Efficient selection of unique and popular oligos for large EST databases. - Jie Zheng 002; Timothy J. Close; Tao Jiang 001; Stefano Lonardi (Bioinform., 2004)

Computing the Assignment of Orthologous Genes via Genome Rearrangement. - Xin Chen 037; Jie Zheng 002; Zheng Fu; Peng Nan; Yang Zhong; Stefano Lonardi; Tao Jiang 001 (APBC, 2005)

Discovery of Repetitive Patterns in DNA with Accurate Boundaries. - Jie Zheng 002; Stefano Lonardi (BIBE, 2005)

Assignment of Orthologous Genes via Genome Rearrangement. - Xin Chen 037; Jie Zheng 002; Zheng Fu; Peng Nan; Yang Zhong; Stefano Lonardi; Tao Jiang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2005)

OligoSpawn: a software tool for the design of overgo probes from large unigene datasets. - Jie Zheng 002; Jan T. Svensson; Kavitha Madishetty; Timothy J. Close; Tao Jiang 001; Stefano Lonardi (BMC Bioinform., 2006)

A Rigorous Analysis of the Pattern of Intron Conservation Supports the Coelomata Clade of Animals. - Jie Zheng 002; Igor B. Rogozin; Eugene V. Koonin; Teresa M. Przytycka (RECOMB-CG, 2007)

The crosstalk between EGF, IGF, and Insulin cell signaling pathways - computational and experimental analysis. - Rafal Zielinski; Pawel F. Przytycki; Jie Zheng 002; David Zhang; Teresa M. Przytycka; Jacek Capala (BMC Syst. Biol., 2009)

SimBoolNet - a Cytoscape plugin for dynamic simulation of signaling networks. - Jie Zheng 002; David Zhang; Pawel F. Przytycki; Rafal Zielinski; Jacek Capala; Teresa M. Przytycka (Bioinform., 2010)

Prediction of Trans-regulators of Recombination Hotspots in Mouse Genome. - Min Wu 008; Chee Keong Kwoh 001; Teresa M. Przytycka; Jing Li 002; Jie Zheng 002 (BIBM, 2011)

Integration of Epigenetic Data in Bayesian Network Modeling of Gene Regulatory Network. - Jie Zheng 002; Iti Chaturvedi; Jagath C. Rajapakse (PRIB, 2011)

Integration of genomic and epigenomic features to predict meiotic recombination hotspots in human and mouse. - Min Wu 008; Chee Keong Kwoh 001; Teresa M. Przytycka; Jing Li 002; Jie Zheng 002 (BCB, 2012)

NetPipe: a network-based pipeline for discovery of genes and protein complexes regulating meiotic recombination hotspots. - Min Wu 008; Chee Keong Kwoh 001; Jie Zheng 002; Xiaoli Li 001 (BCB, 2012)

Globalized bipartite local model for drug-target interaction prediction. - Jian-Ping Mei; Chee Keong Kwoh 001; Peng Yang 010; Xiaoli Li 001; Jie Zheng 002 (BIOKDD, 2012)

Teasing Apart Translational and Transcriptional Components of Stochastic Variations in Eukaryotic Gene Expression. - Raheleh Salari; Damian Wójtowicz; Jie Zheng 002; David Levens; Yitzhak Pilpel; Teresa M. Przytycka (PLoS Comput. Biol., 2012)

Meta-analysis of Genomic and Proteomic Features to Predict Synthetic Lethality of Yeast and Human Cancer. - Min Wu 008; Xuejuan Li; Fan Zhang 089; Xiaoli Li 001; Chee Keong Kwoh 001; Jie Zheng 002 (BCB, 2013)

Syn-Lethality: An integrative knowledge base of synthetic lethality towards discovery of selective anticancer therapies. - Xuejuan Li; Shital K. Mishra; Min Wu 008; Fan Zhang 089; Jie Zheng 002 (BIBM, 2013)

Integrating epigenetic prior in dynamic Bayesian network for gene regulatory network inference. - Haifen Chen; D. A. K. Maduranga; Piyushkumar A. Mundra; Jie Zheng 002 (CIBCB, 2013)

Gene Regulatory Networks from Gene Ontology. - Wenting Liu; Kuiyu Chang; Jie Zheng 002; Jain Divya; Jung-Jae Kim 001; Jagath C. Rajapakse (ISBRA, 2013)

Inferring Time-Delayed Gene Regulatory Networks Using Cross-Correlation and Sparse Regression. - Piyushkumar A. Mundra; Jie Zheng 002; Mahesan Niranjan; Roy E. Welsch; Jagath C. Rajapakse (ISBRA, 2013)

