Latest Research

  • Article |

    A massively parallel reporter assay (eSTARR-seq) shows that gene-distal transcription start sites can delineate active enhancers with higher resolution than histone modifications.

    • Nathaniel D. Tippens
    • , Jin Liang
    • , Alden King-Yung Leung
    • , Shayne D. Wierbowski
    • , Abdullah Ozer
    • , James G. Booth
    • , John T. Lis
    •  & Haiyuan Yu
  • Author Correction |

    • Valeria Orrù
    • , Maristella Steri
    • , Carlo Sidore
    • , Michele Marongiu
    • , Valentina Serra
    • , Stefania Olla
    • , Gabriella Sole
    • , Sandra Lai
    • , Mariano Dei
    • , Antonella Mulas
    • , Francesca Virdis
    • , Maria Grazia Piras
    • , Monia Lobina
    • , Mara Marongiu
    • , Maristella Pitzalis
    • , Francesca Deidda
    • , Annalisa Loizedda
    • , Stefano Onano
    • , Magdalena Zoledziewska
    • , Stephen Sawcer
    • , Marcella Devoto
    • , Myriam Gorospe
    • , Gonçalo R. Abecasis
    • , Matteo Floris
    • , Mauro Pala
    • , David Schlessinger
    • , Edoardo Fiorillo
    •  & Francesco Cucca
  • Perspective |

    This Perspective discusses important aspects of data generation, infrastructure and management that affect how the research community uses medical data, including genetic and genomic information.

    • Amalio Telenti
    •  & Xiaoqian Jiang
  • Article |

    An analysis of 3,757 Sardinian genomes identifies 122 association signals for 459 immune cell traits at 69 loci. Some variants are associated with autoimmune disorders.

    • Valeria Orrù
    • , Maristella Steri
    • , Carlo Sidore
    • , Michele Marongiu
    • , Valentina Serra
    • , Stefania Olla
    • , Gabriella Sole
    • , Sandra Lai
    • , Mariano Dei
    • , Antonella Mulas
    • , Francesca Virdis
    • , Maria Grazia Piras
    • , Monia Lobina
    • , Mara Marongiu
    • , Maristella Pitzalis
    • , Francesca Deidda
    • , Annalisa Loizedda
    • , Stefano Onano
    • , Magdalena Zoledziewska
    • , Stephen Sawcer
    • , Marcella Devoto
    • , Myriam Gorospe
    • , Gonçalo R. Abecasis
    • , Matteo Floris
    • , Mauro Pala
    • , David Schlessinger
    • , Edoardo Fiorillo
    •  & Francesco Cucca
  • Article |

    Mathematical modeling of evolutionary dynamics of neoantigens and immune escape in growing tumors shows that strong negative selection for neoantigens inhibits tumor growth but also provides a strong selective pressure for the evolution of immune escape.

    • Eszter Lakatos
    • , Marc J. Williams
    • , Ryan O. Schenck
    • , William C. H. Cross
    • , Jacob Househam
    • , Luis Zapata
    • , Benjamin Werner
    • , Chandler Gatenbee
    • , Mark Robertson-Tessi
    • , Chris P. Barnes
    • , Alexander R. A. Anderson
    • , Andrea Sottoriva
    •  & Trevor A. Graham
  • Author Correction |

    • Anton G. Henssen
    • , Richard Koche
    • , Jiali Zhuang
    • , Eileen Jiang
    • , Casie Reed
    • , Amy Eisenberg
    • , Eric Still
    • , Ian C. MacArthur
    • , Elias Rodríguez-Fos
    • , Santiago Gonzalez
    • , Montserrat Puiggròs
    • , Andrew N. Blackford
    • , Christopher E. Mason
    • , Elisa de Stanchina
    • , Mithat Gönen
    • , Anne-Katrin Emde
    • , Minita Shah
    • , Kanika Arora
    • , Catherine Reeves
    • , Nicholas D. Socci
    • , Elizabeth Perlman
    • , Cristina R. Antonescu
    • , Charles W. M. Roberts
    • , Hanno Steen
    • , Elizabeth Mullen
    • , Stephen P. Jackson
    • , David Torrents
    • , Zhiping Weng
    • , Scott A. Armstrong
    •  & Alex Kentsis
  • Analysis |

    Mendelian randomization (MR) and colocalization analyses are used to estimate causal effects of 1,002 plasma proteins on 225 phenotypes. Evidence from drug developmental programs shows that target-indication pairs with MR and colocalization support were more likely to be approved, highlighting the value of this approach for prioritizing therapeutic targets.

    • Jie Zheng
    • , Valeriia Haberland
    • , Denis Baird
    • , Venexia Walker
    • , Philip C. Haycock
    • , Mark R. Hurle
    • , Alex Gutteridge
    • , Pau Erola
    • , Yi Liu
    • , Shan Luo
    • , Jamie Robinson
    • , Tom G. Richardson
    • , James R. Staley
    • , Benjamin Elsworth
    • , Stephen Burgess
    • , Benjamin B. Sun
    • , John Danesh
    • , Heiko Runz
    • , Joseph C. Maranville
    • , Hannah M. Martin
    • , James Yarmolinsky
    • , Charles Laurin
    • , Michael V. Holmes
    • , Jimmy Z. Liu
    • , Karol Estrada
    • , Rita Santos
    • , Linda McCarthy
    • , Dawn Waterworth
    • , Matthew R. Nelson
    • , George Davey Smith
    • , Adam S. Butterworth
    • , Gibran Hemani
    • , Robert A. Scott
    •  & Tom R. Gaunt
  • Author Correction |

    • Andrea Lunardi
    • , Ugo Ala
    • , Mirjam T. Epping
    • , Leonardo Salmena
    • , John G. Clohessy
    • , Kaitlyn A. Webster
    • , Guocan Wang
    • , Roberta Mazzucchelli
    • , Maristella Bianconi
    • , Edward C. Stack
    • , Rosina Lis
    • , Akash Patnaik
    • , Lewis C. Cantley
    • , Glenn Bubley
    • , Carlos Cordon-Cardo
    • , William L. Gerald
    • , Rodolfo Montironi
    • , Sabina Signoretti
    • , Massimo Loda
    • , Caterina Nardella
    •  & Pier Paolo Pandolfi
  • Article |

    MOBSTER is an approach for subclonal reconstruction of tumors from cancer genomics data on the basis of models that combine machine learning with evolutionary theory, thus leading to more accurate evolutionary histories of tumors.

    • Giulio Caravagna
    • , Timon Heide
    • , Marc J. Williams
    • , Luis Zapata
    • , Daniel Nichol
    • , Ketevan Chkhaidze
    • , William Cross
    • , George D. Cresswell
    • , Benjamin Werner
    • , Ahmet Acar
    • , Louis Chesler
    • , Chris P. Barnes
    • , Guido Sanguinetti
    • , Trevor A. Graham
    •  & Andrea Sottoriva
  • Article |

    Insertion of a tissue-invariant chromatin domain boundary into 16 ectopic loci leads to various structural phenotypes, which depend on local chromatin features, CTCF binding and transcriptional status.

