Jie Zheng

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 26

Top Topics

Ensemble Learning

Influenza Virus

Encoding Scheme

Regulatory Networks

Top Venues

IEEE ACM Trans. Comput. Biol. Bioinform.

BMC Syst. Biol.

Publications

Ke Zhang, Yimiao Feng, Jie Zheng
Prompt-based Generation of Natural Language Explanations of Synthetic Lethality for Cancer Drug Discovery. LREC/COLING (2024)
Xin Liu, Jieni Hu, Jie Zheng
SL-Miner: a web server for mining evidence and prioritization of cancer-specific synthetic lethality. Bioinform. 40 (2) (2024)
Zongquan Li, Pengxuan Ren, Hao Yang, Jie Zheng, Fang Bai
TEFDTA: a transformer encoder and fingerprint representation combined prediction method for bonded and non-bonded drug-target affinities. Bioinform. 40 (1) (2024)
Ke Zhang, Min Wu, Yong Liu, Yimiao Feng, Jie Zheng
KR4SL: knowledge graph reasoning for explainable prediction of synthetic lethality. Bioinform. 39 (Supplement-1) (2023)
Ke Zhang, Chenxi Wang, Liping Sun, Jie Zheng
Prediction of gene co-expression from chromatin contacts with graph attention network. Bioinform. 38 (19) (2022)
Jie Wang, Min Wu, Xuhui Huang, Li Wang, Sophia Zhang, Hui Liu, Jie Zheng
SynLethDB 2.0: a web-based knowledge graph database on synthetic lethality for novel anticancer drug discovery. Database J. Biol. Databases Curation 2022 (2022) (2022)
Yahui Long, Min Wu, Yong Liu, Jie Zheng, Chee Keong Kwoh, Jiawei Luo, Xiaoli Li
Graph contextualized attention network for predicting synthetic lethality in human cancers. Bioinform. 37 (16) (2021)
Xin Wang, Jie Zheng
Velo-Predictor: an ensemble learning pipeline for RNA velocity prediction. BMC Bioinform. 22 (1) (2021)
Xinnan Dai, Fan Xu, Shike Wang, Piyushkumar A. Mundra, Jie Zheng
PIKE-R2P: Protein-protein interaction network-based knowledge embedding with graph neural network for single-cell RNA to protein prediction. BMC Bioinform. (6) (2021)
Shike Wang, Fan Xu, Yunyang Li, Jie Wang, Ke Zhang, Yong Liu, Min Wu, Jie Zheng
KG4SL: knowledge graph neural network for synthetic lethality prediction in human cancers. Bioinform. 37 (Supplement) (2021)
Mincai Lai, Guangyao Chen, Haochen Yang, Jingkang Yang, Zhihao Jiang, Min Wu, Jie Zheng
Predicting Synthetic Lethality in Human Cancers via Multi-Graph Ensemble Neural Network. EMBC (2021)
Yong Liu, Min Wu, Chenghao Liu, Xiaoli Li, Jie Zheng
MF: Predicting Synthetic Lethality in Human Cancers via Logistic Matrix Factorization. IEEE ACM Trans. Comput. Biol. Bioinform. 17 (3) (2020)
Haifen Chen, D. A. K. Maduranga, Piyushkumar A. Mundra, Jie Zheng
Bayesian Data Fusion of Gene Expression and Histone Modification Profiles for Inference of Gene Regulatory Network. IEEE ACM Trans. Comput. Biol. Bioinform. 17 (2) (2020)
Jie Zheng, Jinyan Li, Yun Zheng
Guest Editorial for the 29th International Conference on Genome Informatics (GIW 2018). IEEE ACM Trans. Comput. Biol. Bioinform. 17 (3) (2020)
Xinrui Zhou, Rui Yin, Jie Zheng, Chee Keong Kwoh
An Encoding Scheme Capturing Generic Priors and Properties of Amino Acids Improves Protein Classification. IEEE Access 7 (2019)
Yong Liu, Min Wu, Chenghao Liu, Xiaoli Li, Jie Zheng
MF: Predicting Synthetic Lethality in Human Cancers via Logistic Matrix Factorization. CoRR (2018)
Rui Yin, Xinrui Zhou, Jie Zheng, Chee Keong Kwoh
Computational identification of physicochemical signatures for host tropism of influenza A virus. J. Bioinform. Comput. Biol. 16 (6) (2018)
Xinrui Zhou, Jie Zheng, Fransiskus Xaverius Ivan, Rui Yin, Shoba Ranganathan, Vincent T. K. Chow, Chee-Keong Kwoh
Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses. BMC Genom. 19 (S2) (2018)
Fransiskus Xaverius Ivan, Xinrui Zhou, Akhila Deshpande, Rui Yin, Jie Zheng, Chee Keong Kwoh
Phylogenetic Tree based Method for Uncovering Co-mutational Site-pairs in Influenza Viruses. BCB (2017)
Jing Guo, Jie Zheng
HopLand: single-cell pseudotime recovery using continuous Hopfield network-based modeling of Waddington's epigenetic landscape. Bioinform. 33 (14) (2017)
