Browse Articles

  • Publisher Correction |

    • Jisen Zhang
    • , Xingtan Zhang
    • , Haibao Tang
    • , Qing Zhang
    • , Xiuting Hua
    • , Xiaokai Ma
    • , Fan Zhu
    • , Tyler Jones
    • , Xinguang Zhu
    • , John Bowers
    • , Ching Man Wai
    • , Chunfang Zheng
    • , Yan Shi
    • , Shuai Chen
    • , Xiuming Xu
    • , Jingjing Yue
    • , David R. Nelson
    • , Lixian Huang
    • , Zhen Li
    • , Huimin Xu
    • , Dong Zhou
    • , Yongjun Wang
    • , Weichang Hu
    • , Jishan Lin
    • , Youjin Deng
    • , Neha Pandey
    • , Melina Mancini
    • , Dessireé Zerpa
    • , Julie K. Nguyen
    • , Liming Wang
    • , Liang Yu
    • , Yinghui Xin
    • , Liangfa Ge
    • , Jie Arro
    • , Jennifer O. Han
    • , Setu Chakrabarty
    • , Marija Pushko
    • , Wenping Zhang
    • , Yanhong Ma
    • , Panpan Ma
    • , Mingju Lv
    • , Faming Chen
    • , Guangyong Zheng
    • , Jingsheng Xu
    • , Zhenhui Yang
    • , Fang Deng
    • , Xuequn Chen
    • , Zhenyang Liao
    • , Xunxiao Zhang
    • , Zhicong Lin
    • , Hai Lin
    • , Hansong Yan
    • , Zheng Kuang
    • , Weimin Zhong
    • , Pingping Liang
    • , Guofeng Wang
    • , Yuan Yuan
    • , Jiaxian Shi
    • , Jinxiang Hou
    • , Jingxian Lin
    • , Jingjing Jin
    • , Peijian Cao
    • , Qiaochu Shen
    • , Qing Jiang
    • , Ping Zhou
    • , Yaying Ma
    • , Xiaodan Zhang
    • , Rongrong Xu
    • , Juan Liu
    • , Yongmei Zhou
    • , Haifeng Jia
    • , Qing Ma
    • , Rui Qi
    • , Zhiliang Zhang
    • , Jingping Fang
    • , Hongkun Fang
    • , Jinjin Song
    • , Mengjuan Wang
    • , Guangrui Dong
    • , Gang Wang
    • , Zheng Chen
    • , Teng Ma
    • , Hong Liu
    • , Singha R. Dhungana
    • , Sarah E. Huss
    • , Xiping Yang
    • , Anupma Sharma
    • , Jhon H. Trujillo
    • , Maria C. Martinez
    • , Matthew Hudson
    • , John J. Riascos
    • , Mary Schuler
    • , Li-Qing Chen
    • , David M. Braun
    • , Lei Li
    • , Qingyi Yu
    • , Jianping Wang
    • , Kai Wang
    • , Michael C. Schatz
    • , David Heckerman
    • , Marie-Anne Van Sluys
    • , Glaucia Mendes Souza
    • , Paul H. Moore
    • , David Sankoff
    • , Robert VanBuren
    • , Andrew H. Paterson
    • , Chifumi Nagai
    •  & Ray Ming
  • Letter |

    In zebrafish, cilia-driven flow of cerebrospinal fluid transports adrenergic signals that induce urotensin neuropeptides in spinal cord neurons. In turn, these neuropeptides activate their receptor on nearby muscle fibers, straightening the body axis.

    • Xiaoli Zhang
    • , Shuo Jia
    • , Zhe Chen
    • , Yan Ling Chong
    • , Haibo Xie
    • , Dong Feng
    • , Xiaotong Wu
    • , Don Zhu Song
    • , Sudipto Roy
    •  & Chengtian Zhao
  • Article |

    Integrated analysis of transcriptome, open chromatin region and chromatin conformation capture data from subjects with acute myeloid leukemia (AML) harboring defined transcription factor and signaling molecule alterations provide insights into the subtype-specific regulatory network in AML.

    • Salam A. Assi
    • , Maria Rosaria Imperato
    • , Daniel J. L. Coleman
    • , Anna Pickin
    • , Sandeep Potluri
    • , Anetta Ptasinska
    • , Paulynn Suyin Chin
    • , Helen Blair
    • , Pierre Cauchy
    • , Sally R. James
    • , Joaquin Zacarias-Cabeza
    • , L. Niall Gilding
    • , Andrew Beggs
    • , Sam Clokie
    • , Justin C. Loke
    • , Phil Jenkin
    • , Ash Uddin
    • , Ruud Delwel
    • , Stephen J. Richards
    • , Manoj Raghavan
    • , Michael J. Griffiths
    • , Olaf Heidenreich
    • , Peter N. Cockerill
    •  & Constanze Bonifer
  • Article |

    Analysis of genotyping-by-sequencing data for more than 20,000 barley accessions from a German genebank provides a framework for genomics-assisted genebank management and analysis of large germplasm collections for important crops.

    • Sara G. Milner
    • , Matthias Jost
    • , Shin Taketa
    • , Elena Rey Mazón
    • , Axel Himmelbach
    • , Markus Oppermann
    • , Stephan Weise
    • , Helmut Knüpffer
    • , Martín Basterrechea
    • , Patrick König
    • , Danuta Schüler
    • , Rajiv Sharma
    • , Raj K. Pasam
    • , Twan Rutten
    • , Ganggang Guo
    • , Dongdong Xu
    • , Jing Zhang
    • , Gerhard Herren
    • , Thomas Müller
    • , Simon G. Krattinger
    • , Beat Keller
    • , Yong Jiang
    • , Maria Y. González
    • , Yusheng Zhao
    • , Antje Habekuß
    • , Sandra Färber
    • , Frank Ordon
    • , Matthias Lange
    • , Andreas Börner
    • , Andreas Graner
    • , Jochen C. Reif
    • , Uwe Scholz
    • , Martin Mascher
    •  & Nils Stein
  • News & Views |

    A new study identifies loss-of-function mutations in HAVCR2, which encodes TIM-3, in patients with a rare cutaneous T cell lymphoma associated with aberrant immunological activation. These mutations lead to loss of the TIM-3 immunological checkpoint, thus promoting inflammation and malignancy.

