张艳菊，女，华侨大学计算机学院教授、硕士研究生导师。2010年获得欧洲科学基金“功能基因组学研究前沿(FFG)”奖励。2015年作为广西“百人计划”海外高层次引进人才就职于桂林电子科技大学计算机与信息安全学院，并被遴选为硕士研究生导师。2019年被评选为广西第一批高层次人才E层次人才。现为CCF中国计算机学会生物信息专委会和广西人工智能学会委员。以第一作者在Briefings in Bioinformatics、Bioinformatics等TOP期刊发表科研论文8篇，其中最高影响因子为13.994；以合作者身份在Nature子刊Nature Communications、Nucleic Acids Research、Twin Research and Human Genetics等期刊发表论文12篇，其中最高影响因子为19.160。近年来，主持国家自然科学基金1项、广西自然科学基金2项，并指导研究生18名，其中8人已获学位，1人获得校级优秀论文。
研究领域：生物信息学和医学图像处理
研究方向：高通量基因测序技术和生物芯片技术算法开发、基因组注释、精准医疗、生物医学大数据挖掘以及医学图像的分割、统计分析和建模等。
研究生招生：学硕和专硕
招生要求：勤奋踏实、具有钻研精神、有一定编程能力和写作能力。
欢迎邮件咨询：yanjuzhang@hqu.edu.cn
教育经历
1. 2006/4–2011/11，荷兰莱顿大学，生物信息，博士，导师：Fons J. Verbeek
2. 2003/10–2005/09，德国德累斯顿工业大学，分子生物工程，硕士，导师：Michael Schroeder
3. 1998/09–2002/07，桂林电子科技大学，计算机应用，学士
科研与学术工作经历
1. 2023/03-至今，华侨大学，计算机科学与技术学院，研究员
2. 2016/12-2023/02，桂林电子科技大学，计算机与信息安全学院，研究员
3. 2015/3-2016/12，桂林电子科技大学，计算机与信息安全学院
4. 2011/9-2014/9，荷兰莱顿大学医学中心，博士后
主持或参加科研项目（课题）及人才计划项目情况
1. 2019年认定为广西第一批高级E层次人才
2. 国家自然科学基金地区基金，面向第三代RNA测序长读段的定位算法研究，2019/01-2022/12，39万，在研，主持
3. 广西自然科学基金联合资助培育项目，第三代转录组测序数据检测剪切位点算法研究，2018/07-2020/07，20万，结题，主持
4. 广西自然科学基金回国基金项目，针对第三代转录组测序数据检测剪切位点的算法开发，2016/09-2019/08，10万，结题，主持
5. 2015年入选广西高校引进海外高层次人才 “百人计划”
代表性研究成果和学术奖励情况：
一、期刊论文
1. 第一作者或通讯作者论文
(1) Ruopeng Xie, Jiahui Li, Jiawei Wang, Wei Dai, André Leier, Tatiana T Marquez-Lago, Tatsuya Akutsu, Trevor Lithgow, Jiangning Song, Yanju Zhang. DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy, Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, https://doi.org/10.1093/bib/bbaa125
(2) Yanju Zhang, Sha Yu, Ruopeng Xie, Jiahui Li, André Leier, Tatiana T Marquez-Lago, Tatsuya Akutsu, A. Ian Smith, Zongyuan Ge, Jiawei Wang, Trevor Lithgow, Jiangning Song; PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins, Bioinformatics, Volume 36, Issue 3, 1 February 2020, Pages 704–712, https://doi.org/10.1093/bioinformatics/btz629
(3) Yanju Zhang, Ruopeng Xie, Jiawei Wang, André Leier, Tatiana T Marquez-Lago, Tatsuya Akutsu, Geoffrey I Webb, Kuo-Chen Chou, Jiangning Song; Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework, Briefings in Bioinformatics, Volume 20, Issue 6, November 2019, Pages 2185–2199, https://doi.org/10.1093/bib/bby079
(4) Yanju Zhang, Eric-Wubbo Lameijer, Peter A. C. 't Hoen, Zemin Ning, P. Eline Slagboom, Kai Ye: PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data. Bioinformatics 28(4): 479-486 (2012).
