Publications
- CTFacTomo: Reconstructing 3D spatial structures of RNA tomography transcriptomes by collapsed tensor factorization, , PLOS Computational Biology, 22, 3, e1013457, Public Library of Science, 2026
- Predicting spatially resolved gene expression via tissue morphology using adaptive spatial GNNs, , Bioinformatics, Special Issue of The Proceedings of The 23rd European Conference on Computational Biology (ECCB), 40, Supplement_2, ii111-ii119, Oxford University Press, 2024
- Deciphering high-order structures in spatial transcriptomes with graph-guided Tucker decomposition, , Bioinformatics, Special Issue of The Proceedings of The 32nd International Conference on Intelligent Systems for Molecular Biology (ISMB), 40, Supplement_1, i529-i538, Oxford University Press, 2024, ⭐ Outstanding Student Paper
- A ventriculomegaly feature computational pipeline to improve the screening of normal pressure hydrocephalus on CT, , Journal of neurosurgery, 141, 3, 822-832, American Association of Neurological Surgeons, 2024
- Structural neuroimaging markers of normal pressure hydrocephalus versus Alzheimer’s dementia and Parkinson’s disease, and hydrocephalus versus atrophy in chronic TBI—a narrative review, , Frontiers in Neurology, 15, 1347200, Frontiers Media SA, 2024
- Orchard: building large cancer phylogenies using stochastic combinatorial search, , PLoS computational biology, 20, 12, e1012653, Public Library of Science San Francisco, CA USA, 2024
- GNTD: reconstructing spatial transcriptomes with graph-guided neural tensor decomposition informed by spatial and functional relations, , Nature communications, 14, 1, 8276, Nature Publishing Group UK London, 2023
- Detecting spatially co-expressed gene clusters with functional coherence by graph-regularized convolutional neural network, , Bioinformatics, 38, 5, 1344-1352, Oxford University Press, 2022
- Imputation of spatially-resolved transcriptomes by graph-regularized tensor completion, , PLoS computational biology, 17, 4, e1008218, Public Library of Science San Francisco, CA USA, 2021
- Scalable label propagation for multi-relational learning on the tensor product of graphs, , IEEE Transactions on Knowledge and Data Engineering, 34, 12, 5964-5978, IEEE, 2021
- Efficient sequencing, assembly, and annotation of human KIR haplotypes, , Frontiers in immunology, 11, 582927, Frontiers Media SA, 2020
- Accurate and efficient KIR gene and haplotype inference from genome sequencing reads with novel K-mer signatures, , Frontiers in immunology, 11, 583013, Frontiers Media SA, 2020
- A large-scale comparative study of isoform expressions measured on four platforms, , BMC genomics, 21, 1-14, Springer, 2020
- Hierarchical canonical correlation analysis reveals phenotype, genotype, and geoclimate associations in plants, , Plant Phenomics, AAAS, 2020
- A detailed view of KIR haplotype structures and gene families as provided by a new motif-based multiple sequence alignment, , Frontiers in immunology, 11, 585731, Frontiers Media SA, 2020
- Machine learning and statistical methods for clustering single-cell RNA-sequencing data, , Briefings in bioinformatics, 21, 4, 1209-1223, Oxford University Press, 2020
- Platform-integrated mRNA isoform quantification, , Bioinformatics, 36, 8, 2466-2473, Oxford University Press, 2020
- Path segmentation for movement trajectories with irregular sampling frequency using space-time interpolation and density-based spatial clustering, , Transactions in GIS, 23, 3, 558-578, Wiley Online Library, 2019
- mTOR-regulated U2af1 tandem exon splicing specifies transcriptome features for translational control, , Nucleic acids research, 47, 19, 10373-10387, Oxford University Press, 2019
- Scalable remote homology detection and fold recognition in massive protein networks, , Proteins: Structure, Function, and Bioinformatics, 87, 6, 478-491, Wiley Online Library, 2019
- Learning a low-rank tensor of pharmacogenomic multi-relations from biomedical networks, , 2019 IEEE International Conference on Data Mining (ICDM), 409-418, IEEE, 2019
- Obesity-induced protein carbonylation in murine adipose tissue regulates the DNA-binding domain of nuclear zinc finger proteins, , Journal of Biological Chemistry, 293, 35, 13464-13476, Elsevier, 2018
- An integrative model for alternative polyadenylation, IntMAP, delineates mTOR-modulated endoplasmic reticulum stress response, , Nucleic acids research, 46, 12, 5996-6008, Oxford University Press, 2018
- Vasodilator-stimulated phosphoprotein promotes liver metastasis of gastrointestinal cancer by activating a $\beta$1-integrin-FAK-YAP1/TAZ signaling pathway, , NPJ precision oncology, 2, 1, 2, Nature Publishing Group UK London, 2018
- HRB2 and BBX21 interaction modulates Arabidopsis ABI5 locus and stomatal aperture, , Plant, Cell \& Environment, 41, 8, 1912-1925, Wiley Online Library, 2018
- A multitask clustering approach for single-cell RNA-seq analysis in recessive dystrophic epidermolysis bullosa, , PLoS computational biology, 14, 4, e1006053, Public Library of Science San Francisco, CA USA, 2018
- DARPP-32 and t-DARPP promote non-small cell lung cancer growth through regulation of IKK$\alpha$-dependent cell migration, , Communications biology, 1, 1, 43, Nature Publishing Group UK London, 2018
