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Method

Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie

Krzysztof H. Banecki
Haoxi Chai
Yijun Ruan
Dariusz Plewczynski

First Published April 8, 2026

Research

Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation

Vanessa L. Porter
Michelle Ng
Kieran O'Neill
Signe MacLennan
Richard D. Corbett
Luka Culibrk Zeid Hamadeh Marissa Iden Rachel Schmidt Shirng-Wern Tsaih Carolyn Nakisige Martin Origa Jackson Orem Glenn Chang Jeremy Fan Ka Ming Nip Vahid Akbari Simon K. Chan James Hopkins Richard A. Moore Eric Chuah Karen L. Mungall Andrew J. Mungall
... [+18 authors] ...,
Inanc Birol
Steven J.M. Jones
Janet S. Rader
Marco A. Marra

First Published December 5, 2024

Research

Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary

Satyam P. Srivastav
Cédric Feschotte
Andrew G. Clark

First Published May 15, 2024

Research

High-resolution structural genomics reveals new therapeutic vulnerabilities in glioblastoma

Michael J. Johnston
Ana Nikolic
Nicoletta Ninkovic
Paul Guilhamon
Florence M.G. Cavalli
Steven Seaman Franz J. Zemp John Lee Aly Abdelkareem Katrina Ellestad Alex Murison Michelle M. Kushida Fiona J. Coutinho Yussanne Ma Andrew J. Mungall Richard Moore Marco A. Marra Michael D. Taylor Peter B. Dirks Trevor J. Pugh Sorana Morrissy
... [+16 authors] ...,
Bradley St Croix
Douglas J. Mahoney
Mathieu Lupien
Marco Gallo

First Published June 27, 2019

Research

An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells

Zhizhuo Zhang
Kern Rei Chng
Shreyas Lingadahalli
Zikai Chen
Mei Hui Liu
Huy Hoang Do Shaojiang Cai Nicola Rinaldi Huay Mei Poh Guoliang Li Ying Ying Sung Charlie L. Heng Leighton J. Core Si Kee Tan Xiaoan Ruan John T. Lis
... [+11 authors] ...,
Manolis Kellis
Yijun Ruan
Wing-Kin Sung
Edwin Cheung

First Published January 3, 2019

Method

An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization

Przemysław Szałaj
Zhonghui Tang
Paul Michalski
Michal J. Pietal
Oscar J. Luo
Michał Sadowski
... [+1 authors] ...,
Xingwang Li
Kamen Radew
Yijun Ruan
Dariusz Plewczynski

First Published October 27, 2016

Research

Evidence for the fixation of gene duplications by positive selection in Drosophila

Margarida Cardoso-Moreira
J. Roman Arguello
Srikanth Gottipati
L.G. Harshman
Jennifer K. Grenier
Andrew G. Clark

First Published April 12, 2016

Research

Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations

Juan L. Rodriguez-Flores
Khalid Fakhro
Francisco Agosto-Perez
Monica D. Ramstetter
Leonardo Arbiza
Thomas L. Vincent Amal Robay Joel A. Malek Karsten Suhre Lotfi Chouchane Ramin Badii Ajayeb Al-Nabet Al-Marri Charbel Abi Khalil Mahmoud Zirie Amin Jayyousi Jacqueline Salit
... [+11 authors] ...,
Alon Keinan
Andrew G. Clark
Ronald G. Crystal
Jason G. Mezey

First Published January 4, 2016

Method

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data

Gavin Ha
Andrew Roth
Jaswinder Khattra
Julie Ho
Damian Yap
Leah M. Prentice Nataliya Melnyk Andrew McPherson Ali Bashashati Emma Laks Justina Biele Jiarui Ding Alan Le Jamie Rosner Karey Shumansky Marco A. Marra C. Blake Gilks
... [+12 authors] ...,
David G. Huntsman
Jessica N. McAlpine
Samuel Aparicio
Sohrab P. Shah

First Published July 24, 2014

Research

Chromosome-wide profiling of X-chromosome inactivation and epigenetic states in fetal brain and placenta of the opossum, Monodelphis domestica

Xu Wang
Kory C. Douglas
John L. VandeBerg
Andrew G. Clark
Paul B. Samollow

First Published September 24, 2013

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