Professor & Associate Director

Department of High-Performance Computing Technology and Application Development

The Supercomputing Center of Chinese Academy of Sciences

Beijing, China, 100190


Research Areas

My main research field is the development of computational methods for the analysis of biological datasets, especially cancer genomic and metagenomic data using high-performance computing technology. In particular, I have been developing computational tools for working with data from the next generation sequencing technology ( Illumina && 454 ).



Ph.D. in Computer Software and Theory, Super Computing Center, Chinese Academy of Sciences, Beijing, China.

Thesis Title: Research on Short Oligonucleotide Alignment and Assembly Algorithm. 

Advisor: Professor Xuebin Chi

1998 – 2002

S.B. in Computer Science, Shandong Agriculture University, Shandong, China


Work Experience

2015 – present

Professor (100 Talents Program of Chinese Academy of Sciences), (Computational Cancer Genomics and precision medicine big data analysis), The Supercomputing Center of  Chinese Academy of Sciences, Beijing, China.

Sponsor: Chinese Academy of Sciences.

·  Lead the development of Precision Medicine Workstation (PMW) pipeline for the precision medicine big data analysis.

·  Lead the development of HotSpot3D software. HotSpot3D is an automated, statistically-based approach for spatial clustering of mutations and drugs presents an opportunity for identifying novel functional mutations and therapeutic targets in human diseases, including cancer.


Staff Scientist, (Computational Cancer Genomics), The Genome Institute, School of Medicine, Washington University in St. Louis, Missouri, US.

Sponsor: Professor Li Ding.

·  Lead the development of computational pipeline (MUSIC2) for the discovering the significance of somatic mutations   found within a given cohort of cancer samples, and with respect to a variety   of external data sources. Involved in the analysis of 3d mutation proximity.

·  Setupcloud computing environments using Apache Hadoop (MapReduce framework) for large scale cancer genomic BD2K (Big   Data to Knowledge) project from ICGC (International Cancer Genome Consortium).

·  Identifying and characterizing somatic/germline genetic changes relevant to cancer initiation and progression as well as drug response by integrating various data types including DNA, RNA, and proteomics data.

·  Development of algorithms and computational tools to facilitate the translation of genomic findings to clinical practice.


Postdoctoral Associate, (Bioinformatics & Parallel computing), California Institute for Telecommunications and Information Technology(CALIT2) & The Center for Research in Biological   Systems(CRBS) & San Diego Supercomputer Center(SDSC), University of California, San Diego, California, US.

Sponsor: Doctor Weizhong Li.

·  Developing novel computational methods for HMP (Human   Metagenome Project) and other metagenomics projects. Developing computational and informatics tools for next generation sequencing data analysis.

·  Testing Gordon supercomputer in SDSC (San Diego Super Computer   Center) using big bioinformatics data for NSF XSEDE (eXtreme Science and Engineering Discovery Environment) Project.

·  Study of artifacts detecting to 454 pyrosequencing data. Designed one algorithm for detecting artifacts in metagenomics sequencing data under 454 pyrosequencing technology.

·  Assembly  improvement of metagenome by using pre-clustering method.

2007 – 2008

Research Intern, (Bioinformatics), Beijing Genomics Institute (BGI), Beijing, China.

Sponsor: Professor Jun Wang

·  Study of parallelization of short reads assembly algorithm based on de Bruijn graphs.

2003 – 2007

Research Assistant, (Parallel Computing), Supercomputing Center of Chinese Academy of Sciences, Beijing, China.

Sponsor: Professor Xuebin Chi.

·  Study of parallel computing, grid computing and bioinformatics (short oligonucleotide alignment and assembly algorithm).

·  Conducted parallel research on the alternative splicing of mRNA, executed parallelization of AltSplice program MPI_AltSplice.  MPI_AltSplice was designed and implemented under MPI environment.

·  Development of a commodity supercomputing environment, ScBioGrid, for supporting bioinformatics research.

·  Linux system administration using ROCKS and Sun Grid Engine.



[1].      Xinyin Han*, Shuying Zhang*, Daniel Cui Zhou, Dongliang Wang, Xiaoyu He, Danyang Yuan, Ruilin Li, Jiayin He, Xiaohong Duan, Michael C Wendl, Li Ding#, Beifang Niu#. (2021). MSIsensor-ct: microsatellite instability detection using cfDNA sequencing data. Briefings in Bioinformatics, bbaa402,

[2].      Danyang Yuan, Xiaoyu He, Xinyin Han, Chunyan Yang, Fei Liu, Shuying Zhang, Haijing Luan, Ruilin Li, Jiayin He, Xiaohong Duan, Dongliang Wang, Qiming Zhou, Sujun Gao #, Beifang Niu#. (2021). Comprehensive review and evaluation of computational methods for identifying FLT3-internal tandem duplication in acute myeloid leukaemia. Briefings in Bioinformatics, bbab099,

