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

SynChro: A Fast and Easy Tool to Reconstruct and Visualize Synteny Blocks along Eukaryotic Chromosomes

(2014) Guénola Drillon et al.   PLoS One

Evolutionary Mobility of the Ribosomal DNA Array in Yeasts

(2013) Estelle Proux-Wéra et al.   Genome Biology and Evolution

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

Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser

(2012) David A Fitzpatrick et al.   BMC GENOMICS

Normalization of a chromosomal contact map

(2012) Axel Cournac et al.   BMC GENOMICS

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

A Predictive Computational Model of the Dynamic 3D Interphase Yeast Nucleus

(2012) Hua Wong et al.   CURRENT BIOLOGY

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

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

(2012) Maxim Imakaev et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Pichia sorbitophila , an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization

(2012) Véronique Leh Louis et al.   G3-Genes Genomes Genetics

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr 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

Mechanisms of Chromosome Number Evolution in Yeast

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

Population Polymorphism of Nuclear Mitochondrial DNA Insertions Reveals Widespread Diploidy Associated with Loss of Heterozygosity in Debaryomyces hansenii

(2010) Noémie Jacques et al.   EUKARYOTIC CELL

Chromosomal G + C Content Evolution in Yeasts: Systematic Interspecies Differences, and GC-Poor Troughs at Centromeres

(2010) Denise B. Lynch et al.   Genome Biology and Evolution

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery

(2009) P. Oza et al.   GENES & DEVELOPMENT

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

Additions, Losses, and Rearrangements on the Evolutionary Route from a Reconstructed Ancestor to the Modern Saccharomyces cerevisiae Genome

(2009) Jonathan L. Gordon et al.   PLoS Genetics