    • Karen O. Dixon
    • , Madhumita Das
    •  & Vijay K. Kuchroo
  • Technical Report |

    A machine learning approach for refinement of somatic variant calls automates this process and reduces bias stemming from inter-reviewer variability.

    • Benjamin J. Ainscough
    • , Erica K. Barnell
    • , Peter Ronning
    • , Katie M. Campbell
    • , Alex H. Wagner
    • , Todd A. Fehniger
    • , Gavin P. Dunn
    • , Ravindra Uppaluri
    • , Ramaswamy Govindan
    • , Thomas E. Rohan
    • , Malachi Griffith
    • , Elaine R. Mardis
    • , S. Joshua Swamidass
    •  & Obi L. Griffith
  • Article | | open

    Comparative study of 81 genomes of parasitic and non-parasitic worms identifies gene family births and expanded gene families at key nodes in the phylogeny that are relevant to parasitism and proteins historically targeted for drug development.

    • Avril Coghlan
    • , Rahul Tyagi
    • , James A. Cotton
    • , Nancy Holroyd
    • , Bruce A. Rosa
    • , Isheng Jason Tsai
    • , Dominik R. Laetsch
    • , Robin N. Beech
    • , Tim A. Day
    • , Kymberlie Hallsworth-Pepin
    • , Huei-Mien Ke
    • , Tzu-Hao Kuo
    • , Tracy J. Lee
    • , John Martin
    • , Rick M. Maizels
    • , Prudence Mutowo
    • , Philip Ozersky
    • , John Parkinson
    • , Adam J. Reid
    • , Neil D. Rawlings
    • , Diogo M. Ribeiro
    • , Lakshmipuram Seshadri Swapna
    • , Eleanor Stanley
    • , David W. Taylor
    • , Nicolas J. Wheeler
    • , Mostafa Zamanian
    • , Xu Zhang
    • , Fiona Allan
    • , Judith E. Allen
    • , Kazuhito Asano
    • , Simon A. Babayan
    • , Germanus Bah
    • , Helen Beasley
    • , Hayley M. Bennett
    • , Stewart A. Bisset
    • , Estela Castillo
    • , Joseph Cook
    • , Philip J. Cooper
    • , Teresa Cruz-Bustos
    • , Carmen Cuéllar
    • , Eileen Devaney
    • , Stephen R. Doyle
    • , Mark L. Eberhard
    • , Aidan Emery
    • , Keeseon S. Eom
    • , John S. Gilleard
    • , Daria Gordon
    • , Yvonne Harcus
    • , Bhavana Harsha
    • , John M. Hawdon
    • , Dolores E. Hill
    • , Jane Hodgkinson
    • , Petr Horák
    • , Kevin L. Howe
    • , Thomas Huckvale
    • , Martin Kalbe
    • , Gaganjot Kaur
    • , Taisei Kikuchi
    • , Georgios Koutsovoulos
    • , Sujai Kumar
    • , Andrew R. Leach
    • , Jane Lomax
    • , Benjamin Makepeace
    • , Jacqueline B. Matthews
    • , Antonio Muro
    • , Noel Michael O’Boyle
    • , Peter D. Olson
    • , Antonio Osuna
    • , Felix Partono
    • , Kenneth Pfarr
    • , Gabriel Rinaldi
    • , Pilar Foronda
    • , David Rollinson
    • , Mercedes Gomez Samblas
    • , Hiroshi Sato
    • , Manuela Schnyder
    • , Tomáš Scholz
    • , Myriam Shafie
    • , Vincent N. Tanya
    • , Rafael Toledo
    • , Alan Tracey
    • , Joseph F. Urban
    • , Lian-Chen Wang
    • , Dante Zarlenga
    • , Mark L. Blaxter
    • , Makedonka Mitreva
    •  & Matthew Berriman
  • Article |

    Whole-genome sequencing of 175 Mongolians representing six tribes highlights population-specific genetic architecture and substantial gene flow among northern Eurasian populations, including derived alleles shared by Mongolians and Finns.

    • Haihua Bai
    • , Xiaosen Guo
    • , Narisu Narisu
    • , Tianming Lan
    • , Qizhu Wu
    • , Yanping Xing
    • , Yong Zhang
    • , Stephen R. Bond
    • , Zhili Pei
    • , Yanru Zhang
    • , Dandan Zhang
    • , Jirimutu Jirimutu
    • , Dong Zhang
    • , Xukui Yang
    • , Morigenbatu Morigenbatu
    • , Li Zhang
    • , Bingyi Ding
    • , Baozhu Guan
    • , Junwei Cao
    • , Haorong Lu
    • , Yiyi Liu
    • , Wangsheng Li
    • , Ningxin Dang
    • , Mingyang Jiang
    • , Shenyuan Wang
    • , Huixin Xu
    • , Dingzhu Wang
    • , Chunxia Liu
    • , Xin Luo
    • , Ying Gao
    • , Xueqiong Li
    • , Zongze Wu
    • , Liqing Yang
    • , Fanhua Meng
    • , Xiaolian Ning
    • , Hashenqimuge Hashenqimuge
    • , Kaifeng Wu
    • , Bo Wang
    • , Suyalatu Suyalatu
    • , Yingchun Liu
    • , Chen Ye
    • , Huiguang Wu
    • , Kalle Leppälä
    • , Lu Li
    • , Lin Fang
    • , Yujie Chen
    • , Wenhao Xu
    • , Tao Li
    • , Xin Liu
    • , Xun Xu
    • , Christopher R. Gignoux
    • , Huanming Yang
    • , Lawrence C. Brody
    • , Jun Wang
    • , Karsten Kristiansen
    • , Burenbatu Burenbatu
    • , Huanmin Zhou
    •  & Ye Yin
  • Letter |

    Analysis of 1,007 sibling pairs from 251 families identifies 878 de novo mutations shared by siblings at 448 sites. Recurrence probability based on parental somatic mosaicism, sibling sharing, parent of origin, mutation type and genomic position can range from 0.011% to 28.5%.

