Beifang Niu

Senior Bioinformatics Research Scientist(Genomics)
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Overview

Dr. Beifang Niu is a Senior Bioinformatics Research Scientist at the Genomics Group, the Center for Applied Bioinformatics (CAB) in the St Jude Children’s Research Hospital (SJCRH). He is a bioinformatics researcher with over 20 years of experience in genome informatics and high-performance computing, focusing on pan-cancer genomics. His work integrates omics data, machine learning, and algorithm development to identify tumor-specific drivers, such as microsatellite instability (MSI) and pan-cancer spacial somatic mutation hotspots. As the principal developer of widely used software such as MSIsensor, HotSpot3D, and the CD-HIT suite, his research has contributed to over 80 publications with more than 40,000 citations, advancing the fields of cancer genomics and precision medicine.

Education

  • PhD, Computer Science (Bioinformatics), University of Chinese Academy of Sciences, Beijing, China (2009)
  • Research Fellowship, Genome Informatics, Beijing Genomics Institute (BGI), Beijing, China (2007)
  • BS, Coumputer Science, Shandong Agricultural University, Shandong, China (2002)

Professional Experience

Time Position PI/Supervisor Institution
2025- Senior Bioinformatics Research Scientist Gang Wu /Ti-Cheng Chang St. Jude Children’s Research Hospital, Memphis, TN, USA
2015-2025 Professor - Computer Network Information Center, Chinese Acedemy of Sciences, Beijing, China
2012-2015 Staff Research Scientist Li Ding McDonnell Genome Institute, Washington University in St. Louis, MO, USA
2009-2012 Postdoctoral Associate Weizhong Li Center for Research in Biological Systems, University of California San Diego, CA, USA

📌 Bioinformatics Tools

  • MSIsensor
    A fast and accurate microsatellite instability (MSI) detection tool for paired tumor-normal sequencing data.
    👉 Paper (PMID: 24371154) | GitHub

  • MSIsensor2
    An improved MSI detection machine learning model supporting both paired and unpaired tumor samples.
    👉 Paper (PMID: 33461213) | GitHub

  • HotSpot3D A tool for identifying spatial variant hotspots (clusters), functionally important cancer mutations using protein 3D structure.
    👉 Paper (PMID: 27294619) | GitHub

  • HotSpot3D Web Server
    An interactive web platform for visualizing and analyzing spatial clusters of somatic mutations in protein 3D structures.
    👉 Paper (PMID: 32315389) | Web Server

  • Docker-FLT3-ITD
    A Docker image for accurate FLT3-internal tandem duplication (FLT3-ITD) identification in acute myeloid leukaemia (AML).
    👉 Paper (PMID: 33851200) | github

  • CD-HIT
    A widely used tool for clustering and comparing large sets of protein or nucleotide sequences at high speed.
    👉 Paper (PMID: 23060610) | Website

Selected Publications

For a full list - Google Scholar

*denotes equal contribution, #denotes corresponding

2025:1

  1. npj Precision Oncolo
    Breast cancer homologous recombination deficiency prediction from pathological images with a sufficient and representative Transformer
    Luan Haijing*, Hu Taiyuan*, Hu Jifang, Liu Weier, Yang Kaixing, Pei Yue, Li Ruilin, He Jiayin, Gao Yajun, Sun Dawei, Duan Xiaohong, Yan Rui#, Zhou S. Kevin#, Niu Beifang#
    npj Precision Oncology 2025
    DOI

2024:1

  1. IEEE BIBM
    Transformer-Based Multi-Scale Fusion for Robust Predicting Microsatellite Instability from Pathological Images
    Hu Taiyuan*, Luan Haijing*, Yan Rui, Hu Jifang, Yang Kaixing, Han Xinyin, Liu Weier, He Jiayin, Duan Xiaohong, Li Ruilin, Zhang Fa, Niu Beifang#
    In 2024
    DOI

2021:2

  1. Briefings in Bioinfo
    Comprehensive review and evaluation of computational methods for identifying FLT3-internal tandem duplication in acute myeloid leukaemia
    Yuan Danyang*, He Xiaoyu, Han Xinyin, Yang Chunyan, Liu Fei, Zhang Shuying, Luan Haijing, Li Ruilin, He Jiayin, Duan Xiaohong, Wang Dongliang, Zhou Qiming, Gao Sujun, Niu Beifang#
    Briefings in Bioinformatics 2021
    DOI
  2. Briefings in Bioinfo
    MSIsensor-ct: microsatellite instability detection using cfDNA sequencing data
    Han Xinyin*, Zhang Shuying*, Zhou Daniel Cui, Wang Dongliang, He Xiaoyu, Yuan Danyang, Li Ruilin, He Jiayin, Duan Xiaohong, Wendl Michael C, Ding Li#, Niu Beifang#
    Briefings in Bioinformatics 2021
    DOI

2020:1

  1. Bioinformatics
    HotSpot3D web server: an integrated resource for mutation analysis in protein 3D structures
    Chen Shanyu*, He Xiaoyu, Li Ruilin, Duan Xiaohong, Niu Beifang#
    Bioinformatics 2020
    DOI

