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We are pleased to share with you our October content update, featuring journal news, top articles and our most recent table of contents.

 
Journal News

 
 

The special issue on Benchmarking Studies, guest edited by Olga Vitek and Mark D. Robinson has launched. This special issue contains studies that benchmark tools and methods on a wide range of datasets to provide insights into challenges and best practices for their use.


Barbara Cheifet will be attending the 4DN-ASCB Satellite Meeting in Washington, D. C. from December 5-6thEmail us to set up a meeting.

 
Featured articles

 
 
understanding the evolutionary and medical implications of human single nucleotide variations in diverse populations

PGG.SNV: understanding the evolutionary and medical implications of human single nucleotide variations in diverse populations


A new database gives higher weight to genetic variants of previously under-investigated Asian populations.

Full text | Download PDF

 
 
 
Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny

Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny


Amato et al. compare the gut microbiome composition of 14 human populations and 18 species of wild primates.

Full text | Download PDF

 
 
 
Endogenous retroviral insertions drive non-canonical imprinting in extra-embryonic tissues

Endogenous retroviral insertions drive non-canonical imprinting in extra-embryonic tissues


Zhao and colleagues show the regulatory roles of poly(A)-binding proteins on the expression of endogenous genes in Arabidopsis.

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Table of contents
 

  

 

Comment

EDITORIAL

Benchmarking comes of age

Mark D. Robinson and Olga Vitek

 


Review


REVIEW

DNA extraction for human microbiome studies: the issue of standardization

K. Leigh Greathouse et al.

 

Research

SHORT REPORT

Comparison of cytosine base editors and development of the BEable-GPS database for targeting pathogenic SNVs

Ying Wang et al.


RESEARCH

Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny

Katherine R. Amato et al.


RESEARCH

Benchmark of computational methods for predicting microRNA-disease associations

Zhou Huang et al.


RESEARCH

Identifying significantly impacted pathways: a comprehensive review and assessment

Tuan-Minh Nguyen et al.


RESEARCH

Birth, expansion, and death of VCY-containing palindromes on the human Y chromosome

Wentao Shi et al.


RESEARCH

Global impact of somatic structural variation on the DNA methylome of human cancers

Yiqun Zhang et al.


RESEARCH

Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses

Ciara H. O’Flanagan et al.


RESEARCH

Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods

Brian J. Haas et al.


RESEARCH

SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines

Abraham Gihawi et al.

RESEARCH

The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation

Andrea Hildebrandt et al.


RESEARCH

Soil domestication by rice cultivation results in plant-soil feedback through shifts in soil microbiota

Joseph Edwards et al.


RESEARCH

Endogenous retroviral insertions drive non-canonical imprinting in extra-embryonic tissues

Courtney W. Hanna et al.


METHOD

MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions

Yael Baran et al.


METHOD

DeepImpute: an accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq data

Cédric Arisdakessian et al.


METHOD

Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT

F. A. Bastiaan von Meijenfeldt et al.

METHOD

IMAGE: high-powered detection of genetic effects on DNA methylation using integrated methylation QTL mapping and allele-specific analysis

Yue Fan et al.

METHOD

HOPS: a quantitative score reveals pervasive horizontal pleiotropy in human genetic variation is driven by extreme polygenicity of human traits and diseases

Daniel M. Jordan et al.


METHOD

RaGOO: fast and accurate reference-guided scaffolding of draft genomes

Michael Alonge et al.


METHOD

Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads

Jon G. Sanders et al.


DATABASE

PGG.SNV: understanding the evolutionary and medical implications of human single nucleotide variations in diverse populations

Chao Zhang et al.

 

Interactions

CORRECTION

Correction to: African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations

Shaohua Fan et al.


CORRECTION

Correction to: MicroPro: using metagenomic unmapped reads to provide insights into human microbiota and disease associations

Zifan Zhu et al.

 
 
 
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