基本信息
牛北方  男  博导  中国科学院计算机网络信息中心
电子邮件: bniu@sccas.cn
通信地址: 北京市海淀区东升南路2号院中国科学院信息化大厦
邮政编码: 100083

研究领域

      长期从事临床肿瘤基因组学、医学生物信息学与高性能计算交叉领域的研究工作。聚焦于肿瘤驱动信号及免疫治疗标志物的发现算法和软件技术研发,开发基因组数据建模和机器学习新模型。基于新一代高通量测序技术,提出了基因组微卫星不稳定(MSI)信号印记及精准探测的新方法,形成了国际上引用率最高的肿瘤样本多层次临床应用场景的MSI算法体系,推动了肿瘤免疫治疗领域基础研究的发展。基于蛋白质结构生物学理论,发展了肿瘤驱动突变预测的空间聚类计算方法,发现了药物与癌突变间的多维相互关系及具有前景的泛癌种可成药靶点。基于启发式算法理论,发展了生物序列去冗余的新型分布式并行优化算法和病原微生物全长基因组序列的聚类算法,形成了国际上具有核心地位的生物序列聚类分析算法与软件工具包。迄今发表同行评审论文70余篇,包括Nature、Nature Genetics等期刊,总被引用17000余次,ESI高被引(1%)论文10余篇,其中多项研究成果被媒体报道。是MSIsensor、MuSiC/MuSiC2、HotSpot3D、CD-HIT系列等流行癌症基因检测软件的主要作者。其中的MSIsensor/MSIsensor2/MSIsensor-ct癌症基因组微卫星不稳定性(MSI)检测系统已作为该领域的核心方法之一,在国际上被多家科研单位、医疗机构和公司广泛使用,并被成功应用于FDA批准的首个基于NGS的癌症多基因检测试剂盒(MSK-IMPACT)。主持国家自然科学基金面上项目、国家重点研发计划课题、中科院信息化专项课题等。目前担任中国运筹学会计算生物学分会理事,中国计算机学会高性能计算专委与生物信息学专委委员等。

招生信息

   
招生专业
081202-计算机软件与理论
1001Z1-精准医学
招生方向
高性能计算,医学生物信息学
临床肿瘤基因组学

教育背景

2002-09--2009-02   中国科学院计算机网络信息中心   工学博士
1998-09--2002-07   山东农业大学计算机系   工学学士
学历
研究生

学位
博士

工作经历

   
工作简历
2012-08~2015-01,美国圣路易斯华盛顿大学(WUSTL), Research Scientist
2009-03~2012-07,美国加州大学圣迭戈(UCSD), 博士后
社会兼职
2019-10-23-今,中国科学院计算技术研究所西部高等研究院, 特聘研究员
2018-10-20-今,中国计算机学会高性能计算专业委员会, 会员
2018-10-13-今,中国计算机学会生物信息专业委员会, 会员
2017-09-30-今,贵州大学特聘教授, 兼职教授
2016-11-30-今,中国计算机学会, 会员
2015-08-13-今,中国运筹学会计算生物学分会, 理事
2015-08-11-今,中国运筹学会, 会员

专利与奖励

   
奖励信息
(1) Top 10 Clinical Research Achievement Awards for 2015(2015年美国10大临床研究成就奖), , 国家级, 2015
专利成果
[1] 陈义夫, 冯仰德, 牛北方, 刘威尔. 基于国家高性能计算环境的中小企业计算社区系统. CN: CN112416565A, 2021-02-26.

[2] 邓笋根, 牛北方. 一种共深度点CDP的确定方法及装置. CN: CN110068863A, 2019-07-30.

[3] 陆忠华, 李铄, 孙永泽, 代闯闯, 邓笋根, 牛北方. 一种基于Mesos的分布式超参数优化系统及方法. CN: CN110046046A, 2019-07-23.

