1.教研室简介
专业定位：
重庆医科大学生物信息学专业结合本校“立足重庆、服务中国、面向世界”的办学定位和大数据时代对生物信息学人才日益增长的需求，秉承“掌握医学、生物学和信息学等多学科基本理论，具备生物信息收集、加工、分析、利用等基本技能”高水平复合型人才的专业培养要求，为国家大数据精准医疗计划提供生物信息学人才支持，为医院、科研机构、公共卫生等相关部门与行业等提供高质量的生物信息学后备人才。
历史沿革：
重庆医科大学是一所医药类专门院校，是全市唯一一所具有医学特色的生物信息学专业的学校，也是重庆市生物信息学学会理事长所在单位。我校生物信息学本科专业于2013年开办，也是全国较早开办的几个生物信息学本科专业之一。2019年获批生物信息学二级学科硕士点，在遗传学专业上招收生物信息学方向博士，现已形成“学士-硕士-博士-博士后”的完整人才培养体系。现任教研室主任为冉隆科，副主任为詹晓慧。
现状简介：
经过11年的建设，生物信息学专业形成了本科-硕士-博士-博士后的完整人才培养体系。现具有四个学位授予点（生物信息学专业学士学位授予点，生物信息学专业学术型硕士学位授予点、电子信息学专业专业型硕士学位（生物信息学方向）授予点、病理学与病理生理学专业博士学位（生物信息学方向）授予点）。建设有专业专用高通量计算中心、数据中心、实训基地、实验智慧教室等先进的教学科研软硬件平台。
特色优势：
生物信息学本科专业一直坚持学系与医院、企业合作的培养模式。从大学二年级开始，本科生按照个人兴趣可在生物信息学教研室、遗传学教研室、生物化学与分子生物学教研室、第一附属医院、第二附属医院、华大基因等企业实习实训。目前本专业已与国内多个顶尖的生物信息学相关公司和机构达成意向，接受生物信息学本科生毕业实习，这为培养应用性生物信息学本科人才提供了有力条件。
2.师资队伍
生物信息学教研室现有教师15人，其中博士学历12人，博士后经历10人。其中教授3人（含兼职教授1名），副教授及副研究员6人，硕士研究生导师7人，博士后合作导师2名，多名教师具有国内外访学经历。新兴的交叉学科的大量人才需求以及高水平的专职教师团队为重庆医科大学发展生物信息学打造了坚持的学科优势基础。
3.教学工作：课程，教材建设，教学课题简介，人才培养（本科生研究生）
人才培养：
目前生物信息学本科专业招生规模40人/届，在读硕士博士约30人，在站博士后3人。迄今为止，生物信息学本科专业已累计培养七届本科毕业生，毕业总人数250人。培养硕士、博士生共计30余人。为社会输送了一批批合格的生物信息学专业人才，绝大多数毕业生在生物技术公司、制药公司、高校、医院和科研院所工作。生物信息学本科专业近5年来的升学就业率平均高于86%，毕业生颇受用人单位好评。历届毕业生平均有12%进入国内一流高校或海外知名高校继续深造，其余的毕业生大都在北上广深等大城市的医院、高校、生物技术和制药公司等从事生物信息学相关工作。
教学任务：
本科生课程：
生物信息学本科专业课程（17门）：生物信息学专业导论、生物信息学、基因组学、蛋白质组学、代谢组学、生物信息数据挖掘、系统生物学、计算机辅助药物设计、生物统计学、生物信息学前沿技术及应用、数据库原理及应用、现代生物计算环境、C语言程序设计、python程序设计、R语言、数据结构与算法分析、基于Linux的Web开发。
其他本科专业核心课程（11门）：高等数学、线性代数、概率统计、分子生物学、细胞生物学、遗传学、基础化学、普通生物学、系统解剖学、生理学、生物化学。生物信息学本科专业的生物学和医学基础课程由基础医学院多个国家级、省级教学名师领衔的国家级教学团队承担。
研究生课程：
生物信息学（全校研究生选修课）、大数据与生物信息学（基础医学院研究生必修课）
总教学时数：约1000学时/学年
4.科学研究：定位，研究方向，代表性团队及论文
生物信息学系的教师在肿瘤、神经性疾病等领域开展生物信息学相关的研究工作。目前主持的在研项目共11项，累计经费共336万元。
近两年的代表性论文：
1. Ruihan Luo; Chuang Ge; Xiao Xiao; Jing Song; Shiqi Miao; Yongyao Tang; Jiayi Lai; Weiqi Nian; Fangzhou Song;Longke Ran*; Identification of genetic variations associated with drug resistance in non-small cell lung cancer patients undergoing systemic treatment, Briefings in Bioinformatics, 2021, 22(6): 1-13
2. Jing Song; Yongyao Tang; Xiaoyong Luo; Xinpeng Shi; Fangzhou Song;Longke Ran*; Pan Cancer Analysis Reveals the Signature of TMC Family of Genes as a Promising Biomarker for Prognosis and Immunotherapeutic Response, Frontiers in Immunology, 2021, 12: 715508