    • Hákon Jónsson
    • , Patrick Sulem
    • , Gudny A. Arnadottir
    • , Gunnar Pálsson
    • , Hannes P. Eggertsson
    • , Snaedis Kristmundsdottir
    • , Florian Zink
    • , Birte Kehr
    • , Kristjan E. Hjorleifsson
    • , Brynjar Ö. Jensson
    • , Ingileif Jonsdottir
    • , Sigurdur Einar Marelsson
    • , Sigurjon Axel Gudjonsson
    • , Arnaldur Gylfason
    • , Adalbjorg Jonasdottir
    • , Aslaug Jonasdottir
    • , Simon N. Stacey
    • , Olafur Th. Magnusson
    • , Unnur Thorsteinsdottir
    • , Gisli Masson
    • , Augustine Kong
    • , Bjarni V. Halldorsson
    • , Agnar Helgason
    • , Daniel F. Gudbjartsson
    •  & Kari Stefansson
  • Letter |

    Retinoic acid and BMP4 signaling, together with p63, contribute to dynamic long-range chromatin interactions during keratinocyte differentiation. TP63 decreases chromatin accessibility and promotes H3K27me3 accumulation at enhancers.

    • Jillian M. Pattison
    • , Sandra P. Melo
    • , Samantha N. Piekos
    • , Jessica L. Torkelson
    • , Elizaveta Bashkirova
    • , Maxwell R. Mumbach
    • , Charlotte Rajasingh
    • , Hanson Hui Zhen
    • , Lingjie Li
    • , Eric Liaw
    • , Daniel Alber
    • , Adam J. Rubin
    • , Gautam Shankar
    • , Xiaomin Bao
    • , Howard Y. Chang
    • , Paul A. Khavari
    •  & Anthony E. Oro
  • Article |

    Eight genome-wide CRISPR screens identify genes required for substrate-specific phagocytosis. The study highlights roles for NHLRC2 in filopodia formation, very-long-chain fatty acids in substrate-specific phagocytosis and TM2D3 in uptake of amyloid-β aggregates.

    • Michael S. Haney
    • , Christopher J. Bohlen
    • , David W. Morgens
    • , James A. Ousey
    • , Amira A. Barkal
    • , C. Kimberly Tsui
    • , Braeden K. Ego
    • , Roni Levin
    • , Roarke A. Kamber
    • , Hannah Collins
    • , Andrew Tucker
    • , Amy Li
    • , Daan Vorselen
    • , Lorenzo Labitigan
    • , Emily Crane
    • , Evan Boyle
    • , Lihua Jiang
    • , Joanne Chan
    • , Esther Rincón
    • , William J. Greenleaf
    • , Billy Li
    • , Michael P. Snyder
    • , Irving L. Weissman
    • , Julie A. Theriot
    • , Sean R. Collins
    • , Ben A. Barres
    •  & Michael C. Bassik
  • Author Correction |

    • Valentina Iotchkova
    • , Jie Huang
    • , John A Morris
    • , Deepti Jain
    • , Caterina Barbieri
    • , Klaudia Walter
    • , Josine L Min
    • , Lu Chen
    • , William Astle
    • , Massimilian Cocca
    • , Patrick Deelen
    • , Heather Elding
    • , Aliki-Eleni Farmaki
    • , Christopher S Franklin
    • , Mattias Franberg
    • , Tom R Gaunt
    • , Albert Hofman
    • , Tao Jiang
    • , Marcus E Kleber
    • , Genevieve Lachance
    • , Jian’an Luan
    • , Giovanni Malerba
    • , Angela Matchan
    • , Daniel Mead
    • , Yasin Memari
    • , Ioanna Ntalla
    • , Kalliope Panoutsopoulou
    • , Raha Pazoki
    • , John R B Perry
    • , Fernando Rivadeneira
    • , Maria Sabater-Lleal
    • , Bengt Sennblad
    • , So-Youn Shin
    • , Lorraine Southam
    • , Michela Traglia
    • , Freerk van Dijk
    • , Elisabeth M van Leeuwen
    • , Gianluigi Zaza
    • , Weihua Zhang
    • , Najaf Amin
    • , Adam Butterworth
    • , John C Chambers
    • , George Dedoussis
    • , Abbas Dehghan
    • , Oscar H Franco
    • , Lude Franke
    • , Mattia Frontini
    • , Giovanni Gambaro
    • , Paolo Gasparini
    • , Anders Hamsten
    • , Aaron Isaacs
    • , Jaspal S Kooner
    • , Charles Kooperberg
    • , Claudia Langenberg
    • , Winfried Marz
    • , Robert A Scott
    • , Morris A Swertz
    • , Daniela Toniolo
    • , Andre G Uitterlinden
    • , Cornelia M van Duijn
    • , Hugh Watkins
    • , Eleftheria Zeggini
    • , Mathew T Maurano
    • , Nicholas J Timpson
    • , Alexander P Reiner
    • , Paul L Auer
    •  & Nicole Soranzo
  • Perspective |

    Mitochondrial variants are important to consider when analyzing the genetics of various metabolic or age-related diseases. These mtDNA variants can influence the penetrance of a phenotype or interact differentially with nuclear DNA variants.

    • Douglas C. Wallace
  • Technical Report |

    Tri-C is a new 3C approach to identify concurrent chromatin interactions at individual alleles. The authors observe specific higher-order structures involving simultaneous interactions between multiple enhancers and promoters, called regulatory hubs.