    • Di Zhang
    • , Peng Huang
    • , Malini Sharma
    • , Cheryl A. Keller
    • , Belinda Giardine
    • , Haoyue Zhang
    • , Thomas G. Gilgenast
    • , Jennifer E. Phillips-Cremins
    • , Ross C. Hardison
    •  & Gerd A. Blobel
  • Letter |

    LSD1 promotes FOXA1 chromatin binding by demethylating lysine 270 of FOXA1 in prostate cancer cells. LSD1 inhibition decreases growth of prostate cancer cells.

    • Shuai Gao
    • , Sujun Chen
    • , Dong Han
    • , Zifeng Wang
    • , Muqing Li
    • , Wanting Han
    • , Anna Besschetnova
    • , Mingyu Liu
    • , Feng Zhou
    • , David Barrett
    • , My Phu Luong
    • , Jude Owiredu
    • , Yi Liang
    • , Musaddeque Ahmed
    • , Jessica Petricca
    • , Susan Patalano
    • , Jill A. Macoska
    • , Eva Corey
    • , Sen Chen
    • , Steven P. Balk
    • , Housheng Hansen He
    •  & Changmeng Cai
  • Technical Report |

    STAAR is a powerful rare variant association test that incorporates variant functional categories and complementary functional annotations using a dynamic weighting scheme based on annotation principal components. STAAR accounts for population structure and relatedness and is scalable for analyzing large whole-genome sequencing studies.