3. Ruihan Luo; Jing Song; Xiao Xiao; Zhengbo Xie; Zhiyuan Zhao; Wanfeng Zhang; Shiqi Miao; Yongyao Tang;Longke Ran*; Identifying CpG methylation signature as a promising biomarker for recurrence and immunotherapy in non-small-cell lung carcinoma, Aging (Albany NY), 2020, 12(14): 14649-14676
4. Guang Li; Meng Yang;Longke Ran*; Fu Jin* ; Classification prediction of early pulmonary nodes based on weighted gene correlation network analysis and machine learning, Journal of Cancer Research and Clinical Oncology, 2022, 149: :3915-:3924
5. Jing Song; Fangzhou Song; Kun Liu; Wanfeng Zhang;Ruihan Luo*; Yongyao Tang; Longke Ran ; Multi-omics analysis reveals epithelial-mesenchymal transition-related gene FOXM1 as a novel prognostic biomarker in clear cell renal carcinoma, Aging (Albany NY), 2019, 11(22): 10316- 10337
6.Wei Wei#, Bo Ye#, Zhenting Huang , Xiaoling Mu, Jing Qiao, Peng Zhao , Yuehang Jiang , Jingxian Wu*,Xiaohui Zhan*. Prediction of Prognosis, Immunotherapy and Chemotherapy with an Immune-Related Risk Score Model for Endometrial Cancer. Cancers (Basel). 2023 Jul 19;15(14):3673.
7.Xiaohui Zhan, Yusong Liu, Asha Jacob Jannu , Shaoyang Huang, Bo Ye, Wei Wei, Pankita H Pandya, Xiufen Ye, Karen E Pollok, Jamie L Renbarger, Kun Huang, Jie Zhang. Identify potential driver genes for PAX-FOXO1 fusion-negative rhabdomyosarcoma through frequent gene co-expression network mining. Front Oncol. 2023 Jan 30;13:1080989.
8. Zixiao Lu#,Xiaohui Zhan#, Yi Wu, Jun Cheng , Wei Shao, Dong Ni, Zhi Han, Jie Zhang, Qianjin Feng , Kun Huang. BrcaSeg: A Deep Learning Approach for Tissue Quantification and Genomic Correlations of Histopathological Images. Genomics Proteomics Bioinformatics. 2021 Dec;19(6):1032-1042. doi: 10.1016/j.gpb.2020.06.026. Epub 2021 Jul 17.
9.Xiaohui Zhan, Yusong Liu, Christina Y Yu , Tian-Fu Wang , Jie Zhang, Dong Ni , Kun Huang. A pan-kidney cancer study identifies subtype specific perturbations on pathways with potential drivers in renal cell carcinoma. BMC Med Genomics. 2020 Dec 28;13(Suppl 11):190.
10.Xiaohui Zhan, Jun Cheng, Zhi Huang, Zhi Han , Bryan Helm , Xiaowen Liu, Jie Zhang, Tian-Fu Wang, Dong Ni, Kun Huang. Correlation Analysis of Histopathology and Proteogenomics Data for Breast Cancer. Mol Cell Proteomics. 2019 Aug 9;18(8 suppl 1):S37-S51.