Inferring Gene Regulatory Networks from Time-Series Expressions Using Random Forests Ensemble. - D. A. K. Maduranga; Jie Zheng 002; Piyushkumar A. Mundra; Jagath C. Rajapakse (PRIB, 2013)

Drug-target interaction prediction by learning from local information and neighbors. - Jian-Ping Mei; Chee Keong Kwoh 001; Peng Yang 010; Xiaoli Li 001; Jie Zheng 002 (Bioinform., 2013)

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. - Chinh Tran To Su; Xuchang Ouyang; Jie Zheng 002; Chee Keong Kwoh 001 (BMC Bioinform., 2013)

Data-driven prediction of cancer cell fates with a nonlinear model of signaling pathways. - Fan Zhang 089; Chee Keong Kwoh 001; Min Wu 008; Jie Zheng 002 (BCB, 2014)

INGOT: Towards network-driven in silico combination therapy. - Sourav S. Bhowmick; Huey-Eng Chua; Jie Zheng 002 (BigComp, 2014)

CUDAGRN: Parallel Speedup of Inferring Large Gene Regulatory Networks from Expression Data Using Random Forest. - Seyed Ziaeddin Alborzi; D. A. K. Maduranga; Rui Fan; Jagath C. Rajapakse; Jie Zheng 002 (PRIB, 2014)

Extracting rate changes in transcriptional regulation from MEDLINE abstracts. - Wenting Liu; Kui Miao; Guangxia Li; Kuiyu Chang; Jie Zheng 002; Jagath C. Rajapakse (BMC Bioinform., 2014)

IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking. - Chinh Tran To Su; Thuy-Diem Nguyen; Jie Zheng 002; Chee Keong Kwoh 001 (BMC Bioinform., 2014)

LDsplit: screening for cis-regulatory motifs stimulating meiotic recombination hotspots by analysis of DNA sequence polymorphisms. - Peng Yang 010; Min Wu 008; Jing Guo; Chee Keong Kwoh 001; Teresa M. Przytycka; Jie Zheng 002 (BMC Bioinform., 2014)

Highly sensitive inference of time-delayed gene regulation by network deconvolution. - Haifen Chen; Piyushkumar A. Mundra; Li Na Zhao; Feng Lin; Jie Zheng 002 (BMC Syst. Biol., 2014)

Finding trans-regulatory genes and protein complexes modulating meiotic recombination hotspots of human, mouse and yeast. - Min Wu 008; Chee Keong Kwoh 001; Xiaoli Li 001; Jie Zheng 002 (BMC Syst. Biol., 2014)

Deciphering histone code of transcriptional regulation in malaria parasites by large-scale data mining. - Haifen Chen; Stefano Lonardi; Jie Zheng 002 (Comput. Biol. Chem., 2014)

Reliable and Fast Estimation of Recombination Rates by Convergence Diagnosis and Parallel Markov Chain Monte Carlo. - Jing Guo; Ritika Jain; Peng Yang 010; Rui Fan; Chee Keong Kwoh 001; Jie Zheng 002 (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Single-cell transcriptional analysis to uncover regulatory circuits driving cell fate decisions in early mouse development. - Haifen Chen; Jing Guo; Shital K. Mishra; Paul Robson 001; Mahesan Niranjan; Jie Zheng 002 (Bioinform., 2015)

Improving compound-protein interaction prediction by building up highly credible negative samples. - Hui Liu 026; Jianjiang Sun; Jihong Guan; Jie Zheng 002; Shuigeng Zhou (Bioinform., 2015)

Computational cell fate modelling for discovery of rewiring in apoptotic network for enhanced cancer drug sensitivity. - Shital K. Mishra; Sourav S. Bhowmick; Huey-Eng Chua; Fan Zhang 089; Jie Zheng 002 (BMC Syst. Biol., 2015)

Introduction to the CSBio2014 special issue. - Xiaoli Li 001; Jie Zheng 002 (J. Bioinform. Comput. Biol., 2015)

Predicting essential genes and synthetic lethality via influence propagation in signaling pathways of cancer cell fates. - Fan Zhang 089; Min Wu 008; Xuejuan Li; Xiaoli Li 001; Chee Keong Kwoh 001; Jie Zheng 002 (J. Bioinform. Comput. Biol., 2015)

TAPESTRY: Network-centric Target Prioritization in Disease-related Signaling Networks. - Huey-Eng Chua; Sourav S. Bhowmick; Jie Zheng 002; Lisa Tucker-Kellogg (BCB, 2016)

Predictive Modeling of Drug Effects on Signaling Pathways in Diverse Cancer Cell Lines. - Shital Kumar Mishra; Sourav S. Bhowmick; Huey-Eng Chua; Jie Zheng 002 (BCB, 2016)