    • A. Marieke Oudelaar
    • , James O. J. Davies
    • , Lars L. P. Hanssen
    • , Jelena M. Telenius
    • , Ron Schwessinger
    • , Yu Liu
    • , Jill M. Brown
    • , Damien J. Downes
    • , Andrea M. Chiariello
    • , Simona Bianco
    • , Mario Nicodemi
    • , Veronica J. Buckle
    • , Job Dekker
    • , Douglas R. Higgs
    •  & Jim R. Hughes
  • Correspondence |

    • Maxime Tarabichi
    • , Iñigo Martincorena
    • , Moritz Gerstung
    • , Armand M. Leroi
    • , Florian Markowetz
    • , Stefan C. Dentro
    • , Ignaty Leshchiner
    • , Moritz Gerstung
    • , Clemency Jolly
    • , Kerstin Haase
    • , Maxime Tarabichi
    • , Jeff Wintersinger
    • , Amit G. Deshwar
    • , Kaixian Yu
    • , Santiago Gonzalez
    • , Yulia Rubanova
    • , Geoff Macintyre
    • , David J. Adams
    • , Pavana Anur
    • , Rameen Beroukhim
    • , Paul C. Boutros
    • , David D. Bowtell
    • , Peter J. Campbell
    • , Shaolong Cao
    • , Elizabeth L. Christie
    • , Marek Cmero
    • , Yupeng Cun
    • , Kevin J. Dawson
    • , Jonas Demeulemeester
    • , Nilgun Donmez
    • , Ruben M. Drews
    • , Roland Eils
    • , Yu Fan
    • , Matthew Fittall
    • , Dale W. Garsed
    • , Gad Getz
    • , Gavin Ha
    • , Marcin Imielinski
    • , Lara Jerman
    • , Yuan Ji
    • , Kortine Kleinheinz
    • , Juhee Lee
    • , Henry Lee-Six
    • , Dimitri G. Livitz
    • , Salem Malikic
    • , Florian Markowetz
    • , Iñigo Martincorena
    • , Thomas J. Mitchell
    • , Ville Mustonen
    • , Layla Oesper
    • , Martin Peifer
    • , Myron Peto
    • , Benjamin J. Raphael
    • , Daniel Rosebrock
    • , S. Cenk Sahinalp
    • , Adriana Salcedo
    • , Matthias Schlesner
    • , Steven Schumacher
    • , Subhajit Sengupta
    • , Ruian Shi
    • , Seung Jun Shin
    • , Lincoln D. Stein
    • , Ignacio Vázquez-García
    • , Shankar Vembu
    • , David A. Wheeler
    • , Tsun-Po Yang
    • , Xiaotong Yao
    • , Ke Yuan
    • , Hongtu Zhu
    • , Wenyi Wang
    • , Quaid D. Morris
    • , Paul T. Spellman
    • , David C. Wedge
    • , Peter Van Loo
    • , Paul T. Spellman
    • , Quaid D. Morris
    • , Ole Christian Lingjærde
    • , David C. Wedge
    •  & Peter Van Loo
  • Letter |

    This study finds germline loss-of-function mutations in HAVCR2, which encodes the immune modulator TIM-3, in individuals with subcutaneous panniculitis-like T cell lymphomas and hemophagocytic lymphohistiocytosis, a life-threatening inflammatory condition.

    • Tenzin Gayden
    • , Fernando E. Sepulveda
    • , Dong-Anh Khuong-Quang
    • , Jonathan Pratt
    • , Elvis T. Valera
    • , Alexandrine Garrigue
    • , Susan Kelso
    • , Frank Sicheri
    • , Leonie G. Mikael
    • , Nancy Hamel
    • , Andrea Bajic
    • , Rola Dali
    • , Shriya Deshmukh
    • , Dzana Dervovic
    • , Daniel Schramek
    • , Frédéric Guerin
    • , Mikko Taipale
    • , Hamid Nikbakht
    • , Jacek Majewski
    • , Despina Moshous
    • , Janie Charlebois
    • , Sharon Abish
    • , Christine Bole-Feysot
    • , Patrick Nitschke
    • , Brigitte Bader-Meunier
    • , David Mitchell
    • , Catherine Thieblemont
    • , Maxime Battistella
    • , Simon Gravel
    • , Van-Hung Nguyen
    • , Rachel Conyers
    • , Jean-Sebastien Diana
    • , Chris McCormack
    • , H. Miles Prince
    • , Marianne Besnard
    • , Stephane Blanche
    • , Paul G. Ekert
    • , Sylvie Fraitag
    • , William D. Foulkes
    • , Alain Fischer
    • , Bénédicte Neven
    • , David Michonneau
    • , Geneviève de Saint Basile
    •  & Nada Jabado
  • Correspondence |

    • Timon Heide
    • , Luis Zapata
    • , Marc J. Williams
    • , Benjamin Werner
    • , Giulio Caravagna
    • , Chris P. Barnes
    • , Trevor A. Graham
    •  & Andrea Sottoriva
  • Letter |

    Genome-wide association meta-analysis of data sets from Iceland and the UK identifies 16 new risk loci for osteoarthritis, including missense variants in SMO, IL11, and COL11A1.

    • Unnur Styrkarsdottir
    • , Sigrun H. Lund
    • , Gudmar Thorleifsson
    • , Florian Zink
    • , Olafur A. Stefansson
    • , Jon K. Sigurdsson
    • , Kristinn Juliusson
    • , Kristbjörg Bjarnadottir
    • , Sara Sigurbjornsdottir
    • , Stefan Jonsson
    • , Kristjan Norland
    • , Lilja Stefansdottir
    • , Asgeir Sigurdsson
    • , Gardar Sveinbjornsson
    • , Asmundur Oddsson
    • , Gyda Bjornsdottir
    • , Reynir L. Gudmundsson
    • , Gisli H. Halldorsson
    • , Thorunn Rafnar
    • , Ingileif Jonsdottir
    • , Eirikur Steingrimsson
    • , Gudmundur L. Norddahl
    • , Gisli Masson
    • , Patrick Sulem
    • , Helgi Jonsson
    • , Thorvaldur Ingvarsson
    • , Daniel F. Gudbjartsson
    • , Unnur Thorsteinsdottir
    •  & Kari Stefansson
  • Correspondence |

    • Lars A. Forsberg
    • , Jonatan Halvardson
    • , Edyta Rychlicka-Buniowska
    • , Marcus Danielsson
    • , Behrooz Torabi Moghadam
    • , Jonas Mattisson
    • , Chiara Rasi
    • , Hanna Davies
    • , Lars Lind
    • , Vilmantas Giedraitis
    • , Lars Lannfelt
    • , Lena Kilander
    • , Martin Ingelsson
    •  & Jan P. Dumanski
  • Editorial |

    We are inviting presubmission enquiries for Articles, Perspectives and Analyses on human, animal, plant and microbial genetics and genomics from Africa, by corresponding authors living and working in African countries, with the aim of publishing an issue of the journal devoted to African genetics.