Rui Yin, Xinrui Zhou, Fransiskus Xaverius Ivan, Jie Zheng, Vincent T. K. Chow, Chee Keong Kwoh
Identification of Potential Critical Virulent Sites Based on Hemagglutinin of Influenza a Virus in Past Pandemic Strains. ICBBS (2017)
Jing Guo, Feng Lin, Xiaomeng Zhang, Vivek Tanavde, Jie Zheng
NetLand: quantitative modeling and visualization of Waddington's epigenetic landscape using probabilistic potential. Bioinform. 33 (10) (2017)
Jing Guo, Hui Liu, Jie Zheng
SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets. Nucleic Acids Res. 44 (Database-Issue) (2016)
Fan Zhang, Runsheng Liu, Jie Zheng
Sig2GRN: a software tool linking signaling pathway with gene regulatory network for dynamic simulation. BMC Syst. Biol. 10 (4) (2016)
Fan Zhang, Haoting Chen, Li Na Zhao, Hui Liu, Teresa M. Przytycka, Jie Zheng
Generalized logical model based on network topology to capture the dynamical trends of cellular signaling pathways. BMC Syst. Biol. 10 (S-1) (2016)
Yifeng Li, Haifen Chen, Jie Zheng, Alioune Ngom
The Max-Min High-Order Dynamic Bayesian Network for Learning Gene Regulatory Networks with Time-Delayed Regulations. IEEE ACM Trans. Comput. Biol. Bioinform. 13 (4) (2016)
Haifen Chen, Jing Guo, Shital K. Mishra, Paul Robson, Mahesan Niranjan, Jie Zheng
Single-cell transcriptional analysis to uncover regulatory circuits driving cell fate decisions in early mouse development. Bioinform. 31 (7) (2015)
Xiaoli Li, Jie Zheng
Introduction to the CSBio2014 special issue. J. Bioinform. Comput. Biol. 13 (3) (2015)
Fan Zhang, Min Wu, Xuejuan Li, Xiaoli Li, Chee Keong Kwoh, Jie Zheng
Predicting essential genes and synthetic lethality via influence propagation in signaling pathways of cancer cell fates. J. Bioinform. Comput. Biol. 13 (3) (2015)
Shital K. Mishra, Sourav S. Bhowmick, Huey-Eng Chua, Fan Zhang, Jie Zheng
Computational cell fate modelling for discovery of rewiring in apoptotic network for enhanced cancer drug sensitivity. BMC Syst. Biol. 9 (S-1) (2015)
Jing Guo, Ritika Jain, Peng Yang, Rui Fan, Chee Keong Kwoh, Jie Zheng
Reliable and Fast Estimation of Recombination Rates by Convergence Diagnosis and Parallel Markov Chain Monte Carlo. IEEE ACM Trans. Comput. Biol. Bioinform. 11 (1) (2014)
Min Wu, Chee Keong Kwoh, Xiaoli Li, Jie Zheng
Finding trans-regulatory genes and protein complexes modulating meiotic recombination hotspots of human, mouse and yeast. BMC Syst. Biol. 8 (2014)
Wenting Liu, Kui Miao, Guangxia Li, Kuiyu Chang, Jie Zheng, Jagath C. Rajapakse
Extracting rate changes in transcriptional regulation from MEDLINE abstracts. BMC Bioinform. 15 (S-2) (2014)
Haifen Chen, Piyushkumar A. Mundra, Li Na Zhao, Feng Lin, Jie Zheng
Highly sensitive inference of time-delayed gene regulation by network deconvolution. BMC Syst. Biol. 8 (S-4) (2014)
Chinh Tran To Su, Thuy-Diem Nguyen, Jie Zheng, Chee Keong Kwoh
IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking. BMC Bioinform. 15 (S-16) (2014)
Haifen Chen, Stefano Lonardi, Jie Zheng
Deciphering histone code of transcriptional regulation in malaria parasites by large-scale data mining. Comput. Biol. Chem. 50 (2014)
Fan Zhang, Chee Keong Kwoh, Min Wu, Jie Zheng
Data-driven prediction of cancer cell fates with a nonlinear model of signaling pathways. BCB (2014)
Seyed Ziaeddin Alborzi, D. A. K. Maduranga, Rui Fan, Jagath C. Rajapakse, Jie Zheng
CUDAGRN: Parallel Speedup of Inferring Large Gene Regulatory Networks from Expression Data Using Random Forest. PRIB (2014)
Peng Yang, Min Wu, Jing Guo, Chee Keong Kwoh, Teresa M. Przytycka, Jie Zheng
LDsplit: screening for cis-regulatory motifs stimulating meiotic recombination hotspots by analysis of DNA sequence polymorphisms. BMC Bioinform. 15 (2014)
Min Wu, Xuejuan Li, Fan Zhang, Xiaoli Li, Chee Keong Kwoh, Jie Zheng
Meta-analysis of Genomic and Proteomic Features to Predict Synthetic Lethality of Yeast and Human Cancer. BCB (2013)