[3].      Xiaoyu He, Shanyu Chen, Ruilin Li, Xinyin Han, Zhipeng He, Danyang Yuan, Shuying Zhang, Xiaohong Duan, Beifang Niu#. (2020). Comprehensive fundamental analysis and quality management strategy for next-generation sequencing data from cancer genomes. Briefings in Bioinformatics, bbaa083,

[4].      Shanyu Chen, Xiaoyu He, Ruilin Li, Xiaohong Duan, Beifang Niu#. (2020). HotSpot3D web server: An Integrated Resource for Mutation Analysis in Protein 3D Structures. Bioinformatics, 36(12): 3944-3946.

[5].       Liping Sun, Yang Yu, Beifang Niu#, Deqing Wang#. (2020). Red blood cells may act as repositories of microRNAs in the circulatory system. Frontiers in Genetics, 11: 442.

[6].      Chuangchuang Dai, Haijing Luan, Qingbing Yu, Xiaoyu He, Yunhao Wang, Bincheng Shuai, Xiaobing Guo#, Zhonghua Lu#, Beifang Niu#. (2020, August). Change-Encryption: Encryption Using Spatiotemporal Information as a Function Model. In 2020 7th IEEE International Conference on Cyber Security and Cloud Computing (CSCloud)/ 6th IEEE International Conference on Edge Computing and Scalable Cloud (EdgeCom) (pp. 281-287).

[7].      Chuangchuang Dai, Xueying Yang, Meikang Qiu, Xiaobing Guo#, Zhonghua Lu#, Beifang Niu#. (2020, September). Digital Currency Investment Strategy Framework Based on Ranking. In Algorithms and Architectures for Parallel Processing (ICA3PP 2020) (pp. 654-662).

[8].      Ruilin Li, Xiaoyu He, Chuangchuang Dai, Haidong Zhu, Xianyu Lang, Wei Chen, Xiaodong Li, Dan Zhao, Yu Zhang, Xinyin Han, Tie Niu, Yi Zhao, Rongqiang Cao, Rong He, Zhonghua Lu, Xuebin Chi, Weizhong Li#Beifang Niu#. (2019). Gclust: A Parallel Clustering Tool for Microbial Genomic Data. Genomics, Proteomics & Bioinformatics, 17(5): 496-502.

[9].      Shanyu Chen, Zhipeng He, Xinyin Han, Xiaoyu He, Ruilin Li, Haidong Zhu, Dan Zhao, Chuangchuang Dai, Yu Zhang, Zhonghua Lu, Xuebin Chi, Beifang Niu#. (2019). How Big Data and High-performance Computing Drive Brain Science. Genomics, Proteomics & Bioinformatics, 17(4): 381-392.

[10].   Zekun Yin, Xiaoming Xu, Kaichao Fan, Ruilin Li, Weizhong Li, Weiguo Liu#Beifang Niu#. (2019, November). DGCF: A Distributed Greedy Clustering Framework for Large-scale Genomic Sequences. In 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (pp. 2272-2279). IEEE.

[11].   Shuo Li, Zhonghua Lu, Yongze Sun, Sungen Deng, Beifang Niu#. (2019, May). Distributed Parameter Optimization Scheduling Strategy and System Design Based on Mesos. In 2019 IEEE 5th Intl Conference on Big Data Security on Cloud (BigDataSecurity), IEEE Intl Conference on High Performance and Smart Computing,(HPSC) and IEEE Intl Conference on Intelligent Data and Security (IDS) (pp. 218-224). IEEE.

[12].   Wei Zhou*, Ruilin Li*, Shuo Yuan, ChangChun Liu, Shaowen Yao, Jing Luo#Beifang Niu#. (2017). MetaSpark: a spark-based distributed processing tool to recruit metagenomic reads to reference genomes. Bioinformatics, 33(7): 1090-1092.

[13].   Beifang Niu*, Adam D. Scott*, Sohini Sengupta*, Matthew H. Bailey, Prag Batra, Jie Ning, Matthew A. Wyczalkowski, Wen-Wei Liang, Qunyuan Zhang, Michael D. McLellan, Sam Q. Sun, Piyush Tripathi, Carolyn Lou, Kai Ye, Robert J. Mashl, John Wallis, Michael C. Wendl, Feng Chen#, Li Ding#. (2016). Protein-structure-guided discovery of functional mutations across 19 cancer types. Nature Genetics, 48(8): 827-837.