    • Xihao Li
    • , Zilin Li
    • , Hufeng Zhou
    • , Sheila M. Gaynor
    • , Yaowu Liu
    • , Han Chen
    • , Ryan Sun
    • , Rounak Dey
    • , Donna K. Arnett
    • , Stella Aslibekyan
    • , Christie M. Ballantyne
    • , Lawrence F. Bielak
    • , John Blangero
    • , Eric Boerwinkle
    • , Donald W. Bowden
    • , Jai G. Broome
    • , Matthew P. Conomos
    • , Adolfo Correa
    • , L. Adrienne Cupples
    • , Joanne E. Curran
    • , Barry I. Freedman
    • , Xiuqing Guo
    • , George Hindy
    • , Marguerite R. Irvin
    • , Sharon L. R. Kardia
    • , Sekar Kathiresan
    • , Alyna T. Khan
    • , Charles L. Kooperberg
    • , Cathy C. Laurie
    • , X. Shirley Liu
    • , Michael C. Mahaney
    • , Ani W. Manichaikul
    • , Lisa W. Martin
    • , Rasika A. Mathias
    • , Stephen T. McGarvey
    • , Braxton D. Mitchell
    • , May E. Montasser
    • , Jill E. Moore
    • , Alanna C. Morrison
    • , Jeffrey R. O’Connell
    • , Nicholette D. Palmer
    • , Akhil Pampana
    • , Juan M. Peralta
    • , Patricia A. Peyser
    • , Bruce M. Psaty
    • , Susan Redline
    • , Kenneth M. Rice
    • , Stephen S. Rich
    • , Jennifer A. Smith
    • , Hemant K. Tiwari
    • , Michael Y. Tsai
    • , Ramachandran S. Vasan
    • , Fei Fei Wang
    • , Daniel E. Weeks
    • , Zhiping Weng
    • , James G. Wilson
    • , Lisa R. Yanek
    • , Namiko Abe
    • , Gonçalo R. Abecasis
    • , Francois Aguet
    • , Christine Albert
    • , Laura Almasy
    • , Alvaro Alonso
    • , Seth Ament
    • , Peter Anderson
    • , Pramod Anugu
    • , Deborah Applebaum-Bowden
    • , Kristin Ardlie
    • , Dan Arking
    • , Donna K. Arnett
    • , Allison Ashley-Koch
    • , Stella Aslibekyan
    • , Tim Assimes
    • , Paul Auer
    • , Dimitrios Avramopoulos
    • , John Barnard
    • , Kathleen Barnes
    • , R. Graham Barr
    • , Emily Barron-Casella
    • , Lucas Barwick
    • , Terri Beaty
    • , Gerald Beck
    • , Diane Becker
    • , Lewis Becker
    • , Rebecca Beer
    • , Amber Beitelshees
    • , Emelia Benjamin
    • , Takis Benos
    • , Marcos Bezerra
    • , Lawrence F. Bielak
    • , Joshua Bis
    • , Thomas Blackwell
    • , John Blangero
    • , Eric Boerwinkle
    • , Donald W. Bowden
    • , Russell Bowler
    • , Jennifer Brody
    • , Ulrich Broeckel
    • , Jai G. Broome
    • , Karen Bunting
    • , Esteban Burchard
    • , Carlos Bustamante
    • , Erin Buth
    • , Brian Cade
    • , Jonathan Cardwell
    • , Vincent Carey
    • , Cara Carty
    • , Richard Casaburi
    • , James Casella
    • , Peter Castaldi
    • , Mark Chaffin
    • , Christy Chang
    • , Yi-Cheng Chang
    • , Daniel Chasman
    • , Sameer Chavan
    • , Bo-Juen Chen
    • , Wei-Min Chen
    • , Yii-Der Ida Chen
    • , Michael Cho
    • , Seung Hoan Choi
    • , Lee-Ming Chuang
    • , Mina Chung
    • , Ren-Hua Chung
    • , Clary Clish
    • , Suzy Comhair
    • , Matthew P. Conomos
    • , Elaine Cornell
    • , Adolfo Correa
    • , Carolyn Crandall
    • , James Crapo
    • , L. Adrienne Cupples
    • , Joanne E. Curran
    • , Jeffrey Curtis
    • , Brian Custer
    • , Coleen Damcott
    • , Dawood Darbar
    • , Sayantan Das
    • , Sean David
    • , Colleen Davis
    • , Michelle Daya
    • , Mariza de Andrade
    • , Lisa de las Fuentes
    • , Michael DeBaun
    • , Ranjan Deka
    • , Dawn DeMeo
    • , Scott Devine
    • , Qing Duan
    • , Ravi Duggirala
    • , Jon Peter Durda
    • , Susan Dutcher
    • , Charles Eaton
    • , Lynette Ekunwe
    • , Adel El Boueiz
    • , Patrick Ellinor
    • , Leslie Emery
    • , Serpil Erzurum
    • , Charles Farber
    • , Tasha Fingerlin
    • , Matthew Flickinger
    • , Myriam Fornage
    • , Nora Franceschini
    • , Chris Frazar
    • , Mao Fu
    • , Stephanie M. Fullerton
    • , Lucinda Fulton
    • , Stacey Gabriel
    • , Weiniu Gan
    • , Shanshan Gao
    • , Yan Gao
    • , Margery Gass
    • , Bruce Gelb
    • , Xiaoqi (Priscilla) Geng
    • , Mark Geraci
    • , Soren Germer
    • , Robert Gerszten
    • , Auyon Ghosh
    • , Richard Gibbs
    • , Chris Gignoux
    • , Mark Gladwin
    • , David Glahn
    • , Stephanie Gogarten
    • , Da-Wei Gong
    • , Harald Goring
    • , Sharon Graw
    • , Daniel Grine
    • , C. Charles Gu
    • , Yue Guan
    • , Xiuqing Guo
    • , Namrata Gupta
    • , Jeff Haessler
    • , Michael Hall
    • , Daniel Harris
    • , Nicola L. Hawley
    • , Jiang He
    • , Susan Heckbert
    • , Ryan Hernandez
    • , David Herrington
    • , Craig Hersh
    • , Bertha Hidalgo
    • , James Hixson
    • , Brian Hobbs
    • , John Hokanson
    • , Elliott Hong
    • , Karin Hoth
    • , Chao (Agnes) Hsiung
    • , Yi-Jen Hung
    • , Haley Huston
    • , Chii Min Hwu
    • , Marguerite R. Irvin
    • , Rebecca Jackson
    • , Deepti Jain
    • , Cashell Jaquish
    • , Min A. Jhun
    • , Jill Johnsen
    • , Andrew Johnson
    • , Craig Johnson
    • , Rich Johnston
    • , Kimberly Jones
    • , Hyun Min Kang
    • , Robert Kaplan
    • , Sharon L. R. Kardia
    • , Sekar Kathiresan
    • , Shannon Kelly
    • , Eimear Kenny
    • , Michael Kessler
    • , Alyna T. Khan
    • , Wonji Kim
    • , Greg Kinney
    • , Barbara Konkle
    • , Charles L. Kooperberg
    • , Holly Kramer
    • , Christoph Lange
    • , Ethan Lange
    • , Leslie Lange
    • , Cathy C. Laurie
    • , Cecelia Laurie
    • , Meryl LeBoff
    • , Jiwon Lee
    • , Seunggeun Shawn Lee
    • , Wen-Jane Lee
    • , Jonathon LeFaive
    • , David Levine
    • , Dan Levy
    • , Joshua Lewis
    • , Xiaohui Li
    • , Yun Li
    • , Henry Lin
    • , Honghuang Lin
    • , Keng Han Lin
    • , Xihong Lin
    • , Simin Liu
    • , Yongmei Liu
    • , Yu Liu
    • , Ruth J. F. Loos
    • , Steven Lubitz
    • , Kathryn Lunetta
    • , James Luo
    • , Michael C. Mahaney
    • , Barry Make
    • , Ani W. Manichaikul
    • , JoAnn Manson
    • , Lauren Margolin
    • , Lisa W. Martin
    • , Susan Mathai
    • , Rasika A. Mathias
    • , Susanne May
    • , Patrick McArdle
    • , Merry-Lynn McDonald
    • , Sean McFarland
    • , Stephen T. McGarvey
    • , Daniel McGoldrick
    • , Caitlin McHugh
    • , Hao Mei
    • , Luisa Mestroni
    • , Deborah A. Meyers
    • , Julie Mikulla
    • , Nancy Min
    • , Mollie Minear
    • , Ryan L. Minster
    • , Braxton D. Mitchell
    • , Matt Moll
    • , May E. Montasser
    • , Courtney Montgomery
    • , Arden Moscati
    • , Solomon Musani
    • , Stanford Mwasongwe
    • , Josyf C. Mychaleckyj
    • , Girish Nadkarni
    • , Rakhi Naik
    • , Take Naseri
    • , Pradeep Natarajan
    • , Sergei Nekhai
    • , Sarah C. Nelson
    • , Bonnie Neltner
    • , Deborah Nickerson
    • , Kari North
    • , Jeffrey R. O’Connell
    • , Tim O’Connor
    • , Heather Ochs-Balcom
    • , David Paik
    • , Nicholette D. Palmer
    • , James Pankow
    • , George Papanicolaou
    • , Afshin Parsa
    • , Juan M. Peralta
    • , Marco Perez
    • , James Perry
    • , Ulrike Peters
    • , Patricia A. Peyser
    • , Lawrence S. Phillips
    • , Toni Pollin
    • , Wendy Post
    • , Julia Powers Becker
    • , Meher Preethi Boorgula
    • , Michael Preuss
    • , Bruce M. Psaty
    • , Pankaj Qasba
    • , Dandi Qiao
    • , Zhaohui Qin
    • , Nicholas Rafaels
    • , Laura Raffield
    • , Ramachandran S. Vasan
    • , D. C. Rao
    • , Laura Rasmussen-Torvik
    • , Aakrosh Ratan
    • , Susan Redline
    • , Robert Reed
    • , Elizabeth Regan
    • , Alex Reiner
    • , Muagututi‘a Sefuiva Reupena
    • , Kenneth M. Rice
    • , Stephen S. Rich
    • , Dan Roden
    • , Carolina Roselli
    • , Jerome I. Rotter
    • , Ingo Ruczinski
    • , Pamela Russell
    • , Sarah Ruuska
    • , Kathleen Ryan
    • , Ester Cerdeira Sabino
    • , Danish Saleheen
    • , Shabnam Salimi
    • , Steven Salzberg
    • , Kevin Sandow
    • , Vijay G. Sankaran
    • , Christopher Scheller
    • , Ellen Schmidt
    • , Karen Schwander
    • , David Schwartz
    • , Frank Sciurba
    • , Christine Seidman
    • , Jonathan Seidman
    • , Vivien Sheehan
    • , Stephanie L. Sherman
    • , Amol Shetty
    • , Aniket Shetty
    • , Wayne Hui-Heng Sheu
    • , M. Benjamin Shoemaker
    • , Brian Silver
    • , Edwin Silverman
    • , Jennifer A. Smith
    • , Josh Smith
    • , Nicholas Smith
    • , Tanja Smith
    • , Sylvia Smoller
    • , Beverly Snively
    • , Michael Snyder
    • , Tamar Sofer
    • , Nona Sotoodehnia
    • , Adrienne M. Stilp
    • , Garrett Storm
    • , Elizabeth Streeten
    • , Jessica Lasky Su
    • , Yun Ju Sung
    • , Jody Sylvia
    • , Adam Szpiro
    • , Carole Sztalryd
    • , Daniel Taliun
    • , Hua Tang
    • , Margaret Taub
    • , Kent D. Taylor
    • , Matthew Taylor
    • , Simeon Taylor
    • , Marilyn Telen
    • , Timothy A. Thornton
    • , Machiko Threlkeld
    • , Lesley Tinker
    • , David Tirschwell
    • , Sarah Tishkoff
    • , Hemant K. Tiwari
    • , Catherine Tong
    • , Russell Tracy
    • , Michael Y. Tsai
    • , Dhananjay Vaidya
    • , David Van Den Berg
    • , Peter VandeHaar
    • , Scott Vrieze
    • , Tarik Walker
    • , Robert Wallace
    • , Avram Walts
    • , Fei Fei Wang
    • , Heming Wang
    • , Karol Watson
    • , Daniel E. Weeks
    • , Bruce Weir
    • , Scott Weiss
    • , Lu-Chen Weng
    • , Jennifer Wessel
    • , Cristen J. Willer
    • , Kayleen Williams
    • , L. Keoki Williams
    • , Carla Wilson
    • , James G. Wilson
    • , Quenna Wong
    • , Joseph Wu
    • , Huichun Xu
    • , Lisa R. Yanek
    • , Ivana Yang
    • , Rongze Yang
    • , Norann Zaghloul
    • , Maryam Zekavat
    • , Yingze Zhang
    • , Snow Xueyan Zhao
    • , Wei Zhao
    • , Degui Zhi
    • , Xiang Zhou
    • , Xiaofeng Zhu
    • , Michael Zody
    • , Sebastian Zoellner
    • , Moustafa Abdalla
    • , Gonçalo R. Abecasis
    • , Donna K. Arnett
    • , Stella Aslibekyan
    • , Tim Assimes
    • , Elizabeth Atkinson
    • , Christie M. Ballantyne
    • , Amber Beitelshees
    • , Lawrence F. Bielak
    • , Joshua Bis
    • , Corneliu Bodea
    • , Eric Boerwinkle
    • , Donald W. Bowden
    • , Jennifer Brody
    • , Brian Cade
    • , Jenna Carlson
    • , I-Shou Chang
    • , Yii-Der Ida Chen
    • , Sung Chun
    • , Ren-Hua Chung
    • , Matthew P. Conomos
    • , Adolfo Correa
    • , L. Adrienne Cupples
    • , Coleen Damcott
    • , Paul de Vries
    • , Ron Do
    • , Amanda Elliott
    • , Mao Fu
    • , Andrea Ganna
    • , Da-Wei Gong
    • , Sarah Graham
    • , Mary Haas
    • , Bernhard Haring
    • , Jiang He
    • , Susan Heckbert
    • , Blanca Himes
    • , James Hixson
    • , Marguerite R. Irvin
    • , Deepti Jain
    • , Gail Jarvik
    • , Min A. Jhun
    • , Jicai Jiang
    • , Goo Jun
    • , Rita Kalyani
    • , Sharon L. R. Kardia
    • , Sekar Kathiresan
    • , Amit Khera
    • , Derek Klarin
    • , Charles L. Kooperberg
    • , Brian Kral
    • , Leslie Lange
    • , Cathy C. Laurie
    • , Cecelia Laurie
    • , Rozenn Lemaitre
    • , Zilin Li
    • , Xihao Li
    • , Xihong Lin
    • , Michael C. Mahaney
    • , Ani W. Manichaikul
    • , Lisa W. Martin
    • , Rasika A. Mathias
    • , Ravi Mathur
    • , Stephen T. McGarvey
    • , Caitlin McHugh
    • , John McLenithan
    • , Julie Mikulla
    • , Braxton D. Mitchell
    • , May E. Montasser
    • , Andrew Moran
    • , Alanna C. Morrison
    • , Tetsushi Nakao
    • , Pradeep Natarajan
    • , Deborah Nickerson
    • , Kari North
    • , Jeffrey R. O’Connell
    • , Christopher O’Donnell
    • , Nicholette D. Palmer
    • , Akhil Pampana
    • , Aniruddh Patel
    • , Gina M. Peloso
    • , James Perry
    • , Ulrike Peters
    • , Patricia A. Peyser
    • , James Pirruccello
    • , Toni Pollin
    • , Michael Preuss
    • , Bruce M. Psaty
    • , D. C. Rao
    • , Susan Redline
    • , Robert Reed
    • , Alex Reiner
    • , Stephen S. Rich
    • , Samantha Rosenthal
    • , Jerome I. Rotter
    • , Jenny Schoenberg
    • , Margaret Sunitha Selvaraj
    • , Wayne Hui-Heng Sheu
    • , Jennifer A. Smith
    • , Tamar Sofer
    • , Adrienne M. Stilp
    • , Shamil R. Sunyaev
    • , Ida Surakka
    • , Carole Sztalryd
    • , Hua Tang
    • , Kent D. Taylor
    • , Michael Y. Tsai
    • , Md Mesbah Uddin
    • , Sarah Urbut
    • , Marie Verbanck
    • , Ann Von Holle
    • , Heming Wang
    • , Fei Fei Wang
    • , Kerri Wiggins
    • , Cristen J. Willer
    • , James G. Wilson
    • , Brooke Wolford
    • , Huichun Xu
    • , Lisa R. Yanek
    • , Norann Zaghloul
    • , Maryam Zekavat
    • , Jingwen Zhang
    • , Benjamin M. Neale
    • , Shamil R. Sunyaev
    • , Gonçalo R. Abecasis
    • , Jerome I. Rotter
    • , Cristen J. Willer
    • , Gina M. Peloso
    • , Pradeep Natarajan
    •  & Xihong Lin
  • Letter |