D. A. K. Maduranga, Jie Zheng, Piyushkumar A. Mundra, Jagath C. Rajapakse
Inferring Gene Regulatory Networks from Time-Series Expressions Using Random Forests Ensemble. PRIB (2013)
Xuejuan Li, Shital K. Mishra, Min Wu, Fan Zhang, Jie Zheng
Syn-Lethality: An integrative knowledge base of synthetic lethality towards discovery of selective anticancer therapies. BIBM (2013)
Wenting Liu, Kuiyu Chang, Jie Zheng, Jain Divya, Jung-Jae Kim, Jagath C. Rajapakse
Gene Regulatory Networks from Gene Ontology. ISBRA (2013)
Piyushkumar A. Mundra, Jie Zheng, Mahesan Niranjan, Roy E. Welsch, Jagath C. Rajapakse
Inferring Time-Delayed Gene Regulatory Networks Using Cross-Correlation and Sparse Regression. ISBRA (2013)
Chinh Tran To Su, Xuchang Ouyang, Jie Zheng, Chee Keong Kwoh
Structural analysis of the novel influenza A (H7N9) viral Neuraminidase interactions with current approved neuraminidase inhibitors Oseltamivir, Zanamivir, and Peramivir in the presence of mutation R289K. BMC Bioinform. 14 (S-16) (2013)
Haifen Chen, D. A. K. Maduranga, Piyushkumar A. Mundra, Jie Zheng
Integrating epigenetic prior in dynamic Bayesian network for gene regulatory network inference. CIBCB (2013)
Jian-Ping Mei, Chee Keong Kwoh, Peng Yang, Xiaoli Li, Jie Zheng
Drug-target interaction prediction by learning from local information and neighbors. Bioinform. 29 (2) (2013)
Jian-Ping Mei, Chee Keong Kwoh, Peng Yang, Xiaoli Li, Jie Zheng
Globalized bipartite local model for drug-target interaction prediction. BIOKDD (2012)
Min Wu, Chee Keong Kwoh, Teresa M. Przytycka, Jing Li, Jie Zheng
Integration of genomic and epigenomic features to predict meiotic recombination hotspots in human and mouse. BCB (2012)
Raheleh Salari, Damian Wójtowicz, Jie Zheng, David Levens, Yitzhak Pilpel, Teresa M. Przytycka
Teasing Apart Translational and Transcriptional Components of Stochastic Variations in Eukaryotic Gene Expression. PLoS Comput. Biol. 8 (8) (2012)
Min Wu, Chee Keong Kwoh, Jie Zheng, Xiaoli Li
NetPipe: a network-based pipeline for discovery of genes and protein complexes regulating meiotic recombination hotspots. BCB (2012)
Jie Zheng, Iti Chaturvedi, Jagath C. Rajapakse
Integration of Epigenetic Data in Bayesian Network Modeling of Gene Regulatory Network. PRIB (2011)
Min Wu, Chee Keong Kwoh, Teresa M. Przytycka, Jing Li, Jie Zheng
Prediction of Trans-regulators of Recombination Hotspots in Mouse Genome. BIBM (2011)
Jie Zheng, David Zhang, Pawel F. Przytycki, Rafal Zielinski, Jacek Capala, Teresa M. Przytycka
SimBoolNet - a Cytoscape plugin for dynamic simulation of signaling networks. Bioinform. 26 (1) (2010)
Rafal Zielinski, Pawel F. Przytycki, Jie Zheng, David Zhang, Teresa M. Przytycka, Jacek Capala
The crosstalk between EGF, IGF, and Insulin cell signaling pathways - computational and experimental analysis. BMC Syst. Biol. 3 (2009)
Jie Zheng, Igor B. Rogozin, Eugene V. Koonin, Teresa M. Przytycka
Clade of Animals. RECOMB-CG (2007)
Jie Zheng, Jan T. Svensson, Kavitha Madishetty, Timothy J. Close, Tao Jiang, Stefano Lonardi
OligoSpawn: a software tool for the design of overgo probes from large unigene datasets. BMC Bioinform. 7 (2006)
Xin Chen, Jie Zheng, Zheng Fu, Peng Nan, Yang Zhong, Stefano Lonardi, Tao Jiang
Computing the Assignment of Orthologous Genes via Genome Rearrangement. APBC (2005)
Jie Zheng, Stefano Lonardi
Discovery of Repetitive Patterns in DNA with Accurate Boundaries. BIBE (2005)
Xin Chen, Jie Zheng, Zheng Fu, Peng Nan, Yang Zhong, Stefano Lonardi, Tao Jiang
Assignment of Orthologous Genes via Genome Rearrangement. IEEE ACM Trans. Comput. Biol. Bioinform. 2 (4) (2005)
Jie Zheng, Timothy J. Close, Tao Jiang, Stefano Lonardi
Efficient selection of unique and popular oligos for large EST databases. Bioinform. 20 (13) (2004)
Jie Zheng, Timothy J. Close, Tao Jiang, Stefano Lonardi
Efficient Selection of Unique and Popular Oligos for Large EST Databases. CPM (2003)