发表论文
(1) ZokorDB: tissue specific regulatory network annotation for non-coding elements of plateau zokor., Quantitative Biology, 2020, 通讯作者(2) Time course regulatory analysis based on paired expression and chromatin accessibility data., Genome Research, 2020, 通讯作者(3) Associating divergent lncRNAs with target genes by integrating genome sequence, gene expression and chromatin accessibility data., NAR Genomics and Bioinformatics, 2020, 通讯作者(4) 3SCover: Identifying safeguard TF from cell type-TF network by an extended minimum set cover model, iScience, 2020, 通讯作者(5) Identifying cell type specific TF combinatorial regulation via a two-stage statistical model, IEEE International Conference on Big Data and Smart Computing (BigComp), 2020, 通讯作者(6) TFAP2Cand p63-Dependent Networks Sequentially Rearrange Chromatin Landscapes to Drive Human Epidermal Lineage Commitment., Cell Stem Cell, 2019, 第 2 作者(7) Lipid-gene regulatory network reveals coregulations of triacylglycerol with phosphatidylinositol/ lysophosphatidylinositol and with hexosyl-ceramide., BBA - Molecular and Cell Biology of Lipids, 2019, 通讯作者(8) Multi-level comparative framework based on gene pair-wise expression across three insulin target tissues for type 2 diabetes., Frontiers in Genetics, 2019, 通讯作者(9) Systems biology intertwines with single cell and AI, BMC Bioinformatics, 2019, 第 1 作者(10) Hierarchical graphical model reveals HFR1 bridging circadian rhythm and flower development in Arabidopsis thaliana., npj Systems Biology and Applications, 2019, 通讯作者(11) DC3 is a method for deconvolution and coupled clustering from bulk and single-cell genomics data., Nature Communications, 2019, 第 4 作者(12) scTIM: Seeking Cell-Type-Indicative Marker from single cell RNA-seq data by consensus optimization., Bioinformatics, 2019, 通讯作者(13) Associating lncRNAs with small molecules via bilevel optimization reveals cancer-related lncRNAs., PLoS Computational Biology, 2019, 通讯作者(14) Integrating distal and proximal information to predict gene expression via a densely con-nected convolutional neural network, Bioinformatics, 2019, 通讯作者(15) Integrative analysis of single cell genomics data by coupled nonnegative matrix factorizations., PNAS, 2018, 第 8 作者(16) ELF: Extract Landmark Features by optimizing topology maintenance, redundancy, and specificity, IEEE/ACM Transactions on Computational Biology and Bioinformatics., 2018, 通讯作者(17) Revealing transcription factor and histone modification co-localization and dynamics across cell lines by integrating ChIP-seq and RNA-seq data, BMC Genomics, 2018, 通讯作者(18) Modeling gene regulation from paired expression and chromatin accessibility data, PNAS, 2017, 通讯作者(19) Models of global gene expression define major 1 domains of cell type and tissue identity, Nucleic Acids Research, 2017, 第 10 作者(20) Drosophila TRF2 and TAF9 regulate lipid droplet size and phospholipid fatty acid composition, PLoS Genetics, 2017, 第 7 作者(21) A Novel Dual Eigen-Analysis of Mouse Multi-Tissues’ Expression Profiles Unveils New Perspectives into Type 2 Diabetes, Scientific Report, 2017, 第 4 作者(22) Modeling the causal regulatory network by integrating chromatin accessibility and transcriptome data, National Science Review, 2016, 第 1 作者(23) Identifying joint biomarker panel from multiple level dataset by an optimization model, Biomarkers in Medicine, 2016, 通讯作者(24) A systematic method to identify modulation of transcriptional regulation via chromatin activity reveals regulatory network during mESC differentiation, Scientific Report, 2016, 通讯作者(25) An extended particle swarm optimization method for folding protein on triangle lattice, IET Systems Biology, 2016, 第 4 作者(26) Simultaneous dimension reduction and adjustment for confounding variation, PNAS, 2016, 第 6 作者(27) Computational probing protein–protein interactions targeting small molecules, Bioinformatics, 2016, 通讯作者(28) NCC-AUC: an AUC optimization