出版信息

   
发表论文
[1] Xi Cheng, Haiming Yu, Jinying Li, Xiaona Han, Erhong Meng, Houqing Zhou, Dongliang Wang, Beifang Niu, Xiaotao Zhang. Dramatic response to local radiotherapy in a refractory metastatic mediastinal yolk sac tumor patient harboring a germline BRCA2 frameshift mutation: a case report. Cancer Biology & Therapy[J]. 2022, [2] 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. MSIsensor-ct: microsatellite instability detection using cfDNA sequencing data. BRIEFINGS IN BIOINFORMATICS[J]. 2021, 22(5): [3] 何小雨, 韩鑫胤, 牛北方. 肿瘤突变印记的求解算法比较. 计算机系统应用[J]. 2021, 30(12): 46-54, [4] He, Xiaoyu, Chen, Shanyu, Li, Ruilin, Han, Xinyin, He, Zhipeng, Yuan, Danyang, Zhang, Shuying, Duan, Xiaohong, Niu, Beifang. Comprehensive fundamental somatic variant calling and quality management strategies for human cancer genomes. BRIEFINGS IN BIOINFORMATICS[J]. 2021, 22(3): [5] 何小雨, 邓笋根, 栾海晶, 牛北方. 国家高性能计算环境的虚拟数据空间运行支撑技术研究. 大数据[J]. 2021, 7(2): 158-171, http://lib.cqvip.com/Qikan/Article/Detail?id=7104093237.
[6] 代闯闯, 栾海晶, 杨雪莹, 过晓冰, 陆忠华, 牛北方. 区块链技术研究综述. 计算机科学[J]. 2021, 48(11A): 500-508, [7] He, Xiaoyu, Zhang, Yu, Yuan, Danyang, Han, Xinyin, He, Jiayin, Duan, Xiaohong, Liu, Siyao, Wang, Xintong, Niu, Beifang. DIVIS: Integrated and Customizable Pipeline for Cancer Genome Sequencing Analysis and Interpretation. FRONTIERS IN ONCOLOGY[J]. 2021, 11: http://dx.doi.org/10.3389/fonc.2021.672597.
[8] Danyang Yuan, Xiaoyu He, Xinyin Han, Chunyan Yang, Fei Liu, Shuying Zhang, Haijing Luan, Ruilin Li, Jiayin He, Duan, Xiaohong, Dongliang Wang, Qiming Zhou, Sujun Gao, Beifang Niu. Comprehensive review and evaluation of computational methods for identifying FLT3-internal tenderm duplication in acute myeloid leukaemia. Briefings in Bioinformatics[J]. 2021, 22(5): [9] Yin, Zekun, Zhang, Hao, Liu, Meiyang, Zhang, Wen, Song, Honglei, Lan, Haidong, Wei, Yanjie, Niu, Beifang, Schmidt, Bertil, Liu, Weiguo. RabbitQC: high-speed scalable quality control for sequencing data. BIOINFORMATICS[J]. 2021, 37(4): 573-574, http://dx.doi.org/10.1093/bioinformatics/btaa719.
[10] Cheng, Shiyu, Li, Xiaochen, Shan, Guihua, Niu, Beifang, Wang, Yang, Luo, MaoKang. ACMViz: a visual analytics approach to understand DRL-based autonomous control model. JOURNAL OF VISUALIZATION[J]. 2021, http://apps.webofknowledge.com/CitedFullRecord.do?product=UA&colName=WOS&SID=5CCFccWmJJRAuMzNPjj&search_mode=CitedFullRecord&isickref=WOS:000700968000001.
[11] 秦广军, 肖利民, 张广艳, 牛北方, 陈志广. 面向国家高性能计算环境的虚拟数据空间系统. 大数据[J]. 2021, 7(2): 101-122, http://lib.cqvip.com/Qikan/Article/Detail?id=7104093234.
[12] 张舒莹, 韩鑫胤, 何小雨, 袁丹阳, 栾海晶, 李瑞琳, 何佳茵, 牛北方. 基于机器学习的基因组微卫星状态探测方法综述. 数据与计算发展前沿[J]. 2021, 126-135, https://t.cnki.net/kcms/detail?v=3uoqIhG8C46NmWw7YpEsKMypi3qVj28LEUDxQXHYyS3fbyEOrIfBzA0n_znVSGEh23VTYlquiImaTFULhBrMsbV5ietEVNWu.
[13] Cheng, Shiyu, Shen, Hanwei, Shan, Guihua, Niu, Beifang, Bai, Weihua. Visual analysis of meteorological satellite data via model-agnostic meta-learning. JOURNAL OF VISUALIZATION[J]. 2021, 24(2): 301-315, http://dx.doi.org/10.1007/s12650-020-00704-4.
