Author
Pennsylvania State University
Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.
7 papers
Recent·Most cited
Tejaswi Iyyanki, Baozhen Zhang, Qixuan Wang, Ye Hou, Qiushi Jin, Jie Xu, Hongbo Yang, Tingting Liu, Xiaotao Wang, Fan Song, Yu Luan, Hironobu Yamashita, Ruby Chien, Huijue Lyu, Lijun Zhang, , Feng Yue
This study identifies subtype-specific epigenomic and 3D genome structures in bladder cancer, linking NPAS2 to luminal subtype regulation and clinical outcomes.
Genome biology · Apr 15, 2021Peer-reviewedGenomics
Tarik J. Salameh, Xiaotao Wang, Fan Song, Bo Zhang, Sage M. Wright, Chachrit Khunsriraksakul, Yijun Ruan, Feng Yue
This paper introduces Peakachu, a Random Forest framework for chromatin loop detection in Hi-C data, showing improved identification of short-range interactions across multiple platforms and species.
Nature Communications · Jul 9, 2020Peer-reviewedBioinformatics
Galip Gürkan Yardımcı, Hakan Özadam, Michael E.G. Sauria, Oana Ursu, Koon‐Kiu Yan, Tao Yang, Abhijit Chakraborty, Arya Kaul, Bryan R. Lajoie, Fan Song, Ye Zhan, Ferhat Ay, Mark Gerstein, Anshul Bharat Kundaje, Qunhua Li, , William Stafford Noble
The paper evaluates reproducibility and quality measures for Hi-C data using real and simulated datasets, showing that specialized methods outperform simple correlation analysis.
Genome biology · Mar 19, 2019Peer-reviewedGenomics
Jie Xu, Fan Song, Emily Schleicher, Christopher Pool, Darrin Bann, Max Hennessy, Kathryn Sheldon, Emma Batchelder, Charyguly Annageldiyev, Arati Sharma, Yuanyuan Chang, Alex Hastie, Barbara Miller, David Goldenberg, Shin Mineishi, , James R. Broach
The paper identifies numerous previously undetected structural variants in leukemia samples using integrated genome analysis and computational methods, revealing their impact on gene expression and patient survival.
bioRxiv · Feb 28, 2019 · PreprintGenomics
Yanli Wang, Fan Song, Bo Zhang, Lijun Zhang, Jie Xu, Da Kuang, Daofeng Li, Mayank N. K. Choudhary, Yun Li, Ming Hu, Ross C. Hardison, Ting Wang, Feng Yue
The paper introduces a web-based browser for visualizing 3D genome organization and chromatin interactions, enabling integration with other omics data to study gene regulation.
Genome biology · Oct 4, 2018Peer-reviewedBioinformatics
Jesse R. Dixon, Jie Xu, Vishnu Dileep, Ye Zhan, Fan Song, Victoria T. Le, Galip Gürkan Yardımcı, Abhijit Chakraborty, Darrin V. Bann, Yanli Wang, Royden A. Clark, Lijun Zhang, Hongbo Yang, Tingting Liu, Sriranga Iyyanki, , Feng Yue
This paper presents an integrative framework to detect structural variants in cancer genomes using multiple methods and finds that non-coding structural variation significantly impacts genome function in cancer cells.
Nature Genetics · Sep 4, 2018Peer-reviewedGenomics
Tao Yang, Feipeng Zhang, Galip Gürkan Yardımcı, Fan Song, Ross C. Hardison, William Stafford Noble, Feng Yue, Qunhua Li
HiCRep assesses Hi-C data reproducibility using a stratum-adjusted correlation coefficient, improving accuracy over existing methods.
Genome Research · Nov 1, 2017Peer-reviewedBioinformatics