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

 
Journal news

 
 

Senior Editor Yixin Yao will be attending the Keystone Engineering the Genome meeting in Banff, British Columbia, Canada from February 8-12th.

Chief Editor Barbara Cheifet will be attending the Keystone Higher-Order Chromatin Architecture in Time and Space meeting in Whistler, British Columbia, Canada from March 15th-19th. 

Email us to set up a meeting.

 
Featured articles

 
 
Transcriptome assembly from long-read RNA-seq alignments with StringTie2

Transcriptome assembly from long-read RNA-seq alignments with StringTie2


Kovaka et al present StringTie2, a reference-guided transcriptome assembler that works with both long and short reads more accurately than existing tools.


Full text | Download PDF

 
 
 
The somatic mutation landscape of the human body

The somatic mutation landscape of the human body


A catalog containing over 280,000 somatic mutations from over 7500 tissue samples shows patterns of tissue-specific somatic evolution.


Full text | Download PDF

 
 
 
Microbial genomes from non-human primate gut metagenomes

Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species


Manara and colleagues reconstruct previously uncharacterized microbial species and show that the majority of microbial diversity associated with non-human primates has been overlooked.


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Table of contents
 

  

 

Comment

EDITORIAL

What is the question?

Itai Yanai and Martin Lercher

EDITORIAL

From Hawaii to PECASE award: tips of success from a female bioinformatician

Lana Garmire

 

Review


REVIEW

Guidelines for benchmarking of optimization-based approaches for fitting mathematical models

Clemens Kreutz

 

Research

SHORT REPORT

Within-species contamination of bacterial whole-genome sequence data has a greater influence on clustering analyses than between-species contamination

Arthur W. Pightling et al.

 

RESEARCH

Distinct epigenetic features of tumor-reactive CD8+ T cells in colorectal cancer patients revealed by genome-wide DNA methylation analysis

Rui Yang et al.

 

RESEARCH

scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation
E. Madissoon et al.

 

RESEARCH

mRNA structural elements immediately upstream of the start codon dictate dependence upon eIF4A helicase activity

Joseph A. Waldron et al.

 

RESEARCH

Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species

Serena Manara et al.

 

RESEARCH

The somatic mutation landscape of the human body

Pablo E. García-Nieto et al.

 

RESEARCH

A comparison framework and guideline of clustering methods for mass cytometry data

Xiao Liu et al.

 

RESEARCH

Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type

Irene Franco et al.

 

RESEARCH

Systematic underestimation of the epigenetic clock and age acceleration in older subjects

Louis Y. El Khoury et al.

 

RESEARCH

Curing hemophilia A by NHEJ-mediated ectopic F8 insertion in the mouse

Jian-Ping Zhang et al.

 

RESEARCH

Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline

Shujun Ou et al.

 

RESEARCH

CTCF modulates allele-specific sub-TAD organization and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains

David Llères et al.

 

RESEARCH

The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans

Alejandro Vasquez-Rifo et al.

 

RESEARCH

Accuracy, robustness and scalability of dimensionality reduction methods for single-cell RNA-seq analysis

Shiquan Sun et al.

 

RESEARCH

The majority of A-to-I RNA editing is not required for mammalian homeostasis

Alistair M. Chalk et al.

 

RESEARCH

Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution

Huizhong Fan et al.

 

RESEARCH

CRISPR-Cas13d mediates robust RNA virus interference in plants

Ahmed Mahas et al.

 

RESEARCH

eIF4A2 drives repression of translation at initiation by Ccr4-Not through purine-rich motifs in the 5′UTR

Ania Wilczynska et al.

 

METHOD

Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression

Christoph Hafemeister and Rahul Satija

 

METHOD

Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model

F. William Townes et al.

 

METHOD

RADAR: differential analysis of MeRIP-seq data with a random effect model

Zijie Zhang et al.

 

METHOD

tmap: an integrative framework based on topological data analysis for population-scale microbiome stratification and association studies

Tianhua Liao et al.

 

METHOD

PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications

Jingwen Fang et al.

 

METHOD

Paragraph: a graph-based structural variant genotyper for short-read sequence data

Sai Chen et al.

 

METHOD

Genotype-free demultiplexing of pooled single-cell RNA-seq

Jun Xu et al.

 

METHOD

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

Angel Ruiz-Reche et al.

 

METHOD

Quantifying the benefit offered by transcript assembly with Scallop-LR on single-molecule long reads

Laura H. Tung et al.

 

METHOD

TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools

Cécline Monat et al.

 

METHOD

OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries

Lin An et al.

 

METHOD

HOPS: automated detection and authentication of pathogen DNA in archaeological remains

Ron Hübler et al.

 

METHOD

PASTMUS: mapping functional elements at single amino acid resolution in human cells

Xinyi Zhang et al.

 

METHOD

Transcriptome assembly from long-read RNA-seq alignments with StringTie2

Sam Kovaka et al.

 

METHOD

deSALT: fast and accurate long transcriptomic read alignment with de Bruijn graph-based index

Bo Liu et al.

 

METHOD

Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference

Yuanhua Huang et al.

 

METHOD

scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data

Jose Alquicira-Hernandez et al.

 

METHOD

Afann: bias adjustment for alignment-free sequence comparison based on sequencing data using neural network regression

Kujin Tang et al.

 

METHOD

Dashing: fast and accurate genomic distances with HyperLogLog

Daniel N. Baker and Ben Langmead

 

SOFTWARE

SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies

Manish Goel et al.

 
 
 
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