Table of Contents

Research

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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,
- Arnav Gupta,
- Miles A. Pufall,
- Robin D. Dowell,
- and Anthony N. Gerber
Genome Res. November 2019 29: 1753-1765; Published in Advance September 13, 2019, doi:10.1101/gr.248187.119
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A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations
- Te-Lun Mai and
- Trees-Juen Chuang
Genome Res. November 2019 29: 1766-1776; Published in Advance September 12, 2019, doi:10.1101/gr.246033.118
OPEN ACCESS ARTICLE
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Global analyses of the dynamics of mammalian microRNA metabolism
- Elena R. Kingston and
- David P. Bartel
Genome Res. November 2019 29: 1777-1790; Published in Advance September 13, 2019, doi:10.1101/gr.251421.119
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Cotargeting among microRNAs in the brain
- Jennifer M. Cherone,
- Vjola Jorgji,
- and Christopher B. Burge
Genome Res. November 2019 29: 1791-1804; Published in Advance October 24, 2019, doi:10.1101/gr.249201.119
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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,
- Qinfeng Liu,
- Chenchen Tang,
- Wei Duan,
- and Shaojun Liu
Genome Res. November 2019 29: 1805-1815; Published in Advance October 24, 2019, doi:10.1101/gr.249805.119
OPEN ACCESS ARTICLE

Methods

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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,
- Michael J. Meaney,
- and Robert B. West
Genome Res. November 2019 29: 1816-1825; Published in Advance September 13, 2019, doi:10.1101/gr.234807.118
OPEN ACCESS ARTICLE
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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,
- and Jason Gertz
Genome Res. November 2019 29: 1826-1835; Published in Advance October 24, 2019, doi:10.1101/gr.249656.119
OPEN ACCESS ARTICLE
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Identification and dynamic quantification of regulatory elements using total RNA
- Sascha H. Duttke,
- Max W. Chang,
- Sven Heinz,
- and Christopher Benner
Genome Res. November 2019 29: 1836-1846; Published in Advance October 24, 2019, doi:10.1101/gr.253492.119
OPEN ACCESS ARTICLE
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SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data
- Hamim Zafar,
- Nicholas Navin,
- Ken Chen,
- and Luay Nakhleh
Genome Res. November 2019 29: 1847-1859; Published in Advance October 18, 2019, doi:10.1101/gr.243121.118
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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,
- Daniel Seidman,
- Faraz Hach,
- Iman Hajirasouliha,
- and S. Cenk Sahinalp
Genome Res. November 2019 29: 1860-1877; Published in Advance October 18, 2019, doi:10.1101/gr.234435.118
OPEN ACCESS ARTICLE
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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,
- Daniela Mari,
- and Jerry W. Shay
Genome Res. November 2019 29: 1878-1888; Published in Advance September 23, 2019, doi:10.1101/gr.250480.119
OPEN ACCESS ARTICLE
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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,
- Zhihua Xie,
- Zhiwen Wang,
- Xiang Zhao,
- and Shaoling Zhang
Genome Res. November 2019 29: 1889-1899; Published in Advance October 24, 2019, doi:10.1101/gr.251033.119
OPEN ACCESS ARTICLE

Resources

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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,
- Barbara J. Wold,
- Richard M. Myers,
- Roderic Guigó,
- and Ali Mortazavi
Genome Res. November 2019 29: 1900-1909; Published in Advance October 23, 2019, doi:10.1101/gr.248997.119
OPEN ACCESS ARTICLE
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Genes essential for embryonic stem cells are associated with neurodevelopmental disorders
- Shahar Shohat and
- Sagiv Shifman
Genome Res. November 2019 29: 1910-1918; Published in Advance October 24, 2019, doi:10.1101/gr.250019.119
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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,
- Paul Flicek,
- Ignas Bunikis,
- Arild Folkvord,
- and Leif Andersson
Genome Res. November 2019 29: 1919-1928; Published in Advance October 24, 2019, doi:10.1101/gr.253435.119
OPEN ACCESS ARTICLE

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

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