[14].   Beifang Niu*, Kai Ye*, Qunyuan Zhang, Charles Lu, Mingchao Xie, Michael D. McLellan, Michael C. Wendl and Li Ding#. (2014). MSIsensor: microsatellite instability detection using paired tu-mor-normal sequence data. Bioinformatics, 30(7):1015-6.

[15].   Beifang Niu, Zhengwei Zhu, Limin Fu, Sitao Wu, Weizhong Li#. (2011). FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes. Bioinformatics, 27(12): 1704-1705.

[16].   Beifang Niu, Limin Fu, Shulei Sun, Weizhong Li#. (2010). Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics, 11:187.

[17].   Beifang Niu#, Xianyu Lang, Zhonghua Lu, Xuebin Chi. (2009). Parallel algorithm research on several important open problems in bioinformatics. Interdisciplinary Sciences: Computational Life Sciences, 1(3): 187-195.

[18].   Beifang Niu#, Xianyu Lang, Zhonghua Lu, Xuebin Chi. (2007). ScBioGrid: a commodity supercomputing environment supporting bioinformatics research. International Journal of Computer Mathematics, 84(2):177-182.

[19]. Shiyu Cheng, Hanwei Shen, Guihua Shan#, Beifang Niu, Weihua Bai. (2021). Visual analysis of meteorological satellite data via model-agnostic meta-learning. Journal of Visualization, 24: 301–315.

[20].   Zekun Yin#, Hao Zhang#, Meiyang Liu, Wen Zhang, Honglei Song, Haidong Lan, Yanjie Wei, Beifang Niu, Bertil Schmidt, Weiguo Liu#. (2020). RabbitQC: high-speed scalable quality control for sequencing data. Bioinformatics, btaa719.

[21].   The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. (2020). Pan-cancer analysis of whole genomes. Nature, 578(7793): 82-93.

[22].   Ludmil B. Alexandrov, Jaegil Kim, Nicholas J. Haradhvala, Mi Ni Huang, Alvin Wei Tian Ng, Yang Wu, Arnoud Boot, Kyle R. Covington, Dmitry A. Gordenin, Erik N. Bergstrom, S. M. Ashiqul Islam, Nuria Lopez-Bigas, Leszek J. Klimczak, John R. McPherson, Sandro Morganella, Radhakrishnan Sabarinathan, David A. Wheeler, Ville Mustonen, PCAWG Mutational Signatures Working Group, Gad Getz, Steven G. Rozen#, Michael R. Stratton#PCAWG Consortium. (2020). The repertoire of mutational signatures in human cancer. Nature, 578(7793): 94-101.

[23].   Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah A. Wala, Ofer Shapira, Grace Tiao, Henrik Hornshøj, Julian M. Hess, Randi Istrup Juul, Ziao Lin, Lars Feuerbach, Radhakrishnan Sabarinathan, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andrés Lanzós, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A. Fonseca, Abel Gonzalez-Perez, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, Andre Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M. C. Tubio, Husen M. Umer, Liis Uusküla-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Benjamin J. Raphael, Mark A. Rubin, Chris Sander, Lincoln D. Stein, Joshua M. Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Jüri Reimand, Mark Gerstein, Ekta Khurana, Peter J. Campbell, Núria López-Bigas, PCAWG Drivers and Functional Interpretation Working Group, PCAWG Structural Variation Working Group, Joachim Weischenfeldt#, Rameen Beroukhim#, Iñigo Martincorena#, Jakob Skou Pedersen#, Gad Getz#PCAWG Consortium. (2020). Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature, 578(7793): 102-111.

[24].   Yilong Li, Nicola D. Roberts, Jeremiah A. Wala, Ofer Shapira, Steven E. Schumacher, Kiran Kumar, Ekta Khurana, Sebastian Waszak, Jan O. Korbel, James E. Haber, Marcin Imielinski, PCAWG Structural Variation Working Group, Joachim Weischenfeldt#, Rameen Beroukhim#, Peter J. Campbell#PCAWG Consortium. (2020). Patterns of somatic structural variation in human cancer genomes. Nature, 578(7793): 112-121.

[25].   Moritz Gerstung#, Clemency Jolly, Ignaty Leshchiner, Stefan C. Dentro, Santiago Gonzalez, Daniel Rosebrock, Thomas J. Mitchell, Yulia Rubanova, Pavana Anur, Kaixian Yu, Maxime Tarabichi, Amit Deshwar, Jeff Wintersinger, Kortine Kleinheinz, Ignacio Vázquez-García, Kerstin Haase, Lara Jerman, Subhajit Sengupta, Geoff Macintyre, Salem Malikic, Nilgun Donmez, Dimitri G. Livitz, Marek Cmero, Jonas Demeulemeester, Steven Schumacher, Yu Fan, Xiaotong Yao, Juhee Lee, Matthias Schlesner, Paul C. Boutros, David D. Bowtell, Hongtu Zhu, Gad Getz, Marcin Imielinski, Rameen Beroukhim, S. Cenk Sahinalp, Yuan Ji, Martin Peifer, Florian Markowetz, Ville Mustonen, Ke Yuan, Wenyi Wang, Quaid D. Morris, PCAWG Evolution & Heterogeneity Working Group, Paul T. Spellman, David C. Wedge, Peter Van Loo#PCAWG Consortium. (2020). The evolutionary history of 2,658 cancers. Nature, 578(7793): 122-128.

