Table of Contents

Research

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Exome-wide assessment of the functional impact and pathogenicity of multinucleotide mutations
- Joanna Kaplanis,
- Nadia Akawi,
- Giuseppe Gallone,
- Jeremy F. McRae,
- Elena Prigmore,
- Caroline F. Wright,
- David R. Fitzpatrick,
- Helen V. Firth,
- Jeffrey C. Barrett,
- Matthew E. Hurles,
- and on behalf of the Deciphering Developmental Disorders study
Genome Res. July 2019 29: 1047-1056; Published in Advance June 21, 2019, doi:10.1101/gr.239756.118
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Growth disrupting mutations in epigenetic regulatory molecules are associated with abnormalities of epigenetic aging
- Aaron R. Jeffries,
- Reza Maroofian,
- Claire G. Salter,
- Barry A. Chioza,
- Harold E. Cross,
- Michael A. Patton,
- Emma Dempster,
- I. Karen Temple,
- Deborah J.G. Mackay,
- Faisal I. Rezwan,
- Lise Aksglaede,
- Diana Baralle,
- Tabib Dabir,
- Matthew F. Hunter,
- Arveen Kamath,
- Ajith Kumar,
- Ruth Newbury-Ecob,
- Angelo Selicorni,
- Amanda Springer,
- Lionel Van Maldergem,
- Vinod Varghese,
- Naomi Yachelevich,
- Katrina Tatton-Brown,
- Jonathan Mill,
- Andrew H. Crosby,
- and Emma L. Baple
Genome Res. July 2019 29: 1057-1066; Published in Advance June 3, 2019, doi:10.1101/gr.243584.118
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Deficiency of nucleotide excision repair is associated with mutational signature observed in cancer
- Myrthe Jager,
- Francis Blokzijl,
- Ewart Kuijk,
- Johanna Bertl,
- Maria Vougioukalaki,
- Roel Janssen,
- Nicolle Besselink,
- Sander Boymans,
- Joep de Ligt,
- Jakob Skou Pedersen,
- Jan Hoeijmakers,
- Joris Pothof,
- Ruben van Boxtel,
- and Edwin Cuppen
Genome Res. July 2019 29: 1067-1077; Published in Advance June 20, 2019, doi:10.1101/gr.246223.118
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Histone methyltransferase PRDM9 is not essential for meiosis in male mice
- Ondrej Mihola,
- Florencia Pratto,
- Kevin Brick,
- Eliska Linhartova,
- Tatyana Kobets,
- Petr Flachs,
- Christopher L. Baker,
- Radislav Sedlacek,
- Kenneth Paigen,
- Petko M. Petkov,
- R. Daniel Camerini-Otero,
- and Zdenek Trachtulec
Genome Res. July 2019 29: 1078-1086; Published in Advance June 11, 2019, doi:10.1101/gr.244426.118
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Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features
- Lisa Barros de Andrade e Sousa,
- Iris Jonkers,
- Laurène Syx,
- Ilona Dunkel,
- Julie Chaumeil,
- Christel Picard,
- Benjamin Foret,
- Chong-Jian Chen,
- John T. Lis,
- Edith Heard,
- Edda G. Schulz,
- and Annalisa Marsico
Genome Res. July 2019 29: 1087-1099; Published in Advance June 7, 2019, doi:10.1101/gr.245027.118
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Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish
- Charles E. Vejnar,
- Mario Abdel Messih,
- Carter M. Takacs,
- Valeria Yartseva,
- Panos Oikonomou,
- Romain Christiano,
- Marlon Stoeckius,
- Stephanie Lau,
- Miler T. Lee,
- Jean-Denis Beaudoin,
- Damir Musaev,
- Hiba Darwich-Codore,
- Tobias C. Walther,
- Saeed Tavazoie,
- Daniel Cifuentes,
- and Antonio J. Giraldez
Genome Res. July 2019 29: 1100-1114; Published in Advance June 21, 2019, doi:10.1101/gr.245159.118
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Haploid selection drives new gene male germline expression
- Julia B. Raices,
- Paulo A. Otto,
- and Maria D. Vibranovski
Genome Res. July 2019 29: 1115-1122; Published in Advance June 20, 2019, doi:10.1101/gr.238824.118
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Nascent chromatin occupancy profiling reveals locus- and factor-specific chromatin maturation dynamics behind the DNA replication fork
- Mónica P. Gutiérrez,
- Heather K. MacAlpine,
- and David M. MacAlpine
Genome Res. July 2019 29: 1123-1133; Published in Advance June 19, 2019, doi:10.1101/gr.243386.118

