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

Journal news

Microbiome Biology Special Issue launched

The special issue on Microbiome Biology, 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), has launched. The special issue, joint with BMC Biology, will be publishing research, methods, and reviews covering diverse areas of microbiome research. Look for our content being published over the next several months here.

Meet the Editors

Senior editor Yixin Yao will be attending The International Bioinformatics Workshop (IBW) from August 3-4th and the Epigenetic and Chromatin Biology Congress from August 15-18th in Beijing. Email us to set up a meeting.

Featured articles

Grob and Grossniklaus

Transgene silencing by KNOT in Arabidopsis

Grob and Grossniklaus show that KNOT-linked silencing is shown to act independently or prior to canonical silencing mechanisms for transgenes in Arabidopsis.

Wang and colleagues

Long term balancing selection in Boechera stricta

The evolutionary processes driving genetic diversity and population differentiation in Beochera stricta is shown by Baosheng Wang and colleagues.

Gunasekara et al

Atlas of systemic human interindividual epigenetic  variation

Gunasekara et al characterize correlated regions of systemic interindividual variation (CoRSIVs) across all three embryonic lineages in GTEx.

Table of contents


Collateral damage: benchmarking off-target effects in genome editing

Dana Caroll


The long walk to African genomics

Serena Tucci and Joshua M. Akey



Bridging the gap between reference and real transcriptomes

Antonin Morillon and Daniel Gautheret


Current status and applications of genome-scale metabolic models

Changdai Gu et al.


Essential guidelines for computational method benchmarking

Lukas M. Weber et al.



A genomic atlas of systemic interindividual epigenetic variation in humans

Chathura J. Gunasekara et al.


Multiplexed promoterless gene expression with CRISPReader

Hengji Zhan et al.


Chromatin accessibility plays a key role in selective targeting of Hox proteins

Damiano Porcelli et al.


Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing

Shunichi Kosugi et al.


Single-cell transcriptomics unveils gene regulatory network plasticity

Giovanni Iacono et al.


A practical guide to methods controlling false discoveries in computational biology

Keegan Korthauer et al.


Codon usage optimization in pluripotent embryonic stem cells

Susanne Bornelöv et al.


Invasive DNA elements modify the nuclear architecture of their insertion site by KNOT-linked silencing in Arabidopsis thaliana

Stefan Grob and Ueli Grossniklaus


Cold stress induces enhanced chromatin accessibility and bivalent histone modifications H3K4me3 and H3K27me3 of active genes in potato

Zixian Zeng et al.


Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta

Baosheng Wang et al.


Trapping a somatic endogenous retrovirus into a germline piRNA cluster immunizes the germline against further invasion

Céline Duc et al.


Performance of neural network basecalling tools for Oxford Nanopore sequencing

Ryan R. Wick et al.


Emphasis on the deep or shallow parts of the tree provides a new characterization of phylogenetic distances

Julia Fukuyama


Haplotype-aware diplotyping from noisy long reads

Jana Ebler et al.




Correction to: VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer

Andrew N. Holding et al.


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

Pierre Murat et al.

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