    A pan-cancer analysis finds that extrachromosomal DNA is pervasive and associated with oncogene amplification and poor patient outcomes.

    • Hoon Kim
    • , Nam-Phuong Nguyen
    • , Kristen Turner
    • , Sihan Wu
    • , Amit D. Gujar
    • , Jens Luebeck
    • , Jihe Liu
    • , Viraj Deshpande
    • , Utkrisht Rajkumar
    • , Sandeep Namburi
    • , Samirkumar B. Amin
    • , Eunhee Yi
    • , Francesca Menghi
    • , Johannes H. Schulte
    • , Anton G. Henssen
    • , Howard Y. Chang
    • , Christine R. Beck
    • , Paul S. Mischel
    • , Vineet Bafna
    •  & Roel G. W. Verhaak
  • Article |

    Single-cell RNA-seq and in vivo lineage tracing identify unique luminal progenitors in the mouse prostate that can contribute to regeneration and oncogenesis. Single-cell RNA-seq analysis of human prostate identifies a similar cell population.

    • Wangxin Guo
    • , Lin Li
    • , Juan He
    • , Zhuang Liu
    • , Ming Han
    • , Fei Li
    • , Xinyi Xia
    • , Xiaoyu Zhang
    • , Yao Zhu
    • , Yu Wei
    • , Yunguang Li
    • , Rebiguli Aji
    • , Hao Dai
    • , Hui Wei
    • , Chunfeng Li
    • , Yu Chen
    • , Luonan Chen
    •  & Dong Gao
  • Letter |

    METTL3-induced deposition of N6-methyladenosine (m6A) in RNA correlates with removal of H3K9me2 genome wide. The m6A reader YTHDC1 recruits the H3K9me2 demethylase KDM3B to chromatin.

