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Dear Colleague,

 

 

Genome Biology is pleased to share with you our October content update, featuring journal news, top articles and our most recent table of contents.

 
 
Journal news

 
 

Check out Genome Biology's latest special issue on Evolutionary Genomics, which contains research and methods from leading researchers in the field.

Genome Biology and BMC Biology are currently inviting submissions to their upcoming joint special issue on Microbiome Biology. This special issue, which is planned for the spring/early summer of 2019, will be guest edited by Rob Knight (UC San Diego), Ruth Ley (MPI Developmental Biology, Tuebingen, Germany) Elizabeth Grice (University of Pennsylvania, USA) and Jeroen Raes (KU Leuven, Belgium).

Genome Biology and its sister journals BMC Biology and Genome Medicine now provide the opportunity for co-submissions, where authors submit a manuscript for joint consideration at two of these journals at the same time. Co-submissions provide a faster publication process, saving authors' time and avoiding the need for multiple submissions. You can learn more about co-submissions here.

 
 
 
Featured articles

 
 
Yue et al

A web-based browser for visualizing the genome in 3D

Yue et al present their interactive Genome Browser for more efficient navigation and visualization of chromatin structures, functional (epi)genomic annotations, and disease/trait-associated SNPs and enhancer-promoter interactions.

 
 
 
Perrin et al

Sex-biased gene expression in common frogs with proto-Y chromosomes

Perrin et al investigate the expression of genes during development of common frogs from embryo to froglet. Sex-biased expression was found to affect genes across developmental stages and increased during development. Further, this expression was not localized to the proto-sex chromosome.

 
 
 
Coller et al

Alternative polyadenylation factors link cell cycle to migration

Coller et al discover that quiescent and proliferating fibroblasts differ with regards to intron and exon expression associated with polyadenylation. When transitioning from a proliferative to quiescent state, levels of gene splicing and polyadenylation are lower.

 
 
 
 
Table of contents
 
 
 


Comment

RESEARCH HIGHLIGHT
Visualizing the dynamics of histone variants in the S-phase nucleus

Maxouri, Tavarias and Lygerou

OPEN LETTER

RefSeg database growth influences the accuracy of the k-mer-based lowest common ancestor species identification

Nasko et al.

MEETING REPORT

Insights from the 2018 Biology of Genomes meeting

Oak and Plon

Q AND A

Parents in science

Perry, Tessmar-Raible and Raible

MEETING REPORT

Diverse model systems reveal common principles of meiosis

Borek and Marston

 
 
 

Research

SHORT REPORT

CRISPR-induced exon skipping is dependent on premature termination codon mutations

Sui et al

RESEARCH

Phytophthora methylomes are modulated by 6mA methyltransferases and associated with adaptive genome regions
Chen et al. 

RESEARCH

CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters
Alkan et al. 

RESEARCH

Alternative polyadenylation factors link cell cycle to migration
Mitra et al. 

RESEARCH

Canonical and single-cell Hi-C reveal distinct chromatin interaction with sub-networks of mammalian transcription factors

Ma et al

RESEARCH

Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes

O’Connor et al.

RESEARCH

Harnessing accurate non-homologous end joining for efficient precise deletion in CRISPR/Cas9-mediated genome editing

Guo et al. 

RESEARCH

Discovering in vivo cytokin-eQTL interactions from a lupus clinical trial
Davenport et al.

RESEARCH
Chromosome evolution at the origin of the ancestral vertebrate genome
Sacredot et al. 

RESEARCH

A comparative study of endoderm differentiation in humans and chimpanzees
Blake et al. 

RESEARCH

CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops

Guo et al. 

RESEARCH

Modularity of genes involved in local adaptation to climate despite physical linkage

Lotterhos et al

RESEARCH

Reconstruction of avian ancestral karyotypes reveals differences in evolutionary history of macro- and microchromosomes

Damas et al. 

RESEARCH

Evolutionary and developmental dynamics of sex-biased gene expression in common frogs with proto-Y chromosomes

Ma et al. 

RESEARCH

A novel long noncoding RNA HOXC-AS3 mediates tumorigenesis of gastric cancer by binding YBX1

Zhang et al

RESEARCH

Predicting microRNA targeting efficacy in Drosophila

Agarwal et al

 
 

 

Method

METHOD

SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation
Budnik et al. 


METHOD

SeqOthello: querying RNA-seq experiments at scale
Yu et al

METHOD
CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis

Schoonenberg et al.

METHOD

Holo-Seq: single-cell sequencing of holo-transcriptome

Xiao et al

METHOD

CRISPhieRmix: a hierarchical mixture model for CRISPR pooled screens

Daley et al. 

METHOD

PHLI-seq: constructing and visualizing cancer genomic maps in 3D in phenotype-based high-throughput laser-aided isolation and sequencing

Kim et al.

METHOD

The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions

Wang et al

SOFTWARE

Clust: automatic extraction of optimal co-expressed gene clusters from gene expression data

Abu-Jamous and Kelly

SOFTWARE
SKESA: a strategic k-mer extension for scrupulous assemblies

Souvorov, Agarwala and Lipman

 
 
 
 
 
 
 
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