Table of Contents

Research

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Slightly deleterious genomic variants and transcriptome perturbations in Down syndrome embryonic selection
- Konstantin Popadin,
- Stephan Peischl,
- Marco Garieri,
- M. Reza Sailani,
- Audrey Letourneau,
- Federico Santoni,
- Samuel W. Lukowski,
- Georgii A. Bazykin,
- Sergey Nikolaev,
- Diogo Meyer,
- Laurent Excoffier,
- Alexandre Reymond,
- and Stylianos E. Antonarakis
Genome Res. January 2018 28: 1-10; Published in Advance December 13, 2017, doi:10.1101/gr.228411.117
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Saturation mutagenesis reveals manifold determinants of exon definition
- Shengdong Ke,
- Vincent Anquetil,
- Jorge Rojas Zamalloa,
- Alisha Maity,
- Anthony Yang,
- Mauricio A. Arias,
- Sergey Kalachikov,
- James J. Russo,
- Jingyue Ju,
- and Lawrence A. Chasin
Genome Res. January 2018 28: 11-24; Published in Advance December 14, 2017, doi:10.1101/gr.219683.116
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Discovery of noncanonical translation initiation sites through mass spectrometric analysis of protein N termini
- Chan Hyun Na,
- Mustafa A. Barbhuiya,
- Min-Sik Kim,
- Steven Verbruggen,
- Stephen M. Eacker,
- Olga Pletnikova,
- Juan C. Troncoso,
- Marc K. Halushka,
- Gerben Menschaert,
- Christopher M. Overall,
- and Akhilesh Pandey
Genome Res. January 2018 28: 25-36; Published in Advance November 21, 2017, doi:10.1101/gr.226050.117
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H3S10ph broadly marks early-replicating domains in interphase ESCs and shows reciprocal antagonism with H3K9me2
- Carol C.L. Chen,
- Preeti Goyal,
- Mohammad M. Karimi,
- Marie H. Abildgaard,
- Hiroshi Kimura,
- and Matthew C. Lorincz
Genome Res. January 2018 28: 37-51; Published in Advance December 11, 2017, doi:10.1101/gr.224717.117
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Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus
- Jaaved Mohammed,
- Alex S. Flynt,
- Alexandra M. Panzarino,
- Md Mosharrof Hossain Mondal,
- Matthew DeCruz,
- Adam Siepel,
- and Eric C. Lai
Genome Res. January 2018 28: 52-65; Published in Advance December 12, 2017, doi:10.1101/gr.226068.117
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DNA mismatch repair preferentially protects genes from mutation
- Eric J. Belfield,
- Zhong Jie Ding,
- Fiona J.C. Jamieson,
- Anne M. Visscher,
- Shao Jian Zheng,
- Aziz Mithani,
- and Nicholas P. Harberd
Genome Res. January 2018 28: 66-74; Published in Advance December 12, 2017, doi:10.1101/gr.219303.116

