Publications (Full list in Google Scholar)

Journals

2021

• Shike Wang#, Fan Xu# (joint first authors), Yunyang Li, Jie Wang, Ke Zhang, Yong Liu, Min Wu*, Jie Zheng*. KG4SL: Knowledge graph neural network for synthetic lethality prediction in human cancers. Bioinformatics (ISMB/ECCB 2021 special issue), in press, 2021 (IF = 5.61).

• 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 Bioinformatics, in press, 2021 (IF = 3.242).

• Fan Xu#, Shike Wang# (joint first authors), Xinnan Dai, Piyushkumar A. Mundra, Jie Zheng*. Ensemble learning models that predict surface protein abundance from single-cell multimodal omics data. Methods, Vol. 189, pp. 65-73, 2021 (IF = 3.641).

2020

• Xiaomeng Zhang#, Ket Hing Chong# (joint first authors), Lin Zhu, Jie Zheng*. A Monte Carlo method for in silico modeling and visualization of Waddington's epigenetic landscape with intermediate details. BioSystems, Vol. 198, 104275, 2020 (IF = 1.652).

• Haifen Chen, Devamuni A.K. Maduranga, Piyushkumar Mundra, Jie Zheng*. Bayesian data fusion of gene expression and histone modification profiles for inference of gene regulatory network. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 17(2): 516-525, 2020 (IF = 3.015).

• Yong Liu, Min Wu*, Chenghao Liu, Xiao-Li Li, Jie Zheng* (joint corresponding authors). SL2MF: Predicting synthetic lethality in human cancers via logistic matrix factorization. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 17(3): 748-757, (special issue of GIW 2018), 2020 (IF = 3.015).

• Jie Zheng, Jinyan Li, Yun Zheng. Guest Editorial for the 29th International Conference on Genome Informatics (GIW 2018). IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 17(3): 726 - 727, 2020 (IF = 3.015).

2019

• Yong Liu, Min Wu*, Chenghao Liu, Xiao-Li Li, Jie Zheng*. SL2MF: Predicting synthetic lethality in human cancers via logistic matrix factorization. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) (special issue of GIW 2018), accepted, 2019 (IF = 2.428).

• Ket Hing Chong, Sandhya Samarasinghe, Don Kulasiri*, Jie Zheng. Mathematical modelling of core regulatory mechanism in p53 protein that activates apoptotic switch. Journal of Theoretical Biology, Vol. 462 (7 Feb.), pp. 134-147, 2019 (IF = 1.833).

2018

• Lichun Ma, Jie Zheng*. Single-cell gene expression data analysis reveals beta-cell dysfunction and deficit mechanisms in type 2 diabetes. BMC Bioinformatics, 19(Suppl 19):515, 2018 (special issue of GIW 2018) (IF = 2.213).

• Xinrui Zhou, Rui Yin, Chee Keong Kwoh*, Jie Zheng*. A context-free encoding scheme of protein sequences for predicting antigenicity of diverse influenza A viruses. BMC Genomics, 19(Suppl 10):936, 2018 (special issue of GIW 2018) (IF = 3.730).

• Rui Yin, Xinrui Zhou, Jie Zheng, Chee Keong Kwoh*. Computational identification of physiochemical signatures for host tropism of influenza A virus. Journal of Bioinformatics and Computational Biology (JBCB), Vol. 16, No. 6, 1840023, 2018 (special issue of GIW 2018) (IF = 0.991).

• Haifen Chen, Devamuni A.K. Maduranga, Piyushkumar Mundra, Jie Zheng*. Bayesian data fusion of gene expression and histone modification profiles for inference of gene regulatory network. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), Early Access, 2018 (IF = 2.428).

• Hongfei Liu, Paolo A Lorenzini, Fan Zhang, Shaohai Xu, Mei Su M Wong, Jie Zheng, Xavier Roca*. Alternative splicing analysis in human monocytes and macrophages reveals MBNL1 as major regulator. Nucleic Acids Research, 46 (12), pp. 6069 – 6086, 2018 (IF = 11.561).