[26].   PCAWG Transcriptome Core Group, Claudia Calabrese, Natalie R. Davidson, Deniz Demircioğlu, Nuno A. Fonseca, Yao He, André Kahles, Kjong-Van Lehmann, Fenglin Liu, Yuichi Shiraishi, Cameron M. Soulette, Lara Urban, Liliana Greger, Siliang Li, Dongbing Liu, Marc D. Perry, Qian Xiang, Fan Zhang, Junjun Zhang, Peter Bailey, Serap Erkek, Katherine A. Hoadley, Yong Hou, Matthew R. Huska, Helena Kilpinen, Jan O. Korbel, Maximillian G. Marin, Julia Markowski, Tannistha Nandi, Qiang Pan-Hammarström, Chandra Sekhar Pedamallu, Reiner Siebert, Stefan G. Stark, Hong Su, Patrick Tan, Sebastian M. Waszak, Christina Yung, Shida Zhu, Philip Awadalla, Chad J. Creighton, Matthew Meyerson, B. F. Francis Ouellette, Kui Wu, Huanming Yang, PCAWG Transcriptome Working Group, Alvis Brazma#, Angela N. Brooks#, Jonathan Göke, Gunnar Rätsch#, Roland F. Schwarz, Oliver Stegle, Zemin Zhang, PCAWG Consortium. (2020). Genomic basis for RNA alterations in cancer. Nature, 578(7793): 129-136.

[27].   Sergei Yakneen#, Sebastian M. Waszak, PCAWG Technical Working Group, Michael Gertz, Jan O. Korbel#PCAWG Consortium. (2020). Butler enables rapid cloud-based analysis of thousands of human genomes. Nature Biotechnology, 38(3): 288-292.

[28].   Kadir C. Akdemir, Victoria T. Le, Sahaana Chandran, Yilong Li, Roel G. Verhaak, Rameen Beroukhim, Peter J. Campbell, Lynda Chin, Jesse R. Dixon, P. Andrew Futreal#, PCAWG Structural Variation Working Group, PCAWG Consortium. (2020). Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer. Nature Genetics, 52(3): 294-305.

[29].   Bernardo Rodriguez-Martin, Eva G. Alvarez, Adrian Baez-Ortega, Jorge Zamora, Fran Supek, Jonas Demeulemeester, Martin Santamarina, Young Seok Ju, Javier Temes, Daniel Garcia-Souto, Harald Detering, Yilong Li, Jorge Rodriguez-Castro, Ana Dueso-Barroso, Alicia L. Bruzos, Stefan C. Dentro, Miguel G. Blanco, Gianmarco Contino, Daniel Ardeljan, Marta Tojo, Nicola D. Roberts, Sonia Zumalave, Paul A. W. Edwards, Joachim Weischenfeldt, Montserrat Puiggròs, Zechen Chong, Ken Chen, Eunjung Alice Lee, Jeremiah A. Wala, Keiran Raine, Adam Butler, Sebastian M. Waszak, Fabio C. P. Navarro, Steven E. Schumacher, Jean Monlong, Francesco Maura, Niccolo Bolli, Guillaume Bourque, Mark Gerstein, Peter J. Park, David C. Wedge, Rameen Beroukhim, David Torrents, Jan O. Korbel, Inigo Martincorena, Rebecca C. Fitzgerald, Peter Van Loo, Haig H. Kazazian, Kathleen H. Burns, PCAWG Structural Variation Working Group, Peter J. Campbell#, Jose M. C. Tubio#PCAWG Consortium. (2020). Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nature Genetics, 52(3): 306-319.

[30].   Marc Zapatka, Ivan Borozan, Daniel S. Brewer, Murat Iskar, Adam Grundhoff, Malik Alawi, Nikita Desai, Holger Sültmann, Holger Moch, PCAWG Pathogens, Colin S. Cooper, Roland Eils, Vincent Ferretti, Peter Lichter#PCAWG Consortium. (2020). The landscape of viral associations in human cancers. Nature Genetics, 52(3): 320-330.