Methods

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SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells
- Kyung Yeon Han,
- Kyu-Tae Kim,
- Je-Gun Joung,
- Dae-Soon Son,
- Yeon Jeong Kim,
- Areum Jo,
- Hyo-Jeong Jeon,
- Hui-Sung Moon,
- Chang Eun Yoo,
- Woosung Chung,
- Hye Hyeon Eum,
- Sangmin Kim,
- Hong Kwan Kim,
- Jeong Eon Lee,
- Myung-Ju Ahn,
- Hae-Ock Lee,
- Donghyun Park,
- and Woong-Yang Park
Genome Res. January 2018 28: 75-87; Published in Advance December 5, 2017, doi:10.1101/gr.223263.117
OPEN ACCESS ARTICLE
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Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI
- Ruben Boers,
- Joachim Boers,
- Bas de Hoon,
- Christel Kockx,
- Zeliha Ozgur,
- Anco Molijn,
- Wilfred van IJcken,
- Joop Laven,
- and Joost Gribnau
Genome Res. January 2018 28: 88-99; Published in Advance December 8, 2017, doi:10.1101/gr.222885.117
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ABCA4 midigenes reveal the full splice spectrum of all reported noncanonical splice site variants in Stargardt disease
- Riccardo Sangermano,
- Mubeen Khan,
- Stéphanie S. Cornelis,
- Valerie Richelle,
- Silvia Albert,
- Alejandro Garanto,
- Duaa Elmelik,
- Raheel Qamar,
- Dorien Lugtenberg,
- L. Ingeborgh van den Born,
- Rob W.J. Collin,
- and Frans P.M. Cremers
Genome Res. January 2018 28: 100-110; Published in Advance November 21, 2017, doi:10.1101/gr.226621.117
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SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site
- Liyang Zhang,
- Gabriella D. Martini,
- H. Tomas Rube,
- Judith F. Kribelbauer,
- Chaitanya Rastogi,
- Vincent D. FitzPatrick,
- Jon C. Houtman,
- Harmen J. Bussemaker,
- and Miles A. Pufall
Genome Res. January 2018 28: 111-121; Published in Advance December 1, 2017, doi:10.1101/gr.222844.117

Resources

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Impact of regulatory variation across human iPSCs and differentiated cells
- Nicholas E. Banovich,
- Yang I. Li,
- Anil Raj,
- Michelle C. Ward,
- Peyton Greenside,
- Diego Calderon,
- Po Yuan Tung,
- Jonathan E. Burnett,
- Marsha Myrthil,
- Samantha M. Thomas,
- Courtney K. Burrows,
- Irene Gallego Romero,
- Bryan J. Pavlovic,
- Anshul Kundaje,
- Jonathan K. Pritchard,
- and Yoav Gilad
Genome Res. January 2018 28: 122-131; Published in Advance December 5, 2017, doi:10.1101/gr.224436.117
OPEN ACCESS ARTICLE
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The landscape of miRNA editing in animals and its impact on miRNA biogenesis and targeting
- Lishi Li,
- Yulong Song,
- Xinrui Shi,
- Jianheng Liu,
- Shaolei Xiong,
- Wanying Chen,
- Qiang Fu,
- Zichao Huang,
- Nannan Gu,
- and Rui Zhang
Genome Res. January 2018 28: 132-143; Published in Advance December 12, 2017, doi:10.1101/gr.224386.117

Corrigendum

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Corrigendum: Discovery and genotyping of structural variation from long-read haploid genome sequence data
- John Huddleston,
- Mark J.P. Chaisson,
- Karyn Meltz Steinberg,
- Wes Warren,
- Kendra Hoekzema,
- David Gordon,
- Tina A. Graves-Lindsay,
- Katherine M. Munson,
- Zev N. Kronenberg,
- Laura Vives,
- Paul Peluso,
- Matthew Boitano,
- Chen-Shin Chin,
- Jonas Korlach,
- Richard K. Wilson,
- and Evan E. Eichler
Genome Res. January 2018 28: 144; doi:10.1101/gr.233007.117
OPEN ACCESS ARTICLE

Research

Slightly deleterious genomic variants and transcriptome perturbations in Down syndrome embryonic selection

Saturation mutagenesis reveals manifold determinants of exon definition

Discovery of noncanonical translation initiation sites through mass spectrometric analysis of protein N termini

H3S10ph broadly marks early-replicating domains in interphase ESCs and shows reciprocal antagonism with H3K9me2

Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus

DNA mismatch repair preferentially protects genes from mutation

Methods

SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells

Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI

ABCA4 midigenes reveal the full splice spectrum of all reported noncanonical splice site variants in Stargardt disease

SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site

Resources

Impact of regulatory variation across human iPSCs and differentiated cells

The landscape of miRNA editing in animals and its impact on miRNA biogenesis and targeting

Corrigendum

Corrigendum: Discovery and genotyping of structural variation from long-read haploid genome sequence data

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