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个人简介

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 工作简历 2012-08~2015-01,美国圣路易斯华盛顿大学(WUSTL), staff research scientist 2009-03~2012-07,美国加州大学圣迭戈(UCSD), 博士后 奖励信息 (1) 2015年美国10大临床研究成就奖, 一等奖, 其他, 2015 专利成果 ( 1 ) 基于国家高性能计算环境的中小企业计算社区系统, 发明, 2019, 第 3 作者, 专利号: 201910769782.8 ( 2 ) 一种基于Mesos的分布式超参数优化系统及方法, 发明, 2019, 第 5 作者, 专利号: 201910278557.4 ( 3 ) 气象卫星数据的处理方法及装置, 发明, 2020, 第 2 作者, 专利号: 202010717906.0 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 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.

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。

近期论文

查看导师新发文章 (温馨提示:请注意重名现象,建议点开原文通过作者单位确认)

(1) MSIsensor-ct: microsatellite instability detection using cfDNA sequencing data, Briefings in Bioinformatics, 2021, 通讯作者 (2) Comprehensive review and evaluation of computational methods for identifying FLT3-internal tenderm duplication in acute myeloid leukaemia, Briefings in Bioinformatics, 2021, 通讯作者 (3) 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, 2021, 通讯作者 (4) Visual analysis of meteorological satellite data via model-agnostic meta-learning, Journal of Visualization, 2021, 第 4 作者 (5) HotSpot3D web server: An Integrated Resource for Mutation Analysis in Protein 3D Structures, Bioinformatics, 2020, 通讯作者 (6) Comprehensive fundamental analysis and quality management strategy for next-generation sequencing data from cancer genomes, Briefings in Bioinformatics, 2020, 通讯作者 (7) Red blood cells may act as repositories of microRNAs in the circulatory system, Frontiers in Genetics, 2020, 通讯作者 (8) Change-Encryption: Encryption using spatiotemporal information as a function model, The 6th IEEE International Conference on Edge Computing and Scalable Cloud, 2020, 通讯作者 (9) Digital Currency Investment Strategy Framework Based on Ranking, 20th International Conference on Algorithms and Architectures for Parallel Processing (ICA3PP 2020), 2020, 通讯作者 (10) 高可用弹性宏基因组学计算平台, 计算机科学, 2020, 通讯作者 (11) RabbitQC: high-speed scalable quality control for sequencing data, Bioinformatics, 2020, 第 8 作者 (12) Pan-cancer analysis of whole genomes, Nature, 2020, 其他(合作组作者) (13) Genomic basis for RNA alterations in cancer, Nature, 2020, 其他(合作组作者) (14) Patterns of somatic structural variation in human cancer genomes, Nature, 2020, 其他(合作组作者) (15) The repertoire of mutational signatures in human cancer, Nature, 2020, 其他(合作组作者) (16) Analyses of non-coding somatic drivers in 2,658 cancer whole genomes, Nature, 2020, 其他(合作组作者) (17) The evolutionary history of 2,658 cancers, Nature, 2020, 其他(合作组作者) (18) Butler enables rapid cloud-based analysis of thousands of human genomes, Nature Biotechnology, 2020, 其他(合作组作者) (19) Comprehensive molecular characterization of mitochondrial genomes in human cancers, Nature Genetics, 2020, 其他(合作组作者) (20) Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition, Nature Genetics, 2020, 其他(合作组作者) (21) Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer, Nature Genetics, 2020, 其他(合作组作者) (22) Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing, Nature Genetics, 2020, 其他(合作组作者) (23) The landscape of viral associations in human cancers, Nature Genetics, 2020, 其他(合作组作者) (24) Sex differences in oncogenic mutational processes, Nature Communications, 2020, 其他(合作组作者) (25) Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples, Nature Communications, 2020, 其他(合作组作者) (26) Divergent mutational processes distinguish hypoxic and normoxic tumours, Nature Communications, 2020, 其他(合作组作者) (27) Integrative pathway enrichment analysis of multivariate omics data, Nature Communications, 2020, 其他(合作组作者) (28) A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns, Nature Communications, 2020, 其他(合作组作者) (29) High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations, Nature Communications, 2020, 其他(合作组作者) (30) Combined burden and functional impact tests for cancer driver discovery using DriverPower, Nature Communications, 2020, 其他(合作组作者) (31) Inferring structural variant cancer cell fraction, Nature Communications, 2020, 其他(合作组作者) (32) Genomic footprints of activated telomere maintenance mechanisms in cancer, Nature Communications, 2020, 其他(合作组作者) (33) Pathway and network analysis of more than 2500 whole cancer genomes, Nature Communications, 2020, 