• Ket Hing Chong, Xiaomeng Zhang, Jie Zheng*. Dynamical analysis of cellular ageing by modeling of gene regulatory network based attractor landscape. PLOS ONE, 13(6), e0197838, 2018 (IF = 2.766).

• Xiaomeng Zhang#, Ket Hing Chong# (joint first authors), Jie Zheng*. A Monte Carlo method for in silico modeling and visualization of Waddington’s epigenetic landscape with intermediate details. bioRxiv 310771, 2018.

• Xinrui Zhou, Jie Zheng, Xaverius Ivan Fransiskus, Rui Yin, Shoba Ranganathan, Vincent T. K. Chow, Chee Keong, Kowh. Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses. BMC Genomics (special issue of APBC 2018) 19 (Suppl 2):88, 2018 (IF = 3.730).

• Bobby Ranjan, Ket Hing Chong, Jie Zheng*. Composite mathematical modeling of calcium signaling behind neuronal cell death in Alzheimer’s disease. BMC Systems Biology (special issue of APBC 2018) 12(Suppl 1):10, 2018 (IF = 2.050).

• Jing Guo, Hao Chen, Peng Yang, Yew Ti Lee, Min Wu, Teresa M. Przytycka, Chee Keong Kwoh, Jie Zheng*. LDSplitDB: A database for studies of meiotic recombination hotspots in MHC using human genomic data. BMC Medical Genomics 11(Suppl 2): 27, special issue of the 28th International Conference on Genome Informatics (GIW/BIOINFO 2017), 2018 (IF = 3.317).
  Website of LDSplitDB: http://histone.scse.ntu.edu.sg/LDSplitDB/

• Huey Eng Chua, Sourav S. Bhowmick*, Jie Zheng. TROVE: A User-friendly Tool for Visualizing and Analyzing Cancer Hallmarks in Signaling Networks. Bioinformatics, 34(2):314-316, 2018 (IF = 5.481).

• Hui Liu, Libo Luo, Zhanzhan Cheng, Jianjiang Sun, Jihong Guan, Jie Zheng*, Shuigeng Zhou* (co-corresponding authors). Group-sparse modeling drug-kinase networks for predicting combinatorial drug sensitivity in cancer cells. Current Bioinformatics, Vol. 13 (E-pub ahead of print), 2018 (IF = 0.540, 5-year IF = 0.777).

• Jing Guo, Hao Chen, Peng Yang, Yew Ti Lee, Min Wu, Teresa M. Przytycka, Chee Keong Kwoh, Jie Zheng. LDSplitDB: A database for studies of meiotic recombination hotspots in MHC using human genomic data. BMC Medical Genomics (special issue of the 28th International Conference on Genome Informatics (GIW/BIOINFO 2017)), 2017, in press (IF = 2.448).

2017

• Lichun Ma, Jie Zheng. A polynomial based model for cell fate prediction in human diseases. BMC Systems Biology (special issue of the 16th International Conference on Bioinformatics (InCoB 2017)), 2017, in press (IF = 2.303). (Best Paper Award, Gold Medal).  

• Jing Guo, Jie Zheng. HopLand: Single-cell pseudotime recovery using continuous Hopfield network based modeling of Waddington’s epigenetic landscape, Bioinformatics, 33(14): i102 – i109 (special issue of conference ISMB/ECCB 2017, acceptance rate 16.5%), 2017 (IF = 7.307).
  Source code of HopLand: https://github.com/NetLand-NTU/HopLand/

• M Pek, SMJM Yatim, Y Chen, J Li, M Gong, X Jiang, F Zhang*, J Zheng, X Wu, Q Yu, Oncogenic KRAS-associate gene signature defines co-targeting of CDK4/6 and MEK as a viable therapeutic strategy in colorectal cancer. Nature Oncogene, 2017, in press (IF = 7.519).