11.Jiliang Hu#, Huanjie Yang#, Jinye Mu, Tiancong Lu, Juli Peng, Xian Deng, Zhaosheng Kong, Shilai Bao, Xiaofeng Cao, JianruZuo*. Nitric oxide regulates protein methylation during stress responses in plants. Molecular Cell, 2017. 67(4):702-710.
12.Jiliang Hu, Xiahe Huang, Lichao Chen, Xuwu Sun, Congming Lu, Lixin Zhang, Yingchun Wang, JianruZuo*. Site-specific nitrosoproteomic identification of endogenously S-nitrosylated proteins in Arabidopsis. Plant Physiology, 2015. 167: 1731-46.
13. Chaochao Tan, Lichun Chen , Xiaoyu Guan , Wenyi Huang , Yinhong Feng, Ziyi Li, Ling Wu, Xiangping Huang, Qianhui Ouyang, Sixiang Liu, Ying Huang,Jiliang Hu. Redox proteomics of PANC-1 cells reveals the significance of HIF-1 signaling protein oxidation in pancreatic ductal adenocarcinoma pathogenesis. J Transl Med. 2024 Mar 16;22(1):287. doi: 10.1186/s12967-024-05068-z. PMID: 38493183; PMCID: PMC10944602.
14. Chang Liu, Yue-Xian He, Jia-Ning Zhang, Fang Yang, Shu-Yuan Wang ,Ji-Liang Hu*, Yang Yu*.Angelica oil restores the intestinal barrier function by suppressing S100A8/A9 signalling in mice with ulcerative colitis. Phytomedicine. 2023;108:154490.
15.Chaochao Tan , Yunfeng Li, Xiahe Huang, Meijin Wei, Ying Huang, Zhouqin Tang, He Huang, Wen Zhou, Yingchun Wang ,Jiliang Hu.Extensive protein S-nitrosylation associated with human pancreatic ductal adenocarcinoma pathogenesis. Cell Death Dis. 2019;10(12):914. Published 2019 Dec 4.
16.J. Tang#, X. L. Wu#, M. J. Mou#, C. Wang, L. D. Wang, F. C. Li, M. Y. Guo, J. Y. Yin, W. Q. Xie, X. N. Wang, Y. X. Wang, Y. B. Ding*, W. W. Xue*, F. Zhu*. GIMICA: host genetic and immune factors shaping human microbiota. Nucleic Acids Res. 49(D1): 715-722 (2021).
17.J. Tang, J. B. Fu, Y. X. Wang, B. Li, Y. H. Li, Q. X. Yang, X. J. Cui, J. J. Hong, X. F. Li, Y. Z. Chen, W. W. Xue, F. Zhu*. ANPELA: analysis and performance-assessment of the label-free quantification workflow for metaproteomic studies. Brief Bioinform. 21(2):621-636 (2020)
18.J. Tang#, M. Mou#, X. Zheng#, J. Yan, Z. Pan, J. Zhang, B. Li, Q. Yang, Y. Wang, Y. Zhang, J. Gao, S Li*, H. Yang*, F. Zhu*. Strategy for Identifying a Robust Metabolomic Signature Reveals the Altered Lipid Metabolism in Pituitary Adenoma. Anal Chem. 96(12): 4745-4755 (2024)
19.J. Tang#, J. B. Fu#, Y. X. Wang#, Y. C. Luo, Q. X. Yang, B. Li, G. Tu, J. J. Hong, X. J. Cui, Y. Z. Chen, L. X. Yao, W. W. Xue, F. Zhu*. Simultaneous improvement in the precision, accuracy and robustness of label-free proteome quantification by optimizing data manipulation chains. Mol Cell Proteomics. 18(8): 1683-1699 (2019).
