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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



All models are wrong, but some organoids may be useful

Benjamin E. Mead and Jeffrey M. Karp


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

Sarah Lebeer and Irina Spacova



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



Measuring the reproducibility and quality of Hi-C data

Galip Gürkan Yardımcı et al.

Analysis of error profiles in deep next-generation sequencing data

Xiaotu Ma et al.





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

Jun Cheng et al.

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

Fangzhou Shen et al.

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

Kin Yau Wong et al.

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

Kieran R. Campbell et al.

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

Satomi Mitsuhashi et al.

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

F. Alexander Wolf et al

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

Lihn Huynh and Fereydoun Hormozdiari

Melissa: Bayesian clustering and imputation of single-cell methylomes

Chantriolnt-Andreas Kapourani and Guido Sanguinetti

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

Aaron T. L. Lun et al.

Alevin efficiently estimates accurate gene abundances from dscRNA-seq data

Avi Srivastava et al.

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

Paul F. Harrison et al.



Assessing taxonomic metagenome profilers with OPAL

Fernando Meyer et al.

RnBeads 2.0: comprehensive analysis of DNA methylation data

Fabian Müller et. al.

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