  • Analysis |

    GeneATLAS is a web resource that presents genetic association results for 118 non-binary and 660 binary traits using UK Biobank data. This atlas allows researchers to query these results without incurring high computational costs.

    • Oriol Canela-Xandri
    • , Konrad Rawlik
    •  & Albert Tenesa
  • Article | | open

    De novo assembly of 23 Aspergillus section Nigri and 6 Aspergillus niger genome sequences allows for inter- and intraspecies comparisons and prediction of secondary metabolite gene clusters.

    • Tammi C. Vesth
    • , Jane L. Nybo
    • , Sebastian Theobald
    • , Jens C. Frisvad
    • , Thomas O. Larsen
    • , Kristian F. Nielsen
    • , Jakob B. Hoof
    • , Julian Brandl
    • , Asaf Salamov
    • , Robert Riley
    • , John M. Gladden
    • , Pallavi Phatale
    • , Morten T. Nielsen
    • , Ellen K. Lyhne
    • , Martin E. Kogle
    • , Kimchi Strasser
    • , Erin McDonnell
    • , Kerrie Barry
    • , Alicia Clum
    • , Cindy Chen
    • , Kurt LaButti
    • , Sajeet Haridas
    • , Matt Nolan
    • , Laura Sandor
    • , Alan Kuo
    • , Anna Lipzen
    • , Matthieu Hainaut
    • , Elodie Drula
    • , Adrian Tsang
    • , Jon K. Magnuson
    • , Bernard Henrissat
    • , Ad Wiebenga
    • , Blake A. Simmons
    • , Miia R. Mäkelä
    • , Ronald P. de Vries
    • , Igor V. Grigoriev
    • , Uffe H. Mortensen
    • , Scott E. Baker
    •  & Mikael R. Andersen
  • Article |

    Chromatin run-on and sequencing (ChRO-seq) is a new method that maps the location of RNA polymerase using virtually any input sample. Here, ChRO-seq is used to study nascent transcription in human glioblastoma, and to identify regulators of tumor subtype.

    • Tinyi Chu
    • , Edward J. Rice
    • , Gregory T. Booth
    • , H. Hans Salamanca
    • , Zhong Wang
    • , Leighton J. Core
    • , Sharon L. Longo
    • , Robert J. Corona
    • , Lawrence S. Chin
    • , John T. Lis
    • , Hojoong Kwak
    •  & Charles G. Danko
  • Article |

    Two hundred and eighty-five methylomes and 11,617 transcriptomes from peripheral blood samples with parent-of-origin-phased haplotypes produce a new map of imprinted methylation and gene expression patterns across the human genome.

    • Florian Zink
    • , Droplaug N. Magnusdottir
    • , Olafur T. Magnusson
    • , Nicolas J. Walker
    • , Tiffany J. Morris
    • , Asgeir Sigurdsson
    • , Gisli H. Halldorsson
    • , Sigurjon A. Gudjonsson
    • , Pall Melsted
    • , Helga Ingimundardottir
    • , Snædis Kristmundsdottir
    • , Kristjan F. Alexandersson
    • , Anna Helgadottir
    • , Julius Gudmundsson
    • , Thorunn Rafnar
    • , Ingileif Jonsdottir
    • , Hilma Holm
    • , Gudmundur Ingi Eyjolfsson
    • , Olof Sigurdardottir
    • , Isleifur Olafsson
    • , Gisli Masson
    • , Daniel F. Gudbjartsson
    • , Unnur Thorsteinsdottir
    • , Bjarni V. Halldorsson
    • , Simon N. Stacey
    •  & Kari Stefansson
  • Article |

    Targeted inactivation, restoration and overexpression of MALAT1 in multiple in vivo models demonstrate that the lncRNA MALAT1 suppresses breast cancer metastasis through binding and inactivation of the pro-metastatic transcription factor TEAD.

    • Jongchan Kim
    • , Hai-Long Piao
    • , Beom-Jun Kim
    • , Fan Yao
    • , Zhenbo Han
    • , Yumeng Wang
    • , Zhenna Xiao
    • , Ashley N. Siverly
    • , Sarah E. Lawhon
    • , Baochau N. Ton
    • , Hyemin Lee
    • , Zhicheng Zhou
    • , Boyi Gan
    • , Shinichi Nakagawa
    • , Matthew J. Ellis
    • , Han Liang
    • , Mien-Chie Hung
    • , M. James You
    • , Yutong Sun
    •  & Li Ma
  • Letter |

    A mapping approach that screens mutants in a sterile interspecific hybrid identifies the genetic determinants of differences in high-temperature growth between divergent Saccharomyces cerevisiae and Saccharomyces paradoxus yeast species.

    • Carly V. Weiss
    • , Jeremy I. Roop
    • , Rylee K. Hackley
    • , Julie N. Chuong
    • , Igor V. Grigoriev
    • , Adam P. Arkin
    • , Jeffrey M. Skerker
    •  & Rachel B. Brem
  • Analysis |

    The authors extend stratified linkage disequilibrium score regression to partition the heritability of both low-frequency and common variants in 40 heritable traits from the UK Biobank, providing insights into low-frequency and rare variant functional architectures.