    • Yuan Li
    • , Linjian Xia
    • , Kaifen Tan
    • , Xidong Ye
    • , Zhixiang Zuo
    • , Minchun Li
    • , Rui Xiao
    • , Zihan Wang
    • , Xiaona Liu
    • , Mingqiang Deng
    • , Jinru Cui
    • , Mengtian Yang
    • , Qizhi Luo
    • , Sun Liu
    • , Xin Cao
    • , Haoran Zhu
    • , Tianqi Liu
    • , Jiaxin Hu
    • , Junfang Shi
    • , Shan Xiao
    •  & Laixin Xia
  • Article |

    Genomic analysis of 118 cervical tumors from Ugandan individuals identifies HPV-clade-specific differences in tumor DNA methylation, regulatory-region-associated histone marks, gene expression and pathway dysregulation.

    • Alessia Gagliardi
    • , Vanessa L. Porter
    • , Zusheng Zong
    • , Reanne Bowlby
    • , Emma Titmuss
    • , Constance Namirembe
    • , Nicholas B. Griner
    • , Hilary Petrello
    • , Jay Bowen
    • , Simon K. Chan
    • , Luka Culibrk
    • , Teresa M. Darragh
    • , Mark H. Stoler
    • , Thomas C. Wright
    • , Patee Gesuwan
    • , Maureen A. Dyer
    • , Yussanne Ma
    • , Karen L. Mungall
    • , Steven J. M. Jones
    • , Carolyn Nakisige
    • , Karen Novik
    • , Jackson Orem
    • , Martin Origa
    • , Julie M. Gastier-Foster
    • , Robert Yarchoan
    • , Corey Casper
    • , Gordon B. Mills
    • , Janet S. Rader
    • , Akinyemi I. Ojesina
    • , Daniela S. Gerhard
    • , Andrew J. Mungall
    •  & Marco A. Marra
  • Letter |

    Quantitative ChIP–seq analysis maps G-quadruplex (G4) DNA structures in breast cancer patient-derived tumor xenograft (PDTX) models. G4-based subtypes highlight additional tumor heterogeneity in the integrative cluster (IC) system.

    • Robert Hänsel-Hertsch
    • , Angela Simeone
    • , Abigail Shea
    • , Winnie W. I. Hui
    • , Katherine G. Zyner
    • , Giovanni Marsico
    • , Oscar M. Rueda
    • , Alejandra Bruna
    • , Alistair Martin
    • , Xiaoyun Zhang
    • , Santosh Adhikari
    • , David Tannahill
    • , Carlos Caldas
    •  & Shankar Balasubramanian
  • Perspective |

    This Perspective discusses the need for mechanistic and quantitative understanding of the ecological and evolutionary dynamics of tumor growth to inform strategies for earlier detection, diagnosis and treatment of cancer.

    • Nastaran Zahir
    • , Ruping Sun
    • , Daniel Gallahan
    • , Robert A. Gatenby
    •  & Christina Curtis
  • Article
    | Open Access

    De novo genome assemblies of four European flint maize lines and comparison with two US Corn Belt genomes provide insights into the dynamics of intraspecies variation in repeat and gene content in maize genomes.

    • Georg Haberer
    • , Nadia Kamal
    • , Eva Bauer
    • , Heidrun Gundlach
    • , Iris Fischer
    • , Michael A. Seidel
    • , Manuel Spannagl
    • , Caroline Marcon
    • , Alevtina Ruban
    • , Claude Urbany
    • , Adnane Nemri
    • , Frank Hochholdinger
    • , Milena Ouzunova
    • , Andreas Houben
    • , Chris-Carolin Schön
    •  & Klaus F. X. Mayer
  • Letter |

    Nucleic acid processing by the cytoplasmic exonuclease TREX1 and cytosine editing by APOBEC3B drive chromothripsis and kataegis during telomere crisis.

    • John Maciejowski
    • , Aikaterini Chatzipli
    • , Alexandra Dananberg
    • , Kevan Chu
    • , Eleonore Toufektchan
    • , Leszek J. Klimczak
    • , Dmitry A. Gordenin
    • , Peter J. Campbell
    •  & Titia de Lange
  • Article |

    Genome-wide analysis of 3D chromatin topologies across gastric cancers suggests that Epstein–Barr virus infection may induce the epigenetic rewiring of EBV-positive tumors through human–viral chromatin interactions, a phenomenon termed ‘enhancer infestation’.

    • Atsushi Okabe
    • , Kie Kyon Huang
    • , Keisuke Matsusaka
    • , Masaki Fukuyo
    • , Manjie Xing
    • , Xuewen Ong
    • , Takayuki Hoshii
    • , Genki Usui
    • , Motoaki Seki
    • , Yasunobu Mano
    • , Bahityar Rahmutulla
    • , Teru Kanda
    • , Takayoshi Suzuki
    • , Sun Young Rha
    • , Tetsuo Ushiku
    • , Masashi Fukayama
    • , Patrick Tan
    •  & Atsushi Kaneda
  • Article |

    Analyses of epigenomic datasets spanning transitions from normal prostate epithelium to localized prostate cancer to metastases show that latent developmental programs are reactivated in metastatic disease and that prostate lineage-specific regulatory elements are strongly enriched for prostate cancer risk heritability.

    • Mark M. Pomerantz
    • , Xintao Qiu
    • , Yanyun Zhu
    • , David Y. Takeda
    • , Wenting Pan
    • , Sylvan C. Baca
    • , Alexander Gusev
    • , Keegan D. Korthauer
    • , Tesa M. Severson
    • , Gavin Ha
    • , Srinivas R. Viswanathan
    • , Ji-Heui Seo
    • , Holly M. Nguyen
    • , Baohui Zhang
    • , Bogdan Pasaniuc
    • , Claudia Giambartolomei
    • , Sarah A. Alaiwi
    • , Connor A. Bell
    • , Edward P. O’Connor
    • , Matthew S. Chabot
    • , David R. Stillman
    • , Rosina Lis
    • , Alba Font-Tello
    • , Lewyn Li
    • , Paloma Cejas
    • , Andries M. Bergman
    • , Joyce Sanders
    • , Henk G. van der Poel
    • , Simon A. Gayther
    • , Kate Lawrenson
    • , Marcos A. S. Fonseca
    • , Jessica Reddy
    • , Rosario I. Corona
    • , Gleb Martovetsky
    • , Brian Egan
    • , Toni Choueiri
    • , Leigh Ellis
    • , Isla P. Garraway
    • , Gwo-Shu Mary Lee
    • , Eva Corey
    • , Henry W. Long
    • , Wilbert Zwart
    •  & Matthew L. Freedman
  • Article |

    Cells lacking TET proteins and DNMT3A and DNMT3B show that DNMT1 has imprecise maintenance activity and weak de novo activity leading to spontaneous ‘epimutations’. These epimutations can be corrected through a neighbor-guided mechanism.

