Jie Zheng

According to our database1, Jie Zheng authored at least 48 papers between 2004 and 2020.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

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Online presence:

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Bibliography

2020
Guest Editorial for the 29th International Conference on Genome Informatics (GIW 2018).
IEEE ACM Trans. Comput. Biol. Bioinform., 2020

SL<sup>2</sup>MF: Predicting Synthetic Lethality in Human Cancers via Logistic Matrix Factorization.
IEEE ACM Trans. Comput. Biol. Bioinform., 2020

Bayesian Data Fusion of Gene Expression and Histone Modification Profiles for Inference of Gene Regulatory Network.
IEEE ACM Trans. Comput. Biol. Bioinform., 2020

2019
Whole Genome Sequencing Analysis.
Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 3, 2019

Genome Analysis - Identification of Genes Involved in Host-Pathogen Protein-Protein Interaction Networks.
Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 3, 2019

An Encoding Scheme Capturing Generic Priors and Properties of Amino Acids Improves Protein Classification.
IEEE Access, 2019

2018
Computational identification of physicochemical signatures for host tropism of influenza A virus.
J. Bioinform. Comput. Biol., 2018

2017
HopLand: single-cell pseudotime recovery using continuous Hopfield network-based modeling of Waddington's epigenetic landscape.
Bioinform., 2017

NetLand: quantitative modeling and visualization of Waddington's epigenetic landscape using probabilistic potential.
Bioinform., 2017

Phylogenetic Tree based Method for Uncovering Co-mutational Site-pairs in Influenza Viruses.
Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

2016
The Max-Min High-Order Dynamic Bayesian Network for Learning Gene Regulatory Networks with Time-Delayed Regulations.
IEEE ACM Trans. Comput. Biol. Bioinform., 2016

SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets.
Nucleic Acids Res., 2016

Sig2GRN: a software tool linking signaling pathway with gene regulatory network for dynamic simulation.
BMC Syst. Biol., 2016

Generalized logical model based on network topology to capture the dynamical trends of cellular signaling pathways.
BMC Syst. Biol., 2016

2015
Predicting essential genes and synthetic lethality via influence propagation in signaling pathways of cancer cell fates.
J. Bioinform. Comput. Biol., 2015

Introduction to the CSBio2014 special issue.
J. Bioinform. Comput. Biol., 2015

Computational cell fate modelling for discovery of rewiring in apoptotic network for enhanced cancer drug sensitivity.
BMC Syst. Biol., 2015

Single-cell transcriptional analysis to uncover regulatory circuits driving cell fate decisions in early mouse development.
Bioinform., 2015

2014
Reliable and Fast Estimation of Recombination Rates by Convergence Diagnosis and Parallel Markov Chain Monte Carlo.
IEEE ACM Trans. Comput. Biol. Bioinform., 2014

Deciphering histone code of transcriptional regulation in malaria parasites by large-scale data mining.
Comput. Biol. Chem., 2014

Finding trans-regulatory genes and protein complexes modulating meiotic recombination hotspots of human, mouse and yeast.
BMC Syst. Biol., 2014

LDsplit: screening for cis-regulatory motifs stimulating meiotic recombination hotspots by analysis of DNA sequence polymorphisms.
BMC Bioinform., 2014

IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking.
BMC Bioinform., 2014

Extracting rate changes in transcriptional regulation from MEDLINE abstracts.
BMC Bioinform., 2014

CUDAGRN: Parallel Speedup of Inferring Large Gene Regulatory Networks from Expression Data Using Random Forest.
Proceedings of the Pattern Recognition in Bioinformatics, 2014

Data-driven prediction of cancer cell fates with a nonlinear model of signaling pathways.
Proceedings of the 5th ACM Conference on Bioinformatics, 2014

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.
BMC Bioinform., 2013

Drug-target interaction prediction by learning from local information and neighbors.
Bioinform., 2013

Inferring Gene Regulatory Networks from Time-Series Expressions Using Random Forests Ensemble.
Proceedings of the Pattern Recognition in Bioinformatics, 2013

Inferring Time-Delayed Gene Regulatory Networks Using Cross-Correlation and Sparse Regression.
Proceedings of the Bioinformatics Research and Applications, 9th International Symposium, 2013

Gene Regulatory Networks from Gene Ontology.
Proceedings of the Bioinformatics Research and Applications, 9th International Symposium, 2013

Integrating epigenetic prior in dynamic Bayesian network for gene regulatory network inference.
Proceedings of the 2013 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2013

Syn-Lethality: An integrative knowledge base of synthetic lethality towards discovery of selective anticancer therapies.
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013

Meta-analysis of Genomic and Proteomic Features to Predict Synthetic Lethality of Yeast and Human Cancer.
Proceedings of the ACM Conference on Bioinformatics, 2013

2012
Teasing Apart Translational and Transcriptional Components of Stochastic Variations in Eukaryotic Gene Expression.
PLoS Comput. Biol., 2012

Globalized bipartite local model for drug-target interaction prediction.
Proceedings of the 11th International Workshop on Data Mining in Bioinformatics, 2012

NetPipe: a network-based pipeline for discovery of genes and protein complexes regulating meiotic recombination hotspots.
Proceedings of the ACM International Conference on Bioinformatics, 2012

Integration of genomic and epigenomic features to predict meiotic recombination hotspots in human and mouse.
Proceedings of the ACM International Conference on Bioinformatics, 2012

2011
Integration of Epigenetic Data in Bayesian Network Modeling of Gene Regulatory Network.
Proceedings of the Pattern Recognition in Bioinformatics, 2011

Prediction of Trans-regulators of Recombination Hotspots in Mouse Genome.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2011

2010
SimBoolNet - a Cytoscape plugin for dynamic simulation of signaling networks.
Bioinform., 2010

2009
The crosstalk between EGF, IGF, and Insulin cell signaling pathways - computational and experimental analysis.
BMC Syst. Biol., 2009

2007
A Rigorous Analysis of the Pattern of Intron Conservation Supports the <i>Coelomata</i> Clade of Animals.
Proceedings of the Comparative Genomics, RECOMB 2007 International Workshop, 2007

2006
OligoSpawn: a software tool for the design of overgo probes from large unigene datasets.
BMC Bioinform., 2006

2005
Assignment of Orthologous Genes via Genome Rearrangement.
IEEE ACM Trans. Comput. Biol. Bioinform., 2005

Discovery of Repetitive Patterns in DNA with Accurate Boundaries.
Proceedings of the Fifth IEEE International Symposium on Bioinformatic and Bioengineering (BIBE 2005), 2005

Computing the Assignment of Orthologous Genes via Genome Rearrangement.
Proceedings of 3rd Asia-Pacific Bioinformatics Conference, 17-21 January 2005, Singapore, 2005

2004
Efficient selection of unique and popular oligos for large EST databases.
Bioinform., 2004


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