    • Steven Gazal
    • , Po-Ru Loh
    • , Hilary K. Finucane
    • , Andrea Ganna
    • , Armin Schoech
    • , Shamil Sunyaev
    •  & Alkes L. Price
  • Article |

    Combining 32 genome-wide association studies with high-density imputation provides a comprehensive view of the genetic contribution to type 2 diabetes in individuals of European ancestry with respect to locus discovery, causal-variant resolution, and mechanistic insight.

    • Anubha Mahajan
    • , Daniel Taliun
    • , Matthias Thurner
    • , Neil R. Robertson
    • , Jason M. Torres
    • , N. William Rayner
    • , Anthony J. Payne
    • , Valgerdur Steinthorsdottir
    • , Robert A. Scott
    • , Niels Grarup
    • , James P. Cook
    • , Ellen M. Schmidt
    • , Matthias Wuttke
    • , Chloé Sarnowski
    • , Reedik Mägi
    • , Jana Nano
    • , Christian Gieger
    • , Stella Trompet
    • , Cécile Lecoeur
    • , Michael H. Preuss
    • , Bram Peter Prins
    • , Xiuqing Guo
    • , Lawrence F. Bielak
    • , Jennifer E. Below
    • , Donald W. Bowden
    • , John Campbell Chambers
    • , Young Jin Kim
    • , Maggie C. Y. Ng
    • , Lauren E. Petty
    • , Xueling Sim
    • , Weihua Zhang
    • , Amanda J. Bennett
    • , Jette Bork-Jensen
    • , Chad M. Brummett
    • , Mickaël Canouil
    • , Kai-Uwe Ec kardt
    • , Krista Fischer
    • , Sharon L. R. Kardia
    • , Florian Kronenberg
    • , Kristi Läll
    • , Ching-Ti Liu
    • , Adam E. Locke
    • , Jian’an Luan
    • , Ioanna Ntalla
    • , Vibe Nylander
    • , Sebastian Schönherr
    • , Claudia Schurmann
    • , Loïc Yengo
    • , Erwin P. Bottinger
    • , Ivan Brandslund
    • , Cramer Christensen
    • , George Dedoussis
    • , Jose C. Florez
    • , Ian Ford
    • , Oscar H. Franco
    • , Timothy M. Frayling
    • , Vilmantas Giedraitis
    • , Sophie Hackinger
    • , Andrew T. Hattersley
    • , Christian Herder
    • , M. Arfan Ikram
    • , Martin Ingelsson
    • , Marit E. Jørgensen
    • , Torben Jørgensen
    • , Jennifer Kriebel
    • , Johanna Kuusisto
    • , Symen Ligthart
    • , Cecilia M. Lindgren
    • , Allan Linneberg
    • , Valeriya Lyssenko
    • , Vasiliki Mamakou
    • , Thomas Meitinger
    • , Karen L. Mohlke
    • , Andrew D. Morris
    • , Girish Nadkarni
    • , James S. Pankow
    • , Annette Peters
    • , Naveed Sattar
    • , Alena Stančáková
    • , Konstantin Strauch
    • , Kent D. Taylor
    • , Barbara Thorand
    • , Gudmar Thorleifsson
    • , Unnur Thorsteinsdottir
    • , Jaakko Tuomilehto
    • , Daniel R. Witte
    • , Josée Dupuis
    • , Patricia A. Peyser
    • , Eleftheria Zeggini
    • , Ruth J. F. Loos
    • , Philippe Froguel
    • , Erik Ingelsson
    • , Lars Lind
    • , Leif Groop
    • , Markku Laakso
    • , Francis S. Collins
    • , J. Wouter Jukema
    • , Colin N. A. Palmer
    • , Harald Grallert
    • , Andres Metspalu
    • , Abbas Dehghan
    • , Anna Köttgen
    • , Goncalo R. Abecasis
    • , James B. Meigs
    • , Jerome I. Rotter
    • , Jonathan Marchini
    • , Oluf Pedersen
    • , Torben Hansen
    • , Claudia Langenberg
    • , Nicholas J. Wareham
    • , Kari Stefansson
    • , Anna L. Gloyn
    • , Andrew P. Morris
    • , Michael Boehnke
    •  & Mark I. McCarthy
  • Article | | open

    Sequencing of haploid sugarcane, Saccharum spontaneum, allows assembly of a prototypical version of the sugarcane chromosome set. This new reference genome will serve as a resource to accelerate sugarcane improvement.

    • Jisen Zhang
    • , Xingtan Zhang
    • , Haibao Tang
    • , Qing Zhang
    • , Xiuting Hua
    • , Xiaokai Ma
    • , Fan Zhu
    • , Tyler Jones
    • , Xinguang Zhu
    • , John Bowers
    • , Ching Man Wai
    • , Chunfang Zheng
    • , Yan Shi
    • , Shuai Chen
    • , Xiuming Xu
    • , Jingjing Yue
    • , David R. Nelson
    • , Lixian Huang
    • , Zhen Li
    • , Huimin Xu
    • , Dong Zhou
    • , Yongjun Wang
    • , Weichang Hu
    • , Jishan Lin
    • , Youjin Deng
    • , Neha Pandey
    • , Melina Mancini
    • , Dessireé Zerpa
    • , Julie K. Nguyen
    • , Liming Wang
    • , Liang Yu
    • , Yinghui Xin
    • , Liangfa Ge
    • , Jie Arro
    • , Jennifer O. Han
    • , Setu Chakrabarty
    • , Marija Pushko
    • , Wenping Zhang
    • , Yanhong Ma
    • , Panpan Ma
    • , Mingju Lv
    • , Faming Chen
    • , Guangyong Zheng
    • , Jingsheng Xu
    • , Zhenhui Yang
    • , Fang Deng
    • , Xuequn Chen
    • , Zhenyang Liao
    • , Xunxiao Zhang
    • , Zhicong Lin
    • , Hai Lin
    • , Hansong Yan
    • , Zheng Kuang
    • , Weimin Zhong
    • , Pingping Liang
    • , Guofeng Wang
    • , Yuan Yuan
    • , Jiaxian Shi
    • , Jinxiang Hou
    • , Jingxian Lin
    • , Jingjing Jin
    • , Peijian Cao
    • , Qiaochu Shen
    • , Qing Jiang
    • , Ping Zhou
    • , Yaying Ma
    • , Xiaodan Zhang
    • , Rongrong Xu
    • , Juan Liu
    • , Yongmei Zhou
    • , Haifeng Jia
    • , Qing Ma
    • , Rui Qi
    • , Zhiliang Zhang
    • , Jingping Fang
    • , Hongkun Fang
    • , Jinjin Song
    • , Mengjuan Wang
    • , Guangrui Dong
    • , Gang Wang
    • , Zheng Chen
    • , Teng Ma
    • , Hong Liu
    • , Singha R. Dhungana
    • , Sarah E. Huss
    • , Xiping Yang
    • , Anupma Sharma
    • , Jhon H. Trujillo
    • , Maria C. Martinez
    • , Matthew Hudson
    • , John J. Riascos
    • , Mary Schuler
    • , Li-Qing Chen
    • , David M. Braun
    • , Lei Li
    • , Qingyi Yu
    • , Jianping Wang
    • , Kai Wang
    • , Michael C. Schatz
    • , David Heckerman
    • , Marie-Anne Van Sluys
    • , Glaucia Mendes Souza
    • , Paul H. Moore
    • , David Sankoff
    • , Robert VanBuren
    • , Andrew H. Paterson
    • , Chifumi Nagai
    •  & Ray Ming
  • News & Views |

