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

东北林业大学生命科学学院（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，东北林业大学引进人才项目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