Methods

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A machine-learning approach for accurate detection of copy number variants from exome sequencing
- Vijay Kumar Pounraja,
- Gopal Jayakar,
- Matthew Jensen,
- Neil Kelkar,
- and Santhosh Girirajan
Genome Res. July 2019 29: 1134-1143; Published in Advance June 6, 2019, doi:10.1101/gr.245928.118
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Genetic variant pathogenicity prediction trained using disease-specific clinical sequencing data sets
- Perry Evans,
- Chao Wu,
- Amanda Lindy,
- Dianalee A. McKnight,
- Matthew Lebo,
- Mahdi Sarmady,
- and Ahmad N. Abou Tayoun
Genome Res. July 2019 29: 1144-1151; Published in Advance June 24, 2019, doi:10.1101/gr.240994.118
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OMA standalone: orthology inference among public and custom genomes and transcriptomes
- Adrian M. Altenhoff,
- Jeremy Levy,
- Magdalena Zarowiecki,
- Bartłomiej Tomiczek,
- Alex Warwick Vesztrocy,
- Daniel A. Dalquen,
- Steven Müller,
- Maximilian J. Telford,
- Natasha M. Glover,
- David Dylus,
- and Christophe Dessimoz
Genome Res. July 2019 29: 1152-1163; Published in Advance June 24, 2019, doi:10.1101/gr.243212.118
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Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs
- Severin Berger,
- Mikhail Pachkov,
- Phil Arnold,
- Saeed Omidi,
- Nicholas Kelley,
- Silvia Salatino,
- and Erik van Nimwegen
Genome Res. July 2019 29: 1164-1177; Published in Advance May 28, 2019, doi:10.1101/gr.239319.118
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Resources

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Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome
- Wouter De Coster,
- Peter De Rijk,
- Arne De Roeck,
- Tim De Pooter,
- Svenn D'Hert,
- Mojca Strazisar,
- Kristel Sleegers,
- and Christine Van Broeckhoven
Genome Res. July 2019 29: 1178-1187; Published in Advance June 11, 2019, doi:10.1101/gr.244939.118
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Early genome activation in Drosophila is extensive with an initial tendency for aborted transcripts and retained introns
- Jamie C. Kwasnieski,
- Terry L. Orr-Weaver,
- and David P. Bartel
Genome Res. July 2019 29: 1188-1197; Published in Advance June 24, 2019, doi:10.1101/gr.242164.118
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Pervasive and dynamic transcription initiation in Saccharomyces cerevisiae
- Zhaolian Lu and
- Zhenguo Lin
Genome Res. July 2019 29: 1198-1210; Published in Advance May 10, 2019, doi:10.1101/gr.245456.118

Research

Exome-wide assessment of the functional impact and pathogenicity of multinucleotide mutations

Growth disrupting mutations in epigenetic regulatory molecules are associated with abnormalities of epigenetic aging

Deficiency of nucleotide excision repair is associated with mutational signature observed in cancer

Histone methyltransferase PRDM9 is not essential for meiosis in male mice

Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features

Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish

Haploid selection drives new gene male germline expression

Nascent chromatin occupancy profiling reveals locus- and factor-specific chromatin maturation dynamics behind the DNA replication fork

Methods

A machine-learning approach for accurate detection of copy number variants from exome sequencing

Genetic variant pathogenicity prediction trained using disease-specific clinical sequencing data sets

OMA standalone: orthology inference among public and custom genomes and transcriptomes

Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs

Resources

Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome

Early genome activation in Drosophila is extensive with an initial tendency for aborted transcripts and retained introns

Pervasive and dynamic transcription initiation in Saccharomyces cerevisiae

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