    The availability of various public resources has hastened the discovery of type 2 diabetes–associated loci in the largest genome-wide association study of the disease reported to date. In addition, these resources have also enabled researchers to get closer to determining the culprit genetic variants and therefore closer to the target effector genes driving these associations.

    • Diana L. Cousminer
    •  & Struan F. A. Grant
  • Analysis |

    Analysis of mRNA splicing in the dorsolateral prefrontal cortex from two cohorts established to study aging identifies variations in pre-mRNA splicing events that are associated with Alzheimer’s disease.

    • Towfique Raj
    • , Yang I. Li
    • , Garrett Wong
    • , Jack Humphrey
    • , Minghui Wang
    • , Satesh Ramdhani
    • , Ying-Chih Wang
    • , Bernard Ng
    • , Ishaan Gupta
    • , Vahram Haroutunian
    • , Eric E. Schadt
    • , Tracy Young-Pearse
    • , Sara Mostafavi
    • , Bin Zhang
    • , Pamela Sklar
    • , David A. Bennett
    •  & Philip L. De Jager
  • Publisher Correction |

    • Joshua C. Stein
    • , Yeisoo Yu
    • , Dario Copetti
    • , Derrick J. Zwickl
    • , Li Zhang
    • , Chengjun Zhang
    • , Kapeel Chougule
    • , Dongying Gao
    • , Aiko Iwata
    • , Jose Luis Goicoechea
    • , Sharon Wei
    • , Jun Wang
    • , Yi Liao
    • , Muhua Wang
    • , Julie Jacquemin
    • , Claude Becker
    • , Dave Kudrna
    • , Jianwei Zhang
    • , Carlos E. M. Londono
    • , Xiang Song
    • , Seunghee Lee
    • , Paul Sanchez
    • , Andrea Zuccolo
    • , Jetty S. S. Ammiraju
    • , Jayson Talag
    • , Ann Danowitz
    • , Luis F. Rivera
    • , Andrea R. Gschwend
    • , Christos Noutsos
    • , Cheng-chieh Wu
    • , Shu-min Kao
    • , Jhih-wun Zeng
    • , Fu-jin Wei
    • , Qiang Zhao
    • , Qi Feng
    • , Moaine El Baidouri
    • , Marie-Christine Carpentier
    • , Eric Lasserre
    • , Richard Cooke
    • , Daniel da Rosa Farias
    • , Luciano Carlos da Maia
    • , Railson S. dos Santos
    • , Kevin G. Nyberg
    • , Kenneth L. McNally
    • , Ramil Mauleon
    • , Nickolai Alexandrov
    • , Jeremy Schmutz
    • , Dave Flowers
    • , Chuanzhu Fan
    • , Detlef Weigel
    • , Kshirod K. Jena
    • , Thomas Wicker
    • , Mingsheng Chen
    • , Bin Han
    • , Robert Henry
    • , Yue-ie C. Hsing
    • , Nori Kurata
    • , Antonio Costa de Oliveira
    • , Olivier Panaud
    • , Scott A. Jackson
    • , Carlos A. Machado
    • , Michael J. Sanderson
    • , Manyuan Long
    • , Doreen Ware
    •  & Rod A. Wing
  • Article |

    Analysis of genetic data and blood lipid measurements from over 300,000 participants in the Million Veteran Program identifies new associations for blood lipid traits.

    • Derek Klarin
    • , Scott M. Damrauer
    • , Kelly Cho
    • , Yan V. Sun
    • , Tanya M. Teslovich
    • , Jacqueline Honerlaw
    • , David R. Gagnon
    • , Scott L. DuVall
    • , Jin Li
    • , Gina M. Peloso
    • , Mark Chaffin
    • , Aeron M. Small
    • , Jie Huang
    • , Hua Tang
    • , Julie A. Lynch
    • , Yuk-Lam Ho
    • , Dajiang J. Liu
    • , Connor A. Emdin
    • , Alexander H. Li
    • , Jennifer E. Huffman
    • , Jennifer S. Lee
    • , Pradeep Natarajan
    • , Rajiv Chowdhury
    • , Danish Saleheen
    • , Marijana Vujkovic
    • , Aris Baras
    • , Saiju Pyarajan
    • , Emanuele Di Angelantonio
    • , Benjamin M. Neale
    • , Aliya Naheed
    • , Amit V. Khera
    • , John Danesh
    • , Kyong-Mi Chang
    • , Gonçalo Abecasis
    • , Cristen Willer
    • , Frederick E. Dewey
    • , David J. Carey
    • , John Concato
    • , J. Michael Gaziano
    • , Christopher J. O’Donnell
    • , Philip S. Tsao
    • , Sekar Kathiresan
    • , Daniel J. Rader
    • , Peter W. F. Wilson
    •  & Themistocles L. Assimes
  • Article | | open

    Sequence assemblies for the genomes of 16 widely used inbred laboratory mouse strains highlight considerable strain-specific haplotype variation and allow for the identification of regions with the greatest sequence diversity between strains.