[31].   Isidro Cortés-Ciriano, Jake June-Koo Lee, Ruibin Xi, Dhawal Jain, Youngsook L. Jung, Lixing Yang, Dmitry Gordenin, Leszek J. Klimczak, Cheng-Zhong Zhang, David S. Pellman, PCAWG Structural Variation Working Group, Peter J. Park#PCAWG Consortium. (2020). Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nature Genetics, 52(3): 331-341.

[32].   Yuan Yuan, Young Seok Ju, Youngwook Kim, Jun Li, Yumeng Wang, Christopher J. Yoon, Yang Yang, Inigo Martincorena, Chad J. Creighton, John N. Weinstein, Yanxun Xu, Leng Han, Hyung-Lae Kim, Hidewaki Nakagawa, Keunchil Park#, Peter J. Campbell#, Han Liang#PCAWG Consortium. (2020). Comprehensive Molecular Characterization of Mitochondrial Genomes in Human Cancers. Nature Genetics, 52(3): 342-352.

[33].   Matthew H. Bailey, William U. Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, Shantao Li, Yize Li, Sean Kelso, MC3 Working Group, PCAWG novel somatic mutation calling methods working group, Gordon Saksena, Kyle Ellrott, Michael C. Wendl, David A. Wheeler, Gad Getz, Jared T. Simpson, Mark B. Gerstein#, Li Ding#, PCAWG Consortium. (2020). Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature Communications, 11:4748.

[34].   Constance H. Li, Stephenie D. Prokopec, Ren X. Sun, Fouad Yousif, Nathaniel Schmitz, PCAWG Tumour Subtypes and Clinical Translation, Paul C. Boutros#, PCAWG Consortium. (2020). Sex differences in oncogenic mutational processes. Nature Communications, 11:4330.

[35].   Wei Jiao, Gurnit Atwal, Paz Polak, Rosa Karlic, Edwin Cuppen, PCAWG Tumor Subtypes and Clinical Translation Working Group, Alexandra Danyi, Jeroen de Ridder, Carla van Herpen, Martijn P. Lolkema, Neeltje Steeghs, Gad Getz, Quaid Morris, Lincoln D. Stein#PCAWG Consortium. (2020). A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns. Nature Communications, 11: 728.

[36].   Matthew A. Reyna, David Haan, Marta Paczkowska, Lieven P. C. Verbeke, Miguel Vazquez, Abdullah Kahraman, Sergio Pulido-Tamayo, Jonathan Barenboim, Lina Wadi, Priyanka Dhingra, Raunak Shrestha, Gad Getz, Michael S. Lawrence, Jakob Skou Pedersen, Mark A. Rubin, David A. Wheeler, Søren Brunak, Jose M. G. Izarzugaza, Ekta Khurana, Kathleen Marchal, Christian von Mering, S. Cenk Sahinalp, Alfonso Valencia, PCAWG Drivers and Functional Interpretation Working Group, Jüri Reimand#, Joshua M. Stuart#, Benjamin J. Raphael#PCAWG Consortium. (2020). Pathway and network analysis of more than 2500 whole cancer genomes. Nature Communications, 11: 729.

[37].   Marek Cmero#, Ke Yuan, Cheng Soon Ong, Jan Schröder, PCAWG Evolution and Heterogeneity Working Group, Niall M. Corcoran, Tony Papenfuss, Christopher M. Hovens, Florian Markowetz, Geoff Macintyre#PCAWG Consortium. (2020). Inferring structural variant cancer cell fraction. Nature Communications, 11: 730.

[38].   Yulia Rubanova, Ruian Shi, Caitlin F. Harrigan, Roujia Li, Jeff Wintersinger, Nil Sahin, Amit Deshwar, PCAWG Evolution and Heterogeneity Working Group, Quaid Morris#PCAWG Consortium. (2020). Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig. Nature Communications, 11: 731.

[39].   Lina Sieverling, Chen Hong, Sandra D. Koser, Philip Ginsbach, Kortine Kleinheinz, Barbara Hutter, Delia M. Braun, Isidro Cortés-Ciriano, Ruibin Xi, Rolf Kabbe, Peter J. Park, Roland Eils, Matthias Schlesner, PCAWG-Structural Variation Working Group, Benedikt Brors, Karsten Rippe, David T. W. Jones, Lars Feuerbach#PCAWG Consortium. (2020). Genomic footprints of activated telomere maintenance mechanisms in cancer. Nature Communications, 11: 733.

[40].   Shimin Shuai#, PCAWG Drivers and Functional Interpretation Working Group, Steven Gallinger, Lincoln Stein#PCAWG Consortium. (2020). Combined burden and functional impact tests for cancer driver discovery using DriverPower. Nature Communications, 11: 734.