[14] Yakneen, Sergei, Waszak, Sebastian M, Gertz, Michael, Korbel, Jan O, Aminou, Brice, Bartolome, Javier, Boroevich, Keith A, Boyce, Rich, Brooks, Angela N, Buchanan, Alex, Buchhalter, Ivo, Butler, Adam P, Byrne, Niall J, Cafferkey, Andy, Campbell, Peter J, Chen, Zhaohong, Cho, Sunghoon, Choi, Wan, Clapham, Peter, DavisDusenbery, Brandi N, De La Vega, Francisco M, Demeulemeester, Jonas, Dow, Michelle T, Dursi, Lewis Jonathan, Eils, Juergen, Eils, Roland, Ellrott, Kyle, Farcas, Claudiu, Favero, Francesco, Fayzullaev, Nodirjon, Ferretti, Vincent, Flicek, Paul, Fonseca, Nuno A, Gelpi, Josep Ll, Getz, Gad, Gibson, Bob, Grossman, Robert L, Harismendy, Olivier, Heath, Allison P, Heinold, Michael C, Hess, Julian M, Hofmann, Oliver, Hong, Jongwhi H, Hudson, Thomas J, Hutter, Barbara, Hutter, Carolyn M, Huebschmann, Daniel, Imoto, Seiya, Ivkovic, Sinisa, Jeon, SeungHyup, Jiao, Wei, Jung, Jongsun, Kabbe, Rolf, Kahles, Andre, Kerssemakers, Jules N A, Kim, HyungLae, Kim, Hyunghwan, Kim, Jihoon, Kim, Youngwook, Kleinheinz, Kortine, Koscher, Michael, Koures, Antonios, Kovacevic, Milena, Lawerenz, Chris, Leshchiner, Ignaty, Liu, Jia, Livitz, Dimitri, Mihaiescu, George L, Mijalkovic, Sanja, Lazic, Ana Mijalkovic, Miyano, Satoru, Miyoshi, Naoki, NahalBose, Hardeep K, Nakagawa, Hidewaki, Nastic, Mia, Newhouse, Steven J, Nicholson, Jonathan, OConnor, Brian D, Ocana, David, Ohi, Kazuhiro, OhnoMachado, Lucila, Omberg, Larsson, Ouellette, B F Francis, Paramasivam, Nagarajan, Perry, Marc D, Pihl, Todd D, Prinz, Manuel, Puiggros, Montserrat, Radovic, Petar, Raine, Keiran M, Rheinbay, Esther, Rosenberg, Mara, Royo, Romina, Raetsch, Gunnar, Saksena, Gordon, Schlesner, Matthias, Shorser, Solomon, I, Short, Charles, Sofia, Heidi J, Spring, Jonathan, Stein, Lincoln D, Struck, Adam J, Tiao, Grace, Tijanic, Nebojsa, Torrents, David, Van Loo, Peter, Vazquez, Miguel, Vicente, David, Wala, Jeremiah A, Wang, Zhining, Weischenfeldt, Joachim, Werner, Johannes, Williams, Ashley, Woo, Youngchoon, Wright, Adam J, Xiang, Qian, Yang, Liming, Yuen, Denis, Yung, Christina K, Zhang, Junjun, PCAWG Tech Working Grp, PCAWG Consortium. Butler enables rapid cloud-based analysis of thousands of human genomes. NATURE BIOTECHNOLOGY[J]. 2020, 38(3): 288-+, https://www.webofscience.com/wos/woscc/full-record/WOS:000511288100001.
[15] 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. Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig. Nature Communications[J]. 2020, 11(1): 1-12, http://dx.doi.org/10.1038/s41467-020-14352-7.
[16] Marta Paczkowska, Jonathan Barenboim, Nardnisa Sintupisut, Natalie S Fox, Helen Zhu, Diala AbdRabbo, Miles W Mee, Paul C Boutros, PCAWG Drivers and Functional Interpretation Working Group, Jri Reimand, PCAWG Consortium. Integrative pathway enrichment analysis of multivariate omics data. Nature Communications[J]. 2020, 11(1): 1-16, https://doaj.org/article/0e1be01e74114d78838f12db1d7166ab.
[17] Sun, Liping, Yu, Yang, Niu, Beifang, Wang, Deqing. Red Blood Cells as Potential Repositories of MicroRNAs in the Circulatory System. FRONTIERS IN GENETICS[J]. 2020, 11: https://doaj.org/article/000ba4a58eae4514b82cb45cf060e7c7.
[18] Constance H Li, Stephenie D Prokopec, Ren X Sun, Fouad Yousif, Nathaniel Schmitz, PCAWG Tumour Subtypes and Clinical Translation, Paul C Boutros, PCAWG Consortium. Sex differences in oncogenic mutational processes. NATURE COMMUNICATIONS[J]. 2020, 11(1): https://doaj.org/article/675a0b63db164a13bc463d8f773c85d4.