method to identify multi-biomarker panel for cancer prognosis from genomic and clinical data, Bioinformatics, 2015, 通讯作者(29) A novel mixed integer programming for multi-biomarker panel identification by distinguishing malignant from benign colorectal tumors, Methods, 2015, 通讯作者(30) Identifying network biomarkers based on protein-protein interactions and expression data, BMC Medical Genomics, 2015, 通讯作者(31) Development of serum parameters panels for the early detection of pancreatic cancer, International Journal of Cancer, 2014, 通讯作者(32) Network predicting drug anatomical therapeutic chemical code, Bioinformatics, 2013, 通讯作者(33) ellipsoidFN: a tool for identifying a heterogeneous set of cancer biomarkers based on gene expressions, Nucleic Acids Research, 2013, 第 1 作者(34) Network-Based Drug Repositioning, Mol. BioSyst., 2013, 通讯作者(35) iPcc: a novel feature extraction method for accurate disease class discovery and prediction., Nucleic Acids Research, 2013, 第 1 作者(36) A New Framework for Repositioning Drugs by Incorporating Various Functional Information, IET Systems Biology, 2013, 通讯作者(37) Bioinformatics studies on induced pluripotent stem cell, Current Bioinformatics, 2013, 第 1 作者(38) Revealing metabolite biomarkers for acupuncture treatment by linear programming based feature selection, BMC Systems Biology, 2012, 第 1 作者(39) A unified computational model for revealing and predicting subtle subtypes of cancers, BMC Bioinformatics, 2012, 通讯作者(40) A combinatorial model and algorithm for globally searching community structure in complex networks, Journal of Combinatorial Optimization, 2012, 通讯作者(41) Community structure detection based on Potts model and network spectral characterization, Europhysics Letters, 2012, 第 2 作者(42) A combinatorial model and algorithm for globally searching community structure in complex networks, Journal of Combinatorial Optimization, 2010, 第 4 作者(43) Network-based analysis of complex, IET Systems Biology, 2010, 第 2 作者(44) Prediction of protein-RNA binding sites by a random forest method with combined features, Bioinformatics, 2010, 第 3 作者(45) Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer disease brains, BMC Systems Biology, 2010, 第 2 作者(46) Computationally probing drug-protein interactions via support vector machine, Letters In Drug Design and Discovery, 2010, 第 3 作者(47) SANA: an algorithm for sequential and non-sequential protein structure alignment, Amino Acid, 2010, 第 3 作者(48) Protein evolution in yeast transcription factor subnetworks, Nucleic Acids Research, 2010, 第 1 作者(49) Optimization meets systems biology, BMC Systems Biology, 2010, 第 1 作者(50) Identifying translation initiation sites in prokaryotes using support vector machine, Journal of Theoretical Biology, 2010, 第 3 作者(51) A Linear Programming Framework for Inferring Gene Regulatory Networks by Integrating Heterogeneous Data, Chapter XIX in Computational Methodologies in Gene Regulatory Networks, 2009, 第 1 作者(52) Evaluating protein similarity from coarse structures, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2009, 第 1 作者(53) Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data, Nucleic Acids Research, 2009, 第 1 作者(54) A network biology study on circadian rhythm by integrating various omics data, OMICS: A Journal of Integrative Biology, 2009, 第 1 作者(55) Analysis on multi-domain cooperation for predicting protein-protein interactions, BMC Bioinformatics, 2008, 第 2 作者(56) Inferring transcriptional regulatory networks from high-throughput data, Bioinformatics, 2007, 第 1 作者(57) Supervised Inference of Gene Regulatory Networks by Linear Programming, Lecture Notes in Bioinformatics, 2006, 第 1 作者(58) Inferring gene regulatory networks from multiple microarray datasets, Bioinformatics, 2006, 第 1 作者(59) Exploring protein optimal HP configurations by self-organizing mapping, Journal of Bioinformatics and Computational Biology, 2005, 第 2 作者