Accurate identification of centromere locations in yeast genomes using Hi-C

Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C

(2015) Ferhat Ay et al.   BMC GENOMICS

Centromeric Heterochromatin: The Primordial Segregation Machine

(2014) Kerry S. Bloom   Annual Review of Genetics

Filling annotation gaps in yeast genomes using genome-wide contact maps

(2014) Hervé Marie-Nelly et al.   BIOINFORMATICS

Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression

(2014) F. Ay et al.   GENOME RESEARCH

Genome-wide Hi-C Analyses in Wild-Type and Mutants Reveal High-Resolution Chromatin Interactions in Arabidopsis

(2014) Suhua Feng et al.   MOLECULAR CELL

Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe

(2014) Takeshi Mizuguchi et al.   NATURE

High-quality genome (re)assembly using chromosomal contact data

(2014) Hervé Marie-Nelly et al.   Nature Communications

Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps

(2014) Joshua N. Burton et al.   G3-Genes Genomes Genetics

GC-Rich DNA Elements Enable Replication Origin Activity in the Methylotrophic Yeast Pichia pastoris

(2014) Ivan Liachko et al.   PLoS Genetics

Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products

(2014) Christopher W. Beitel et al.   PeerJ

An autonomously replicating sequence for use in a wide range of budding yeasts

(2013) Ivan Liachko et al.   FEMS YEAST RESEARCH

High-throughput genome scaffolding from in vivo DNA interaction frequency

(2013) Noam Kaplan et al.   NATURE BIOTECHNOLOGY

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing

(2013) Siddarth Selvaraj et al.   NATURE BIOTECHNOLOGY

CISA: Contig Integrator for Sequence Assembly of Bacterial Genomes

(2013) Shin-Hung Lin et al.   PLoS One

Saccharomyces diversity and evolution: a budding model genus

(2013) Chris Todd Hittinger   TRENDS IN GENETICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Plasmodium falciparumcentromeres display a unique epigenetic makeup and cluster prior to and during schizogony

(2012) Wieteke A. M. Hoeijmakers et al.   CELLULAR MICROBIOLOGY

A genome-wide 3C-method for characterizing the three-dimensional architectures of genomes

(2012) Zhijun Duan et al.   METHODS

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

Functional Centromeres Determine the Activation Time of Pericentric Origins of DNA Replication in Saccharomyces cerevisiae

(2012) Thomas J. Pohl et al.   PLoS Genetics

Principles of chromosomal organization: lessons from yeast

(2011) Christophe Zimmer et al.   JOURNAL OF CELL BIOLOGY

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture

(2011) Eitan Yaffe et al.   NATURE GENETICS

Extensive DNA-binding specificity divergence of a conserved transcription regulator

(2011) C. R. Baker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus

(2011) Devin R. Scannell et al.   G3-Genes Genomes Genetics

Mechanisms of Chromosome Number Evolution in Yeast

(2011) Jonathan L. Gordon et al.   PLoS Genetics

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

Yeast evolutionary genomics

(2010) Bernard Dujon   NATURE REVIEWS GENETICS

Epigenetically-Inherited Centromere and Neocentromere DNA Replicates Earliest in S-Phase

(2010) Amnon Koren et al.   PLoS Genetics

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing

(2009) Philippe Lefrançois et al.   BMC GENOMICS

Major Evolutionary Transitions in Centromere Complexity

(2009) Harmit S. Malik et al.   CELL

Centromere Replication Timing Determines Different Forms of Genomic Instability in Saccharomyces cerevisiae Checkpoint Mutants During Replication Stress

(2009) Wenyi Feng et al.   GENETICS

Comparative genomics of protoploid Saccharomycetaceae

(2009) et al.   GENOME RESEARCH

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

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