[41].   Marta Paczkowska, Jonathan Barenboim, Nardnisa Sintupisut, Natalie S. Fox, Helen Zhu, Diala Abd-Rabbo, Miles W. Mee, Paul C. Boutros, PCAWG Drivers and Functional Interpretation Working Group, Jüri Reimand#PCAWG Consortium. (2020). Integrative pathway enrichment analysis of multivariate omics data. Nature Communications, 11: 735.

[42].   Yiqun Zhang, Fengju Chen, Nuno A. Fonseca, Yao He, Masashi Fujita, Hidewaki Nakagawa, Zemin Zhang, Alvis Brazma, PCAWG Transcriptome Working Group, PCAWG Structural Variation Working Group, Chad J. Creighton#PCAWG Consortium. (2020). High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations. Nature Communications, 11: 736.

[43].   Vinayak Bhandari, Constance H. Li, Robert G. Bristow#, Paul C. Boutros#PCAWG Consortium. (2020). Divergent mutational processes distinguish hypoxic and normoxic tumours. Nature Communications, 11: 737.

[44].   Joana Carlevaro-Fita, Andrés Lanzós, Lars Feuerbach, Chen Hong, David Mas-Ponte, Jakob Skou Pedersen, PCAWG Drivers and Functional Interpretation Group, Rory Johnson#PCAWG Consortium. (2020). Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. Communications Biology, 3: 56.

[45].   Junlan Zhu, Zhongxian Tian, Yang Li, Xiaohui Hua, Dongyun Zhang, Jingxia Li, Honglei Jin, Jiheng Xu, Wei Chen, Beifang Niu, Xue-Ru Wu, Sergio Comincini, Haishan Huang#, Chuanshu Huang#. (2019). ATG7 Promotes Bladder Cancer Invasion via Autophagy‐Mediated Increased ARHGDIB mRNA Stability. Advanced Science, 6(8): 1801927.

[46].   Liping Sun, Fengyan Fan, Ruilin Li, Beifang Niu, Liguo Zhu, Shuai Yu, Shuying Wang, Cuiying Li# and Deqing Wang#. (2018). Different Erythrocyte MicroRNA Profiles in Low- and High-Altitude Individuals. Frontiers in Physiology, 9: 1099.

[47].   Yanan Cao#, Weiwei Zhou, Lin Li, Jiaqian Wang, Zhibo Gao, Yiran Jiang, Xiuli Jiang, Aijing Shan, Matthew H. Bailey, Kuan-lin Huang, Sam Q. Sun, Michael D. McLellan, Beifang Niu, Weiqing Wang, Li Ding#, Guang Ning#. (2018). Pan-Cancer Analysis of Somatic Mutations Across 21 Neuroendocrine Tumor Types. Cell Research, 28(5): 601-604.

[48].   Robert J Mashl*, Adam D Scott, Kuan-lin Huang, Matthew A Wyczalkowski, Christopher J Yoon, Beifang Niu, Erin DeNardo, Venkata D Yellapantula, Robert E Handsaker, Ken Chen, Daniel C Koboldt, Kai Ye, David Fenyö, Benjamin Raphael, Michael C Wendl, Li Ding#. (2017). GenomeVIP: a cloud platform for genomic variant discovery and interpretation. Genome Research, 27(8): 1450-1459.

[49].   Kuan-lin Huang*, Shunqiang Li*, Philipp Mertins*, Song Cao, Harsha P Gunawardena, Kelly V Ruggles, DR Mani, Karl R Clauser, Maki Tanioka, Jerry Usary, Shyam M Kavuri, Ling Xie, Christopher Yoon, Jana W Qiao, John Wrobel, Matthew A Wyczalkowski, Petra Erdmann-Gilmore, Jacqueline E Snider, Jeremy Hoog, Purba Singh, Beifang Niu, Zhanfang Guo, Sam Qiancheng Sun, Souzan Sanati, Emily Kawaler, Xuya Wang, Adam Scott, Kai Ye, Michael D McLellan, Michael C Wendl, Anna Malovannaya, Jason M Held, Michael A Gillette, David Fenyö, Christopher R Kinsinger, Mehdi Mesri, Henry Rodriguez, Sherri R Davies, Charles M Perou, Cynthia Ma, R Reid Townsend, Xian Chen, Steven A Carr, Matthew J Ellis, Li Ding#. (2017). Proteogenomic integration reveals therapeutic targets in breast cancer xenografts. Nature Communications, 8: 14864.