Generalized logical model based on network topology to capture the dynamical trends of cellular signaling pathways. - Fan Zhang 089; Haoting Chen; Li Na Zhao; Hui Liu 026; Teresa M. Przytycka; Jie Zheng 002 (BMC Syst. Biol., 2016)

Sig2GRN: a software tool linking signaling pathway with gene regulatory network for dynamic simulation. - Fan Zhang 089; Runsheng Liu; Jie Zheng 002 (BMC Syst. Biol., 2016)

SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets. - Jing Guo; Hui Liu 026; Jie Zheng 002 (Nucleic Acids Res., 2016)

The Max-Min High-Order Dynamic Bayesian Network for Learning Gene Regulatory Networks with Time-Delayed Regulations. - Yifeng Li 001; Haifen Chen; Jie Zheng 002; Alioune Ngom (IEEE ACM Trans. Comput. Biol. Bioinform., 2016)

Phylogenetic Tree based Method for Uncovering Co-mutational Site-pairs in Influenza Viruses. - Fransiskus Xaverius Ivan; Xinrui Zhou; Akhila Deshpande; Rui Yin 002; Jie Zheng 002; Chee Keong Kwoh 001 (BCB, 2017)

Identification of Potential Critical Virulent Sites Based on Hemagglutinin of Influenza a Virus in Past Pandemic Strains. - Rui Yin 002; Xinrui Zhou; Fransiskus Xaverius Ivan; Jie Zheng 002; Vincent T. K. Chow; Chee Keong Kwoh 001 (ICBBS, 2017)

NetLand: quantitative modeling and visualization of Waddington's epigenetic landscape using probabilistic potential. - Jing Guo; Feng Lin; Xiaomeng Zhang; Vivek Tanavde; Jie Zheng 002 (Bioinform., 2017)

HopLand: single-cell pseudotime recovery using continuous Hopfield network-based modeling of Waddington's epigenetic landscape. - Jing Guo; Jie Zheng 002 (Bioinform., 2017)

A polynomial based model for cell fate prediction in human diseases. - Lichun Ma; Jie Zheng 002 (BMC Syst. Biol., 2017)

TROVE: a user-friendly tool for visualizing and analyzing cancer hallmarks in signaling networks. - Huey-Eng Chua; Sourav S. Bhowmick; Jie Zheng 002 (Bioinform., 2018)

Single-cell gene expression analysis reveals β-cell dysfunction and deficit mechanisms in type 2 diabetes. - Lichun Ma; Jie Zheng 002 (BMC Bioinform., 2018)

Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses. - Xinrui Zhou; Jie Zheng 002; Fransiskus Xaverius Ivan; Rui Yin 002; Shoba Ranganathan; Vincent T. K. Chow; Chee-Keong Kwoh 001 (BMC Genom., 2018)

Composite mathematical modeling of calcium signaling behind neuronal cell death in Alzheimer's disease. - Bobby Ranjan; Ket Hing Chong; Jie Zheng 002 (BMC Syst. Biol., 2018)

Computational identification of physicochemical signatures for host tropism of influenza A virus. - Rui Yin 002; Xinrui Zhou; Jie Zheng 002; Chee Keong Kwoh 001 (J. Bioinform. Comput. Biol., 2018)

Topic Judgment Helps Question Similarity Prediction in Medical FAQ Dialogue Systems. - Lin Zhu; Xinnan Dai; Qihao Huang; Hai Xiang; Jie Zheng 002 (ICDM Workshops, 2019)

An Encoding Scheme Capturing Generic Priors and Properties of Amino Acids Improves Protein Classification. - Xinrui Zhou; Rui Yin 002; Jie Zheng 002; Chee Keong Kwoh 001 (IEEE Access, 2019)

Boolean network modeling of β-cell apoptosis and insulin resistance in type 2 diabetes mellitus. - Pritha Dutta; Lichun Ma; Yusuf Ali; Peter M. A. Sloot; Jie Zheng 002 (BMC Syst. Biol., 2019)

Genome Analysis - Identification of Genes Involved in Host-Pathogen Protein-Protein Interaction Networks. - Fransiskus Xaverius Ivan; Chee-Keong Kwoh 001; Vincent T. K. Chow; Jie Zheng 002 (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

Whole Genome Sequencing Analysis. - Rui Yin 002; Chee Keong Kwoh 001; Jie Zheng 002 (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

A Monte Carlo method for in silico modeling and visualization of Waddington's epigenetic landscape with intermediate details. - Xiaomeng Zhang; Ket Hing Chong; Lin Zhu; Jie Zheng 002 (Biosyst., 2020)

Bayesian Data Fusion of Gene Expression and Histone Modification Profiles for Inference of Gene Regulatory Network. - Haifen Chen; D. A. K. Maduranga; Piyushkumar A. Mundra; Jie Zheng 002 (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

