Jie Zheng

89 papers B 2C 2Journal 60Unranked 23
YearRankTypeTitle / Venue / Authors
2026 J jnl
A survey of downstream applications of evolutionary scale modeling protein language models.
Quant. Biol.
Qingyu Yang, Jiale Yu, Jie Zheng
2025 J jnl
CellVTA: Enhancing Vision Foundation Models for Accurate Cell Segmentation and Classification.
CoRR
Yang Yang, Xijie Xu, Yixun Zhou, Jie Zheng
2025 J jnl
Early tumor volume change as a novel CT RECIST indicator for predicting pathological response and prognosis in NSCLC patients undergoing immunotherapy.
Biomed. Signal Process. Control.
Fan Xu, Mei Xie, Xuwen Lin, Jie Gao, Xidong Ma, Yang Yang, Zhiqiang Xue, Chongchong Wu, Tianjiao Jiang, Yimiao Feng, Jialin Song, Yuanyong Wang, Jie Yao, Xinyu Bao, Xin Zhang, Xuming He, Yuyao Zhang, Jiannan Yao, Jie Zheng, Xinying Xue
2025 J jnl
Interpretable High-order Knowledge Graph Neural Network for Predicting Synthetic Lethality in Human Cancers.
CoRR
Xuexin Chen, Ruichu Cai, Zhengting Huang, Zijian Li, Jie Zheng, Min Wu
2025 J jnl
Interpretable high-order knowledge graph neural network for predicting synthetic lethality in human cancers.
Briefings Bioinform.
Xuexin Chen, Ruichu Cai, Zhengting Huang, Zijian Li, Jie Zheng, Min Wu
2025 J jnl
Learning Universal Knowledge Graph Embedding for Predicting Biomedical Pairwise Interactions.
IEEE Trans. Comput. Biol. Bioinform.
Siyu Tao, Yang Yang, Xin Liu, Yimiao Feng, Jie Zheng
2025 — conf
Prompt-Driven Context-Aware Prediction of Cell Line-Specific Synthetic Lethality via Biomedical Large Language Models.
BIBM
Ting Lu, Yimiao Feng, Ruoyin Zhang, Yingfan Rui, Jie Zheng
2025 J jnl
SLInterpreter: An Exploratory and Iterative Human-AI Collaborative System for GNN-Based Synthetic Lethal Prediction.
IEEE Trans. Vis. Comput. Graph.
Haoran Jiang, Shaohan Shi, Shuhao Zhang, Jie Zheng, Quan Li
2024 — conf
CellSeg2TLS: A Deep Learning Framework for Predicting the Maturation of Tertiary Lymphoid Structures in Pathology Images.
ISBI
Yang Yang, Mei Xie, Yimiao Feng, Xueheng Lv, Jialin Song, Xinying Xue, Jie Zheng
2024 J jnl
GENNDTI: Drug-Target Interaction Prediction Using Graph Neural Network Enhanced by Router Nodes.
IEEE J. Biomed. Health Informatics
Beiyuan Yang, Yule Liu, Junfeng Wu, Fang Bai, Mingyue Zheng, Jie Zheng
2024 — conf
Prompt-based Generation of Natural Language Explanations of Synthetic Lethality for Cancer Drug Discovery.
LREC/COLING
Ke Zhang, Yimiao Feng, Jie Zheng
2024 J jnl
SL-Miner: a web server for mining evidence and prioritization of cancer-specific synthetic lethality.
Bioinform.
Xin Liu, Jieni Hu, Jie Zheng
2024 J jnl
SLInterpreter: An Exploratory and Iterative Human-AI Collaborative System for GNN-based Synthetic Lethal Prediction.
CoRR
Haoran Jiang, Shaohan Shi, Shuhao Zhang, Jie Zheng, Quan Li
2024 J jnl
TEFDTA: a transformer encoder and fingerprint representation combined prediction method for bonded and non-bonded drug-target affinities.
Bioinform.
Zongquan Li, Pengxuan Ren, Hao Yang, Jie Zheng, Fang Bai
2024 J jnl
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.
Lin Zhu, Xin Kang, Chunhe Li, Jie Zheng
2023 J jnl
KR4SL: knowledge graph reasoning for explainable prediction of synthetic lethality.
Bioinform.