(5) Yanju Zhang, Elia Stupka, Christiaan V. Henkel, Hans J. Jansen, Herman P. Spaink and Fons J. Verbeek. Identification of Common Carp Innate Immune Genes with Whole-Genome Sequencing and RNA-Seq Data. Journal of Integrative Bioinformatics, 8(2):169, 2011. Online Journal: http://journal.imbio.de/index.php?paper id=169.
(6) Yanju Zhang and Fons J. Verbeek. Comparison and Integration of Target Prediction Algorithms for microRNA Studies. Journal of Integrative Bioinformatics, 7(3):127, 2010. Online Journal: http://journal.imbio.de/index.php?paper id=127.
(7) Yanju Zhang, Joost M. Woltering, Fons J. Verbeek. Screen of microRNA targets in zebrafish using heterogeneous data sources: a case study for dre-miR-10 and dre-miR-196. International Journal of Mathematical, Physical and Engineering Sciences, Vol. 2 (1), 10-17, 2007.
2. 既非第一作者又非通讯作者论文
(8) Jiawei Wang, Wei Dai, Jiahui Li, Qi Li, Ruopeng Xie, Yanju Zhang, Christopher Stubenrauch, Trevor Lithgow, AcrHub: an integrative hub for investigating, predicting and mapping anti-CRISPR proteins, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D630–D638, https://doi.org/10.1093/nar/gkaa951
(9) Jiawei Wang, Jiahui Li, Yi Hou, Wei Dai, Ruopeng Xie, Tatiana T Marquez-Lago, André Leier, Tieli Zhou, Von Torres, Iain Hay, Christopher Stubenrauch, Yanju Zhang, Jiangning Song, Trevor Lithgow, BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D651–D659, https://doi.org/10.1093/nar/gkaa899
(10) Jiawei Wang, Wei Dai, Jiahui Li, Ruopeng Xie, Rhys A Dunstan, Christopher Stubenrauch, Yanju Zhang, Trevor Lithgow, PaCRISPR: a server for predicting and visualizing anti-CRISPR proteins, Nucleic Acids Research, Volume 48, Issue W1, 02 July 2020, Pages W348–W357, https://doi.org/10.1093/nar/gkaa432
(11) Jiawei Wang, Jiahui Li, Bingjiao Yang, Ruopeng Xie, Tatiana T Marquez-Lago, André Leier, Morihiro Hayashida, Tatsuya Akutsu, Yanju Zhang, Kuo-Chen Chou, Joel Selkrig, Tieli Zhou, Jiangning Song, Trevor Lithgow, Bastion3: a two-layer ensemble predictor of type III secreted effectors, Bioinformatics, Volume 35, Issue 12, June 2019, Pages 2017–2028, https://doi.org/10.1093/bioinformatics/bty914
(12) Jiawei Wang, Bingjiao Yang, André Leier, Tatiana T Marquez-Lago, Morihiro Hayashida, Andrea Rocker, Yanju Zhang, Tatsuya Akutsu, Kuo-Chen Chou, Richard A Strugnell, Jiangning Song, Trevor Lithgow; Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors, Bioinformatics, Volume 34, Issue 15, 1 August 2018, Pages 2546–2555, https://doi.org/10.1093/bioinformatics/bty155
(13) Shengtao Xu，Guangyu Wang，Yan Lin，Yanju Zhang，Lingling Pei，Hong Yao，Mei Hu，Yangyi Qiu，Zhangjian Huang，Yihua Zhang，Jinyi Xu. Novel anticancer oridonin derivatives possessing a diazen-1-ium-1,2-diolate nitric oxide donor moiety: Design, synthesis, biological evaluation and nitric oxide release studies. Bioorganic & Medicinal Chemistry Letters, 2016/4/24.
(14) Tobi EW, Goeman JJ, Monajemi R, Gu H, Putter H, Zhang Y, Slieker RC, Stok AP, Thijssen PE, Müller F, van Zwet EW, Bock C, Meissner A, Lumey LH, Eline Slagboom P, Heijmans BT. DNA methylation signatures link prenatal famine exposure to growth and metabolism. Nat Commun. 2014 Nov 26;5:5592. doi: 10.1038/ncomms6592.
