PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data. - Kuo Ping Chiu; Chee-Hong Wong; Qiongyu Chen; Pramila Ariyaratne; Hong Sain Ooi; Chia-Lin Wei; Wing-Kin Sung; Yijun Ruan (BMC Bioinform., 2006)

A Streamlined and Generalized Analysis of Chromatin ImmunoPrecipitation Paired-End diTag Data. - Vinsensius B. Vega; Yijun Ruan; Wing-Kin Sung (ICCS (3), 2008)

3D-GNOME: an integrated web service for structural modeling of the 3D genome. - Przemyslaw Szalaj; Paul J. Michalski; Przemyslaw Wróblewski; Zhonghui Tang; Michal Kadlof; Giovanni Mazzocco; Yijun Ruan; Dariusz Plewczynski (Nucleic Acids Res., 2016)

QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks. - Asa Thibodeau; Eladio J. Márquez; Oscar Luo; Yijun Ruan; Francesca Menghi; Dong-Guk Shin; Michael L. Stitzel; Paola Vera-Licona; Duygu Ucar (PLoS Comput. Biol., 2016)

Highlights from the 11th ISCB Student Council Symposium 2015: Dublin, Ireland. 10 July 2015. - Katie Wilkins; Mehedi Hassan; Margherita Francescatto; Jakob B. Jespersen; R. Gonzalo Parra; Bart Cuypers; Dan F. DeBlasio; Alexander Junge; Anupama Jigisha; Farzana Rahman; Griet Laenen; Sander Willems; et al. (BMC Bioinform., 2016)

pyBedGraph: a python package for fast operations on 1D genomic signal tracks. - Henry B. Zhang; Minji Kim 007; Jeffrey H. Chuang; Yijun Ruan (Bioinform., 2020)

3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome. - Michal Wlasnowolski; Michal Sadowski; Tymon Czarnota; Karolina Jodkowska; Przemyslaw Szalaj; Zhonghui Tang; Yijun Ruan; Dariusz Plewczynski (Nucleic Acids Res., 2020)

Virus Infection Induces Immune Gene Activation with CTCF-anchored Enhancers and Chromatin Interactions in Pig Genome. - Jianhua Cao; Ruimin Ren; Xiaolong Li; Xiaoqian Zhang; Yan Sun; Xiaohuan Tian; Ru Liu; Xiangdong Liu; Yijun Ruan; Guoliang Li 002; Shuhong Zhao (Genom. Proteom. Bioinform., 2024)