[19] Zapatka, Marc, Borozan, Ivan, Brewer, Daniel S, Iskar, Murat, Grundhoff, Adam, Alawi, Malik, Desai, Nikita, Sueltmann, Holger, Moch, Holger, Cooper, Colin S, Eils, Roland, Ferretti, Vincent, Lichter, Peter, PCAWG Pathogens, PCAWG Consortium. The landscape of viral associations in human cancers. NATURE GENETICS[J]. 2020, 52(3): 320-+, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8076016/.
[20] CortesCiriano, Isidro, Lee, Jake JuneKoo, Xi, Ruibin, Jain, Dhawal, Jung, Youngsook L, Yang, Lixing, Gordenin, Dmitry, Klimczak, Leszek J, Zhang, ChengZhong, Pellman, David S, Park, Peter J, Akdemir, Kadir C, Alvarez, Eva G, BaezOrtega, Adrian, Beroukhim, Rameen, Boutros, Paul C, Bowtell, David D L, Brors, Benedikt, Burns, Kathleen H, Campbell, Peter J, Chan, Kin, Chen, Ken, DuesoBarroso, Ana, Dunford, Andrew J, Edwards, Paul A, Estivill, Xavier, Etemadmoghadam, Dariush, Feuerbach, Lars, Fink, J Lynn, FrenkelMorgenstern, Milana, Garsed, Dale W, Gerstein, Mark, Gordenin, Dmitry A, Haan, David, Haber, James E, Hess, Julian M, Hutter, Barbara, Imielinski, Marcin, Jones, David T W, Ju, Young Seok, Kazanov, Marat D, Koh, Youngil, Korbel, Jan O, Kumar, Kiran, Lee, Eunjung Alice, Li, Yilong, Lynch, Andy G, Macintyre, Geoff, Markowetz, Florian, Martincorena, Inigo, MartinezFundichely, Alexander, Miyano, Satoru, Nakagawa, Hidewaki, Navarro, Fabio C P, Ossowski, Stephan, Pearson, John, V, Puiggros, Montserrat, Rippe, Karsten, Roberts, Nicola D, Roberts, Steven A, RodriguezMartin, Bernardo, Schumacher, Steven E, Scully, Ralph, Shackleton, Mark, Sidiropoulos, Nikos, Sieverling, Lina, Stewart, Chip, Torrents, David, Tubio, Jose M C, Villasante, Izar, Waddell, Nicola, Wala, Jeremiah A, Weischenfeldt, Joachim, Yao, Xiaotong, Yoon, SungSoo, Zamora, Jorge, PCAWG Struct Variation Working Grp, PCAWG Consortium. Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. NATURE GENETICS[J]. 2020, 52(3): 331-+, https://www.webofscience.com/wos/woscc/full-record/WOS:000511282900004.
[21] Dai, Chuangchuang, Yang, Xueying, Qiu, Meikang, Guo, Xiaobing, Lu, Zhonghua, Niu, Beifang. Digital Currency Investment Strategy Framework Based on Ranking. ALGORITHMS AND ARCHITECTURES FOR PARALLEL PROCESSING, ICA3PP 2020, PT IIInull. 2020, 12454: 654-662, [22] Calabrese, Claudia, Davidson, Natalie R, Demircioglu, Deniz, Fonseca, Nuno A, He, Yao, Kahles, Andre, KjongVan Lehmann, Liu, Fenglin, Shiraishi, Yuichi, Soulette, Cameron M, Urban, Lara, Greger, Liliana, Li, Siliang, Liu, Dongbing, Perry, Marc D, Xiang, Qian, Zhang, Fan, Zhang, Junjun, Bailey, Peter, Erkek, Serap, Hoadley, Katherine A, Hou, Yong, Huska, Matthew R, Kilpinen, Helena, Korbel, Jan O, Marin, Maximillian G, Markowski, Julia, Nandi, Tannistha, PanHammarstrom, Qiang, Pedamallu, Chandra Sekhar, Siebert, Reiner, Stark, Stefan G, Su, Hong, Tan, Patrick, Waszak, Sebastian M, Yung, Christina, Zhu, Shida, Awadalla, Philip, Creighton, Chad J, Meyerson, Matthew, Ouellette, B F Francis, Wu, Kui, Yang, Huanming, Brazma, Alvis, Brooks, Angela N, Goke, Jonathan, Raetsch, Gunnar, Schwarz, Roland F, Stegle, Oliver, Zhang, Zemin, PCAWG Transcriptome Core Grp, PCAWG Transcriptome Working Grp, PCAWG Consortium. Genomic basis for RNA alterations in cancer. NATURE[J]. 2020, 578(7793): 129-+, https://www.webofscience.com/wos/woscc/full-record/WOS:000529097800012.
