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We are pleased to share with you our August 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.

Featured articles

Reproducibility of CRISPR-Cas9 methods for generation of conditional mouse alleles: a multi-center evaluation

A study of 20 laboratories worldwide demonstrates that one-donor methods for generation of cKO animal models are more efficient than two-donor methods.
RNA methylomes reveal the m6A-mediated regulation of DNA demethylase gene SlDML2 in tomato fruit ripening

Qin and colleagues show a novel gene regulation mechanism between DNA methylation and mRNA m6A methylation during fruit ripening.
An enhanced genetic model of colorectal cancer progression history

A study from Park et al shows a tumor progression model that identifies key events in the evolution of colorectal cancer.
Table of contents





Of funding and finches

Verena Jantsch and Michael Jantsch


Funding research, a Chinese perspective

Hui Yang

The changing landscape of research funding: challenges for mid-career researchers
Nick Wong

Night science
Itai Yanai and Martin Lercher




Is it time to change the reference genome?

Sara Ballouz et al.



Genomic GPS: using genetic distance from individuals to public data for genomic analysis without disclosing personal genomes

Kunhee Kim et al.

Alternative splicing is required for stage differentiation in malaria parasites

Lee M. Yeoh et al.

RNA methylomes reveal the m6A-mediated regulation of DNA demethylase gene SlDML2 in tomato fruit ripening
Leilei Zhou et al.

Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis
Kinga Rutowicz et al.

A systematic assessment of current genome-scale metabolic reconstruction tools
Sebastián N. Mendoza et al.

Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes
Jingyi Jessica Li et al.

Analysis of Vibrio cholerae genomes identifies new type VI secretion system gene clusters
Cristian V. Crisan et al.

Screening for genes that accelerate the epigenetic aging clock in humans reveals a role for the H3K36 methyltransferase NSD1
Daniel E. Martin-Herranz et al.

An enhanced genetic model of colorectal cancer progression history
Lixing Yang et al.

Benchmarking software tools for detecting and quantifying selection in evolve and resequencing studies
Christos Vlachos et al.

Diurnal regulation of SDG2 and JMJ14 by circadian clock oscillators orchestrates histone modification rhythms in Arabidopsis
Qingxin Song et al.

Regulation of rumen development in neonatal ruminants through microbial metagenomes and host transcriptomes
Nilusha Malmuthuge et al.

Reproducibility of CRISPR-Cas9 methods for generation of conditional mouse alleles: a multi-center evaluation
Channabasavaiah B. Gurumurthy et al.

Maturation of the infant rhesus macaque gut microbiome and its role in the development of diarrheal disease
Nicholas Rhoades et al.

Raptor genomes reveal evolutionary signatures of predatory and nocturnal lifestyles
Yun Sung Cho et al.

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation
Derek M. Bickhart et al.

BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis
Fatma Uzbas et al.

BERMUDA: a novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes
Tongxin Wang et al.

scAlign: a tool for alignment, integration, and rare cell identification from scRNA-seq data
Nelson Johansen and Gerald Quon

AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design
Kathleen C. Keough et al.

MetaCarvel: linking assembly graph motifs to biological variants
Jay Ghurye et al.

MicroPro: using metagenomic unmapped reads to provide insights into human microbiota and disease associations
Zifan Zhu et al.

A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types
Maxwell W. Libbrecht et al.



The registry of software tools and data resources for the life sciences
Jon Ison et al.

A statistical and biological response to an informatics appraisal of healthy aging gene signatures
James A. Timmons et al.

Correction to: Identification of novel Y chromosome encoded transcripts by testis transcriptome analysis of mice with deletions of the Y chromosome long arm
Aminata Touré et al.

Correction to: Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta
Baosheng Wang et al.

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