(15) Kai Ye, Marian Beekman, Eric-Wubbo Lameijer, Yanju Zhang, Matthijs H. Moed, Erik B. van den Akker, Joris Deelen, Jeanine J. Houwing-Duistermaat, Dennis Kremer, Seyed Yahya Anvar, Jeroen F. J. Laros, David Jones, Keiran Raine, Ben Blackburne, Shobha Potluri, Quan Long, Victor Guryev, Ruud van der Breggen, Rudi G. J. Westendorp, Peter A. C. ‘t Hoen, Johan den Dunnen, Gert Jan B. van Ommen, Gonneke Willemsen, Steven J. Pitts, David R. Cox, Zemin Ning, Dorret I. Boomsma, and P. Eline Slagboom. Aging as Accelerated Accumulation of Somatic Variants: Whole-Genome Sequencing of Centenarian and Middle-Aged Monozygotic Twin Pairs. Twin Research and Human Genetics. Vol. 16, No. 6. (December 2013), pp. 1026-1032, doi:10.1017/thg.2013.73.
(16) Roderick C Slieker, Steffan D Bos, Jelle J Goeman, Judith VMG Bovée, Rudolf P Talens, Ruud van der Breggen, H Eka D Suchiman, Eric-Wubbo Lameijer, Hein Putter, Erik B van den Akker, Yanju Zhang, J Wouter Jukema, P Eline Slagboom, Ingrid Meulenbelt, and Bastiaan T Heijmans. Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array. Epigenetics & Chromatin, 2013, 6:26.
(17) Gihan Dawelbait, Christof Winter, Yanju Zhang, Chrisitian Pilarky, Robert Grtz-mann, Jrg-Chrisitan Heinrich and Michael Schroeder. Structural templates predict novel protein interactions and targets from pancreas tumour gene expression data. Bioinformatics, 23:i115–24, 2007.
二 、会议论文
1. 第一作者论文
(18) Jiahao Chen, Ruohan Lin, Xiaobin Lan, Rongxing Wang, Xipeng Pan, Yanju Zhang; Transfer Learning for Semi-Supervised 3D Left Atrium Segmentation through Dual-Task Consistency Framework, International Symposium on Bioinformatics Research and Applications, November 14-17, 2022.
(19) Yanju Zhang, Jeroen S. de Bruin, Fons J. Verbeek. miRNA target prediction through mining of miRNA relationships. Proceedings of the 8th IEEE International Conference on Bioinformatics and Bioengineering. ISBN: 978-1-4244-2844-1, 1-6, 2008.
三、其他论文成果
(20) Yanju Zhang, Jeroen S. de Bruin and Fons J. Verbeek. Specificity Enhancement in microRNA Target Prediction through Knowledge Discovery. Chapter 20 In: Machine Learning, Eds. Yagang Zhang, ISBN: 978-953-307-033-9, INTECH, February 2010.
四、专利
(1) 张艳菊; 李琪; 王荣兴; 齐王璟; 一种基于WFA算法的第三代测序RNA-seq比对方法, 2022-02-28, 中国专利, ZL202210186243.3.
(2) 张艳菊; 许峻玮; 齐王璟; 王荣兴; 一种双端成对的剪接位点预测方法, 2022-02-25, 中国专利, ZL202210178009.6.
(3) 张艳菊; 李琪; 王荣兴; 齐王璟; 一种基于GPU并行计算的第三代测序RNA-seq比对方法, 2022-02-28, 中国专利, ZL202210186254.1.
(4) 张艳菊; 许峻玮; 齐王璟; 王荣兴; 一种基于注意力机制的剪接位点预测及解释性方法, 2022-02-25, 中国专利, ZL202210178010.9.
(5) 张艳菊; 王鹤杰; 陈嘉豪; 蓝小斌; 一种基于深度学习的第三代测序数据的自校正纠错方法, 2022-04-12, 中国专利, ZL202210380222.5.
(6) 张艳菊; 王鹤杰; 林若翰; 周帆; 一种PacBio测序数据纠错结果的自动化评估方法, 2022-04-12, 中国专利, ZL202210380137.9.