Read Our Latest Monthly Round Up - February 2020
 
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We are pleased to share with you our February content update, featuring journal news, top articles and our most recent table of contents.

 
Journal news

 
 

Call for papers: the special issue on Cancer Evolution and Metastasis, guest edited by Christina Curtis and Florian Markowetz, has launched. The deadline for submissions is April 30th 2020. Please see the landing page for more details.

 
Featured articles

 
 
Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice

Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice


A study that highlights the value of using nanopore sequencing to produce chromosome-level genome assemblies for an iconic rice variety group.


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Admixture-enabled selection for rapid adaptive evolution in the Americas

Admixture-enabled selection for rapid adaptive evolution in the Americas


Norris and colleagues report significant evidence for admixture-enabled selection in Latin American populations that were formed by admixture among diverse African, European, and Native American source populations dating back five centuries.


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A framework for transcriptome-wide association studies in breast cancer

A framework for transcriptome-wide association studies in breast cancer in diverse study populations


Transcriptome-wide association studies (TWAS), in comparison to genome-wide association studies (GWAS), are showing increased power in detecting functionally relevant loci by leveraging expression quantitative trait loci (eQTLs) from external reference panels in relevant tissues.


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Table of contents
 

  

 

Comment

EDITORIAL

The Deep Genome Project
C. Kent Lloyd et al. 



 

Review


REVIEW

From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis

Feng Yang et al.

 

REVIEW

Opportunities and challenges in long-read sequencing data analysis

Shanika L. Amarasinghe et al.

 

REVIEW

Eleven grand challenges in single-cell data science

David Lähnemann et al.

 

REVIEW

Mutational signatures: experimental design and analytical framework

Gene Koh et al.


Research

SHORT REPORT

Protein velocity and acceleration from single-cell multiomics experiments

Gennady Gorin et al.

 

SHORT REPORT

Histone H3K27 acetylation is dispensable for enhancer activity in mouse embryonic stem cells

Tiantian Zhang et al.

 

RESEARCH

Host-associated microbiomes are predicted by immune system complexity and climate

Douglas C. Woodhams et al.

 

RESEARCH

Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana

Hainan Zhao et al.

 

RESEARCH

Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice

Jae Young Choi et al.

 

RESEARCH

Purifying selection of long dsRNA is the first line of defense against false activation of innate immunity

Michal Barak et al.

 

RESEARCH

Systematic functional identification of cancer multi-drug resistance genes

Man-Tat Lau et al.

 

RESEARCH

Admixture-enabled selection for rapid adaptive evolution in the Americas

Emily T. Norris et al.

 

RESEARCH

A post-transcriptional program of chemoresistance by AU-rich elements and TTP in quiescent leukemic cells

Sooncheol Lee et al.

 

RESEARCH

Assembly of hundreds of novel bacterial genomes from the chicken caecum

Laura Glendinning et al.

 

RESEARCH

Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data

Christian H. Holland et al.

 

RESEARCH

A willow sex chromosome reveals convergent evolution of complex palindromic repeats

Ran Zhou et al.

 

RESEARCH

A framework for transcriptome-wide association studies in breast cancer in diverse study populations

Arjun Bhattacharya et al.

 

RESEARCH

Comprehensive assessment of computational algorithms in predicting cancer driver mutations

Hu Chen et al.

 

RESEARCH

Allosteric inhibition of CRISPR-Cas9 by bacteriophage-derived peptides

Yan-ru Cui et al.

 

RESEARCH

A rare codon-based translational program of cell proliferation

Joao C. Guimaraes et al.

RESEARCH

Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility

Hyung Joo Lee et al.

 

METHOD

scAI: an unsupervised approach for the integrative analysis of parallel single-cell transcriptomic and epigenomic profiles

Suoqin Jin et al.

 

METHOD

Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data

Qian Qin et al.

 

METHOD

Genotyping structural variants in pangenome graphs using the vg toolkit

Glenn Hickey et al.

 

METHOD

Carnelian uncovers hidden functional patterns across diverse study populations from whole metagenome sequencing reads

Sumaiya Nazeem et al.

 

METHOD

ncHMR detector: a computational framework to systematically reveal non-classical functions of histone modification regulators

Shengen Hu et al.

 

METHOD

Linked optical and gene expression profiling of single cells at high-throughput

Jesse Q. Zhang et al.

Interactions

PUBLISHER CORRECTION

Publisher Correction: Co-opted transposons help perpetuate conserved higher-order chromosomal structures

Mayank N. K. Choudhary et al.

 

PUBLISHER CORRECTION

Publisher Correction: Host-associated microbiomes are predicted by immune system complexity and climate

Douglas C. Woodhams et al.

 

AUTHOR CORRECTION

Author Correction: Interaction between the microbiome and TP53 in human lung cancer
Leigh Greathouse et al. 

 

AUTHOR CORRECTION

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

Ming-Li Li et al.

 

AUTHOR CORRECTION

Author Correction: 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.

 

 
 
 
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