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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

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
Research

Yeast genetic interaction screen of human genes associated with amyotrophic lateral sclerosis: identification of MAP2K5 kinase as a potential drug target

  • Myungjin Jo
  • Ah Young Chung
  • Nozomu Yachie
  • Minchul Seo
  • Hyejin Jeon
  • Youngpyo Nam Yeojin Seo Eunmi Kim Quan Zhong
  • ... [+4 authors] ...,
  • Marc Vidal
  • Hae Chul Park
  • Frederick P. Roth
  • Kyoungho Suk
  • First Published June 8, 2017
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
Method

An extended set of yeast-based functional assays accurately identifies human disease mutations

  • Song Sun
  • Fan Yang
  • Guihong Tan
  • Michael Costanzo
  • Rose Oughtred
  • Jodi Hirschman Chandra L. Theesfeld Pritpal Bansal Nidhi Sahni Song Yi Analyn Yu Tanya Tyagi Cathy Tie David E. Hill Marc Vidal
  • ... [+10 authors] ...,
  • Brenda J. Andrews
  • Charles Boone
  • Kara Dolinski
  • Frederick P. Roth
  • First Published March 14, 2016
Research

Understanding transcriptional regulation by integrative analysis of transcription factor binding data

  • Chao Cheng
  • Roger Alexander
  • Renqiang Min
  • Jing Leng
  • Kevin Y. Yip
  • Joel Rozowsky Koon-Kiu Yan Xianjun Dong Sarah Djebali Yijun Ruan Carrie A. Davis Piero Carninci Timo Lassman Thomas R. Gingeras Roderic Guigó
  • ... [+10 authors] ...,
  • Ewan Birney
  • Zhiping Weng
  • Michael Snyder
  • Mark Gerstein
  • First Published September 5, 2012
Resource

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

  • Thomas Derrien
  • Rory Johnson
  • Giovanni Bussotti
  • Andrea Tanzer
  • Sarah Djebali
  • Hagen Tilgner Gregory Guernec David Martin Angelika Merkel David G. Knowles Julien Lagarde Lavanya Veeravalli Xiaoan Ruan Yijun Ruan Timo Lassmann Piero Carninci James B. Brown Leonard Lipovich Jose M. Gonzalez Mark Thomas Carrie A. Davis Ramin Shiekhattar Thomas R. Gingeras
  • ... [+18 authors] ...,
  • Tim J. Hubbard
  • Cedric Notredame
  • Jennifer Harrow
  • Roderic Guigó
  • First Published September 5, 2012
Research

Transcriptional consequences of genomic structural aberrations in breast cancer

  • Koichiro Inaki
  • Axel M. Hillmer
  • Leena Ukil
  • Fei Yao
  • Xing Yi Woo
  • Leah A. Vardy Kelson Folkvard Braaten Zawack Charlie Wah Heng Lee Pramila Nuwantha Ariyaratne Yang Sun Chan Kartiki Vasant Desai Jonas Bergh Per Hall Thomas Choudary Putti Wai Loon Ong Atif Shahab Valere Cacheux-Rataboul Radha Krishna Murthy Karuturi Wing-Kin Sung
  • ... [+14 authors] ...,
  • Xiaoan Ruan
  • Guillaume Bourque
  • Yijun Ruan
  • Edison T. Liu
  • First Published April 5, 2011
Research

Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes

  • Axel M. Hillmer
  • Fei Yao
  • Koichiro Inaki
  • Wah Heng Lee
  • Pramila N. Ariyaratne
  • Audrey S.M. Teo Xing Yi Woo Zhenshui Zhang Hao Zhao Leena Ukil Jieqi P. Chen Feng Zhu Jimmy B.Y. So Manuel Salto-Tellez Wan Ting Poh Kelson F.B. Zawack Niranjan Nagarajan Song Gao Guoliang Li Vikrant Kumar Hui Ping J. Lim Yee Yen Sia Chee Seng Chan See Ting Leong Say Chuan Neo Poh Sum D. Choi Hervé Thoreau Patrick B.O. Tan Atif Shahab Xiaoan Ruan Jonas Bergh Per Hall Valère Cacheux-Rataboul Chia-Lin Wei Khay Guan Yeoh
  • ... [+30 authors] ...,
  • Wing-Kin Sung
  • Guillaume Bourque
  • Edison T. Liu
  • Yijun Ruan
  • First Published April 5, 2011
Resource

C. elegans ORFeome" > Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome

  • Kourosh Salehi-Ashtiani
  • Chenwei Lin
  • Tong Hao
  • Yun Shen
  • David Szeto
  • Xinping Yang Lila Ghamsari HanJoo Lee Changyu Fan Ryan R. Murray Stuart Milstein Nenad Svrzikapa
  • ... [+7 authors] ...,
  • Michael E. Cusick
  • Frederick P. Roth
  • David E. Hill
  • Marc Vidal
  • First Published October 2, 2009
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