• Jing Guo, Feng Lin, Xiaomeng Zhang, Vivek Tanavde, Jie Zheng. NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential. Bioinformatics, 33(10), pp. 1583 - 1585, 2017 (IF = 7.307).
  Software source code and user manual: https://github.com/NetLand-NTU/NetLand/

2016

• Jing Guo, Hui Liu, Jie Zheng. SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets. Nucleic Acids Research, 44 (D1), D1011 - 1017 (Database issue, open access on-line), 2016 (IF = 10.162).
  SynLethDB website: http://histone.scse.ntu.edu.sg/SynLethDB/

• Hui Liu, Fan Zhang, Shital Kumar Mishra, Shuigeng Zhou, Jie Zheng. Knowledge-guided fuzzy logic modeling to infer cellular signaling networks from proteomic data. Scientific Reports, 6:35652, 2016 (IF = 5.228).
  Source code and dataset: http://www.ntu.edu.sg/home/zhengjie/software/fuzzySigNet/

• Fan Zhang, Min Wu, Chee Keong Kwoh, Jie Zheng. Power-law modeling of cancer cell fates driven by signaling data to reveal drug effects. PLOS ONE, 11(10):e0165049, 2016 (IF = 3.54).

• Haifen Chen, Xinrui Zhou, Jie Zheng, Chee Keong Kwoh. Rules of co-occurring mutations characterize the antigenic evolution of human influenza A/H3N2, A/H1N1 and B viruses. BMC Medical Genomics, 9:230, 2016 (special issue of the 15th International Conference on Bioinformatics, INCOB 2016, IF = 2.726).

• Fan Zhang, Runsheng Liu, Jie Zheng. Sig2GRN: a software tool linking signaling pathway with gene regulatory network for dynamic simulation. BMC Systems Biology, 10(4), 541, 2016 (special issue of the 27th International Conference on Genome Informatics, GIW 2016, IF = 2.65).
  Source code: http://histone.scse.ntu.edu.sg/Sig2GRN/

• Fan Zhang, Haoting Chen, Li Na Zhao, Hui Liu, Teresa M. Przytycka and Jie Zheng. Generalized logical model based on network topology to capture the dynamical trends of cellular signaling pathways. BMC Systems Biology, 10 Suppl 1:7, 2016 (special issue of APBC 2016, IF = 2.65).

• Yifeng Li*, Haifen Chen* (*joint first authors), Jie Zheng, Alioune Ngom. The Max-Min High-Order Dynamic Bayesian Network for Learning Gene Regulatory Networks with Time-Delayed Regulations. IEEE/ACM Transactions on Computational Biology and Bioinformatics (IEEE/ACM TCBB), Vol. 13, Issue 4, pp. 792 - 803, 2016 (IF = 1.438).

2015 and before

• Hao Chen, Peng Yang, Jing Guo, Chee Keong Kwoh, Teresa M. Przytycka, Jie Zheng. ARG-walker: Inference of Individual Specific Strengths of Meiotic Recombination Hotspots by Population Genomics Analysis. BMC Genomics, 16(Suppl 12):S1, 2015 (IF = 3.99).

• 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. Bioinformatics, 31(7), pp. 1060 – 1066, 2015 (IF = 5.766).

• Hui Liu, Jianjiang Sun, Jihong Guan, Jie Zheng and Shuigeng Zhou. Improving compound–protein interaction prediction by building up highly credible negative samples. Bioinformatics 31 (12), i221 – i229, (special issue of ISMB/ECCB 2015), 2015 (IF = 5.766, 5-year IF = 6.968).

• 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 Systems Biology, 9 (Suppl. 1):S4, 2015 (presented at APBC 2015, IF = 2.853).

• María Muñoz‐Amatriaín, Stefano Lonardi, …, Jie Zheng, …, Timothy J Close. Sequencing of 15 622 gene‐bearing BACs clarifies the gene‐dense regions of the barley genome. The Plant Journal, Volume 84, Issue 1, pages 216 – 227, 2015 (open access, IF =  5.972).

• 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. Journal of Bioinformatics and Computational Biology, Vol. 13, No. 03, 1541002 (14 pages), 2015.