[23] Chen, Shanyu, He, Xiaoyu, Li, Ruilin, Duan, Xiaohong, Niu, Beifang. HotSpot3D web server: an integrated resource for mutation analysis in protein 3D structures. BIOINFORMATICS[J]. 2020, 36(12): 3944-3946, https://www.webofscience.com/wos/woscc/full-record/WOS:000550127500061.
[24] CarlevaroFita, Joana, Lanzos, Andres, Feuerbach, Lars, Hong, Chen, MasPonte, David, Pedersen, Jakob Skou, Johnson, Rory, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Barenboim, Jonathan, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Brunak, Soren, Campbell, Peter J, CarlevaroFita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, DeuPons, Jordi, Dhingra, Priyanka, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, GambacortiPasserini, Carlo, Garsed, Dale W, Gerstein, Mark, Getz, Gad, GonzalezPerez, Abel, Guo, Qianyun, Gut, Ivo G, Haan, David, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Hornshoj, Henrik, Isaev, Keren, Izarzugaza, Jose M G, Johnson, Todd A, Juul, Malene, Juul, Randi Istrup, Kahles, Andre, Kahraman, Abdullah, Kellis, Manolis, Khurana, Ekta, Kim, Jaegil, Kim, Jong K, Kim, Youngwook, Komorowski, Jan, Korbel, Jan O, Kumar, Sushant, Lanzos, Andres, Larsson, Erik, Lawrence, Michael S, Lee, Donghoon, Lehmann, KjongVan, Li, Shantao, Li, Xiaotong, Lin, Ziao, Liu, Eric Minwei, Lochovsky, Lucas, Lou, Shaoke, Madsen, Tobias, Marchal, Kathleen, Martincorena, Inigo, MartinezFundichely, Alexander, Maruvka, Yosef E, McGillivray, Patrick D, Meyerson, William, Muinos, Ferran, Mularoni, Loris, Nakagawa, Hidewaki, Nielsen, Morten Muhlig, Paczkowska, Marta, Park, Keunchil, Park, Kiejung, Pedersen, Jakob Skou, Pich, Oriol, Pons, Tirso, PulidoTamayo, Sergio, Raphael, Benjamin J, Reimand, Juri, ReyesSalazar, Iker, Reyna, Matthew A, Rheinbay, Esther, Rubin, Mark A, RubioPerez, Carlota, Sabarinathan, Radhakrishnan, Sahinalp, S Cenk, Saksena, Gordon, Salichos, Leonidas, Sander, Chris, Schumacher, Steven E, Shackleton, Mark, Shapira, Ofer, Shen, Ciyue, Shrestha, Raunak, Shuai, Shimin, Sidiropoulos, Nikos, Sieverling, Lina, SinnottArmstrong, Nasa, Stein, Lincoln D, Stuart, Joshua M, Tamborero, David, Tiao, Grace, Tsunoda, Tatsuhiko, Umer, Husen M, UuskulaReimand, Liis, Valencia, Alfonso, Vazquez, Miguel, Verbeke, Lieven P C, Wadelius, Claes, Wadi, Lina, Wang, Jiayin, Warrell, Jonathan, Waszak, Sebastian M, Weischenfeldt, Joachim, Wheeler, David A, Wu, Guanming, Yu, Jun, Zhang, Jing, Zhang, Xuanping, Zhang, Yan, Zhao, Zhongming, Zou, Lihua, von Mering, Christian, PCAWG Drivers Functional, PCAWG Consortium. Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. COMMUNICATIONS BIOLOGY[J]. 2020, 3(1): http://dx.doi.org/10.1038/s42003-019-0741-7.
[25] Yuan, Yuan, Ju, Young Seok, Kim, Youngwook, Li, Jun, Wang, Yumeng, Yoon, Christopher J, Yang, Yang, Martincorena, Inigo, Creighton, Chad J, Weinstein, John N, Xu, Yanxun, Han, Leng, Kim, HyungLae, Nakagawa, Hidewaki, Park, Keunchil, Campbell, Peter J, Liang, Han, PCAWG Consortium. Comprehensive molecular characterization of mitochondrial genomes in human cancers. NATURE GENETICS[J]. 2020, 52(3): 342-+, https://www.webofscience.com/wos/woscc/full-record/WOS:000511282900005.