20. Y. Wu#, L. P. Yang#, X. L. Wu#, L. D. Wang, H. B. Qi, Q. Feng, Bin. Peng, Y. B. Ding*,J. Tang*. Identification of the hub genes in polycystic ovary syndrome based on disease-associated molecule network. FASEB J. 37(7): e23056 (2023),
21.Shenglong Li; Wang Wang; Tingting Li; Xiaojian Han; Chao Hu; Yingming Wang; Meiying Shen; Li Du; Yaru Nai; Jianwei Wang; Aishun Jin ; Immune characteristics analysis reveals two key infla mmatory factors correlated to the expressions of SARS-CoV-2 S1-specific antibodies, Genes & disea se, 2022.春季, 9(2): 522-530
22.Shenglong Li; Masahiro Ajimura; Zhiwei Chen; Jianqiu Liu; Enxiang Chen; Huizhen Guo; Vidya Tadapatri; Chilakala Gangi Reddy; Jiwei Zhang; Hirohisa Kishino; Hiroaki Abe; Qingyou Xia; Kallare P. Arunkumar; Kazuei Mita ; A new approach for comprehensively describing heterogametic sex chromosomes, DNA research, 2018, 25(4): 375-382
23. Xiaojian Han; Yingming Wang;Shenglong Li; Chao Hu; Tingting L; Chenjian Gu; Kai Wang; Me iying Shen; Jianwei Wang; Jie Hu; Ruixin Wu; Song Mu; Fang Gong; Qian Chen; Fengxia Gao; Jingjing Huang; Yingyi Long; Feiyang Luo; Shuyi Song; Shunhua Long; Yanan Hao; Luo Li; Yang Wu; Wei Xu; Xi a Cai; Qingzhu Gao; Guiji Zhang; Changlong He; Kun Deng; Li Du; Yaru Nai; Wang Wang; Youhua Xie; Di Qu; Ailong Huang; Ni Tang; Aishun Jin ; A rapid and efficient screening system for neutralizin g antibodies and its application for SARS-CoV-2, Frontiers in Immunology
24. Chen, Siyin; Zhang, Jing; Shen, Meiying; Han, Xiaojian;Li, Shenglong; Hu, Chao; Wang, Wang; Li, Luo; Du, Li; Pang, Da; Tao, Kun; Jin, Aishun ; p38 inhibition enhances TCR-T cell functio n and antagonizes the immunosuppressive activity of TGF-beta, International Immunopharmacology, 2021, 98: 0-107848
25. Tingting Li; Xiaojian Han; Chenjian Gu; Hangtian Guo; Huajun Zhang; Yingming Wang; Chao H u; Kai Wang; Fengjiang Liu; Feiyang Luo; Yanan Zhang; Jie Hu; Wang Wang; Shenglong Li; Yanan Hao; Meiying Shen; Jingjing Huang; Yingyi Long; Shuyi Song; Ruixin Wu; Song Mu; Qian Chen; Fengxia Gao ; Jianwei Wang; Shunhua Long; Luo Li; Yang Wu; Yan Gao; Wei Xu; Xia Cai; Di Qu; Zherui Zhang; Hon gqing Zhang; Na Li; Qingzhu Gao; Guiji Zhang; Changlong He; Wei Wang; Xiaoyun Ji; Ni Tang; Zhengh ong Yuan; Youhua Xie; Haitao Yang; Bo Zhang; Ailong Huang; Aishun Jin ; Potent SARS-CoV-2 neutral izing antibodies with protective efficacy against newly emerged mutational variants, Nature Communications, 2021, 12
26.Xiaoxu Yang#, Changhong Yang#, Xianing Zheng#, Luoxing Xiong, Yutian Tao, Meng Wang, Adam Yongxin Ye, Qixi Wu, Yanmei Dou, Junyu Luo, Liping Wei*., August Yue Huang*. MosaicBase: A knowledgebase for postzygotic mosaic variants for non-cancer diseases and asymptomatic human individuals. GENOMICS PROTEOMICS & BIOINFORMATICS, 2020, 18(2): 140-149.