    • Qiujun Wang
    • , Guang Yu
    • , Xuan Ming
    • , Weikun Xia
    • , Xiguang Xu
    • , Yu Zhang
    • , Wenhao Zhang
    • , Yuanyuan Li
    • , Chunyi Huang
    • , Hehuang Xie
    • , Bing Zhu
    •  & Wei Xie
  • Article |

    Whole-genome bisulfite sequencing along with whole-genome and transcriptome sequencing of 100 prostate cancer metastases identifies genomic regions that are differentially methylated during disease progression and a novel epigenomic subtype.

    • Shuang G. Zhao
    • , William S. Chen
    • , Haolong Li
    • , Adam Foye
    • , Meng Zhang
    • , Martin Sjöström
    • , Rahul Aggarwal
    • , Denise Playdle
    • , Arnold Liao
    • , Joshi J. Alumkal
    • , Rajdeep Das
    • , Jonathan Chou
    • , Junjie T. Hua
    • , Travis J. Barnard
    • , Adina M. Bailey
    • , Eric D. Chow
    • , Marc D. Perry
    • , Ha X. Dang
    • , Rendong Yang
    • , Ruhollah Moussavi-Baygi
    • , Li Zhang
    • , Mohammed Alshalalfa
    • , S. Laura Chang
    • , Kathleen E. Houlahan
    • , Yu-Jia Shiah
    • , Tomasz M. Beer
    • , George Thomas
    • , Kim N. Chi
    • , Martin Gleave
    • , Amina Zoubeidi
    • , Robert E. Reiter
    • , Matthew B. Rettig
    • , Owen Witte
    • , M. Yvonne Kim
    • , Lawrence Fong
    • , Daniel E. Spratt
    • , Todd M. Morgan
    • , Rohit Bose
    • , Franklin W. Huang
    • , Hui Li
    • , Lisa Chesner
    • , Tanushree Shenoy
    • , Hani Goodarzi
    • , Irfan A. Asangani
    • , Shahneen Sandhu
    • , Joshua M. Lang
    • , Nupam P. Mahajan
    • , Primo N. Lara
    • , Christopher P. Evans
    • , Phillip Febbo
    • , Serafim Batzoglou
    • , Karen E. Knudsen
    • , Housheng H. He
    • , Jiaoti Huang
    • , Wilbert Zwart
    • , Joseph F. Costello
    • , Jianhua Luo
    • , Scott A. Tomlins
    • , Alexander W. Wyatt
    • , Scott M. Dehm
    • , Alan Ashworth
    • , Luke A. Gilbert
    • , Paul C. Boutros
    • , Kyle Farh
    • , Arul M. Chinnaiyan
    • , Christopher A. Maher
    • , Eric J. Small
    • , David A. Quigley
    •  & Felix Y. Feng
  • Article |

    A new computational method integrates whole-genome sequencing and transcriptomic data to identify regulatory noncoding variants in an individual cancer genome.

    • Yu Liu
    • , Chunliang Li
    • , Shuhong Shen
    • , Xiaolong Chen
    • , Karol Szlachta
    • , Michael N. Edmonson
    • , Ying Shao
    • , Xiaotu Ma
    • , Judith Hyle
    • , Shaela Wright
    • , Bensheng Ju
    • , Michael C. Rusch
    • , Yanling Liu
    • , Benshang Li
    • , Michael Macias
    • , Liqing Tian
    • , John Easton
    • , Maoxiang Qian
    • , Jun J. Yang
    • , Shaoyan Hu
    • , A. Thomas Look
    •  & Jinghui Zhang
  • Review Article |

    This review discusses major privacy threats relevant to collection and analysis of genomic data in the context of direct-to-consumer applications and provides suggestions for improving the design of privacy-protecting approaches.

    • Luca Bonomi
    • , Yingxiang Huang
    •  & Lucila Ohno-Machado
  • Article |

    Quantitative trait locus (QTL) mapping of N6-methyladenosine (m6A) in human cells highlights the role of RNA-binding proteins, RNA secondary structure and context-dependent m6A effects. m6A QTLs are enriched in loci associated with immune and blood-related traits.

    • Zijie Zhang
    • , Kaixuan Luo
    • , Zhongyu Zou
    • , Maguanyun Qiu
    • , Jiakun Tian
    • , Laura Sieh
    • , Hailing Shi
    • , Yuxin Zou
    • , Gao Wang
    • , Jean Morrison
    • , Allen C. Zhu
    • , Min Qiao
    • , Zhongshan Li
    • , Matthew Stephens
    • , Xin He
    •  & Chuan He
  • Article |

    Computational analyses integrating whole-genome sequencing, cardiac epigenomic data and RNA-binding-protein data identify a role for noncoding de novo mutations in congenital heart disease.

    • Felix Richter
    • , Sarah U. Morton
    • , Seong Won Kim
    • , Alexander Kitaygorodsky
    • , Lauren K. Wasson
    • , Kathleen M. Chen
    • , Jian Zhou
    • , Hongjian Qi
    • , Nihir Patel
    • , Steven R. DePalma
    • , Michael Parfenov
    • , Jason Homsy
    • , Joshua M. Gorham
    • , Kathryn B. Manheimer
    • , Matthew Velinder
    • , Andrew Farrell
    • , Gabor Marth
    • , Eric E. Schadt
    • , Jonathan R. Kaltman
    • , Jane W. Newburger
    • , Alessandro Giardini
    • , Elizabeth Goldmuntz
    • , Martina Brueckner
    • , Richard Kim
    • , George A. Porter Jr.
    • , Daniel Bernstein
    • , Wendy K. Chung
    • , Deepak Srivastava
    • , Martin Tristani-Firouzi
    • , Olga G. Troyanskaya
    • , Diane E. Dickel
    • , Yufeng Shen
    • , Jonathan G. Seidman
    • , Christine E. Seidman
    •  & Bruce D. Gelb
  • Article |

    A combination of super-resolution microscopy and Oligopaint technology shows that TAD boundaries are variable at the single-cell level. Loss of cohesin, in contrast to WAPL or CTCF depletion, reduces interactions across boundaries and alters transcriptional bursting of genes near boundaries.

    • Jennifer M. Luppino
    • , Daniel S. Park
    • , Son C. Nguyen
    • , Yemin Lan
    • , Zhuxuan Xu
    • , Rebecca Yunker
    •  & Eric F. Joyce
  • Article |

    Genome-wide detection of inversions in great ape genomes by using long-read sequencing and single-cell DNA template strand sequencing (Strand-seq) expands the number of known ape inversions and identifies several regions that have recurrently toggled between a direct and an inverted state during primate evolution.

