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Dear Colleague,

 

 

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

 
 
Journal news

 
 
Call for Papers: Special Issue on Graph Genomes
 
 
 

Guest edited by Mike Schatz


Find more information on this collection here.

 
 
Call for Papers: Special Issue on Benchmarking Studies
 
 
 

Guest edited by Mark Robinson and Olga Vitek


Submission Deadline
: May 18th 2019


Find more information on this special issue here.

 
 
Meet the Editors
 
 
 

Associate Editor Kevin Pang will be attending the Biology of Genomes meeting in Cold Spring Harbor, New York from May 7-11th.


Email us
to set up a meeting.

 
 
Featured articles

 
 
 
Wolf et al

Using graph abstraction for single-cell analysis


Wolf et al develop PAGA, a method that reconstructs branching gene expression changes across different datasets and reconstructs the lineage of a whole animal.

 
 
 
Yardimci et al

Evaluation of reproducibility and quality of Hi-C data


Yardımcı and colleagues compare the performance of several recently published methods for assessing reproducibility of Hi-C data and describe best practices for quality assessment.

 
 
 
Meyer et al

An Open-community Profiling Assessment Tool (OPAL) for taxonomic profiling


Meyer et al describe a new framework for comparing and assessing taxonomic profilers to help the community decide which method is best suited for an analysis.

 
 
 
 
Table of contents
 
 
 


Comment

EDITORIAL

All models are wrong, but some organoids may be useful

Benjamin E. Mead and Jeffrey M. Karp


MEETING REPORT

Exploring human host-microbiome interactions in health and disease—how to not get lost in translation

Sarah Lebeer and Irina Spacova

 
 
 


Review

REVIEW
Interactive roles of chromatin regulation and circadian clock functions in plants
Z. Jeffrey Chen and Paloma Mas

 
 
 

Research

RESEARCH
Measuring the reproducibility and quality of Hi-C data

Galip Gürkan Yardımcı et al.

RESEARCH
Analysis of error profiles in deep next-generation sequencing data

Xiaotu Ma et al.

 
 

 

Method

METHOD

MMSplice: modular modeling improves the predictions of genetic variant effects on splicing

Jun Cheng et al.

METHOD
Genome-scale network model of metabolism and histone acetylation reveals metabolic dependencies of histone deacetylase inhibitors

Fangzhou Shen et al.

METHOD
I-Boost: an integrative boosting approach for predicting survival time with multiple genomics platforms

Kin Yau Wong et al.

METHOD
clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers

Kieran R. Campbell et al.

METHOD
Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads

Satomi Mitsuhashi et al.

METHOD
PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells

F. Alexander Wolf et al

METHOD
TAD fusion score: discovery and ranking the contribution of deletions to genome structure

Lihn Huynh and Fereydoun Hormozdiari

METHOD
Melissa: Bayesian clustering and imputation of single-cell methylomes

Chantriolnt-Andreas Kapourani and Guido Sanguinetti

METHOD
EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data

Aaron T. L. Lun et al.

METHOD
Alevin efficiently estimates accurate gene abundances from dscRNA-seq data

Avi Srivastava et al.

METHOD
Topconfects: a package for confident effect sizes in differential expression analysis provides a more biologically useful ranked gene list

Paul F. Harrison et al.

 
 
 

Software

SOFTWARE
Assessing taxonomic metagenome profilers with OPAL

Fernando Meyer et al.

SOFTWARE
RnBeads 2.0: comprehensive analysis of DNA methylation data

Fabian Müller et. al.

 
 
 
 
 
 
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