Volume 29, Issue 11 | November 2019

Research
- - Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression
    Sarah K. Sasse
    Margaret Gruca
    Mary A. Allen
    Vineela Kadiyala
    Tengyao Song
    Fabienne Gally
    ...[+1 authors]...,
    Arnav Gupta
    Miles A. Pufall
    Robin D. Dowell
    Anthony N. Gerber
    First Published September 13, 2019
  - A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations
    Te-Lun Mai
    Trees-Juen Chuang
    First Published September 12, 2019
  - Global analyses of the dynamics of mammalian microRNA metabolism
    Elena R. Kingston
    David P. Bartel
    First Published September 13, 2019
  - Cotargeting among microRNAs in the brain
    Jennifer M. Cherone
    Vjola Jorgji
    Christopher B. Burge
    First Published October 24, 2019
  - The subgenomes show asymmetric expression of alleles in hybrid lineages of Megalobrama amblycephala × Culter alburnus
    Li Ren
    Wuhui Li
    Qinbo Qin
    He Dai
    Fengming Han
    Jun Xiao Xin Gao Jialin Cui Chang Wu Xiaojing Yan Guoliang Wang Guiming Liu Jia Liu Jiaming Li Zhong Wan Conghui Yang Chun Zhang Min Tao Jing Wang Kaikun Luo Shi Wang Fangzhou Hu Rurong Zhao Xuming Li Min Liu Hongkun Zheng Rong Zhou Yuqin Shu Yude Wang
    ...[+24 authors]...,
    Qinfeng Liu
    Chenchen Tang
    Wei Duan
    Shaojun Liu
    First Published October 24, 2019
Methods
- - Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ
    Joseph W. Foley
    Chunfang Zhu
    Philippe Jolivet
    Shirley X. Zhu
    Peipei Lu
    First Published September 13, 2019
  - FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples
    Jeffery M. Vahrenkamp
    Kathryn Szczotka
    Mark K. Dodson
    Elke A. Jarboe
    Andrew P. Soisson
    First Published October 24, 2019
  - Identification and dynamic quantification of regulatory elements using total RNA
    Sascha H. Duttke
    Max W. Chang
    Sven Heinz
    Christopher Benner
    First Published October 24, 2019
  - SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data
    Hamim Zafar
    Nicholas Navin
    Ken Chen
    Luay Nakhleh
    First Published October 18, 2019
  - PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data
    Salem Malikic
    Farid Rashidi Mehrabadi
    Simone Ciccolella
    Md. Khaledur Rahman
    Camir Ricketts
    Ehsan Haghshenas
    ...[+1 authors]...,
    Daniel Seidman
    Faraz Hach
    Iman Hajirasouliha
    S. Cenk Sahinalp
    First Published October 18, 2019
  - Quantitative mitochondrial DNA copy number determination using droplet digital PCR with single-cell resolution
    Ryan O'Hara
    Enzo Tedone
    Andrew Ludlow
    Ejun Huang
    Beatrice Arosio
    First Published September 23, 2019
  - Single-pollen-cell sequencing for gamete-based phased diploid genome assembly in plants
    Dongqing Shi
    Jun Wu
    Haibao Tang
    Hao Yin
    Hongtao Wang
    Ran Wang Runze Wang Ming Qian Juyou Wu Kaijie Qi
    ...[+5 authors]...,
    Zhihua Xie
    Zhiwen Wang
    Xiang Zhao
    Shaoling Zhang
    First Published October 24, 2019
Resources
- - Dynamics of microRNA expression during mouse prenatal development
    Sorena Rahmanian
    Rabi Murad
    Alessandra Breschi
    Weihua Zeng
    Mark Mackiewicz
    Brian Williams Carrie A. Davis Brian Roberts Sarah Meadows Dianna Moore Diane Trout Chris Zaleski Alex Dobin Lei-Hoon Sei Jorg Drenkow Alex Scavelli Thomas R. Gingeras
    ...[+12 authors]...,
    Barbara J. Wold
    Richard M. Myers
    Roderic Guigó
    Ali Mortazavi
    First Published October 23, 2019
  - Genes essential for embryonic stem cells are associated with neurodevelopmental disorders
    Shahar Shohat
    Sagiv Shifman
    First Published October 24, 2019
  - A chromosome-level assembly of the Atlantic herring genome—detection of a supergene and other signals of selection
    Mats E. Pettersson
    Christina M. Rochus
    Fan Han
    Junfeng Chen
    Jason Hill
    Ola Wallerman Guangyi Fan Xiaoning Hong Qiwu Xu He Zhang Shanshan Liu Xin Liu Leanne Haggerty Toby Hunt Fergal J. Martin
    ...[+10 authors]...,
    Paul Flicek
    Ignas Bunikis
    Arild Folkvord
    Leif Andersson
    First Published October 24, 2019

Table of Contents

Volume 29, Issue 11 | November 2019

Research

Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression

A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations

Global analyses of the dynamics of mammalian microRNA metabolism

Cotargeting among microRNAs in the brain

The subgenomes show asymmetric expression of alleles in hybrid lineages of Megalobrama amblycephala × Culter alburnus

Methods

Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ

FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples

Identification and dynamic quantification of regulatory elements using total RNA

SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data

PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data

Quantitative mitochondrial DNA copy number determination using droplet digital PCR with single-cell resolution

Single-pollen-cell sequencing for gamete-based phased diploid genome assembly in plants

Resources

Dynamics of microRNA expression during mouse prenatal development

Genes essential for embryonic stem cells are associated with neurodevelopmental disorders

A chromosome-level assembly of the Atlantic herring genome—detection of a supergene and other signals of selection

Table of Contents

Volume 29, Issue 11 | November 2019

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Research

Methods

Resources