Dynamic reorganization of the genome shapes the recombination landscape in meiotic prophase

(2019) Lucas Patel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Reprogramming of Meiotic Chromatin Architecture during Spermatogenesis

(2019) Yao Wang et al.   MOLECULAR CELL

Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis

(2019) Covadonga Vara et al.   Cell Reports

Small RNA-Mediated trans -Nuclear and trans -Element Communications in Tetrahymena DNA Elimination

(2018) Tomoko Noto et al.   CURRENT BIOLOGY

High-resolution TADs reveal DNA sequences underlying genome organization in flies

(2018) Fidel Ramírez et al.   Nature Communications

Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells

(2018) Bogdan Bintu et al.   SCIENCE

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

(2017) Ilya M. Flyamer et al.   NATURE

Cell-cycle dynamics of chromosomal organization at single-cell resolution

(2017) Takashi Nagano et al.   NATURE

Massively multiplex single-cell Hi-C

(2017) Vijay Ramani et al.   NATURE METHODS

Whats, hows and whys of programmed DNA elimination in Tetrahymena

(2017) Tomoko Noto et al.   Open Biology

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

Programmed Minichromosome Elimination as a Mechanism for Somatic Genome Reduction in Tetrahymena thermophila

(2016) Chih-Yi Gabriela Lin et al.   PLoS Genetics

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

(2016) Eileen P Hamilton et al.   eLife

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

(2015) Tsung-Han S. Hsieh et al.   CELL

Condensin- and Replication-Mediated Bacterial Chromosome Folding and Origin Condensation Revealed by Hi-C and Super-resolution Imaging

(2015) Martial Marbouty et al.   MOLECULAR CELL

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome

(2013) T. B. K. Le et al.   SCIENCE

A Single Cohesin Complex Performs Mitotic and Meiotic Functions in the Protist Tetrahymena

(2013) Rachel A. Howard-Till et al.   PLoS Genetics

A fast algorithm for matrix balancing

(2012) P. A. Knight et al.   IMA JOURNAL OF NUMERICAL ANALYSIS

The Tetrahymena meiotic chromosome bouquet is organized by centromeres and promotes interhomolog recombination

(2012) J. Loidl et al.   JOURNAL OF CELL SCIENCE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Developmentally programmed, RNA-directed genome rearrangement in Tetrahymena

(2011) Kazufumi Mochizuki   DEVELOPMENT GROWTH & DIFFERENTIATION

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Dynamic nuclear reorganization during genome remodeling of Tetrahymena

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

Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure

(2008) Robert S Coyne et al.   BMC GENOMICS

DNA double-strand breaks, but not crossovers, are required for the reorganization of meiotic nuclei in Tetrahymena

(2008) K. Mochizuki et al.   JOURNAL OF CELL SCIENCE