Ke Zhang, Min Wu, Yong Liu, Yimiao Feng, Jie Zheng
2022 J jnl
NSF4SL: negative-sample-free contrastive learning for ranking synthetic lethal partner genes in human cancers.
Bioinform.
Shike Wang, Yimiao Feng, Xin Liu, Yong Liu, Min Wu, Jie Zheng
2022 J jnl
PiLSL: pairwise interaction learning-based graph neural network for synthetic lethality prediction in human cancers.
Bioinform.
Xin Liu, Jiale Yu, Siyu Tao, Beiyuan Yang, Shike Wang, Lin Wang, Fang Bai, Jie Zheng
2022 J jnl
Prediction of gene co-expression from chromatin contacts with graph attention network.
Bioinform.
Ke Zhang, Chenxi Wang, Liping Sun, Jie Zheng
2022 J jnl
SynLethDB 2.0: a web-based knowledge graph database on synthetic lethality for novel anticancer drug discovery.
Database J. Biol. Databases Curation
Jie Wang, Min Wu, Xuhui Huang, Li Wang, Sophia Zhang, Hui Liu, Jie Zheng
2021 J jnl
Graph contextualized attention network for predicting synthetic lethality in human cancers.
Bioinform.
Yahui Long, Min Wu, Yong Liu, Jie Zheng, Chee Keong Kwoh, Jiawei Luo, Xiaoli Li
2021 J jnl
KG4SL: knowledge graph neural network for synthetic lethality prediction in human cancers.
Bioinform.
Shike Wang, Fan Xu, Yunyang Li, Jie Wang, Ke Zhang, Yong Liu, Min Wu, Jie Zheng
2021 J jnl
PIKE-R2P: Protein-protein interaction network-based knowledge embedding with graph neural network for single-cell RNA to protein prediction.
BMC Bioinform.
Xinnan Dai, Fan Xu, Shike Wang, Piyushkumar A. Mundra, Jie Zheng
2021 — conf
Predicting Synthetic Lethality in Human Cancers via Multi-Graph Ensemble Neural Network.
EMBC
Mincai Lai, Guangyao Chen, Haochen Yang, Jingkang Yang, Zhihao Jiang, Min Wu, Jie Zheng
2021 J jnl
Velo-Predictor: an ensemble learning pipeline for RNA velocity prediction.
BMC Bioinform.
Xin Wang, Jie Zheng
2020 J jnl
A Monte Carlo method for
Biosyst.
Xiaomeng Zhang, Ket Hing Chong, Lin Zhu, Jie Zheng
2020 J jnl
Bayesian Data Fusion of Gene Expression and Histone Modification Profiles for Inference of Gene Regulatory Network.
IEEE ACM Trans. Comput. Biol. Bioinform.
Haifen Chen, D. A. K. Maduranga, Piyushkumar A. Mundra, Jie Zheng
2020 J jnl
Guest Editorial for the 29th International Conference on Genome Informatics (GIW 2018).
IEEE ACM Trans. Comput. Biol. Bioinform.
Jie Zheng, Jinyan Li, Yun Zheng
2020 J jnl
SL
IEEE ACM Trans. Comput. Biol. Bioinform.
Yong Liu, Min Wu, Chenghao Liu, Xiaoli Li, Jie Zheng
2019 J jnl
An Encoding Scheme Capturing Generic Priors and Properties of Amino Acids Improves Protein Classification.
IEEE Access
Xinrui Zhou, Rui Yin, Jie Zheng, Chee Keong Kwoh
2019 J jnl
Boolean network modeling of β-cell apoptosis and insulin resistance in type 2 diabetes mellitus.
BMC Syst. Biol.
Pritha Dutta, Lichun Ma, Yusuf Ali, Peter M. A. Sloot, Jie Zheng
2019 — ch.
Genome Analysis - Identification of Genes Involved in Host-Pathogen Protein-Protein Interaction Networks.
Encyclopedia of Bioinformatics and Computational Biology (3)
Fransiskus Xaverius Ivan, Chee-Keong Kwoh, Vincent T. K. Chow, Jie Zheng
2019 — conf
Topic Judgment Helps Question Similarity Prediction in Medical FAQ Dialogue Systems.
ICDM Workshops
Lin Zhu, Xinnan Dai, Qihao Huang, Hai Xiang, Jie Zheng
2019 — ch.