27.Changhong Yang, Jiarui Li, Qixi Wu, Xiaoxu Yang, August Yue Huang, Jie Zhang, Adam Yongxin Ye, Yanmei Dou, Linlin Yan, Wei-zhen Zhou, Lei Kong, Meng Wang, Chen Ai, Dechang Yang, Liping Wei. AutismKB 2.0: a knowledgebase for the genetic evidence of autism spectrum disorder. Database, 2018, 1:8.
28.Changhong Yang, Jialei Chen, Zhe Yu, Jing Luo, Xuemei Li, Baoyong Zhou*, Ning Jiang*. Mining of RNA Methylation-Related Genes and Elucidation of Their Molecular Biology in Gallbladder Carcinoma. Front Oncol. 2021 Feb 25;11:621806.
29.Wei-Zhen Zhou, Jie Zhang, Ziyi Li, Xiaojing Lin, Jiarui Li, Sheng Wang,Changhong Yang, Qixi Wu, Adam Yongxin Ye, Meng Wang, Dandan Wang, Tad Zhengzhang Pu, Yu-Yu Wu, Liping Wei. Targeted re-sequencing with a comprehensive gene panel for autism spectrum disorder in a Chinese cohort. Human Mutation, 2019,2,14
30.Yanmei Dou, Xiaoxu Yang, Ziyi Li, Sheng Wang, Zheng Zhang, Adam Yongxin Ye, Linlin Yan,Changhong Yang, Qixi Wu, Jiarui Li, Boxun Zhao, August Yue Huang, Liping Wei. Post-zygotic single nucleotide mosaicisms contribute to the etiology of autism spectrum disorder and autistic traits and the origin of mutations. Human Mutation, 2017, 1002-1013.
31.Wei Sun#;Kunyan Liu#; Hongyu Zhou; Fang Zhao; Yan Dong; Yu Xu; Yunyi Kong; Minghe Wang; Xi Cheng; Yong Chen*; Whole-exome sequencing reveals mutational profiles of anorectal and gynecological melanoma, 2023, 40:330.
32.Xin Wei#;Kunyan Liu#; Yanxin Zhang#; Qi Feng#; Linhai Wang#; Yan Zhao; Donghua Li; Qiang Zhao; Xiaodong Zhu; Xiaofeng Zhu; Wenjun Li; Danlin Fan; Yuan Gao; Yiqi Lu; Xianmei Zhang; Xiumei Tang; Congcong Zhou; Chuanrang Zhu; Lifeng Liu; Ruichun Zhong; Qilin Tian; Ziruo Wen; Qijun Weng; Bin Han; Xuehui Huang*; Xiurong Zhangb*; Genetic discovery for oil production and quality in sesame, Nature communication, 2015, 6:8609.
33. Yong Heng Wang # , Pan Pan Luo #, Ao Yi Geng, Xinwei Li, Tai-Hang Liu , Yi Jie He , Lin Huang ,Ya Qin Tang.Identification of highly reliable risk genes for Alzheimer’s disease through joint-tissue integrative analysis.Front Aging Neurosci. 2023;15:1183119.
34.Ya-Shi Wu # , Wen-Han Zheng # , Tai-Hang Liu # , Yan Sun , Yu-Ting Xu, Li-Zhen Shao, Qin-Yu Cai ,Ya Qin Tang.Joint-tissue integrative analysis identifies high-risk genes for Parkinson's disease.Front Neurosci. 2024;18:1309684. Published 2024 Mar 21.