• Li Na Zhao, Jie Zheng, Lock Yue Chew, Yuguang Mu. An Investigation on the Fundamental Interaction between Abeta Peptides and the AT-Rich DNA. The Journal of Physical Chemistry B, Volume 119, Issue 26, Pages 8247 – 8259, 2015 (IF = 3.302).

• Hongliang Hu, Qinghua Zhang, Shen Li, Xiaona Zhang, Junsong Han, Huasheng Xiao, David Yan, Jie Zheng, Biaoru Li. A Therapeutic Targeting Identification from Microarray Data and Quantitative Network Analysis. The Open Access Journal of Science & Technology, Volume 3, Article ID 101114, Pages 10, 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. ACM/IEEE Transactions on Computational Biology and Bioinformatics (TCBB), 11(1), pp. 1-10, 2014 (presented at GIW 2013, IF = 1.62).

• 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 Systems Biology, 8:107, 2014 (IF = 2.853).

• Haifen Chen, Piyushkumar A Mundra, Li Na Zhao, Feng Lin, Jie Zheng. Highly sensitive inference of time-delayed gene regulation by network deconvolution. BMC Systems Biology, 8 (Suppl. 4), S6, 2014 (special issue of InCoB 2014, IF = 2.853).

• 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 Bioinformatics, 15:48, 2014 (IF = 2.67).

• Wenting Liu, Kui Miao, Guangxia Li, Kuiyu Chang, Jie Zheng, Jagath C Rajapakse. Extracting rate changes in transcriptional regulation from MEDLINE abstracts. BMC Bioinformatics, 15(Suppl 2):S4, 2014 (presented at APBC 2014, IF = 2.67).

• 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 Bioinformatics, 15 (Suppl. 16), S9, 2014. (presented at InCoB 2014, IF = 2.67).

• Ragini Rai, Lei Zhu, Haifen Chen*, Archana Patkar Gupta, Siu Kwan Sze, Jie Zheng, Christiane Ruedl, Zbynek Bozdech, Mark Featherstone. Genome-wide analysis in Plasmodium falciparum reveals early and late phases of RNA polymerase II occupancy during the infectious cycle. BMC Genomics, 15:959, 2014 (IF = 4.04).

• Xue-juan 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. BioMed Research International, Vol. 2014, Article ID 196034, 7 pages, 2014 (IF = 2.706).

• Haifen Chen, Stefano Lonardi, Jie Zheng. Deciphering Histone Code of Transcriptional Regulation in Malaria Parasites by Large-scale Data Mining. Computational Biology and Chemistry, Vol. 50, pp. 3-10, 2014 (presented at APBC 2014, IF = 1.595).

• Min Wu, Xuejuan Li, Fan Zhang, Xiaoli Li, Chee-Keong Kwoh, Jie Zheng. In Silico Prediction of Synthetic Lethality by Meta-Analysis of Genetic Interactions, Functions, and Pathways in Yeast and Human Cancer. Cancer Informatics, 13(Suppl. 3), pp. 71-80, 2014 (IF = 1.36).

• Pamela Thompson, Kevin Urayama, Jie Zheng, Peng Yang, Matt Ford, Patricia Buffler, Anand Chokkalingam, Tracy Lightfoot, Malcolm Taylor. Differences in meiotic recombination rates in childhood acute lymphoblastic leukemia at an MHC class II hotspot close to disease associated haplotypes. PLOS ONE, 9(6):e100480, 2014 (IF = 3.534).

• Yunbo Xu, Hongliang Hu, Jie Zheng#, Biaoru Li# (co-corresponding author). Feasibility of Whole RNA Sequencing from Single-Cell mRNA Amplification, Genetics Research International, Vol. 2013, No. 724124, 2013.

• M. Wu, Q. Yu, X-L, Li, J. Zheng, J-F Huang, C-K Kwoh. Benchmarking Human Protein Complexes to Investigate Drug-Related Systems and Evaluate Predicted Protein Complexes. PLOS ONE 8(2): e53197, 2013 (IF = 4.092).