Whole Genome Sequencing Analysis.
Encyclopedia of Bioinformatics and Computational Biology (3)
Rui Yin, Chee Keong Kwoh, Jie Zheng
2018 J jnl
Composite mathematical modeling of calcium signaling behind neuronal cell death in Alzheimer's disease.
BMC Syst. Biol.
Bobby Ranjan, Ket Hing Chong, Jie Zheng
2018 J jnl
Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses.
BMC Genom.
Xinrui Zhou, Jie Zheng, Fransiskus Xaverius Ivan, Rui Yin, Shoba Ranganathan, Vincent T. K. Chow, Chee-Keong Kwoh
2018 J jnl
Computational identification of physicochemical signatures for host tropism of influenza A virus.
J. Bioinform. Comput. Biol.
Rui Yin, Xinrui Zhou, Jie Zheng, Chee Keong Kwoh
2018 J jnl
SL
CoRR
Yong Liu, Min Wu, Chenghao Liu, Xiaoli Li, Jie Zheng
2018 J jnl
Single-cell gene expression analysis reveals β-cell dysfunction and deficit mechanisms in type 2 diabetes.
BMC Bioinform.
Lichun Ma, Jie Zheng
2018 J jnl
TROVE: a user-friendly tool for visualizing and analyzing cancer hallmarks in signaling networks.
Bioinform.
Huey-Eng Chua, Sourav S. Bhowmick, Jie Zheng
2017 J jnl
A polynomial based model for cell fate prediction in human diseases.
BMC Syst. Biol.
Lichun Ma, Jie Zheng
2017 J jnl
HopLand: single-cell pseudotime recovery using continuous Hopfield network-based modeling of Waddington's epigenetic landscape.
Bioinform.
Jing Guo, Jie Zheng
2017 — conf
Identification of Potential Critical Virulent Sites Based on Hemagglutinin of Influenza a Virus in Past Pandemic Strains.
ICBBS
Rui Yin, Xinrui Zhou, Fransiskus Xaverius Ivan, Jie Zheng, Vincent T. K. Chow, Chee Keong Kwoh
2017 J jnl
NetLand: quantitative modeling and visualization of Waddington's epigenetic landscape using probabilistic potential.
Bioinform.
Jing Guo, Feng Lin, Xiaomeng Zhang, Vivek Tanavde, Jie Zheng
2017 — conf
Phylogenetic Tree based Method for Uncovering Co-mutational Site-pairs in Influenza Viruses.
BCB
Fransiskus Xaverius Ivan, Xinrui Zhou, Akhila Deshpande, Rui Yin, Jie Zheng, Chee Keong Kwoh
2016 J jnl
Generalized logical model based on network topology to capture the dynamical trends of cellular signaling pathways.
BMC Syst. Biol.
Fan Zhang, Haoting Chen, Li Na Zhao, Hui Liu, Teresa M. Przytycka, Jie Zheng
2016 — conf
Predictive Modeling of Drug Effects on Signaling Pathways in Diverse Cancer Cell Lines.
BCB
Shital Kumar Mishra, Sourav S. Bhowmick, Huey-Eng Chua, Jie Zheng
2016 J jnl
Sig2GRN: a software tool linking signaling pathway with gene regulatory network for dynamic simulation.
BMC Syst. Biol.
Fan Zhang, Runsheng Liu, Jie Zheng
2016 J jnl
SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets.
Nucleic Acids Res.
Jing Guo, Hui Liu, Jie Zheng
2016 — conf
TAPESTRY: Network-centric Target Prioritization in Disease-related Signaling Networks.
BCB
Huey-Eng Chua, Sourav S. Bhowmick, Jie Zheng, Lisa Tucker-Kellogg
2016 J jnl
The Max-Min High-Order Dynamic Bayesian Network for Learning Gene Regulatory Networks with Time-Delayed Regulations.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yifeng Li, Haifen Chen, Jie Zheng, Alioune Ngom
2015 J jnl
Computational cell fate modelling for discovery of rewiring in apoptotic network for enhanced cancer drug sensitivity.
BMC Syst. Biol.
Shital K. Mishra, Sourav S. Bhowmick, Huey-Eng Chua, Fan Zhang, Jie Zheng
2015 J jnl
Improving compound-protein interaction prediction by building up highly credible negative samples.