[26] Lina Sieverling, Chen Hong, Sandra D Koser, Philip Ginsbach, Kortine Kleinheinz, Barbara Hutter, Delia M Braun, Isidro CortsCiriano, Ruibin Xi, Rolf Kabbe, Peter J Park, Roland Eils, Matthias Schlesner, PCAWGStructural Variation Working Group, Benedikt Brors, Karsten Rippe, David T W Jones, Lars Feuerbach, PCAWG Consortium. Genomic footprints of activated telomere maintenance mechanisms in cancer. Nature Communications[J]. 2020, 11(1): 1-13, https://doaj.org/article/f5ba2ff084914f529104ae4627a4c3f7.
[27] Campbell, Peter J, Getz, Gad, Korbel, Jan O, Stuart, Joshua M, Jennings, Jennifer L, Stein, Lincoln D, Perry, Marc D, NahalBose, Hardeep K, Ouellette, B F Francis, Li, Constance H, Rheinbay, Esther, Nielsen, G Petur, Sgroi, Dennis C, Wu, ChinLee, Faquin, William C, Deshpande, Vikram, Boutros, Paul C, Lazar, Alexander J, Hoadley, Katherine A, Louis, David N, Dursi, L Jonathan, Yung, Christina K, Bailey, Matthew H, Saksena, Gordon, Raine, Keiran M, Buchhalter, Ivo, Kleinheinz, Kortine, Schlesner, Matthias, Zhang, Junjun, Wang, Wenyi, Wheeler, David A, Ding, Li, Simpson, Jared T, OConnor, Brian D, Yakneen, Sergei, Ellrott, Kyle, Miyoshi, Naoki, Butler, Adam P, Royo, Romina, Shorser, Solomon, I, Vazquez, Miguel, Rausch, Tobias, Tiao, Grace, Waszak, Sebastian M, RodriguezMartin, Bernardo, Shringarpure, Suyash, Wu, DaiYing, Demidov, German M, Delaneau, Olivier, Hayashi, Shuto, Imoto, Seiya, Habermann, Nina, Segre, Ayellet, V, Garrison, Erik, Cafferkey, Andy, Alvarez, Eva G, Maria HerediaGenestar, Jose, Muyas, Francesc, Drechsel, Oliver, Bruzos, Alicia L, Temes, Javier, Zamora, Jorge, BaezOrtega, Adrian, Kim, HyungLae, Mashl, R Jay, Ye, Kai, DiBiase, Anthony, Huang, Kuanlin, Letunic, Ivica, McLellan, Michael D, Newhouse, Steven J, Shmaya, Tal, Kumar, Sushant, Wedge, David C, Wright, Mark H, Yellapantula, Venkata D, Gerstein, Mark, Khurana, Ekta, MarquesBonet, Tomas, Navarro, Arcadi, Bustamante, Carlos D, Siebert, Reiner, Nakagawa, Hidewaki, Easton, Douglas F, Ossowski, Stephan, Tubio, Jose M C, De La Vega, Francisco M, Estivill, Xavier, Yuen, Denis, Mihaiescu, George L, Omberg, Larsson, Ferretti, Vincent, Sabarinathan, Radhakrishnan, Pich, Oriol, GonzalezPerez, Abel, Weiner, Amaro Taylor, Fittall, Matthew W, Demeulemeester, Jonas, Tarabichi, Maxime, Roberts, Nicola D, Van Loo, Peter, CortesCiriano, Isidro, Urban, Lara, Park, Peter, Bin Zhu, Pitkaenen, Esa, Li, Yilong, Saini, Natalie, Klimczak, Leszek J, Weischenfeldt, Joachim, Sidiropoulos, Nikos, Alexandrov, 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[70] Walter, M J, Shen, D, Shao, J, Ding, L, White, B S, Kandoth, C, Miller, C A, Niu, B, McLellan, M D, Dees, N D, Fulton, R, Elliot, K, Heath, S, Grillot, M, Westervelt, P, Link, D C, DiPersio, J F, Mardis, E, Ley, T J, Wilson, R K, Graubert, T A. Clonal diversity of recurrently mutated genes in myelodysplastic syndromes. LEUKEMIA[J]. 2013, 27(6): 1275-1282, https://www.webofscience.com/wos/woscc/full-record/WOS:000319917500008.
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发表著作
(1) FR-HIT Overview, SpringerReference, 2014-06, 第 1 作者
(2) Clustering-based HMP Sequence Comparison, SpringerReference, 2014-06, 第 1 作者
(3) Fast program for clustering and comparing large sets of protein or nucleotide sequences, SpringerReference, 2014-06, 第 2 作者

