Volume 30, Issue 2 | February 2020

Research
- - A HOTAIR regulatory element modulates glioma cell sensitivity to temozolomide through long-range regulation of multiple target genes
    Lei Zhang
    Anshun He
    Bohan Chen
    Jinfang Bi
    Jun Chen
    Dianhao Guo Yuyang Qian Wenbin Wang Tengfei Shi Zhongfang Zhao
    ...[+5 authors]...,
    Jiandang Shi
    Woojin An
    Frank Attenello
    Wange Lu
    First Published January 17, 2020
  - An efficient RNA-seq-based segregation analysis identifies the sex chromosomes of Cannabis sativa
    Djivan Prentout
    Olga Razumova
    Bénédicte Rhoné
    Hélène Badouin
    Hélène Henri
    First Published February 7, 2020
  - Genome-wide redistribution of 24-nt siRNAs in rice gametes
    Chenxin Li
    Hengping Xu
    Fang-Fang Fu
    Scott D. Russell
    Venkatesan Sundaresan
    First Published January 2, 2020
Methods
- - Ancestry-agnostic estimation of DNA sample contamination from sequence reads
    Fan Zhang
    Matthew Flickinger
    Sarah A. Gagliano Taliun
    Gonçalo R. Abecasis
    Laura J. Scott
    First Published January 24, 2020
  - netNMF-sc: leveraging gene–gene interactions for imputation and dimensionality reduction in single-cell expression analysis
    Rebecca Elyanow
    Bianca Dumitrascu
    Barbara E. Engelhardt
    Benjamin J. Raphael
    First Published January 28, 2020
  - SHARP: hyperfast and accurate processing of single-cell RNA-seq data via ensemble random projection
    Shibiao Wan
    Junil Kim
    Kyoung Jae Won
    First Published January 28, 2020
  - Deep neural networks for interpreting RNA-binding protein target preferences
    Mahsa Ghanbari
    Uwe Ohler
    First Published January 28, 2020
  - MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome
    Dechao Tian
    Ruochi Zhang
    Yang Zhang
    Xiaopeng Zhu
    Jian Ma
    First Published January 6, 2020
  - TraDIS-Xpress: a high-resolution whole-genome assay identifies novel mechanisms of triclosan action and resistance
    Muhammad Yasir
    A. Keith Turner
    Sarah Bastkowski
    David Baker
    Andrew J. Page
    Andrea Telatin Minh-Duy Phan Leigh Monahan
    ...[+3 authors]...,
    George M. Savva
    Aaron Darling
    Mark A. Webber
    Ian G. Charles
    First Published February 12, 2020
Resources
- - A comparison of gene expression and DNA methylation patterns across tissues and species
    Lauren E. Blake
    Julien Roux
    Irene Hernando-Herraez
    Nicholas E. Banovich
    Raquel Garcia Perez
    Chiaowen Joyce Hsiao
    ...[+1 authors]...,
    Ittai Eres
    Claudia Cuevas
    Tomas Marques-Bonet
    Yoav Gilad
    First Published January 17, 2020
  - A time-resolved multi-omic atlas of the developing mouse liver
    Tongqing Gong
    Chunchao Zhang
    Xiaotian Ni
    Xianju Li
    Jin'e Li
    Mingwei Liu Dongdong Zhan Xia Xia Lei Song
    ...[+4 authors]...,
    Quan Zhou
    Chen Ding
    Jun Qin
    Yi Wang
    First Published February 12, 2020
  - Organ-level protein networks as a reference for the host effects of the microbiome
    Robert H. Mills
    Jacob M. Wozniak
    Alison Vrbanac
    Anaamika Campeau
    Benoit Chassaing
    First Published January 28, 2020
  - Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development
    Runsheng Li
    Xiaoliang Ren
    Qiutao Ding
    Yu Bi
    Dongying Xie
    First Published February 5, 2020
  - The full-length transcriptome of C. elegans using direct RNA sequencing
    Nathan P. Roach
    Norah Sadowski
    Amelia F. Alessi
    Winston Timp
    James Taylor
    First Published February 5, 2020
Corrigendum
- - Corrigendum: Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites
    Fiorella C. Grandi
    James M. Rosser
    Simon J. Newkirk
    Jun Yin
    Xiaoling Jiang
    Zhuo Xing Leanne Whitmore Sanum Bashir Zoltán Ivics
    ...[+4 authors]...,
    Zsuzsanna Izsvák
    Ping Ye
    Y. Eugene Yu
    Wenfeng An
    First Published February 20, 2020

Table of Contents

Volume 30, Issue 2 | February 2020

Research

A HOTAIR regulatory element modulates glioma cell sensitivity to temozolomide through long-range regulation of multiple target genes

An efficient RNA-seq-based segregation analysis identifies the sex chromosomes of Cannabis sativa

Genome-wide redistribution of 24-nt siRNAs in rice gametes

Methods

Ancestry-agnostic estimation of DNA sample contamination from sequence reads

netNMF-sc: leveraging gene–gene interactions for imputation and dimensionality reduction in single-cell expression analysis

SHARP: hyperfast and accurate processing of single-cell RNA-seq data via ensemble random projection

Deep neural networks for interpreting RNA-binding protein target preferences

MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome

TraDIS-Xpress: a high-resolution whole-genome assay identifies novel mechanisms of triclosan action and resistance

Resources

A comparison of gene expression and DNA methylation patterns across tissues and species

A time-resolved multi-omic atlas of the developing mouse liver

Organ-level protein networks as a reference for the host effects of the microbiome

Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development

The full-length transcriptome of C. elegans using direct RNA sequencing

Corrigendum

Corrigendum: Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites

Table of Contents

Volume 30, Issue 2 | February 2020

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Research

Methods

Resources

Corrigendum