Bioinform.
Hui Liu, Jianjiang Sun, Jihong Guan, Jie Zheng, Shuigeng Zhou
2015 J jnl
Introduction to the CSBio2014 special issue.
J. Bioinform. Comput. Biol.
Xiaoli Li, Jie Zheng
2015 J jnl
Predicting essential genes and synthetic lethality via influence propagation in signaling pathways of cancer cell fates.
J. Bioinform. Comput. Biol.
Fan Zhang, Min Wu, Xuejuan Li, Xiaoli Li, Chee Keong Kwoh, Jie Zheng
2015 J jnl
Single-cell transcriptional analysis to uncover regulatory circuits driving cell fate decisions in early mouse development.
Bioinform.
Haifen Chen, Jing Guo, Shital K. Mishra, Paul Robson, Mahesan Niranjan, Jie Zheng
2014 — conf
CUDAGRN: Parallel Speedup of Inferring Large Gene Regulatory Networks from Expression Data Using Random Forest.
PRIB
Seyed Ziaeddin Alborzi, D. A. K. Maduranga, Rui Fan, Jagath C. Rajapakse, Jie Zheng
2014 — conf
Data-driven prediction of cancer cell fates with a nonlinear model of signaling pathways.
BCB
Fan Zhang, Chee Keong Kwoh, Min Wu, Jie Zheng
2014 J jnl
Deciphering histone code of transcriptional regulation in malaria parasites by large-scale data mining.
Comput. Biol. Chem.
Haifen Chen, Stefano Lonardi, Jie Zheng
2014 J jnl
Extracting rate changes in transcriptional regulation from MEDLINE abstracts.
BMC Bioinform.
Wenting Liu, Kui Miao, Guangxia Li, Kuiyu Chang, Jie Zheng, Jagath C. Rajapakse
2014 J jnl
Finding trans-regulatory genes and protein complexes modulating meiotic recombination hotspots of human, mouse and yeast.
BMC Syst. Biol.
Min Wu, Chee Keong Kwoh, Xiaoli Li, Jie Zheng
2014 J jnl
Highly sensitive inference of time-delayed gene regulation by network deconvolution.
BMC Syst. Biol.
Haifen Chen, Piyushkumar A. Mundra, Li Na Zhao, Feng Lin, Jie Zheng
2014 J jnl
IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking.
BMC Bioinform.
Chinh Tran To Su, Thuy-Diem Nguyen, Jie Zheng, Chee Keong Kwoh
2014 — conf
INGOT: Towards network-driven in silico combination therapy.
BigComp
Sourav S. Bhowmick, Huey-Eng Chua, Jie Zheng
2014 J jnl
LDsplit: screening for cis-regulatory motifs stimulating meiotic recombination hotspots by analysis of DNA sequence polymorphisms.
BMC Bioinform.
Peng Yang, Min Wu, Jing Guo, Chee Keong Kwoh, Teresa M. Przytycka, Jie Zheng
2014 J jnl
Reliable and Fast Estimation of Recombination Rates by Convergence Diagnosis and Parallel Markov Chain Monte Carlo.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jing Guo, Ritika Jain, Peng Yang, Rui Fan, Chee Keong Kwoh, Jie Zheng
2013 J jnl
Drug-target interaction prediction by learning from local information and neighbors.
Bioinform.
Jian-Ping Mei, Chee Keong Kwoh, Peng Yang, Xiaoli Li, Jie Zheng
2013 — conf
Gene Regulatory Networks from Gene Ontology.
ISBRA
Wenting Liu, Kuiyu Chang, Jie Zheng, Jain Divya, Jung-Jae Kim, Jagath C. Rajapakse
2013 — conf
Inferring Gene Regulatory Networks from Time-Series Expressions Using Random Forests Ensemble.
PRIB
D. A. K. Maduranga, Jie Zheng, Piyushkumar A. Mundra, Jagath C. Rajapakse
2013 — conf
Inferring Time-Delayed Gene Regulatory Networks Using Cross-Correlation and Sparse Regression.
ISBRA
Piyushkumar A. Mundra, Jie Zheng, Mahesan Niranjan, Roy E. Welsch, Jagath C. Rajapakse
2013 C conf
Integrating epigenetic prior in dynamic Bayesian network for gene regulatory network inference.