    • David Porubsky
    • , Ashley D. Sanders
    • , Wolfram Höps
    • , PingHsun Hsieh
    • , Arvis Sulovari
    • , Ruiyang Li
    • , Ludovica Mercuri
    • , Melanie Sorensen
    • , Shwetha C. Murali
    • , David Gordon
    • , Stuart Cantsilieris
    • , Alex A. Pollen
    • , Mario Ventura
    • , Francesca Antonacci
    • , Tobias Marschall
    • , Jan O. Korbel
    •  & Evan E. Eichler
  • Article |

    Genome-wide association meta-analyses among 1.4 million individuals identify 318 new risk loci for type 2 diabetes and provide insight into the contribution of these risk variants to diabetes-related vascular outcomes.

    • Marijana Vujkovic
    • , Jacob M. Keaton
    • , Julie A. Lynch
    • , Donald R. Miller
    • , Jin Zhou
    • , Catherine Tcheandjieu
    • , Jennifer E. Huffman
    • , Themistocles L. Assimes
    • , Kimberly Lorenz
    • , Xiang Zhu
    • , Austin T. Hilliard
    • , Renae L. Judy
    • , Jie Huang
    • , Kyung M. Lee
    • , Derek Klarin
    • , Saiju Pyarajan
    • , John Danesh
    • , Olle Melander
    • , Asif Rasheed
    • , Nadeem H. Mallick
    • , Shahid Hameed
    • , Irshad H. Qureshi
    • , Muhammad Naeem Afzal
    • , Uzma Malik
    • , Anjum Jalal
    • , Shahid Abbas
    • , Xin Sheng
    • , Long Gao
    • , Klaus H. Kaestner
    • , Katalin Susztak
    • , Yan V. Sun
    • , Scott L. DuVall
    • , Kelly Cho
    • , Jennifer S. Lee
    • , J. Michael Gaziano
    • , Lawrence S. Phillips
    • , James B. Meigs
    • , Peter D. Reaven
    • , Peter W. Wilson
    • , Todd L. Edwards
    • , Daniel J. Rader
    • , Scott M. Damrauer
    • , Christopher J. O’Donnell
    • , Philip S. Tsao
    • , Mark A. Atkinson
    • , Al C. Powers
    • , Ali Naji
    • , Klaus H. Kaestner
    • , Goncalo R. Abecasis
    • , Aris Baras
    • , Michael N. Cantor
    • , Giovanni Coppola
    • , Aris N. Economides
    • , Luca A. Lotta
    • , John D. Overton
    • , Jeffrey G. Reid
    • , Alan R. Shuldiner
    • , Christina Beechert
    • , Caitlin Forsythe
    • , Erin D. Fuller
    • , Zhenhua Gu
    • , Michael Lattari
    • , Alexander E. Lopez
    • , Thomas D. Schleicher
    • , Maria Sotiropoulos Padilla
    • , Karina Toledo
    • , Louis Widom
    • , Sarah E. Wolf
    • , Manasi Pradhan
    • , Kia Manoochehri
    • , Ricardo H. Ulloa
    • , Xiaodong Bai
    • , Suganthi Balasubramanian
    • , Leland Barnard
    • , Andrew L. Blumenfeld
    • , Gisu Eom
    • , Lukas Habegger
    • , Alicia Hawes
    • , Shareef Khalid
    • , Evan K. Maxwell
    • , William J. Salerno
    • , Jeffrey C. Staples
    • , Ashish Yadav
    • , Marcus B. Jones
    • , Lyndon J. Mitnaul
    • , Samuel M. Aguayo
    • , Sunil K. Ahuja
    • , Zuhair K. Ballas
    • , Sujata Bhushan
    • , Edward J. Boyko
    • , David M. Cohen
    • , John Concato
    • , Joseph I. Constans
    • , Louis J. Dellitalia
    • , Joseph M. Fayad
    • , Ronald S. Fernando
    • , Hermes J. Florez
    • , Melinda A. Gaddy
    • , Saib S. Gappy
    • , Gretchen Gibson
    • , Michael Godschalk
    • , Jennifer A. Greco
    • , Samir Gupta
    • , Salvador Gutierrez
    • , Kimberly D. Hammer
    • , Mark B. Hamner
    • , John B. Harley
    • , Adriana M. Hung
    • , Mostaqul Huq
    • , Robin A. Hurley
    • , Pran R. Iruvanti
    • , Douglas J. Ivins
    • , Frank J. Jacono
    • , Darshana N. Jhala
    • , Laurence S. Kaminsky
    • , Scott Kinlay
    • , Jon B. Klein
    • , Suthat Liangpunsakul
    • , Jack H. Lichy
    • , Stephen M. Mastorides
    • , Roy O. Mathew
    • , Kristin M. Mattocks
    • , Rachel McArdle
    • , Paul N. Meyer
    • , Laurence J. Meyer
    • , Jonathan P. Moorman
    • , Timothy R. Morgan
    • , Maureen Murdoch
    • , Xuan-Mai T. Nguyen
    • , Olaoluwa O. Okusaga
    • , Kris-Ann K. Oursler
    • , Nora R. Ratcliffe
    • , Michael I. Rauchman
    • , R. Brooks Robey
    • , George W. Ross
    • , Richard J. Servatius
    • , Satish C. Sharma
    • , Scott E. Sherman
    • , Elif Sonel
    • , Peruvemba Sriram
    • , Todd Stapley
    • , Robert T. Striker
    • , Neeraj Tandon
    • , Gerardo Villareal
    • , Agnes S. Wallbom
    • , John M. Wells
    • , Jeffrey C. Whittle
    • , Mary A. Whooley
    • , Junzhe Xu
    • , Shing-Shing Yeh
    • , Michaela Aslan
    • , Jessica V. Brewer
    • , Mary T. Brophy
    • , Todd Connor
    • , Dean P. Argyres
    • , Nhan V. Do
    • , Elizabeth R. Hauser
    • , Donald E. Humphries
    • , Luis E. Selva
    • , Shahpoor Shayan
    • , Brady Stephens
    • , Stacey B. Whitbourne
    • , Hongyu Zhao
    • , Jennifer Moser
    • , Jean C. Beckham
    • , Jim L. Breeling
    • , J. P. Casas Romero
    • , Grant D. Huang
    • , Rachel B. Ramoni
    • , Saiju Pyarajan
    • , Yan V. Sun
    • , Kelly Cho
    • , Peter W. Wilson
    • , Christopher J. O’Donnell
    • , Philip S. Tsao
    • , Kyong-Mi Chang
    • , J. Michael Gaziano
    • , Sumitra Muralidhar
    • , Kyong-Mi Chang
    • , Benjamin F. Voight
    •  & Danish Saleheen
  • Article |

    Whole-genome bisulfite sequencing analysis of human embryonic stem cells shows that DNMT3 deficiency leads to global and local demethylation, which depends on TET activity. Dynamic loci overlap with putative somatic enhancers that are highly methylated in ESCs.

