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We are pleased to share with you our November 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.

 

 
Featured articles

 
 
CAFA challenge reports

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens


The results of the third Critical Assessment of Functional Annotation (CAFA) challenge is announced.


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Genetic regulation of gene expression

Genetic regulation of gene expression and splicing during a 10-year period of human aging


Balliu and colleagues show that small set of genes is shown to be differentially expressed and alternatively spliced in later life.


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

OrthoFinder: phylogenetic orthology inference for comparative genomics


An advance to the OrthoFinder method from Emms and Kelly provides accurate phylogenetic inference of orthologs and gene duplication events.


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Table of contents
 

  

 

Comment

EDITORIAL

Crowdfunding science

Melissa A. Wilson

 

Review


REVIEW

Epigenetic modifications of histones in cancer

Zibo Zhao and Ali Shilatifard

REVIEW

Structural variant calling: the long and the short of it

Medhat Mahmoud et al.

REVIEW

DNA methylation aging clocks: challenges and recommendations

Christopher G. Bell et al.

 

Research

SHORT REPORT

Scaling computational genomics to millions of individuals with GPUs

Amaro Taylor-Weiner et al.

 

SHORT REPORT

Improved metagenomic analysis with Kraken 2

Derrick E. Wood et al.


RESEARCH

Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

Robert C. Kaplan et al.


RESEARCH

Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families

Yan Wang et al.

 

RESEARCH

Genetic regulation of gene expression and splicing during a 10-year period of human aging

Brunilda Balliu et al.

 

RESEARCH

Impact of mouse contamination in genomic profiling of patient-derived models and best practice for robust analysis

Se-Young Jo et al.

 

RESEARCH

Evaluation of commonly used analysis strategies for epigenome- and transcriptome-wide association studies through replication of large-scale population studies

Jeroen van Rooij et al.

 

RESEARCH

Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer

Dharmesh D. Bhuva et al.

 

RESEARCH

Evaluating nanopore sequencing data processing pipelines for structural variation identification

Anbo Zhou et al.

 

RESEARCH

Correlation of homologous recombination deficiency induced mutational signatures with sensitivity to PARP inhibitors and cytotoxic agents

Ádám Póti et al.


RESEARCH

Assessment of computational methods for the analysis of single-cell ATAC-seq data

Huidong Chen et al.

 

RESEARCH

Systematic comparative analysis of single-nucleotide variant detection methods from single-cell RNA sequencing data

Fenglin Liu et al.

 

RESEARCH

Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize

Jing Xu et al.

 

RESEARCH

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Naihui Zhou et al.

RESEARCH

Gut-derived Enterococcus faecium from ulcerative colitis patients promotes colitis in a genetically susceptible mouse host

Jun Seishima et al.


RESEARCH

Pharmacogenomic analysis of patient-derived tumor cells in gynecologic cancers

Jason K. Sa et al.

RESEARCH

Common DNA sequence variation influences 3-dimensional conformation of the human genome

David U. Gorkin et al.

RESEARCH

The Aquilegia genome reveals a hybrid origin of core eudicots

Gökçe Aköz and Magnus Nordborg

 

RESEARCH

547 transcriptomes from 44 brain areas reveal features of the aging brain in non-human primates

Ming-Li Li et al.

RESEARCH

Characterizing the interplay between gene nucleotide composition bias and splicing

Sébastien Lemaire et al.

 

METHOD

Mash Screen: high-throughput sequence containment estimation for genome discovery

Brian D. Ondov et al.


METHOD

DESE: estimating driver tissues by selective expression of genes associated with complex diseases or traits

Lin Jiang et al.


METHOD

CRUP: a comprehensive framework to predict condition-specific regulatory units

Anna Ramisch et al.

 

METHOD

NanoSatellite: accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION

Arne De Roeck et al.

 

METHOD

EpiMethylTag: simultaneous detection of ATAC-seq or ChIP-seq signals with DNA methylation

Priscillia Lhoumaud et al.

METHOD

MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms

Minji Kim et al.

METHOD

RegSNPs-intron: a computational framework for predicting pathogenic impact of intronic single nucleotide variants

Hai Lin et al.

METHOD

ReorientExpress: reference-free orientation of nanopore cDNA reads with deep learning

Angel Ruiz-Reche et al.

METHOD

methylCC: technology-independent estimation of cell type composition using differentially methylated regions

Stephanie C. Hicks and Rafael A. Irizarry

 

SOFTWARE

OrthoFinder: phylogenetic orthology inference for comparative genomics

David M. Emms and Steven Kelly

 

DATABASE

MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect

Daniel Esposito et al.

 

Interactions

CORRECTION

Correction to: Identifying significantly impacted pathways: a comprehensive review and assessment

Tuan-Minh Nguyen et al.

 

CORRECTION

Correction to: scBFA: modeling detection patterns to mitigate technical noise in large-scale single-cell genomics data

Ruoxin Li and Gerald Quon

 
 
 
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