CIBCB
Haifen Chen, D. A. K. Maduranga, Piyushkumar A. Mundra, Jie Zheng
2013 — conf
Meta-analysis of Genomic and Proteomic Features to Predict Synthetic Lethality of Yeast and Human Cancer.
BCB
Min Wu, Xuejuan Li, Fan Zhang, Xiaoli Li, Chee Keong Kwoh, Jie Zheng
2013 J jnl
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.
Chinh Tran To Su, Xuchang Ouyang, Jie Zheng, Chee Keong Kwoh
2013 — conf
Syn-Lethality: An integrative knowledge base of synthetic lethality towards discovery of selective anticancer therapies.
BIBM
Xuejuan Li, Shital K. Mishra, Min Wu, Fan Zhang, Jie Zheng
2012 — conf
Globalized bipartite local model for drug-target interaction prediction.
BIOKDD
Jian-Ping Mei, Chee Keong Kwoh, Peng Yang, Xiaoli Li, Jie Zheng
2012 — conf
Integration of genomic and epigenomic features to predict meiotic recombination hotspots in human and mouse.
BCB
Min Wu, Chee Keong Kwoh, Teresa M. Przytycka, Jing Li, Jie Zheng
2012 — conf
NetPipe: a network-based pipeline for discovery of genes and protein complexes regulating meiotic recombination hotspots.
BCB
Min Wu, Chee Keong Kwoh, Jie Zheng, Xiaoli Li
2012 J jnl
Teasing Apart Translational and Transcriptional Components of Stochastic Variations in Eukaryotic Gene Expression.
PLoS Comput. Biol.
Raheleh Salari, Damian Wójtowicz, Jie Zheng, David Levens, Yitzhak Pilpel, Teresa M. Przytycka
2011 — conf
Integration of Epigenetic Data in Bayesian Network Modeling of Gene Regulatory Network.
PRIB
Jie Zheng, Iti Chaturvedi, Jagath C. Rajapakse
2011 — conf
Prediction of Trans-regulators of Recombination Hotspots in Mouse Genome.
BIBM
Min Wu, Chee Keong Kwoh, Teresa M. Przytycka, Jing Li, Jie Zheng
2010 J jnl
SimBoolNet - a Cytoscape plugin for dynamic simulation of signaling networks.
Bioinform.
Jie Zheng, David Zhang, Pawel F. Przytycki, Rafal Zielinski, Jacek Capala, Teresa M. Przytycka
2009 J jnl
The crosstalk between EGF, IGF, and Insulin cell signaling pathways - computational and experimental analysis.
BMC Syst. Biol.
Rafal Zielinski, Pawel F. Przytycki, Jie Zheng, David Zhang, Teresa M. Przytycka, Jacek Capala
2007 — conf
A Rigorous Analysis of the Pattern of Intron Conservation Supports the
RECOMB-CG
Jie Zheng, Igor B. Rogozin, Eugene V. Koonin, Teresa M. Przytycka
2006 J jnl
OligoSpawn: a software tool for the design of overgo probes from large unigene datasets.
BMC Bioinform.
Jie Zheng, Jan T. Svensson, Kavitha Madishetty, Timothy J. Close, Tao Jiang, Stefano Lonardi
2005 J jnl
Assignment of Orthologous Genes via Genome Rearrangement.
IEEE ACM Trans. Comput. Biol. Bioinform.
Xin Chen, Jie Zheng, Zheng Fu, Peng Nan, Yang Zhong, Stefano Lonardi, Tao Jiang
2005 B conf
Computing the Assignment of Orthologous Genes via Genome Rearrangement.
APBC
Xin Chen, Jie Zheng, Zheng Fu, Peng Nan, Yang Zhong, Stefano Lonardi, Tao Jiang
2005 C conf
Discovery of Repetitive Patterns in DNA with Accurate Boundaries.
BIBE
Jie Zheng, Stefano Lonardi
2004 J jnl
Efficient selection of unique and popular oligos for large EST databases.
Bioinform.
Jie Zheng, Timothy J. Close, Tao Jiang, Stefano Lonardi
2003 B conf
Efficient Selection of Unique and Popular Oligos for Large EST Databases.
CPM
Jie Zheng, Timothy J. Close, Tao Jiang, Stefano Lonardi