Table of Contents

Research

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Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons
- Jiaxu Wang,
- Piroon Jenjaroenpun,
- Akshay Bhinge,
- Vladimir Espinosa Angarica,
- Antonio Del Sol,
- Intawat Nookaew,
- Vladimir A. Kuznetsov,
- and Lawrence W. Stanton
Genome Res. November 2017 27: 1783-1794; Published in Advance October 13, 2017, doi:10.1101/gr.223313.117
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Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data
- Aaron T.L. Lun,
- Fernando J. Calero-Nieto,
- Liora Haim-Vilmovsky,
- Berthold Göttgens,
- and John C. Marioni
Genome Res. November 2017 27: 1795-1806; Published in Advance October 13, 2017, doi:10.1101/gr.222877.117
OPEN ACCESS ARTICLE
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Disease-specific biases in alternative splicing and tissue-specific dysregulation revealed by multitissue profiling of lymphocyte gene expression in type 1 diabetes
- Jeremy R.B. Newman,
- Ana Conesa,
- Matthew Mika,
- Felicia N. New,
- Suna Onengut-Gumuscu,
- Mark A. Atkinson,
- Stephen S. Rich,
- Lauren M. McIntyre,
- and Patrick Concannon
Genome Res. November 2017 27: 1807-1815; Published in Advance October 12, 2017, doi:10.1101/gr.217984.116
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Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol
- Noah Dukler,
- Gregory T. Booth,
- Yi-Fei Huang,
- Nathaniel Tippens,
- Colin T. Waters,
- Charles G. Danko,
- John T. Lis,
- and Adam Siepel
Genome Res. November 2017 27: 1816-1829; Published in Advance October 12, 2017, doi:10.1101/gr.222935.117
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Altered hydroxymethylation is seen at regulatory regions in pancreatic cancer and regulates oncogenic pathways
- Sanchari Bhattacharyya,
- Kith Pradhan,
- Nathaniel Campbell,
- Jozef Mazdo,
- Aparna Vasantkumar,
- Shahina Maqbool,
- Tushar D. Bhagat,
- Sonal Gupta,
- Masako Suzuki,
- Yiting Yu,
- John M. Greally,
- Ulrich Steidl,
- James Bradner,
- Meelad Dawlaty,
- Lucy Godley,
- Anirban Maitra,
- and Amit Verma
Genome Res. November 2017 27: 1830-1842; Published in Advance October 6, 2017, doi:10.1101/gr.222794.117