其他(合作组作者) (34) Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig, Nature Communications, 2020, 其他(合作组作者) (35) Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis, Communications Biology, 2020, 其他(合作组作者) (36) Gclust: A Parallel Clustering Tool for Microbial Genome Data, Genomics, Proteomics & Bioinformatics, 2019, 通讯作者 (37) How Big Data and High-performance Computing Drive Brain Science, Genomics, Proteomics & Bioinformatics, 2019, 通讯作者 (38) DGCF: A Distributed Greedy Clustering Framework for Large-scale Genomic Sequences, 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2019, 通讯作者 (39) Distributed Parameter Optimization Scheduling Strategy and System Design Based on Mesos, The 5th IEEE International Conference on Big Data Security on Cloud(BigDataSecurity 2019), 2019, 通讯作者 (40) 单肿瘤组织微卫星不稳定探测方法, 计算机系统应用, 2019, 通讯作者 (41) 六倍体小麦基因组注释流程构建与优化, 计算机系统应用, 2019, 通讯作者 (42) 基于宏基因组长片段的基因预测算法基准研究, 计算机应用, 2019, 通讯作者 (43) ATG7 Promotes Bladder Cancer Invasion via Autophagy‐Mediated Increased ARHGDIB mRNA Stability, Advanced Science, 2019, 第 10 作者 (44) 肿瘤微卫星不稳定检测方法综述, 计算机系统应用, 2018, 通讯作者 (45) Different Erythrocyte MicroRNA Profiles in Low-and High-Altitude Individuals, Frontiers in Physiology, 2018, 第 4 作者 (46) Pan-cancer analysis of somatic mutations across 21 neuroendocrine tumor types, Cell Research, 2018, 其他(合作组作者) (47) MetaSpark: a spark-based distributed processing tool to recruit metagenomic reads to reference genomes, Bioinformatics, 2017, 通讯作者 (48) GenomeVIP: a cloud platform for genomic variant discovery and interpretation, Genome Research, 2017, 第 6 作者 (49) Proteogenomic integration reveals therapeutic targets in breast cancer xenografts, Nature Communications, 2017, 其他(合作组作者) (50) Protein-structure-guided discovery of functional mutations across 19 cancer types, Nature Genetics, 2016, 第 1 作者 (51) Divergent viral presentation among human tumors and adjacent normal tissues, Scientific Reports, 2016, 第 9 作者 (52) Systematic discovery of complex insertions and deletions in human cancers, Nature Medicine, 2015, 其他(合作组作者) (53) Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes, Nature Genetics, 2015, 第 8 作者 (54) Patterns and functional implications of rare germline variants across 12 cancer types, Nature Communications, 2015, 其他(合作组作者) (55) Sequence and structure-guided approach to identify functional mutations in G-protein coupled receptors, Cancer Research, 2015, 第 4 作者 (56) MSIsensor: microsatellite instability detection using paired tumor-normal sequence data, Bioinformatics, 2014, 第 1 作者 (57) Comprehensive molecular characterization of gastric adenocarcinoma, Nature, 2014, 其他(合作组作者) (58) Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin, Cell, 2014, 第 8 作者 (59) Mutational landscape and significance across 12 major cancer types, Nature, 2013, 第 5 作者 (60) BreakTrans: uncovering the genomic architecture of gene fusions, Genome Biology, 2013, 第 6 作者 (61) Clonal diversity of recurrently mutated genes in myelodysplastic syndromes, Leukem, 2013, 第 8 作者 (62) Mutational and clonal analyses across TCGA cancer types using the MuSiC suite of tools, Cancer Research, 2013, 第 7 作者 (63) MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data, Bioinformatics, 2013, 第 2 作者 (64) Ultrafast clustering algorithms for metagenomic sequence analysis, Briefings in Bioinformatics, 2012, 第 3 作者 (65) CD-HIT: Accelerated for Clustering the Next-Generation Sequencing Data, Bioinformatics, 2012, 第 2 作者 (66) FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes, Bioinformatics, 2011, 第 1 作者 (67) WebMGA: a customizable web server for fast metagenomic sequence analysis, BMC Genomics, 2011, 第 4 作者 (68) Artificial and natural duplicates in pyrosequencing reads of metagenomic data, BMC Bioinformatics, 2010, 第 1 作者 (69) CD-HIT Suite: a web server for clustering and comparing biological sequences, Bioinformatics, 2010, 第 2 作者 (70) Parallel algorithm research on several important open problems in bioinformatics, Interdisciplinary Sciences: Computational Life Sciences, 2009, 第 1 作者 (71) ScBioGrid: a commodity supercomputing environment supporting bioinformatics research, International Journal of Computer Mathematics, 2007, 第 1 作者

学术兼职

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

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