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

 
Journal news

 
 

The special issue on Cancer Evolution and Metastasis, guest edited by Christina Curtis and Florian Markowetz has launched. The deadline for submissions has been extended to May 31st 2020. Please see the landing page for more details.

 
Featured articles

 
 
Avocado

Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome


Schreiber and colleagues use a deep neural network tensor factorization method to impute epigenomic data and to predict gene expression, promoter-enhancer interactions, and replication timing.


Full text | Download PDF

 
 
 
Completing the ENCODE3

Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples


Schrieber et al apply Avocado to data from the ENCODE compendium and show that it  facilitates the addition of assays and biosamples to pre-trained models.


Full text | Download PDF

 
 
 
The genome evolution

The genome evolution and domestication of tropical fruit mango


Wang and colleagues generate the genome assembly of the mango, providing crucial information on the evolution of one of the world’s most important tropical fruits.


Full text | Download PDF

 
 
 
Table of contents
 

  

 

Comment

EDITORIAL
Renaissance minds in 21st century science

Itai Yanai and Martin Lercher



 

Review

REVIEW
A benchmark of algorithms for the analysis of pooled CRISPR screens

Sunil Bodapati et al.

 

Research


SHORT REPORT
Accurate targeted long-read DNA methylation and hydroxymethylation sequencing with TAPS

Yibin Liu et al.

 

SHORT REPORT
WhatsGNU: a tool for identifying proteomic novelty

Ahmed M. Moustafa and Paul J. Planet

 

SHORT REPORT
Decode-seq: a practical approach to improve differential gene expression analysis

Yingshu Li et al.

 

RESEARCH
Longitudinal survey of microbiome associated with particulate matter in a megacity

Nan Qin et al.

 

RESEARCH
The genome evolution and domestication of tropical fruit mango

Peng Wang et al.

 

RESEARCH
Hemispheric asymmetry in the human brain and in Parkinson’s disease is linked to divergent epigenetic patterns in neurons

Peipei Li et al.

 

RESEARCH
High-resolution modeling of the selection on local mRNA folding strength in coding sequences across the tree of life

Michael Peeri and Tamir Tuller

 

RESEARCH
Smarcad1 mediates microbiota-induced inflammation in mouse and coordinates gene expression in the intestinal epithelium

Juri Kazakevych et al.

 

RESEARCH
Benchmarking of computational error-correction methods for next-generation sequencing data

Keith Mitchell et al.

 

RESEARCH
Obstacles to detecting isoforms using full-length scRNA-seq data

Jennifer Westoby et al.

 

RESEARCH
Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection

Zhilian Jia et al.

 

RESEARCH
High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells

Peiyao A. Zhao et al.

 

RESEARCH
A Cas12a ortholog with stringent PAM recognition followed by low off-target editing rates for genome editing

Peng Chen et al.

 

RESEARCH
Diverse genetic mechanisms underlie worldwide convergent rice feralization

Jie Qiu et al.

 

RESEARCH
Characterisation of genetic regulatory effects for osteoporosis risk variants in human osteoclasts

Benjamin H. Mullin et al.

 

RESEARCH
CRISPRi-based radiation modifier screen identifies long non-coding RNA therapeutic targets in glioma
John Liu et al.

 

METHOD
gscreend: modelling asymmetric count ratios in CRISPR screens to decrease experiment size and improve phenotype detection

Katharina Imkeller et al.

 

METHOD
Decontamination of ambient RNA in single-cell RNA-seq with DecontX

Shiyi Yang et al.

 

METHOD
Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9

Xin Liu et al.

 

METHOD
CHOP: haplotype-aware path indexing in population graphs

Tom Mokveld et al.

 

METHOD
BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty

Simone Tiberi and Mark D. Robinson

 

METHOD
VALOR2: characterization of large-scale structural variants using linked-reads

Fatih Karao─člano─člu et al.

 

METHOD
HiNT: a computational method for detecting copy number variations and translocations from Hi-C data

Su Wang et al.

 

METHOD
DeepMILO: a deep learning approach to predict the impact of non-coding sequence variants on 3D chromatin structure

Tuan Trieu et al.

 

METHOD
Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome

Jacob Schreiber et al.

 

METHOD
Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples

Jacob Schreiber et al.

  

SOFTWARE
NanoVar: accurate characterization of patients’ genomic structural variants using low-depth nanopore sequencing

Cheng Yong Tham et al.

 

SOFTWARE
Ultraplexing: increasing the efficiency of long-read sequencing for hybrid assembly with k-mer-based multiplexing

Alexander T. Dilthey et al.

 

 
 
 
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