机器学习和生物信息学实验室联盟

标题: 本课题组开发维护的软件 [打印本页]

作者: zouquan 时间: 2015-10-6 09:30
标题: 本课题组开发维护的软件
数据库
Ricyer(Rice yield related gene database)(开发：邢鹏威，姜晶，目前负责：姜晶)
Ref：Jing Jiang, Fei Xing, Xiangxiang Zeng, Quan Zou. RicyerDB: A Database For Collecting Rice Yield-related Genes with Biological Analysis. International Journal of Biological Sciences. 2018, 14(8):965-970

PMIDB(DNA/RNA binding proteins 功能数据库)（目前负责：江姗姗、徐磊）
Ref:

mAML（人类健康微生物组数据库及web server）（目前负责：杨凤龙）
Ref: Fenglong Yang, Quan Zou. mAML: an automated machine learning pipeline with a microbiome repository for human disease classification. DATABASE-The Journal of Biological Databases and Curation. Accepted.

序列分析软件
Symka (Browser of Symka Genome)(目前负责：邹权)
Ref: Senjie Lin, Shifeng Cheng, Bo Song, Xiao Zhong, Xin Lin, Wujiao Li, Ling Li, Yaqun Zhang, Huan Zhang, Zhiliang Ji, Meichun Cai, Yunyun Zhuang, Xinguo Shi, Lingxiao Lin, Lu Wang, Zhaobao Wang, Xin Liu, Sheng Yu, Peng Zeng, Han Hao, Quan Zou, Chengxuan Chen, Yanjun Li, Ying Wang, Chunyan Xu, Shanshan Meng, Xun Xu, Jun Wang, Huanming Yang, David A. Campbe, Nancy R. Sturm, Steve Dagenais-Bellefeuille, David Morse. The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis. Science. 2015, 350(6261): 691-694

HAlign (Multiple Sequence Alignment with Hadoop)(开发：毛耀宗、万世想，目前负责：万世想)
Ref: Quan Zou, Qinghua Hu, Maozu Guo, Guohua Wang. HAlign: Fast Multiple Similar DNA/RNA Sequence Alignment Based on the Centre Star Strategy. Bioinformatics. 2015,31(15): 2475-2481

HPTree(Building phylogenetics tree for unaligned sequences with Hadoop)(开发：毛耀宗、万世想，目前负责：万世想)
Ref: BIBM2016

sanmog (Sequence And Nework MOtif detection with Gpu)(开发：谢思发)
Ref: 投稿中

RNA计算分析软件
mirnaDetect (a software to predict possible microRNA precursors within genome data) (目前负责：魏乐义)
Ref: Wei L, Liao M, Gao Y, Ji R, He Z, Zou Q. Improved and promising identification of human microRNAs by incorporating a high-quality negative set. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2014, 11(1): 192-201

MDAP (microRNA-disease association prediction) (目前负责：李金金)
Ref: Quan Zou, Jinjin Li, Qingqi Hong, Ziyu Lin, Hua Shi, Yun Wu, Ying Ju. Prediction of microRNA-disease associations based on social network analysis methods. BioMed Research International. 2015, 2015: 810514

ifmda (infer microRNA-disease association)(目前负责：刘元盛)
Ref: Yuansheng Liu, Xiangxiang Zeng, Zengyou He, Quan Zou. Inferring microRNA-disease associations by random walk on a heterogeneous network with multiple data sources. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Doi: 10.1109/TCBB.2016.2550432.

miR-isomiRExp(miRNA-isomiR Expression Analysis) (开发：毛耀宗，合作指导：郭丽，目前负责：邹权)
Ref: Li Guo, Jiafeng Yu, Tingming Liang, Quan Zou. miR-isomiRExp: a web-server for the analysis of expression of miRNA at the miRNA/isomiR levels. Scientific Reports. 2016, 6: 23700

miRClassify (预测miRNA的家族信息)(开发：胡玲玲，目前负责：邹权)
Ref: Quan Zou, Yaozong Mao, Lingling Hu, Yunfeng Wu, Zhiliang Ji. miRClassify: An advanced web server for miRNA family classification and annotation. Computers in Biology and Medicine. 2014, 45:157-160

tRNA-Predict(预测是否是tRNA序列)(目前负责：郭佳盛)
Ref: Quan Zou, Jiasheng Guo, Ying Ju, Meihong Wu, Xiangxiang Zeng, Zhiling Hong. Improving tRNAscan-SE annotation results via ensemble classifiers. Molecular Informatics. Molecular Informatics.2015,34(11-12):761-770.

RAM-ESVM(Detecting N6-methyladenosine sites from RNA transcriptomes using ensemble Support Vector Machines)(目前负责：邢鹏威)
Ref: Wei Chen, Pengwei Xing, Quan Zou. Detecting N6-methyladenosine sites from RNA transcriptomes using ensemble Support Vector Machines. Scientific Reports. 2017, 7: 40242

MMCOP (利用miRNA和甲基化表达谱探测肿瘤起始位置)（开发：唐伟，万世想；目前负责：万世想）
Ref: Wei Tang, Shixiang Wan, Zhen Yang, Andrew E. Teschendorff, Quan Zou. Tumor Origin Detection with Tissue-Specific miRNA and DNA methylation Markers. Bioinformatics. 2018, 34(3): 398-406

CirRNAPL (circleRNA预测)（开发：牛梦婷；目前负责：牛梦婷）
Ref: Mengting Niu, et al. CirRNAPL: A web server for the identification of circRNA based on extreme learning machine. Computational and Structural Biotechnology Journal. Accepted

蛋白质分类软件
PFPA(a web server for protein fold prediction) (目前负责：魏乐义)
Ref: Wei L, Liao M, Gao X, Zou Q. Enhanced Protein Fold Prediction Method Through a Novel Feature Extraction Technique. IEEE Transactions on NanoBioscience, 2015, 14(6): 649-659.

