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ORCIDJie Zheng 0002
Person information
- affiliation: ShanghaiTech University, School of Information Science and Technology, Shanghai, China
- affiliation: Nanyang Technological University, School of Computer Engineering, Bioinformatics Research Centre, Singapore
- affiliation: A*STAR, Genome Institute of Singapore, Singapore
- affiliation (2006 - 2011): National Institutes of Health, Bethesda, MD, USA
- affiliation (PhD 2006): University of California Riverside, CA, USA
Other persons with the same name
- Jie Zheng — disambiguation page
- Jie Zheng 0001
![[0000-0002-2999-0103]](https://dblp.uni-trier.de./img/orcid-mark.12x12.png "0000-0002-2999-0103")
— University of Pennsylvania, Perelman School of Medicine, Department of Genetics, Philadelphia, PA, USA - Jie Zheng 0003 — University of Akron, Department of Chemical and Biomolecular Engineering, OH, USA (and 1 more)
- Jie Zheng 0004 — Tsinghua University, School of Economics and Management, Beijing, China (and 1 more)
- Jie Zheng 0005 — Northwest University, School of Information and Technology, Xi'an, China (and 1 more)
- Jie Zheng 0006 — University of Bristol, School of Social and Community Medicine, UK (and 1 more)
- Jie Zheng 0007 — State Key Laboratory of Information Engineering in Surveying, Mapping and Remote Sensing, LIESMARS, Wuhan, China (and 1 more)
- Jie Zheng 0008 — Tianjin Agricultural University, College of computer and Information Engineering, China
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2020 – today
- 2025
[j52]Haoran Jiang, Shaohan Shi, Shuhao Zhang, Jie Zheng, Quan Li:
SLInterpreter: An Exploratory and Iterative Human-AI Collaborative System for GNN-Based Synthetic Lethal Prediction. IEEE Trans. Vis. Comput. Graph. 31(1): 919-929 (2025)- 2024
- [j51]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) - [j50]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) - [j49]Lin Zhu, Xin Kang, Chunhe Li, Jie Zheng:
TMELand: An End-to-End Pipeline for Quantification and Visualization of Waddington's Epigenetic Landscape Based on Gene Regulatory Network. IEEE ACM Trans. Comput. Biol. Bioinform. 21(6): 1604-1612 (2024) - [j48]Beiyuan Yang, Yule Liu, Junfeng Wu, Fang Bai, Mingyue Zheng, Jie Zheng:
GENNDTI: Drug-Target Interaction Prediction Using Graph Neural Network Enhanced by Router Nodes. IEEE J. Biomed. Health Informatics 28(12): 7588-7598 (2024) - [c25]Ke Zhang, Yimiao Feng, Jie Zheng:
Prompt-based Generation of Natural Language Explanations of Synthetic Lethality for Cancer Drug Discovery. LREC/COLING 2024: 13131-13142 - 2023
- [j47]Ke Zhang, Min Wu, Yong Liu, Yimiao Feng, Jie Zheng:
KR4SL: knowledge graph reasoning for explainable prediction of synthetic lethality. Bioinform. 39(Supplement-1): 158-167 (2023) - 2022
- [j46]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) - [j45]Ke Zhang, Chenxi Wang, Liping Sun, Jie Zheng:
Prediction of gene co-expression from chromatin contacts with graph attention network. Bioinform. 38(19): 4457-4465 (2022) - [j44]Xin Liu, Jiale Yu, Siyu Tao, Beiyuan Yang, Shike Wang, Lin Wang, Fang Bai, Jie Zheng:
PiLSL: pairwise interaction learning-based graph neural network for synthetic lethality prediction in human cancers. Bioinform. 38(Supplement_2): ii106-ii112 (2022) - [j43]Shike Wang, Yimiao Feng, Xin Liu, Yong Liu, Min Wu, Jie Zheng:
NSF4SL: negative-sample-free contrastive learning for ranking synthetic lethal partner genes in human cancers. Bioinform. 38(Supplement_2): ii13-ii19 (2022) - 2021
- [j42]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): 2432-2440 (2021) - [j41]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): 418-425 (2021) - [j40]Xin Wang, Jie Zheng:
Velo-Predictor: an ensemble learning pipeline for RNA velocity prediction. BMC Bioinform. 22(1): 419 (2021) - [j39]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. 22-S(6): 139 (2021) - [c24]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: 1731-1734 - 2020
- [j38]Xiaomeng Zhang, Ket Hing Chong, Lin Zhu, Jie Zheng:
A Monte Carlo method for in silico modeling and visualization of Waddington's epigenetic landscape with intermediate details. Biosyst. 198: 104275 (2020) - [j37]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): 516-525 (2020) - [j36]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): 726-727 (2020) - [j35]Yong Liu, Min Wu, Chenghao Liu, Xiaoli Li, Jie Zheng:
SL2MF: Predicting Synthetic Lethality in Human Cancers via Logistic Matrix Factorization. IEEE ACM Trans. Comput. Biol. Bioinform. 17(3): 748-757 (2020)
2010 – 2019
- 2019
- [j34]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: 7348-7356 (2019) - [j33]Pritha Dutta, Lichun Ma, Yusuf Ali, Peter M. A. Sloot, Jie Zheng:
Boolean network modeling of β-cell apoptosis and insulin resistance in type 2 diabetes mellitus. BMC Syst. Biol. 13-S(2): 36:1-36:12 (2019) - [c23]Lin Zhu, Xinnan Dai, Qihao Huang, Hai Xiang, Jie Zheng:
Topic Judgment Helps Question Similarity Prediction in Medical FAQ Dialogue Systems. ICDM Workshops 2019: 966-972 - [r2]Rui Yin, Chee Keong Kwoh, Jie Zheng:
Whole Genome Sequencing Analysis. Encyclopedia of Bioinformatics and Computational Biology (3) 2019: 176-183 - [r1]Fransiskus Xaverius Ivan, Chee-Keong Kwoh, Vincent T. K. Chow, Jie Zheng:
Genome Analysis - Identification of Genes Involved in Host-Pathogen Protein-Protein Interaction Networks. Encyclopedia of Bioinformatics and Computational Biology (3) 2019: 410-424 - 2018
- [j32]Huey-Eng Chua, Sourav S. Bhowmick, Jie Zheng:
TROVE: a user-friendly tool for visualizing and analyzing cancer hallmarks in signaling networks. Bioinform. 34(2): 314-316 (2018) - [j31]Lichun Ma, Jie Zheng:
Single-cell gene expression analysis reveals β-cell dysfunction and deficit mechanisms in type 2 diabetes. BMC Bioinform. 19-S(19): 37-48 (2018) - [j30]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) - [j29]Bobby Ranjan, Ket Hing Chong, Jie Zheng:
Composite mathematical modeling of calcium signaling behind neuronal cell death in Alzheimer's disease. BMC Syst. Biol. 12(1): 61-74 (2018) - [j28]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): 1840023:1-1840023:21 (2018) - [i1]Yong Liu, Min Wu, Chenghao Liu, Xiaoli Li, Jie Zheng:
SL2MF: Predicting Synthetic Lethality in Human Cancers via Logistic Matrix Factorization. CoRR abs/1810.08726 (2018) - 2017
- [j27]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): 1583-1585 (2017) - [j26]Jing Guo, Jie Zheng:
HopLand: single-cell pseudotime recovery using continuous Hopfield network-based modeling of Waddington's epigenetic landscape. Bioinform. 33(14): i102-i109 (2017) - [j25]Lichun Ma, Jie Zheng:
A polynomial based model for cell fate prediction in human diseases. BMC Syst. Biol. 11(S-7): 15-27 (2017) - [c22]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: 21-26 - [c21]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: 30-36 - 2016
- [j24]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): 541-548 (2016) - [j23]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): 7 (2016) - [j22]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): 1011-1017 (2016) - [j21]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): 792-803 (2016) - [c20]Huey-Eng Chua, Sourav S. Bhowmick, Jie Zheng, Lisa Tucker-Kellogg:
TAPESTRY: Network-centric Target Prioritization in Disease-related Signaling Networks. BCB 2016: 108-117 - [c19]Shital Kumar Mishra, Sourav S. Bhowmick, Huey-Eng Chua, Jie Zheng:
Predictive Modeling of Drug Effects on Signaling Pathways in Diverse Cancer Cell Lines. BCB 2016: 200-209 - 2015
- [j20]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): 1060-1066 (2015) - [j19]Hui Liu, Jianjiang Sun, Jihong Guan, Jie Zheng, Shuigeng Zhou:
Improving compound-protein interaction prediction by building up highly credible negative samples. Bioinform. 31(12): 221-229 (2015) - [j18]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): S4 (2015) - [j17]Xiaoli Li, Jie Zheng:
Introduction to the CSBio2014 special issue. J. Bioinform. Comput. Biol. 13(3): 1502002:1-1502002:4 (2015) - [j16]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): 1541002:1-1541002:14 (2015) - 2014
- [j15]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: 48 (2014) - [j14]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): S9 (2014) - [j13]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): S4 (2014) - [j12]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: 107 (2014) - [j11]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): S6 (2014) - [j10]Haifen Chen, Stefano Lonardi, Jie Zheng:
Deciphering histone code of transcriptional regulation in malaria parasites by large-scale data mining. Comput. Biol. Chem. 50: 3-10 (2014) - [j9]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): 63-72 (2014) - [c18]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: 436-444 - [c17]Sourav S. Bhowmick, Huey-Eng Chua, Jie Zheng:
INGOT: Towards network-driven in silico combination therapy. BigComp 2014: 34-39 - [c16]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: 85-97 - 2013
- [j8]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): 238-245 (2013) - [j7]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): S7 (2013) - [c15]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: 384 - [c14]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: 4 - [c13]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: 76-82 - [c12]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: 64-75 - [c11]Wenting Liu, Kuiyu Chang, Jie Zheng, Jain Divya, Jung-Jae Kim, Jagath C. Rajapakse:
Gene Regulatory Networks from Gene Ontology. ISBRA 2013: 87-98 - [c10]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: 13-22 - 2012
- [j6]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) - [c9]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: 20-27 - [c8]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: 297-304 - [c7]Jian-Ping Mei, Chee Keong Kwoh, Peng Yang, Xiaoli Li, Jie Zheng:
Globalized bipartite local model for drug-target interaction prediction. BIOKDD 2012: 8-14 - 2011
- [c6]Min Wu, Chee Keong Kwoh, Teresa M. Przytycka, Jing Li, Jie Zheng:
Prediction of Trans-regulators of Recombination Hotspots in Mouse Genome. BIBM 2011: 57-62 - [c5]Jie Zheng, Iti Chaturvedi, Jagath C. Rajapakse:
Integration of Epigenetic Data in Bayesian Network Modeling of Gene Regulatory Network. PRIB 2011: 87-96 - 2010
- [j5]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): 141-142 (2010)
2000 – 2009
- 2009
- [j4]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: 88 (2009) - 2007
- [c4]Jie Zheng, Igor B. Rogozin, Eugene V. Koonin, Teresa M. Przytycka:
A Rigorous Analysis of the Pattern of Intron Conservation Supports the Coelomata Clade of Animals. RECOMB-CG 2007: 177-191 - 2006
- [j3]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: 7 (2006) - 2005
- [j2]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): 302-315 (2005) - [c3]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: 363-378 - [c2]Jie Zheng, Stefano Lonardi:
Discovery of Repetitive Patterns in DNA with Accurate Boundaries. BIBE 2005: 105-112 - 2004
- [j1]Jie Zheng, Timothy J. Close, Tao Jiang, Stefano Lonardi:
Efficient selection of unique and popular oligos for large EST databases. Bioinform. 20(13): 2101-2112 (2004) - 2003
- [c1]Jie Zheng, Timothy J. Close, Tao Jiang, Stefano Lonardi:
Efficient Selection of Unique and Popular Oligos for Large EST Databases. CPM 2003: 384-401
Coauthor Index
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