• J. Mei, C-K Kwoh, P. Yang, X-L Li, J. Zheng. Drug-Target Interaction Prediction by Learning from Local Information and Neighbors. Bioinformatics, 29(2): 238-245, 2013 (IF = 5.766) .

• Daniel Lin-Kit Wong, Xiao-Li Li, Min Wu, Jie Zheng, See-Kiong Ng. PLW: Probabilistic Local Walks for detecting protein complexes from protein interaction networks. BMC Genomics, 14(Suppl 5): S15, 2013 (IF = 4.40, conference version presented at Twelfth International Conference on Bioinformatics (InCoB2013), Taicang, China, Sept. 20-22, 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 Bioinformatics, 14 (Suppl 16), S7, 2013 (IF = 3.02, conference version presented at Twelfth International Conference on Bioinformatics (InCoB2013), Taicang, China, Sept. 20-22, 2013).

• Min Wu, Zhipeng Xie, Xiaoli Li, Chee‐Keong Kwoh, Jie Zheng. Identifying protein complexes from heterogeneous biological data. Proteins: Structure, Function, and Bioinformatics, 81(11), 2023-2033, 2013 (IF = 3.337).

• R. Salari#, D. Wojtowicz#, J. Zheng# (joint first authors in alphabetical order), D. Levens. Y. Pilpel, TM Przytycka. Teasing Apart Translational and Transcriptional Components of Stochastic Variations in Eukaryotic Gene Expression. PLoS Computational Biology, 8(8):e1002644, 2012 (IF = 5.515).

• Min Wu, Chee-Keong Kwoh, Teresa Przytycka, Jing Li, and Jie Zheng. Epigenetic Functions Enriched in Transcription Factors Binding to Mouse Recombination Hotspots. Proteome Science, 10(Suppl 1):S11, 2012 (IF = 2.42).

• J. Zheng, T. Jiang. International Conference on Research in Computational Molecular Biology. Communications of China Computer Federation (CCCF), vol. 59, 2011.

• J. Zheng, PP Khil, RD Camerini-Otero, TM Przytycka. Detecting sequence polymorphisms associated with meiotic recombination hotspots in the human genome. Genome Biology, 11:R103. 2010 (Highlighted on daily news of GenomeWeb) (IF = 11.313).

• J. Zheng*, D. Zhang, PF Przytycki, R. Zielinski, J. Capala, TM Przytycka* (co-corresponding author). SimBoolNet - A Cytoscape plugin for dynamic simulation of signaling networks. Bioinformatics, 26(1): 141-142, 2010 (IF = 5.766).

• R. Zielinski, PF Przytycki, J. Zheng, D. Zhang, TM Przytycka, J. Capala. The crosstalk between EGF, IGF, and Insulin cell signaling pathways – computational and experimental analysis. BMC Systems Biology, 3(88), 2009 (IF = 3.148).

• J. Zheng, IB Rogozin, EV Koonin, TM Przytycka. Support for the Coelomata Clade of animals from a rigorous analysis of the pattern of intron conservation. Molecular Biology and Evolution, 24(11):2583-92, 2007 (IF = 13.649).

• J. Zheng, J. Svensson, K. Madishetty, T. Close, T. Jiang, S. Lonardi. OligoSpawn: a software tool for the design of overgo probes from large unigene databases. BMC Bioinformatics, 7:7, 2006 (IF = 2.751).

• X. Chen, J. Zheng, Z. Fu, P. Nan, Y. Zhong, S. Lonardi and T. Jiang. Assignment of orthologous genes via genome rearrangement. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2(4), 302-315, 2005 (IF = 1.543).

• A. Goldstein, P. Kolman, J. Zheng (authors in alphabetical order). Minimum common string partition problem: hardness and approximation. Electronic Journal of Combinatorics, 12(1), 2005.

• J. Zheng, T. Close, T. Jiang, S. Lonardi. Efficient Selection of Unique and Popular Oligos for Large EST Databases. Bioinformatics, 20(13), 2101-2112, 2004 (IF = 5.766).

