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Dear Colleague,

 

 

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

 
 
Journal news

 
 
Call for Papers: Benchmarking Studies
 
 
 

Guest edited by Olga Vitek and Mark D Robinson


Submission deadline: May 19th 2019

We are accepting submissions for our forthcoming Special Issue to be published in the second half of 2019, covering papers reporting in-depth analyses of state-of-the-art computational tools on a wide range of datasets, with clear guidelines and recommendations given for the user. Submit your outstanding work today!

 
 
Meet the Editors
 
 
 

Associate Editor Kevin Pang will be attending the Keystone 3D Genome: Gene Regulation and Disease conference from March 17th - 21st in Banff, Canada.

Senior Editor Tim Sands will be attending Reconstructing the Human Past – Using Ancient and Modern Genomics in Heidelberg, Germany from March 31st - April 3rd.

Email us to set up a meeting.

 
 
Featured articles

 
 
 
Moreno-Romero

Predicting and identifying paternally expressed genes in Arabidopsis

Moreno-Romero and colleagues reveal that there are substantially more paternally-expressed genes than previously identified and show insight into the pathways involved in genomic imprinting.

 
 
 
Peach breeding history

Peach breeding history

A comprehensive analysis of 480 wild and cultivated accessions shows distinct phases of domestication and improvement.

 
 
 
Sato et al

CellFishing.jl to search atlas-scale single-cell datasets

A new method from Kenta Sato and colleagues can detect noteworthy genes with high accuracy and throughput.

 
 
 
 
Table of contents
 
 
 


Comment

EDITORIAL

Graph genomes article collection

Michael C. Schatz and Andrew Cosgrove

EDITORIAL
Improving the usability and archival stability of bioinformatics software

Serghei Mangul et al.

RESEARCH HIGHLIGHT

Fragile DNA contributes to repeated evolution

Claudius F. Kratochwil and Axel Meyer

OPINION

Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA

Caroline Pont et al.

 
 
 

Research

SHORT REPORT

Enhanced mammalian genome editing by new Cas12a orthologs with optimized crRNA scaffolds

Fei Tang et al.

RESEARCH

Evolutionarily significant A-to-I RNA editing originated through G-to-A mutations in primates

Ni A. An et al.

RESEARCH

A comparative evaluation of hybrid error correction methods for error-prone long reads

Shuhua Fu et al.

RESEARCH

Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects

Emanuel Gonçalves et al.

RESEARCH

Modeling double strand susceptibility to interrogate structural variation in cancer

Tracy J. Ballinger et al.

RESEARCH

Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

Stephanie M. Linker et al.

RESEARCH

Dynamic inosinome profiles reveal novel patient stratification and gender-specific differences in glioblastoma

Domenico Alessandro Silvestris et al.

RESEARCH

Rapid turnover of life-cycle-related genes in the brown algae

Agnieszka P. Lipinska et al.

RESEARCH

Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history

Yong Li et al.

RESEARCH

Mitochondrial hypoxic stress induces widespread RNA editing by APOBEC3G in natural killer cells

Shraddha Sharma et al.

RESEARCH

Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants

Xin Qiao et al.

RESEARCH

Epigenetic signatures associated with imprinted paternally expressed genes in the Arabidopsis endosperm

Jordi Moreno-Romero et al.

RESEARCH

Reproducible interference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling

Aslihan Karabacak Calviello et al.

 
 

 

Method

METHOD

CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing

Kenta Sato et al.

METHOD

NCBoost classifies pathogenic non-coding variants in Mendelian diseases through supervised learning on purifying selection signals in humans

Barthélémy Caron et al.

METHOD

Skmer: assembly-free and alignment-free sample identification using genome skims

Shahab Sarmashghi et al.

METHOD

dStruct: identifying differentially reactive regions from RNA structurome profiling data

Krishna Choudhary et al.

METHOD

Identification of transcription factor binding sites using ATAC-seq

Zhijian Li et al.

SOFTWARE

bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes
Matthew Z. DeMaere and Aaron E. Darling

 
 
 

Interactions

CORRECTION

Correction to: Rapid turnover of life-cycle-related genes in the brown algae

Agnieszka P. Lipinska et al.

CORRECTION

Correction to: Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data

Nelly Olova et al.

 
 
 
 
 
 
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