35.Wanfeng Zhang; Fang Huang; Xia Tang; Longke Ran ; The clonal expression genes associated with poor prognosis of liver cancer., Frontiers in Genetics, 2022, 13(1664-8021): 808273
36.Wanfeng Zhang; Sen Wang; Xianqin Zhang; Kun Liu; Jing Song; Xue Leng; Ruihan Luo; Longke Ran ; Transmembrane Channel-Like 5 (TMC5) promotes prostate cancer cell proliferation through cell cycle regulation, Biochimie, 2019, 165: 122
37.Wanfeng Zhang; Peng Shu; Sen Wang; Jing Song; Kun Liu; Changdong Wang; LongKe Ran ; ZNF154 is a promising diagnosis biomarker and predicts biochemical recurrence in prostate cancer,
Gene, 2018, 675: 136
38. Xin Li;Wanfeng Zhang; Jing Song; Xianqin Zhang; Longke Ran; Yunfeng He ; SLCO4C1 promoter methylation is a potential biomarker for prognosis associated with biochemical recurrence-free survival after radical prostatectomy, Clinical Epigenetics, 2019, 11(1): 99
39. Min Yan; Ruixin Wu; Han Fu; Chao Hu; Yanan Hao; Jie Zeng; Tong Chen; Yingming Wang; Yingying Wang; Jing Hu; Aishun Jin ; Integrated analysis of single-cell and bulk RNA sequencing data reveals the association between hypoxic tumor cells and exhausted T cells in predicting immune therapy response, Computers in Biology and Medicine, 2024, 171(108179)
40.Min Yan; Jing Hu; Huating Yuan; Liwen Xu; Gaoming Liao; Zedong Jiang; Jiali Zhu; Bo Pang; Yanyan Ping; Yunpeng Zhang; Yun Xiao; Xia Li ; Dynamic regulatory networks of T cell trajectory dissect transcriptional control of T cell state transition, Molecular Therapy - Nucleic Acids, 2021, 26: 1115-1129
41.Min Yan; Jing Hu; Yanyan Ping; Liwen Xu; Gaoming Liao; Zedong Jiang; Bo Pang; Shangqin Sun; Yunpeng Zhang; Yun Xiao; Xia Li ; Single-Cell Transcriptomic Analysis Reveals a Tumor- Reactive T Cell Signature Associated With Clinical Outcome and Immunotherapy Response In Melanoma, Frontiers in Immunology, 2021, 12: 12:758288-12:758288
42. Jiali Zhu#;Min Yan#; Haoteng Yan; Liwen Xu; Zedong Jiang; Gaoming Liao; Yao Zhou; Wei Liu; Xin Liang; Xia Li; Yun Xiao; Yunpeng Zhang ; Single-Cell Transcriptomic Analysis Reveals the Crosstalk Propensity Between the Tumor Intermediate State and the CD8+ T Exhausted State to be Associated with Clinical Benefits in Melanoma, Frontiers in Immunology, 2022, 13: 13:766852- 13:766852
43. Huating Yuan#;Min Yan#; Xin Liang; Wei Liu; Shengyuan He; Shangqin Sun; Xinxin Zhang; Yujia Lan ; Decoding the associations between cell functional states in head and neck cancer based on single-cell transcriptome., Oral Oncology, 2022, 134: 106110-106110
5.荣誉与奖励
1. 2024/06第十届全国大学生基础医学创新研究暨实验设计论坛总决赛金奖、银奖、铜奖
2. 2024/08第九届全国大学生生命科学竞赛三等奖（创新创业类，国家级）
3. 2024/06全国大学生生命科学竞赛重庆赛区三等奖（创新创业类，省部级级）
4. 2024/05首届全国大学生职业规划大赛全国总决赛银奖（国家级）
5. 2024/04成渝地区双城经济圈首届大学生职业规划大赛冠军争夺赛金奖（省部级）
6.第十一届本科生国际学术论坛海报展一等奖（省部级）
7.首届全国大学生职业规划大赛暨重庆市2023大学生职业规划大赛（重庆市级决赛）金奖
8. 2023/06第九届全国大学生基础医学创新研究暨实验设计论坛总决赛铜奖（国家级）
9. 2023/02第八届全国大学生基础医学创新研究暨实验设计论坛总决赛金奖/最佳团队合作奖（国家级）
10. 2022/11第八届全国大学生基础医学创新研究暨实验设计论坛-西部赛区（一等奖）
11. 2022/08全国大学生生命科学竞赛（2022，科学探究类）重庆赛区三等奖
13. 2021/12第七届全国大学生基础医学创新研究暨实验设计论坛总决赛优秀成果奖铜奖（国家级）
14. 2021/11第七届全国大学生基础医学创新研究暨实验设计论坛（西部赛区）二等奖(省部级)
6、科室合影