Conferences

1. Xin Wang, Jie Zheng*. Velo-Predictor: An ensemble learning pipeline for RNA velocity prediction. The 19th Asia Pacific Bioinformatics Conference (APBC), Online Virtual Conference, Feb. 3 - 5, 2021.

2. Lin Zhu, Xinnan Dai, Qihao Huang, Hai Xiang, Jie Zheng*. Topic judgment helps question similarity prediction in medical FAQ dialogue systems. IEEE International Conference on Data Mining (ICDM), Workshop on Data Mining in Biomedical Informatics and Healthcare (DMBIH), pp. 966-972, Beijing, China, Nov. 8th, 2019.

3. Jing Guo, Hao Chen, Peng Yang, Yew Ti Lee, Min Wu, Teresa M. Przytycka, Chee Keong Kwoh, Jie Zheng. LDSplitDB: A database for studies of meiotic recombination hotspots in MHC using human genomic data. The 28th International Conference on Genome Informatics (GIW/BIOINFO 2017)), Seoul, Korea, 31 Oct. – 3 Nov. 2017.

4. Lichun Ma, Jie Zheng. A polynomial based model for cell fate prediction in human diseases. The 16th International Conference on Bioinformatics (InCoB 2017), Shenzhen, China, 20 – 22 Sept., 2017.

5. Fransiskus Xavier Ivan, Xinrui Zhou, Akhila Deshpande, Rui Ying, Jie Zheng, Chee Keong Kwoh. Phylogenetic tree based method for uncovering co-mutational site-pairs in influenza viruses. Proc. of 8th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), pages 21 – 26, Boston, MA, USA, 20 – 23 August, 2017.

6. Jing Guo, Jie Zheng. HopLand: Single-cell pseudotime recovery using continuous Hopfield network based modeling of Waddington’s epigenetic landscape. Proc. Intelligent Systems for Molecular Biology and European Conference on Computational Biology (ISMB/ECCB) 2017, to appear, Prague, Czech Republic, 21 – 25 July, 2017. [acceptance rate 16.5%].

7. Rui Yin, Xinrui Zhou, Fransiskus Xavier 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. Proc. 6th International Conference on Bioinformatics and Biomedical Science (ICBBS), Singapore, June 22 – 24, 2017.

8. Shital Kumar Mishra, Sourav S Bhowmick, Huey Eng Chua and Jie Zheng. Predictive Modeling of Drug Effects on Signaling Pathways in Diverse Cancer Cell Lines. The 7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB 2016), pp. 200 – 209, Seattle, WA, USA, 2 – 5 Oct. 2016.

9. Huey Eng Chua, Sourav S Bhowmick, Jie Zheng and Lisa Tucker-Kellogg. TAPESTRY: Network-centric Target Prioritization in Disease-related Signaling Networks. The 7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB 2016), pp. 108 – 117, Seattle, WA, USA, 2 – 5 Oct. 2016.

10. Hui Liu, Zhanzhan Cheng, Jiangjiang Sun, Jihong Guan, Jie Zheng, Shuigeng Zhou. Sparse linear modeling kinase inhibition network for predicting combinatorial drug sensitivity in cancer cells. The first CCF Bioinformatics Conference (CBC 2016), Chongqing, China, 10 – 13 Nov. 2016.

11. Haifen Chen, Xinrui Zhou, Jie Zheng, Chee Keong Kwoh. Rules of co-occurring mutations characterize the antigenic evolution of human influenza A/H3N2, A/H1N1 and B viruses. Proc. 15th International Conference on Bioinformatics (INCOB 2016), Biopolis, Singapore, 21st – 23rd Sept. 2016.

12. Fan Zhang*, Runsheng Liu*, Jie Zheng. Sig2GRN: a software tool linking signaling pathway with gene regulatory network for dynamic simulation. The 27th International Conference on Genome Informatics (GIW2016), Shanghai, China, 3 – 5 Oct. 2016.