SL2MF: Predicting Synthetic Lethality in Human Cancers via Logistic Matrix Factorization. - Yong Liu 020; Min Wu 008; Chenghao Liu; Xiaoli Li 001; Jie Zheng 002 (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

Guest Editorial for the 29th International Conference on Genome Informatics (GIW 2018). - Jie Zheng 002; Jinyan Li 001; Yun Zheng (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

Predicting Synthetic Lethality in Human Cancers via Multi-Graph Ensemble Neural Network. - Mincai Lai; Guangyao Chen; Haochen Yang 002; Jingkang Yang; Zhihao Jiang; Min Wu 008; Jie Zheng 002 (EMBC, 2021)

Graph contextualized attention network for predicting synthetic lethality in human cancers. - Yahui Long; Min Wu 008; Yong Liu 020; Jie Zheng 002; Chee Keong Kwoh 001; Jiawei Luo 001; Xiaoli Li 001 (Bioinform., 2021)

KG4SL: knowledge graph neural network for synthetic lethality prediction in human cancers. - Shike Wang; Fan Xu; Yunyang Li; Jie Wang; Ke Zhang; Yong Liu 020; Min Wu 008; Jie Zheng 002 (Bioinform., 2021)

PIKE-R2P: Protein-protein interaction network-based knowledge embedding with graph neural network for single-cell RNA to protein prediction. - Xinnan Dai; Fan Xu; Shike Wang; Piyushkumar A. Mundra; Jie Zheng 002 (BMC Bioinform., 2021)

Velo-Predictor: an ensemble learning pipeline for RNA velocity prediction. - Xin Wang; Jie Zheng 002 (BMC Bioinform., 2021)

SynLethDB 2.0: a web-based knowledge graph database on synthetic lethality for novel anticancer drug discovery. - Jie Wang; Min Wu 008; Xuhui Huang; Li Wang; Sophia Zhang; Hui Liu 026; Jie Zheng 002 (Database J. Biol. Databases Curation, 2022)

PiLSL: pairwise interaction learning-based graph neural network for synthetic lethality prediction in human cancers. - Xin Liu 027; Jiale Yu; Siyu Tao; Beiyuan Yang; Shike Wang; Lin Wang; Fang Bai; Jie Zheng 002 (Bioinform., 2022)

NSF4SL: negative-sample-free contrastive learning for ranking synthetic lethal partner genes in human cancers. - Shike Wang; Yimiao Feng; Xin Liu 027; Yong Liu 020; Min Wu 008; Jie Zheng 002 (Bioinform., 2022)

Prediction of gene co-expression from chromatin contacts with graph attention network. - Ke Zhang; Chenxi Wang; Liping Sun; Jie Zheng 002 (Bioinform., 2022)

KR4SL: knowledge graph reasoning for explainable prediction of synthetic lethality. - Ke Zhang; Min Wu 008; Yong Liu 020; Yimiao Feng; Jie Zheng 002 (Bioinform., 2023)

Prompt-based Generation of Natural Language Explanations of Synthetic Lethality for Cancer Drug Discovery. - Ke Zhang; Yimiao Feng; Jie Zheng 002 (LREC/COLING, 2024)

TMELand: An End-to-End Pipeline for Quantification and Visualization of Waddington's Epigenetic Landscape Based on Gene Regulatory Network. - Lin Zhu; Xin Kang; Chunhe Li 001; Jie Zheng 002 (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

TEFDTA: a transformer encoder and fingerprint representation combined prediction method for bonded and non-bonded drug-target affinities. - Zongquan Li; Pengxuan Ren; Hao Yang 060; Jie Zheng 002; Fang Bai (Bioinform., 2024)

SL-Miner: a web server for mining evidence and prioritization of cancer-specific synthetic lethality. - Xin Liu 027; Jieni Hu; Jie Zheng 002 (Bioinform., 2024)

GENNDTI: Drug-Target Interaction Prediction Using Graph Neural Network Enhanced by Router Nodes. - Beiyuan Yang; Yule Liu; Junfeng Wu; Fang Bai; Mingyue Zheng; Jie Zheng 002 (IEEE J. Biomed. Health Informatics, 2024)

Interpretable high-order knowledge graph neural network for predicting synthetic lethality in human cancers. - Xuexin Chen; Ruichu Cai; Zhengting Huang; Zijian Li 001; Jie Zheng 002; Min Wu 008 (Briefings Bioinform., 2025)

SLInterpreter: An Exploratory and Iterative Human-AI Collaborative System for GNN-Based Synthetic Lethal Prediction. - Haoran Jiang; Shaohan Shi; Shuhao Zhang; Jie Zheng 002; Quan Li (IEEE Trans. Vis. Comput. Graph., 2025)