    • Jingtao Lilue
    • , Anthony G. Doran
    • , Ian T. Fiddes
    • , Monica Abrudan
    • , Joel Armstrong
    • , Ruth Bennett
    • , William Chow
    • , Joanna Collins
    • , Stephan Collins
    • , Anne Czechanski
    • , Petr Danecek
    • , Mark Diekhans
    • , Dirk-Dominik Dolle
    • , Matt Dunn
    • , Richard Durbin
    • , Dent Earl
    • , Anne Ferguson-Smith
    • , Paul Flicek
    • , Jonathan Flint
    • , Adam Frankish
    • , Beiyuan Fu
    • , Mark Gerstein
    • , James Gilbert
    • , Leo Goodstadt
    • , Jennifer Harrow
    • , Kerstin Howe
    • , Ximena Ibarra-Soria
    • , Mikhail Kolmogorov
    • , Chris J. Lelliott
    • , Darren W. Logan
    • , Jane Loveland
    • , Clayton E. Mathews
    • , Richard Mott
    • , Paul Muir
    • , Stefanie Nachtweide
    • , Fabio C. P. Navarro
    • , Duncan T. Odom
    • , Naomi Park
    • , Sarah Pelan
    • , Son K. Pham
    • , Mike Quail
    • , Laura Reinholdt
    • , Lars Romoth
    • , Lesley Shirley
    • , Cristina Sisu
    • , Marcela Sjoberg-Herrera
    • , Mario Stanke
    • , Charles Steward
    • , Mark Thomas
    • , Glen Threadgold
    • , David Thybert
    • , James Torrance
    • , Kim Wong
    • , Jonathan Wood
    • , Binnaz Yalcin
    • , Fengtang Yang
    • , David J. Adams
    • , Benedict Paten
    •  & Thomas M. Keane
  • Perspective |

    • Marc A. Marti-Renom
    • , Genevieve Almouzni
    • , Wendy A. Bickmore
    • , Kerstin Bystricky
    • , Giacomo Cavalli
    • , Peter Fraser
    • , Susan M. Gasser
    • , Luca Giorgetti
    • , Edith Heard
    • , Mario Nicodemi
    • , Marcelo Nollmann
    • , Modesto Orozco
    • , Ana Pombo
    •  & Maria-Elena Torres-Padilla
  • Article |

    A Pitx1 enhancer shows activity in forelimbs and hindlimbs but only interacts with Pitx1 in hindlimbs because of its three-dimensional configuration. Structural variants that affect three-dimensional conformation induce Pitx1 expression in forelimbs and cause partial arm-to-leg transformation in mice and humans.

    • Bjørt K. Kragesteen
    • , Malte Spielmann
    • , Christina Paliou
    • , Verena Heinrich
    • , Robert Schöpflin
    • , Andrea Esposito
    • , Carlo Annunziatella
    • , Simona Bianco
    • , Andrea M. Chiariello
    • , Ivana Jerković
    • , Izabela Harabula
    • , Philine Guckelberger
    • , Michael Pechstein
    • , Lars Wittler
    • , Wing-Lee Chan
    • , Martin Franke
    • , Darío G. Lupiáñez
    • , Katerina Kraft
    • , Bernd Timmermann
    • , Martin Vingron
    • , Axel Visel
    • , Mario Nicodemi
    • , Stefan Mundlos
    •  & Guillaume Andrey
  • Editorial |

    A number of journalistic reports over the last year have drawn attention to dismaying trends in maternal and fetal health in the United States, particularly among African Americans. This public health crisis highlights the need for research into the genetic basis of maternal–fetal health and consideration of the genetic risk factors and exposures of women and children in diverse populations more broadly.

  • Article |

    Analysis of genomic and transcriptomic data from 462 patient-derived tumor cell (PDC) samples across 14 cancer types, along with pharmacological responses to 60 agents, indicates that PDC-derived drug sensitivities might be predictive of clinical response to targeted therapies.

    • Jin-Ku Lee
    • , Zhaoqi Liu
    • , Jason K. Sa
    • , Sang Shin
    • , Jiguang Wang
    • , Mykola Bordyuh
    • , Hee Jin Cho
    • , Oliver Elliott
    • , Timothy Chu
    • , Seung Won Choi
    • , Daniel I. S. Rosenbloom
    • , In-Hee Lee
    • , Yong Jae Shin
    • , Hyun Ju Kang
    • , Donggeon Kim
    • , Sun Young Kim
    • , Moon-Hee Sim
    • , Jusun Kim
    • , Taehyang Lee
    • , Yun Jee Seo
    • , Hyemi Shin
    • , Mijeong Lee
    • , Sung Heon Kim
    • , Yong-Jun Kwon
    • , Jeong-Woo Oh
    • , Minsuk Song
    • , Misuk Kim
    • , Doo-Sik Kong
    • , Jung Won Choi
    • , Ho Jun Seol
    • , Jung-Il Lee
    • , Seung Tae Kim
    • , Joon Oh Park
    • , Kyoung-Mee Kim
    • , Sang-Yong Song
    • , Jeong-Won Lee
    • , Hee-Cheol Kim
    • , Jeong Eon Lee
    • , Min Gew Choi
    • , Sung Wook Seo
    • , Young Mog Shim
    • , Jae Ill Zo
    • , Byong Chang Jeong
    • , Yeup Yoon
    • , Gyu Ha Ryu
    • , Nayoung K. D. Kim
    • , Joon Seol Bae
    • , Woong-Yang Park
    • , Jeongwu Lee
    • , Roel G. W. Verhaak
    • , Antonio Iavarone
    • , Jeeyun Lee
    • , Raul Rabadan
    •  & Do-Hyun Nam