13. Fan Zhang, Haoting Chen, Li Na Zhao, Hui Liu, Teresa M. Przytycka and Jie Zheng. Generalized logical model based on network topology to capture the dynamical trends of cellular signaling pathways. Proc. 14th Asia Pacific Bioinformatics Conference (APBC 2016), San Francisco, California, USA, 11 – 13 January, 2016.

14. Hao Chen, Peng Yang, Jing Guo, Chee Keong Kwoh, Teresa M. Przytycka, Jie Zheng. ARG-walker: Inference of Individual Specific Strengths of Meiotic Recombination Hotspots by Population Genomics Analysis. The 26th Genome Informatics Workshop and 14th International Conference on Bioinformatics (GIW/InCoB 2015), Odaiba, Tokyo, Japan, 9 – 11 Sept. 2015.

15. Hui Liu, Jianjiang Sun, Jihong Guan, Jie Zheng and Shuigeng Zhou. Improving compound–protein interaction prediction by building up highly credible negative samples. The 23rd Annual International Conference on Intelligent Systems for Molecular Biology & 14th European Conference on Computational Biology (ISMB/ECCB 2015), Dublin, Ireland, 10 – 14, July, 2015.

16. 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. The 2nd Symposium on Complex Biodynamics & Networks (cBio 2015), Tsuruoka, Japan, 11 – 13 May 2015.

17. 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. The 13th Asia Pacific Bioinformatics Conference (APBC 2015), HsinChu, Taiwan, China, 21 – 23 January 2015.

18. 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. The 5th International Conference on Computational Systems Biology and Bioinformatics (CSBio 2014), Singapore, 10 - 12 Nov. 2014.

19. Fan Zhang, Chee-Keong Kwoh, Min Wu, Jie Zheng. Data-driven prediction of cancer cell fates with a nonlinear model of signaling pathways. Proc. 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB2014), pp. 436 – 444, Newport Beach, California, USA, 20 – 23 Sept. 2014.

20. Seyed Ziaeddin Alborzi, DAK Maduranga, Rui Fan, Jagath C Rajapakse, Jie Zheng. CUDAGRN: Parallel Speedup of Inferring Large Gene Regulatory Networks from Expression Data Using Random Forest. Proc. 9th IAPR International Conference of Pattern Recognition in Bioinformatics (PRIB2014), LNCS 8626, pp. 85 – 97, Stockholm, Sweden, 21 – 23 Aug. 2014.

21. Sourav S Bhowmick, Huey-Eng Chua, Jie Zheng. INGOT: Towards Network-driven In Silico Combination Therapy. Proc. of 1st International Conference on Big Data and Smart Computing (BigComp 2014), Bangkok, Thailand, 15 – 17 Jan. 2014.

22. Xue-juan Li, Shital Kumar Mishra, Min Wu, Fan Zhang, and Jie Zheng. Syn-Lethality: An Integrative Knowledge Base of Synthetic Lethality towards Discovery of Selective Anticancer Therapies. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Workshop "Biomolecular Networks and Human Diseases", Shanghai, China, 2013.

23. 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. Proc. the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics (ACM-BCB), pp. 384- 391, 2013.

24. D.A.K. Maduranga, Jie Zheng, Piyushkumar A. Mundra, Jagath C. Rajapakse. Inferring gene regulatory networks from time-series expressions using random forests ensembl. Proc. Pattern Recognition in Bioinformatics (PRIB), LNBI 7986, pp. 13-22, 2013.

25. 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. Proc. Bioinformatics Research and Applications (ISBRA), LNCS 7875, pp. 64-75, 2013.

26. Wenting Liu, Kuiyu Chang, Jie Zheng, Jain Divya, Jung-Jae Kim, Jagath C. Rajapakse. Gene Regulatory Networks from Gene Ontology. Proc. Bioinformatics Research and Applications (ISBRA), LNCS 7875, pp. 87-98, 2013.

27. Haifen Chen#, D.A.K. Maduranga# (joint first authors), Piyushkumar A. Mundra, Jie Zheng*. Integrating Epigenetic Prior in Dynamic Bayesian Network for Gene Regulatory Network Inference. Proc. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), pp. 76-82, Singapore, as part of IEEE Symposium Series on Computational Intelligence (SSCI), 2013.

