孙善文 教授/博士生导师
联系方式:
E-mail: sunshanwen@nefu.edu.cn
地址:黑龙江省哈尔滨市香坊区和兴路26号
99905i银河官方网(新逸夫教学楼)226房间
教育经历:
2014-10至2019-04,德国拜罗伊特大学,博士,导师:Bettina Engelbrecht
2010-09至2014-07,中国科学院西双版纳热带植物园,硕士,导师:曹坤芳研究员
2006-09至2010-07,东北师范大学,城市与环境科学学院,学士
工作经历:
2019-09至2021-04,电子科技大学,博士后,导师:邹权教授
研究领域:
生物信息学,生物序列分析,植物功能基因挖掘,人工智能
科研项目:
主持国家自然基金委项目2项,99905i银河官方网引进人才项目1项,中央高校项目1项,黑龙江省项目3项,各类项目到账经费总额200余万元。
学术兼职:
JDSIS期刊编辑,Frontiers集团杂志的Guest Editor,主持专刊一份,Nature chemical biology等期刊审稿人
中国自动化学会委员
中国人工智能学会委员
中国计算机学会委员
发明专利:
一种RNA测序数据的基因表达量计算方法。专利号:ZL 2020 1 0603775.3
论文发表:
Xueying Xie, Lin Gui, Baixue Qiao, Guohua Wang, Shan Huang, Yuming Zhao, Shanwen Sun* (2024) Deep learning in template-free de novo biosynthetic pathway design of natural products. Briefings in Bioinformatics. 25(6): bbae495 (自动化学会生物信息学A类期刊,TOP期刊)
Baixue Qiao, Shuda Wang, Mingjun Hou, Haodi Chen, Zhengwenyang Zhou, Xueying Xie, Shaozi Pang, Chunxue Yang, Fenglong Yang, Quan Zou, Shanwen Sun* (2024) Identifying nucleotide-binding leucine-rich repeat receptor and pathogen effector pairing using transfer-learning and bilinear attention network. Bioinformatics. 40(10): btae581 (自动化学会生物信息学A类期刊)
Zhao Y, Gui L, Hou C, Zhang D, and Sun S* (2024) GwasWA: A GWAS one-stop analysis platform from WGS data to variant effect assessment. Computers in Biology and Medicine. 169:107820. (影响因子7.7,小类中科院一区,Top期刊)
Sun S, Ye X*, and Zou Q* (2023) Editorial: Machine learning on understanding the epigenetic mechanisms underlying plant adaptation and domestication. Front. Plant Sci. 14:1236787. (影响因子:5.6,中科院二区,Top期刊)
Chen B, Guo Y, Zhang X, Wang L, Cao L, Zhang T, Zhang Z, Zhou W, Xie L, Wang J, Sun S* (共同通讯), Yang C*, and Zhang Q* (2022) Climate-responsive DNA methylation is involved in the biosynthesis of lignin in birch. Front. Plant Sci. 13:1090967. (影响因子:5.6,中科院二区,Top期刊)
Wang X, Sun S (共同第一作者), Sedio B, Glomglieng S, Cao M, Cao K, Yang J, Zhang J*, and Yang J* (2022). Niche differentiation along multiple functional-trait dimensions contributes to high local diversity of Euphorbiaceae in a tropical tree assemblage. Journal of Ecology, 110, 2731–2744. (影响因子:6.381,中科院一区,Top期刊)
Ding K, Sun S (共同第一作者), Luo Y, Long C, Zhai J, Zhai Y, and Wang G* (2023) PlantCADB: A Comprehensive Plant Chromatin Accessibility Database. Genomics, Proteomics & Bioinformatics, 21, 311-323. (影响因子:11.5,中科院一区,Top期刊)
Sun S, Dong B*, and Zou Q*. Revisiting genome-wide association studies from statistical modelling to machine learning. Briefings in Bioinformatics. 22 (4), bbaa263. (影响因子:13.994,中科院一区,Top期刊)
Sun S, Xu L*, Zou Q*, and Wang G*. BP4RNAseq: a babysitter package for retrospective and newly generated RNA-seq data analyses using both alignment-based and alignment-free quantification method. Bioinformatics. 37 (9), 1319–1321. (影响因子:5.610,中科院一区,Top期刊)
Sun S*, Jung E, Gaviria J, and Engelbrecht B M J. Drought survival is positively associated with high turgor loss point in temperate perennial grassland species. Functional Ecology, 2020, 34:788-798. (影响因子:4.43,中科院一区,Top期刊)
Sun S, Ding H, Wang D*, and Han S*. Identifying antifreeze proteins based on key evolutionary information. Frontiers in Bioengineering and Biotechnology, 2020, 8:1-8. (影响因子:3.644,中科院二区)
Sun S, Wang C, Ding H, and Zou Q*. Machine learning and its applications in plant molecular studies. Briefings in functional genomics, 2020, 19:40-48. (影响因子:2.941,中科院二区)
Sun S, Ao C, Wang D*, and Dong B*. The frequencies of oppositely charged, uncharged polar, and β-branched amino acids determine proteins' thermostability. IEEE Access, 2020, 8:66839-66845. (影响因子:3.745,中科院二区,Top期刊)
Jung E, Gaviria J, Sun S, and Engelbrecht B M J*. Comparative drought resistance of temperate grassland species: testing performance trade-offs and the relation to distribution. Oecologia, 2020:1-14. (影响因子:2.915,中科院二区)
Bartlett M K*, Zhang Y, Yang J, Kreidler N, Sun S, et al. Drought tolerance as a driver of tropical forest assembly: resolving spatial signatures for multiple processes. Ecology, 2016, 97:503-514. (影响因子:4.7,中科院一区,Top期刊)
Bartlett M K*, Zhang Y, Kreidler N, Sun S, et al. Global analysis of plasticity in turgor loss point, a key drought tolerance trait. Ecology Letters, 2014, 17:1580-1590. (影响因子:8.665,中科院一区,Top期刊)
Bartlett M K*, Scoffoni C, Ardy R, Zhang Y, Sun S, et al. Rapid determination of comparative drought tolerance traits: using an osmometer to predict turgor loss point. Methods in Ecology and Evolution, 2012, 3:880-888. (影响因子:6.51,中科院一区,Top期刊)
本科人才培养:
论文:
1. Xueying Xie, Lin Gui, Baixue Qiao, Guohua Wang, Shan Huang, Yuming Zhao, Shanwen Sun* (2024) Deep learning in template-free de novo biosynthetic pathway design of natural products. Briefings in Bioinformatics. 25(6): bbae495 (本科生第一作者论文)
2. Baixue Qiao, Shuda Wang, Mingjun Hou, Haodi Chen, Zhengwenyang Zhou, Xueying Xie, Shaozi Pang, Chunxue Yang, Fenglong Yang, Quan Zou, Shanwen Sun* (2024) Identifying nucleotide-binding leucine-rich repeat receptor and pathogen effector pairing using transfer-learning and bilinear attention network. Bioinformatics. 40(10): btae581 (本科生参与论文)
专利:
1. 一种基于元分析构建基因调控网络的方法 (本科生第一发明人)
2. 基于迁移学习的植物 NLR-无毒蛋白 Avr 对应关系识别方法 (本科生合作发明)
3. 一种植物抗盐碱基因的识别方法及系统 (本科生第一发明人)
4. 一种基于深度学习的植物抗旱基因的识别方法 (本科生第一发明人)
课程:
生物信息学、生物实验设计与统计分析