[50].   Song Cao, Michael C. Wendl, Matthew A. Wyczalkowski, Kristine Wylie, Kai Ye, Reyka Jayasinghe, Mingchao Xie, Song Wu, Beifang Niu, Robert Grubb III, Kimberly J. Johnson, Hiram Gay, Ken Chen, Janet S. Rader, John F. Dipersio, Feng Chen, Li Ding#. (2016). Divergent viral presentation among human tumors and adjacent normal tissues. Scientific Reports, 6: 28294.

[51].   Kai Ye*, Jiayin Wang*, Reyka Jayasinghe, Eric-Wubbo Lameijer, Joshua F McMichael, Jie Ning, Michael D McLellan, Mingchao Xie, Song Cao, Venkata Yellapantula, Kuan-lin Huang, Adam Scott, Steven Foltz, Beifang Niu, Kimberly J Johnson, Matthijs Moed, PEline Slagboom, Feng Chen, Michael C Wendl, Li Ding#. (2015). Systematic discovery of complex insertions and deletions in human cancers. Nature Medicine, 22(1): 97-104.

[52].   Charles Lu*, Mingchao Xie*, Michael C. Wendl, Jiayin Wang, Michael D. McLellan, Mark D. M. Leiserson, Kuan-lin Huang, Matthew A. Wyczalkowski, Reyka Jayasinghe, Tapahsama Banerjee, Jie Ning, Piyush Tripathi, Qunyuan Zhang, Beifang Niu, Kai Ye, Heather K. Schmidt, Robert S. Fulton,Joshua F. McMichael, Prag Batra, Cyriac Kandoth, Maheetha Bharadwaj, Daniel C. Koboldt, Christopher A. Miller, Krishna L. Kanchi, James M. Eldred, David E. Larson, John S. Welch, Ming You, Bradley A. Ozenberger, Ramaswamy Govindan, Matthew J. Walter, Matthew J. Ellis, Elaine R. Mardis, Timothy A. Graubert,  John F. Dipersio, Timothy J. Ley, Richard K. Wilson, Paul J. Goodfellow, Benjamin J. Raphael, Feng Chen, Kimberly J. Johnson, Jeffrey D. Parvin, Li Ding#. (2015). Patterns and functional implications of rare germline variants across 12 cancer types. Nature Communications, 6: 10086.

[53].   Mark DM Leiserson*, Fabio Vandin*, Hsin-Ta Wu, Jason R Dobson, Jonathan V Eldridge, Jacob L Thomas, Alexandra Papoutsaki, Younhun Kim, Beifang Niu, Michael McLellan, Michael S Lawrence, Abel Gonzalez-Perez, David Tamborero, Yuwei Cheng, Gregory A Ryslik, Nuria Lopez-Bigas, Gad Getz, Li Ding, Benjamin J Raphael#. (2015). Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes. Nature Genetics, 47(2): 106-144.

[54].   The Cancer Genome Atlas Research Network. (2014). Comprehensive molecular characterization of gastric adenocarcinoma. Nature, 513(7517): 202-209.

[55].   Katherine A Hoadley*, Christina Yau*, Denise M Wolf*, Andrew D Cherniack*, David Tamborero, Sam Ng, Max DM Leiserson, Beifang Niu, Michael D McLellan, Vladislav Uzunangelov, Jiashan Zhang, Cyriac Kandoth, Rehan Akbani, Hui Shen, Larsson Omberg, Andy Chu, Adam A Margolin, Laura J van’t Veer, Nuria Lopez-Bigas, Peter W Laird, Benjamin J Raphael, Li Ding, A Gordon Robertson, Lauren A Byers, Gordon B Mills, John N Weinstein, Carter Van Waes, Zhong Chen, Eric A Collisson, Christopher C Benz#, Charles M Perou#, Joshua M Stuart#, Cancer Genome Atlas Research Network. (2014). Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell, 158(4): 929-944.

[56].   Cyriac Kandoth*, Michael D McLellan*, Fabio Vandin, Kai Ye, Beifang Niu, Charles Lu, Mingchao Xie, Qunyuan Zhang, Joshua F McMichael, Matthew A Wyczalkowski, Mark DM Leiserson, Christopher A Miller, John S Welch, Matthew J Walter, Michael C Wendl, Timothy J Ley, Richard K Wilson, Benjamin J Raphael, Li Ding#. (2013). Mutational landscape and significance across 12 major cancer types. Nature, 502 (7471): 333-339.

[57].   Ken Chen#, Nicholas E Navin, Yong Wang, Heather K Schmidt, John W Wallis, Beifang Niu, Xian Fan, Hao Zhao, Michael D Mclellan, Katherine A Hoadley, Elaine R Mardis, Timothy J Ley, Charles M Perou, Richard K Wilson, Li Ding#. (2013). BreakTrans: uncovering the genomic architecture of gene fusions. Genome Biology, 14(8): R87.