28. M. Wu, C-K Kwoh, X-L Li, J. Zheng*. NetPipe: A Network-based Pipeline for Discovery of Genes and Protein Complexes Regulating Meiotic Recombination Hotspots. Proc. ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), Orlando, FL, USA, pp. 20-27, 2012.

29. M. Wu, C-K Kwoh, TM Przytycka, J. Li, J. Zheng*. Integration of Genomic and Epigenomic Features to Predict Meiotic Recombination Hotspots in Human and Mouse. Proc. ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), Orlando, FL, USA, pp. 297-304, 2012.

30. J. Mei, C-K Kwoh, P. Yang, X-L Li, J. Zheng. Globalized Bipartite Local Learning Model for Drug-Target Interaction Prediction. International Workshop on Data Mining in Bioinformatics (BIOKDD), Beijing, China, 2012.

31. P. Yang, M. Wu, C-K Kwoh, PP Khil, RD Camerini-Otero, TM Przytycka, J. Zheng*. Predicting DNA Sequence Motifs of Recombination Hotspots by Integrative Visualization and Analysis. Proc. International Symposium on Integrative Bioinformatics, pp. 52-58, 2012.

32. J. Zheng, I. Chaturvedi, J. C. Rajapakse. Integration of epigenetic data in Bayesian Network modeling of Gene Regulatory Network. The 6th IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB), LNCS 7036, pp. 87-96, 2011.

33. M. Wu, C-K Kwoh, TM Przytycka, J. Li, J. Zheng*. Prediction of trans-regulators of recombination hotspots in mouse genome. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 57-62, 2011.

34. Z. Wang, H. Hu, J. Zheng*, B. Li* (co-corresponding authors). Gene expression and pathway analysis of quiescent CD8+ T Cells from liver cancer, liver sinusoid and peripheral blood -- study on toxicogenomics and prevention targeting. IEEE International Symposium on BioInformatics and BioEngineering (BIBE), pp. 72-77, 2011.

35. J. Zheng, IB Rogozin, EV Koonin, TM Przytycka. A rigorous analysis of the pattern of intron conservation supports the Coelomata clade of animals. RECOMB Comparative Genomics, LNCS 4751, pp. 177-191, 2007.

36. J. Zheng, S. Lonardi. Discovery of repetitive patterns in DNA with accurate boundaries. Proc. of IEEE International Symposium on BioInformatics and BioEngineering (BIBE), pp. 105-112, 2005.

37. X. Chen, J. Zheng, Z. Fu, P. Nan, Y. Zhong, S. Lonardi and T. Jiang. Assignment of orthologous genes via genome rearrangement. Proc. of Asia-Pacific Bioinformatics Conference (APBC), pp. 363-378, 2005

38. A. Goldstein, P. Kolman, J. Zheng (authors in alphabetical order). Minimum common string partition problem: hardness and approximation. Proc. of International Symposium on Algorithms and Computation (ISAAC), pp. 484-495, LNCS 3341, 2004.

39. J. Zheng, T. Close, T. Jiang, S. Lonardi. Efficient Selection of Unique and Popular Oligos for Large EST Databases. Proc. of Symposium on Combinatorial Pattern Matching (CPM), pp. 384-401, LNCS 2676, 2003.

Book Chapters

1. Biaoru Li, Xiaomeng Zhang, Jie Zheng. Single-Cell Next-Generation Sequencing and Its Applications in Cancer Biology. Next Generation Sequencing in Cancer Research, Volume 2, pages 1 – 18, Springer International Publishing, 2015.

2. Teresa M. Przytycka, Jie Zheng. Hidden Markov Models. Encyclopedia of Life Sciences, 2011.

3. Yang Huang*, Jie Zheng*, Teresa M. Przytycka (*co-first author). Discovery of regulatory mechanisms from gene expression variation by eQTL analysis. Biological Data Mining, Chapman and Hall/CRC Press, 2009.