RF_PSCP (a web server for protein fold prediction)(目前负责：魏乐义)
Ref: Leyi Wei, Minghong Liao, Xing Gao, Quan Zou. An Improved Protein Structural Class Prediction Method by Incorporating Both Sequence and Structure Information, IEEE Transactions on NanoBioscience, 2015, 14(4): 339-349.

P2F3(a web server for protein fold prediction)(开发：赵雪薇，目前负责：邹权)
Ref: Xuewei Zhao, Quan Zou, Bin Liu, Xiangrong Liu. Exploratory predicting protein folding model with random forest and hybrid features. Current Proteomics. 2014, 11(4):289-299

nDNA-Prot(a web server for distinguishing DNA-binding proteins)(开发：宋莉，目前负责：邹权)
Ref: Li Song, Dapeng Li, Xiangxiang Zeng, Yunfeng Wu, Li Guo, Quan Zou. nDNA-prot: Identification of DNA-binding Proteins Based on Unbalanced Classification. BMC Bioinformatics. 2014, 15:298

bdscyto(a web server for distingguishing cytokine proteins)(目前负责：万世想)
Ref: Quan Zou, Shixiang Wan, Bing Han,Zhihui Zhan. BDSCyto: An Automated Approach for Identifying Cytokines Based onBest Dimension Searching. Pacific Rim International Conference on ArtificialIntelligence (PRICAI2016).Springer International Publishing, 2016: 713-725

PPIpre (Predicting Protein-Protein Interaction)(目前负责：邹权)
Ref: 投稿中

MEC (Multifunctional Enzyme Classification)(开发：车玉馨，目前负责：邹权)
Ref: PLoS ONE

HPFP (Hierarchical Protein Fold Prediction)(开发：邹莹，目前负责：邹权)
Ref: Chen Lin, Ying Zou, Ji Qin, Xiangrong Liu, Yi Jiang, Caihuan Ke, Quan Zou. Hierarchical Classification of Protein Folds Using a Novel Ensemble Classifier. PLoS One. 2013, 8(2):e56499

SkipCPP-Pred (A webserver for predicting cell-penetrating peptides) (目前负责：魏乐义)
Ref: ISBRA2016

PreTATA (Predicting TATA-binding proteins)(目前负责：万世想)
Ref: Quan Zou, Shixiang Wan, Ying Ju, Jijun Tang,Xiangxiang Zeng. Pretata: predicting TATA binding proteins with novel features and dimensionality reduction strategy. BMC System Biology. 2016, 10(Suppl 4): 114

mGOF-loc (Human Protein Subcellular Localization Prediction)(目前负责：魏乐义)
Ref: Leyi Wei, Minghong Liao, Xing Gao, Jingjing Wang, Weiqi Lin. mGOF-Loc: A Novel Ensemble Learning Method for Human Protein Subcellular Localization Prediction. Neurocomputing. 2016. 217:73-82

Local-DPP ( An Improved DNA-binding Protein PredictionMethod by Exploring Local Evolutionary Information(目前负责：魏乐义)
Ref: Leyi Wei, Jijun Tang, Quan Zou. Local-DPP: An Improved DNA-binding Protein Prediction Method by Exploring Local Evolutionary Information. Information Sciences. 2017. 384:135-144

MePred-RF (fast prediction of protein methylation sites using sequence-based feature selection technique)(目前负责：邢鹏威)
Ref: Leyi Wei, Pengwei Xing, Gaotao Shi, Zhiliang Ji*, Quan Zou*. Fast prediction of protein methylation sites using a sequence-based feature selection technique. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Doi: 10.1109/TCBB.2017.2670558.

IKP-DBPPred (识别DNA binding proteins)（目前负责：曲凯扬）
Ref: Kaiyang Qu, Ke Han, Song Wu, Guohua Wang, Leyi Wei. Identification of DNA-Binding Proteins Using Mixed Feature Representation Methods. Molecules. 2017, 22: 1602

机器学习软件
libD3C (an emsemble classifier)(目前负责：郭佳盛)
Ref: Chen Lin, Wenqiang Chen, Cheng Qiu, Yunfeng Wu, Sridhar Krishnan, Quan Zou. LibD3C: Ensemble Classifiers with a Clustering and Dynamic Selection Strategy. Neurocomputing. 2014,123:424-435

MRMD(论坛)(2.0版本)(a software for feature ranking and selection)(目前负责：万世想)
Ref: Quan Zou, Jiancang Zeng, Liujuan Cao, Rongrong Ji. A Novel Features Ranking Metric with Application to Scalable Visual and Bioinformatics Data Classification. Neurocomputing. 2016, 173:346-354

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