[58].   Matthew J. Walter*, Dong Shen*, Jin Shao*, Li Ding, Brian White, Cyriac Kandoth, Christopher A. Miller, Beifang Niu, Michael D. McLellan, Nathan D. Dees, Robert Fulton, Kevin Elliot, Sharon Heath, Marcus Grillot, Peter Westervelt, Daniel C. Link, John F. DiPersio, Elaine Mardis, Timothy J. Ley, Richard K. Wilson, Timothy A. Graubert#. (2013). Clonal Diversity of Recurrently Mutated Genes in Myelodysplastic Syndromes. Leukemia, 27: 1275–1282.

[59].   Zhengwei Zhu*Beifang Niu, Sitao Wu, Weizhong Li#. (2013). MGAviewer: A desktop visualization tool for analysis of metage-nomics alignment data. Bioinformatics, 29(1): 122-123.

[60].   Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu and Weizhong Li#. (2012). CD-HIT: accelerated for clustering the next generation sequencing data. Bioinformatics, 28(23): 3150–3152.

[61].   Weizhong Li#, Limin Fu, Beifang Niu, Sitao Wu, John Wooley. (2012). Ultrafast clustering algorithms for metagenomic sequence analysis. Briefings in Bioinformatics, 13 (6): 656-668.

[62].   Sitao Wu, Zhengwei Zhu, Limin Fu, Beifang Niu, Weizhong Li#. (2011). WebMGA: a Customizable Web Server for Fast Metagenomic Sequence Analysis. BMC Genomics, 12: 444.

[63].   Ying Huang, Beifang Niu, Ying Gao, Limin Fu, Weizhong Li#. (2010). CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics, 26(5): 680–682.

Research Interests

  • Bioinformatics software development and algorithm optimization.

  • Cancer genomics and Metagenomics.

  • Large scale precision medicine data analysis and sequence clustering, alignment and assembly algorithm for next generation sequencing data. 

  • High performance parallel computing and cloud computing.


Beifang Niu, John Wallis, Qunyuan Zhang, PiyushTripathi, Mike McLellan, Matt Wyczalkowski, CyriacKandoth, MaheethaBharadwa, Kai Ye, R. Jay Mash, Mike Wendl, Feng Chen, Li Ding. HOTSPOT3D: A novel computational tool for inferring functional importance of cancer mutations through 3D proximity analyses. Genome Informatics 2013, Cold Spring harbor, New York, US. Oct 31-Nov 2,2013. Poster.

Beifang Niu, Limin Fu, Sitao Wu and Weizhong Li. Filtering out extra redundancy significantly improve the assembly of metagenomic short reads, International Human Microbiome Congress (IHMC),  St Louis, US. March 9-11, 2011. Poster.

Beifang Niu, Zhengwei Zhu, Limin Fu, Sitao Wu, and Weizhong Li. FR-HIT, a Very Fast Program to Recruit Metagenomic Reads to Homologous Reference Genomes. International Human Microbiome Congress (IHMC),  St Louis, US. March 9-11, 2011. Poster.

Beifang Niu, Xianyu Lang, Zhonghua Lu and Xuebin Chi. ScBioGrid: a commodity supercomputing environment supporting bioinformatics research. Distributed Computing and its Applications in Business, Engineering, and Sciences/ International Conference on Parallel Algorithms and Computational Environment (DCABES/ICPACE), August 25-27, 2005, London. UK. Presentation.


The  McDonnell Genome Institute, School of Medicine, Washington University in St. Louis, Missouri, US.

San Diego Supercomputer Center(SDSC), University of California, San Diego, California, US.

The J. Craig Venter Institute (JCVI), La Jolla, San Diego, California, US. 

The General Hospital of the People's Liberation Army (PLAGH), Beijing, China.

Honors & Distinctions


Top 10 Clinical Research Achievement Awards for 2015(US)(Multiplatform analysis of 12 cancer types reveals   molecular classification within and across tissues of origin)


Member, The Clinical Proteomic Tumor Analysis Consortium (CPTAC) Cancer Biology Working Group


American Association for Cancer Research (AACR)


Member, iSeqTools Network


Member, International Cancer Genome Consortium(ICGC)


Member, The Cancer Genome Atlas (TCGA) Pan Cancer Working Group


Member, The Cancer Genome Atlas (TCGA) Lung Cancer Analysis Working Group


Member, The Cancer Genome Atlas (TCGA) Endometrial Cancer Analysis Working Group


Member, The International Society for Computational Biology (ISCB)


Genome Research, Bioinformatics, Nucleic Acid Research, BMC Bioinformatics and BMC Genomics journals, IEEE Transactions on Computational Biology and Bioinformatics (TCCB)