Methods

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Co-expression networks reveal the tissue-specific regulation of transcription and splicing
- Ashis Saha,
- Yungil Kim,
- Ariel D.H. Gewirtz,
- Brian Jo,
- Chuan Gao,
- Ian C. McDowell,
- The GTEx Consortium,
- Barbara E. Engelhardt,
- and Alexis Battle
Genome Res. November 2017 27: 1843-1858; Published in Advance October 11, 2017, doi:10.1101/gr.216721.116
OPEN ACCESS ARTICLE
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Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis
- Fan Yang,
- Jiebiao Wang,
- The GTEx Consortium,
- Brandon L. Pierce,
- and Lin S. Chen
Genome Res. November 2017 27: 1859-1871; Published in Advance October 11, 2017, doi:10.1101/gr.216754.116
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Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change
- Pejman Mohammadi,
- Stephane E. Castel,
- Andrew A. Brown,
- and Tuuli Lappalainen
Genome Res. November 2017 27: 1872-1884; Published in Advance October 11, 2017, doi:10.1101/gr.216747.116
OPEN ACCESS ARTICLE
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Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors
- Jack Kuipers,
- Katharina Jahn,
- Benjamin J. Raphael,
- and Niko Beerenwinkel
Genome Res. November 2017 27: 1885-1894; Published in Advance October 13, 2017, doi:10.1101/gr.220707.117
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Detection of long repeat expansions from PCR-free whole-genome sequence data
- Egor Dolzhenko,
- Joke J.F.A. van Vugt,
- Richard J. Shaw,
- Mitchell A. Bekritsky,
- Marka van Blitterswijk,
- Giuseppe Narzisi,
- Subramanian S. Ajay,
- Vani Rajan,
- Bryan R. Lajoie,
- Nathan H. Johnson,
- Zoya Kingsbury,
- Sean J. Humphray,
- Raymond D. Schellevis,
- William J. Brands,
- Matt Baker,
- Rosa Rademakers,
- Maarten Kooyman,
- Gijs H.P. Tazelaar,
- Michael A. van Es,
- Russell McLaughlin,
- William Sproviero,
- Aleksey Shatunov,
- Ashley Jones,
- Ahmad Al Khleifat,
- Alan Pittman,
- Sarah Morgan,
- Orla Hardiman,
- Ammar Al-Chalabi,
- Chris Shaw,
- Bradley Smith,
- Edmund J. Neo,
- Karen Morrison,
- Pamela J. Shaw,
- Catherine Reeves,
- Lara Winterkorn,
- Nancy S. Wexler,
- The US–Venezuela Collaborative Research Group,
- David E. Housman,
- Christopher W. Ng,
- Alina L. Li,
- Ryan J. Taft,
- Leonard H. van den Berg,
- David R. Bentley,
- Jan H. Veldink,
- and Michael A. Eberle
Genome Res. November 2017 27: 1895-1903; Published in Advance September 8, 2017, doi:10.1101/gr.225672.117
OPEN ACCESS ARTICLE
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High-throughput single-molecule telomere characterization
- Jennifer McCaffrey,
- Eleanor Young,
- Katy Lassahn,
- Justin Sibert,
- Steven Pastor,
- Harold Riethman,
- and Ming Xiao
Genome Res. November 2017 27: 1904-1915; Published in Advance October 12, 2017, doi:10.1101/gr.222422.117
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The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology
- Eugene J. Gardner,
- Vincent K. Lam,
- Daniel N. Harris,
- Nelson T. Chuang,
- Emma C. Scott,
- W. Stephen Pittard,
- Ryan E. Mills,
- The 1000 Genomes Project Consortium,
- and Scott E. Devine
Genome Res. November 2017 27: 1916-1929; Published in Advance August 30, 2017, doi:10.1101/gr.218032.116
OPEN ACCESS ARTICLE
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Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data
- Mingxiang Teng and
- Rafael A. Irizarry
Genome Res. November 2017 27: 1930-1938; Published in Advance October 12, 2017, doi:10.1101/gr.220673.117
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HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient
- Tao Yang,
- Feipeng Zhang,
- Galip Gürkan Yardımcı,
- Fan Song,
- Ross C. Hardison,
- William Stafford Noble,
- Feng Yue,
- and Qunhua Li
Genome Res. November 2017 27: 1939-1949; Published in Advance August 30, 2017, doi:10.1101/gr.220640.117

Resource

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A genome-wide interactome of DNA-associated proteins in the human liver
- Ryne C. Ramaker,
- Daniel Savic,
- Andrew A. Hardigan,
- Kimberly Newberry,
- Gregory M. Cooper,
- Richard M. Myers,
- and Sara J. Cooper
Genome Res. November 2017 27: 1950-1960; Published in Advance October 11, 2017, doi:10.1101/gr.222083.117

Research

Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons

Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data

Disease-specific biases in alternative splicing and tissue-specific dysregulation revealed by multitissue profiling of lymphocyte gene expression in type 1 diabetes

Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol

Altered hydroxymethylation is seen at regulatory regions in pancreatic cancer and regulates oncogenic pathways

Methods

Co-expression networks reveal the tissue-specific regulation of transcription and splicing

Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis

Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change

Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors

Detection of long repeat expansions from PCR-free whole-genome sequence data

High-throughput single-molecule telomere characterization

The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology

Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

Resource

A genome-wide interactome of DNA-associated proteins in the human liver

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