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

Journal news


Genome Biology and BMC Biology are currently inviting submissions to their upcoming joint special issue on Microbiome Biology. The special issue, which is planned for the spring/early summer of 2019, will be guest edited by Rob Knight (UC San Diego, USA), Ruth Ley (MPI for Developmental Biology, Tuebingen, Germany), Elizabeth Grice (University of Pennsylvania, USA) and Jeroen Raes (KU Leuven, Belgium). The deadline for the special issue submission has been extended to January 31st.

Chief Editor Barbara Cheifet will be attending the Keystone Single-Cell Genomics conference in Breckenridge, Colorado from January 13th-17th. Email us to set up a meeting.

Senior Editor Yixin Yao will be attending the Keystone Genome Engineering: From Mechanisms to Therapies conference in Victoria, British Columbia from February 19th-23rd. Email us to set up a meeting.

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.

From 1st January 2019, all research reviewed at Genome Biology will undergo transparent peer review. Please see our Editorial for more details.

Featured articles

Yuan and colleagues

Linking live cell imaging and single-cell RNA sequencing with SCOPE-Seq

Yuan and colleagues link cellular phenotypes to single-cell sequencing by combing dual barcoded beads and bead-free DNA libraries.

Husquin et al

The impact of DNA methylation on immune gene regulation

Using a system-level approach, Husquin et al combine DNA methylation variation data with genome-wide genotyping, whole-exome sequencing data, and monocyte RNA-sequencing profiles to assess causal impacts of population-level variation in DNA methylation on transcriptional activity related to immune responses.

Zufferey et al

On computational methods used to identify topologically associating domains

Zufferey et al compare the performance of 22 methods used to identify chromatin domains. They find mean size of chromatin domains to be extremely variable between the different methodological approaches. Methods TopDom, HiCseg, and CaTCh are identified as top scoring.

Table of contents



Making supplemental information more accessible



Understanding tumor ecosystems by single-cell sequencing: promises and limitations
Ren, Kang and Zhang


Illuminating the genome-wide activity of genome editors for safe and effective therapeutics
Cheng and Tsai


Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses
Begley et al.


We simply cannot go on being so vague about 'function'




Predicting age from the transcriptome of human dermal fibroblasts
Navlakha et al. 


SCOPE-Seq: a scalable technology for linking live cell imaging and single-cell RNA sequencing
Yuan, Sheng and Sims


Downregulation of RdDM during strawberry fruit ripening
Lang et al. 


NmeCas9 is an intrinsically high-fidelity genome-editing platform
Sontheimer et al. 


Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis
Poetsch, Boulton and Luscombe


Comparison of computational methods for the identification of topologically associating domains
Ciriello et al.


Enhancers in the Peril lincRNA locus regulate distant but not local genes
Rinn et al.


A novel FLI1 exonic circular RNA promotes metastasis in breast cancer by coordinately regulating TET1 and DNMT1

Cui et al.


Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate
Skok et al


Exploring the genetic basis of human population differences in DNA methylation and their casual impact on immune gene regulation
Quintana-Murci et al


RNA G-quadruplexes at upstream open reading frames cause DHX36- and DHX9-dependent translation of human mRNAs

Balasubramanian et al. 





miRTrace reveals the organismal origins of microRNA sequencing data

Friedländer et al.


Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics
Satija et al




FORGe: prioritizing variants for graph genomes

Pritt, Chen and Langmead

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