    • Jocelyn Charlton
    • , Eunmi J. Jung
    • , Alexandra L. Mattei
    • , Nina Bailly
    • , Jing Liao
    • , Eric J. Martin
    • , Pay Giesselmann
    • , Björn Brändl
    • , Elena K. Stamenova
    • , Franz-Josef Müller
    • , Evangelos Kiskinis
    • , Andreas Gnirke
    • , Zachary D. Smith
    •  & Alexander Meissner
  • Letter |

    Genome-wide analysis in 212,453 Japanese individuals identifies loci associated with 42 diseases. Comparative analysis with European populations identifies East Asian–specific associations.

    • Kazuyoshi Ishigaki
    • , Masato Akiyama
    • , Masahiro Kanai
    • , Atsushi Takahashi
    • , Eiryo Kawakami
    • , Hiroki Sugishita
    • , Saori Sakaue
    • , Nana Matoba
    • , Siew-Kee Low
    • , Yukinori Okada
    • , Chikashi Terao
    • , Tiffany Amariuta
    • , Steven Gazal
    • , Yuta Kochi
    • , Momoko Horikoshi
    • , Ken Suzuki
    • , Kaoru Ito
    • , Satoshi Koyama
    • , Kouichi Ozaki
    • , Shumpei Niida
    • , Yasushi Sakata
    • , Yasuhiko Sakata
    • , Takashi Kohno
    • , Kouya Shiraishi
    • , Yukihide Momozawa
    • , Makoto Hirata
    • , Koichi Matsuda
    • , Masashi Ikeda
    • , Nakao Iwata
    • , Shiro Ikegawa
    • , Ikuyo Kou
    • , Toshihiro Tanaka
    • , Hidewaki Nakagawa
    • , Akari Suzuki
    • , Tomomitsu Hirota
    • , Mayumi Tamari
    • , Kazuaki Chayama
    • , Daiki Miki
    • , Masaki Mori
    • , Satoshi Nagayama
    • , Yataro Daigo
    • , Yoshio Miki
    • , Toyomasa Katagiri
    • , Osamu Ogawa
    • , Wataru Obara
    • , Hidemi Ito
    • , Teruhiko Yoshida
    • , Issei Imoto
    • , Takashi Takahashi
    • , Chizu Tanikawa
    • , Takao Suzuki
    • , Nobuaki Sinozaki
    • , Shiro Minami
    • , Hiroki Yamaguchi
    • , Satoshi Asai
    • , Yasuo Takahashi
    • , Ken Yamaji
    • , Kazuhisa Takahashi
    • , Tomoaki Fujioka
    • , Ryo Takata
    • , Hideki Yanai
    • , Akihide Masumoto
    • , Yukihiro Koretsune
    • , Hiromu Kutsumi
    • , Masahiko Higashiyama
    • , Shigeo Murayama
    • , Naoko Minegishi
    • , Kichiya Suzuki
    • , Kozo Tanno
    • , Atsushi Shimizu
    • , Taiki Yamaji
    • , Motoki Iwasaki
    • , Norie Sawada
    • , Hirokazu Uemura
    • , Keitaro Tanaka
    • , Mariko Naito
    • , Makoto Sasaki
    • , Kenji Wakai
    • , Shoichiro Tsugane
    • , Masayuki Yamamoto
    • , Kazuhiko Yamamoto
    • , Yoshinori Murakami
    • , Yusuke Nakamura
    • , Soumya Raychaudhuri
    • , Johji Inazawa
    • , Toshimasa Yamauchi
    • , Takashi Kadowaki
    • , Michiaki Kubo
    •  & Yoichiro Kamatani
  • Letter |

    CTCF is dispensable for transdifferentiation of B cells into induced macrophages despite widespread loss of topologically associating domains. CTCF depletion impairs upregulation of inflammatory genes after endotoxin exposure by destabilizing promoter–enhancer interactions.

    • Grégoire Stik
    • , Enrique Vidal
    • , Mercedes Barrero
    • , Sergi Cuartero
    • , Maria Vila-Casadesús
    • , Julen Mendieta-Esteban
    • , Tian V. Tian
    • , Jinmi Choi
    • , Clara Berenguer
    • , Amaya Abad
    • , Beatrice Borsari
    • , François le Dily
    • , Patrick Cramer
    • , Marc A. Marti-Renom
    • , Ralph Stadhouders
    •  & Thomas Graf
  • Article |

    Analysis with alleles encoding pharmacologically degradable Mediator subunits shows that Mediator acts as a global coactivator that facilitates transcription globally but is acutely required for cell-type-specific gene regulatory circuits.

    • Martin G. Jaeger
    • , Björn Schwalb
    • , Sebastian D. Mackowiak
    • , Taras Velychko
    • , Alexander Hanzl
    • , Hana Imrichova
    • , Matthias Brand
    • , Benedikt Agerer
    • , Someth Chorn
    • , Behnam Nabet
    • , Fleur M. Ferguson
    • , André C. Müller
    • , Andreas Bergthaler
    • , Nathanael S. Gray
    • , James E. Bradner
    • , Christoph Bock
    • , Denes Hnisz
    • , Patrick Cramer
    •  & Georg E. Winter
  • Article |

    Immunogenomic analyses of advanced high-grade serous ovarian cancer samples before and after neoadjuvant chemotherapy show that the tumor–immune microenvironment is intrinsically heterogeneous and that chemotherapy induces local immune activation.

    • Alejandro Jiménez-Sánchez
    • , Paulina Cybulska
    • , Katherine LaVigne Mager
    • , Simon Koplev
    • , Oliver Cast
    • , Dominique-Laurent Couturier
    • , Danish Memon
    • , Pier Selenica
    • , Ines Nikolovski
    • , Yousef Mazaheri
    • , Yonina Bykov
    • , Felipe C. Geyer
    • , Geoff Macintyre
    • , Lena Morrill Gavarró
    • , Ruben M. Drews
    • , Michael B. Gill
    • , Anastasios D. Papanastasiou
    • , Ramon E. Sosa
    • , Robert A. Soslow
    • , Tyler Walther
    • , Ronglai Shen
    • , Dennis S. Chi
    • , Kay J. Park
    • , Travis Hollmann
    • , Jorge S. Reis-Filho
    • , Florian Markowetz
    • , Pedro Beltrao
    • , Hebert Alberto Vargas
    • , Dmitriy Zamarin
    • , James D. Brenton
    • , Alexandra Snyder
    • , Britta Weigelt
    • , Evis Sala
    •  & Martin L. Miller
  • Author Correction |

    • Andrea Cortese
    • , Yi Zhu
    • , Adriana P. Rebelo
    • , Sara Negri
    • , Steve Courel
    • , Lisa Abreu
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    Analysis of metastases using a mathematical framework and multi-region sampling data shows that lymph node metastases have higher levels of intratumor heterogeneity than distant metastases, and that these form via different evolutionary mechanisms.

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    • , Onno Kranenburg
    • , Jochen K. Lennerz
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