科研活动

   
科研项目
( 1 ) 泛癌体细胞突变热点分析算法研究, 主持, 国家级, 2018-05--2021-12
( 2 ) 国家高性能计算环境中虚拟数据空间运行支撑技术, 主持, 国家级, 2018-05--2021-04
( 3 ) 生态环境损害鉴定评估业务化技术研究, 主持, 国家级, 2016-07--2020-12
( 4 ) 组学数据挖掘的高性能开源软件系统, 主持, 部委级, 2016-01--2018-12
( 5 ) 大尺度基因组重构与注释的高性能软件系统, 主持, 部委级, 2017-01--2020-12
( 6 ) 个性化药物—基于疾病分子分型的惠普新药研发, 参与, 部委级, 2015-10--2018-12
( 7 ) 基于高通量测序技术的新生儿出生缺陷筛查新技术研究与示范, 主持, 省级, 2016-01--2018-12
( 8 ) 宫颈癌组学数据深度挖掘分析, 主持, 研究所(学校), 2017-05--2019-12
( 9 ) 面向生命健康大数据分析的新计算架构与人工智能方法, 主持, 部委级, 2020-01--2024-12
参与会议
(1)MSI及TMB高表达人群数据挖掘算法   第二十二届“全国临床肿瘤学大会暨2019年CSCO学术年”   2018-09-18
(2)Pan-cancer Analysis of Genomics Sequencing Big Data   International Workshop on CO-DESIGN   2016-10-27
(3)Protein-structure-guided discovery of functional mutations across 19 cancer types   International Symposium on Clinical and Translational Medicine   2016-09-22
(4)Mutational Landscape and Significance Across Pan-Cancer   第四届“数学、计算机与生命科学交叉研究”青年学者论坛   2016-05-21

合作情况


项目协作单位

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.

指导学生

已指导学生

李瑞琳  博士研究生  081202-计算机软件与理论  

赵丹  硕士研究生  085211-计算机技术  

张裕  硕士研究生  081202-计算机软件与理论  

祝海栋  硕士研究生  081203-计算机应用技术  

何小雨  博士研究生  081202-计算机软件与理论  

陈玮  硕士研究生  081202-计算机软件与理论  

陈珊羽  硕士研究生  085211-计算机技术  

何志鹏  硕士研究生  085211-计算机技术  

张舒莹  硕士研究生  085211-计算机技术  

袁丹阳  硕士研究生  081202-计算机软件与理论  

余果  硕士研究生  025100-金融  

刘月琳  硕士研究生  025100-金融  

现指导学生

郝卉群  博士研究生  081202-计算机软件与理论  

代闯闯  博士研究生  081202-计算机软件与理论  

程世宇  博士研究生  081202-计算机软件与理论  

冀德韬  硕士研究生  081202-计算机软件与理论  

胡季芳  硕士研究生  081202-计算机软件与理论  

栾海晶  博士研究生  081202-计算机软件与理论