2019:1

  1. Genomics, Proteomic
    Gclust: A Parallel Clustering Tool for Microbial Genomic Data
    Li Ruilin*, He Xiaoyu, Dai Chuangchuang, Zhu Haidong, Lang Xianyu, Chen Wei, Li Xiaodong, Zhao Dan, Zhang Yu, Han Xinyin, Niu Tie, Zhao Yi, Cao Rongqiang, He Rong, Lu Zhonghua, Chi Xuebin, Li Weizhong, Niu Beifang#
    Genomics, Proteomics & Bioinformatics 2019
    DOI

2018:1

  1. Cell Research
    Pan-cancer analysis of somatic mutations across 21 neuroendocrine tumor types
    Cao Yanan*, Zhou Weiwei*, Li Lin*, Wang Jiaqian*, Gao Zhibo*, Jiang Yiran, Jiang Xiuli, Shan Aijing, Bailey Matthew H., Huang Kuan-lin, Sun Sam Q., McLellan Michael D., Niu Beifang, Wang Weiqing, Ding Li#, Ning Guang#
    Cell Research 2018
    DOI

2016:1

  1. Nature Genetics
    Protein-structure-guided discovery of functional mutations across 19 cancer types
    Niu Beifang*, Scott Adam D*, Sengupta Sohini*, Bailey Matthew H, Batra Prag, Ning Jie, Wyczalkowski Matthew A, Liang Wen-Wei, Zhang Qunyuan, McLellan Michael D, Sun Sam Q, Tripathi Piyush, Lou Carolyn, Ye Kai, Mashl R Jay, Wallis John, Wendl Michael C, Chen Feng#, Ding Li#
    Nature Genetics 2016
    DOI

2015:1

  1. Nature Communication
    Patterns and functional implications of rare germline variants across 12 cancer types
    Lu Charles*, Xie Mingchao*, Wendl Michael C., Wang Jiayin, McLellan Michael D., Leiserson Mark D. M., Huang Kuan-lin, Wyczalkowski Matthew A., Jayasinghe Reyka, Banerjee Tapahsama, Ning Jie, Tripathi Piyush, Zhang Qunyuan, Niu Beifang, Ye Kai, Schmidt Heather K., Fulton Robert S., McMichael Joshua F., Batra Prag, Kandoth Cyriac, Bharadwaj Maheetha, Koboldt Daniel C., Miller Christopher A., Kanchi Krishna L., Eldred James M., Larson David E., Welch John S., You Ming, Ozenberger Bradley A., Govindan Ramaswamy, Walter Matthew J., Ellis Matthew J., Mardis Elaine R., Graubert Timothy A., Dipersio John F., Ley Timothy J., Wilson Richard K., Goodfellow Paul J., Raphael Benjamin J., Chen Feng, Johnson Kimberly J., Parvin Jeffrey D., Ding Li#
    Nature Communications 2015
    DOI

2014:2

  1. Cell
    Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin
    Hoadley Katherine A.*, Yau Christina, Wolf Denise M., Cherniack Andrew D., Tamborero David, Ng Sam, Leiserson Max D.M., Niu Beifang, McLellan Michael D., Uzunangelov Vladislav, Zhang Jiashan, Kandoth Cyriac, Akbani Rehan, Shen Hui, Omberg Larsson, Chu Andy, Margolin Adam A., Veer Laura J., Lopez-Bigas Nuria, Laird Peter W., Raphael Benjamin J., Ding Li, Robertson A. Gordon, Byers Lauren A., Mills Gordon B., Weinstein John N., Van Waes Carter, Chen Zhong, Collisson Eric A., Benz Christopher C.#, Perou Charles M.#, Stuart Joshua M.#
    Cell 2014
    DOI
  2. Bioinformatics
    MSIsensor: microsatellite instability detection using paired tumor-normal sequence data
    Niu Beifang*, Ye Kai*, Zhang Qunyuan, Lu Charles, Xie Mingchao, McLellan Michael D., Wendl Michael C., Ding Li#
    Bioinformatics 2014
    DOI

2013:1

  1. Nature
    Mutational landscape and significance across 12 major cancer types
    Kandoth Cyriac*, McLellan Michael D.*, Vandin Fabio, Ye Kai, Niu Beifang, Lu Charles, Xie Mingchao, Zhang Qunyuan, McMichael Joshua F., Wyczalkowski Matthew A., Leiserson Mark D. M., Miller Christopher A., Welch John S., Walter Matthew J., Wendl Michael C., Ley Timothy J., Wilson Richard K., Raphael Benjamin J., Ding Li#
    Nature 2013
    DOI

2012:1

  1. Bioinformatics
    CD-HIT: accelerated for clustering the next-generation sequencing data
    Fu Limin*, Niu Beifang, Zhu Zhengwei, Wu Sitao, Li Weizhong#
    Bioinformatics 2012
    DOI

2010:1

  1. BMC Bioinformatics
    Artificial and natural duplicates in pyrosequencing reads of metagenomic data
    Niu Beifang*, Fu Limin, Sun Shulei, Li Weizhong#
    BMC Bioinformatics 2010
    DOI

Awards/Presentations/Posters

2015 Top 10 Clinical Research Achievement Awards of the United States
International symposium on clinical and translational medicine 2016, Shanghai, China. Invited speaker
International Workshop on CO-DESIGN 2016, Xian, China. Invited speaker
Genome Informatics 2013, Cold Spring Harbor, NY, USA, Oct 31-Nov 2, 2013. Poster
International Human Microbiome Congress (IHMC), Vancouver, Canada, March 9-11, 2011. Poster