- Transfer learning across ontologies for phenome-genome association prediction, , Bioinformatics, 33, 4, 529-536, Oxford University Press, 2017
- Dropout prediction in home care training, , Proc. 10th Int. Conf. Educ. Data Mining, 442-443, ERIC, 2017
- Revealing complete complex KIR haplotypes phased by long-read sequencing technology, , Genes \& Immunity, 18, 3, 127-134, Nature Publishing Group, 2017
- Detecting population-differentiation copy number variants in human population tree by sparse group selection, , IEEE/ACM Transactions on Computational Biology and Bioinformatics, 16, 2, 538-549, IEEE, 2017
- Global analysis of canola genes targeted by SHORT HYPOCOTYL UNDER BLUE 1 during endosperm and embryo development, , The Plant Journal, 91, 1, 158-171, Wiley Online Library, 2017
- Network-based machine learning and graph theory algorithms for precision oncology, , NPJ precision oncology, 1, 1, 25, Nature Publishing Group UK London, 2017
- Estimating KIR haplotype frequencies on a cohort of 10,000 individuals: a comprehensive study on population variations, typing resolutions, and reference haplotypes, , PLoS One, 11, 10, e0163973, Public Library of Science San Francisco, CA USA, 2016
- Meta-analysis of EMT datasets reveals different types of EMT, , PloS one, 11, 6, e0156839, Public Library of Science San Francisco, CA USA, 2016
- Predicting small group accretion in social networks: A topology based incremental approach, , Proceedings of the 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining 2015, 408-415, 2015
- TP53 mutations, tetraploidy and homologous recombination repair defects in early stage high-grade serous ovarian cancer, , Nucleic acids research, 43, 14, 6945-6958, Oxford University Press, 2015
- Network-based phenome-genome association prediction by bi-random walk, , PloS one, 10, 5, e0125138, Public Library of Science San Francisco, CA USA, 2015
- mRNA 3′-UTR shortening is a molecular signature of mTORC1 activation, , Nature communications, 6, 1, 7218, Nature Publishing Group UK London, 2015
- Predicting and exploring network components involved in pathogenesis in the malaria parasite via novel subnetwork alignments, , BMC systems biology, 9, 1-11, Springer, 2015
- Network-based isoform quantification with RNA-seq data for cancer transcriptome analysis, , PLoS computational biology, 11, 12, e1004465, Public Library of Science San Francisco, CA USA, 2015
- SubPatCNV: approximate subspace pattern mining for mapping copy-number variations, , BMC bioinformatics, 16, 1-12, Springer, 2015
- Platinum-sensitive recurrence in ovarian cancer: the role of tumor microenvironment, , Frontiers in oncology, 3, 251, Frontiers Media SA, 2013
- Large-scale integrative network-based analysis identifies common pathways disrupted by copy number alterations across cancers, , BMC genomics, 14, 1-13, Springer, 2013
- Network-based survival analysis reveals subnetwork signatures for predicting outcomes of ovarian cancer treatment, , PLoS computational biology, 9, 3, e1002975, Public Library of Science San Francisco, USA, 2013
- Transfer learning across cancers on DNA copy number variation analysis, , 2013 IEEE 13th International Conference on Data Mining, 1283-1288, IEEE, 2013
- A novel subnetwork alignment approach predicts new components of the cell cycle regulatory apparatus in Plasmodium falciparum, , BMC bioinformatics, 14, 1-13, Springer, 2013
- Co-clustering phenome-genome for phenotype classification and disease gene discovery, , Nucleic acids research, 40, 19, e146—e146, Oxford University Press, 2012
- Module-based subnetwork alignments reveal novel transcriptional regulators in malaria parasite Plasmodium falciparum, , BMC systems biology, 6, 1-13, Springer, 2012
- Prediction of novel systems components in cell cycle regulation in malaria parasite by subnetwork alignments, , 2012 IEEE International Conference on Bioinformatics and Biomedicine, 1-6, IEEE, 2012
- Global linear neighborhoods for efficient label propagation, , Proceedings of the 2012 SIAM international conference on data mining, 863-872, SIAM, 2012
- Prioritizing disease genes by bi-random walk, , Advances in Knowledge Discovery and Data Mining: 16th Pacific-Asia Conference, PAKDD 2012, Kuala Lumpur, Malaysia, May 29—June 1, 2012, Proceedings, Part II 16, 292-303, Springer, 2012
- Signed network propagation for detecting differential gene expressions and DNA copy number variations, , Proceedings of the ACM conference on bioinformatics, computational biology and biomedicine, 337-344, 2012
- Approximate subspace pattern mining for mapping copy-number variations, , Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 616-616, 2012
- Sparse group selection on fused lasso components for identifying group-specific DNA copy number variations, , 2012 IEEE 12th International Conference on Data Mining, 665-674, IEEE, 2012, ⭐ Best Student Paper
- Inferring disease and gene set associations with rank coherence in networks, , Bioinformatics, 27, 19, 2692-2699, Oxford University Press, 2011
- Proteases in malaria parasites-a phylogenomic perspective, , Current Genomics, 12, 6, 417-427, Bentham Science Publishers, 2011
- A heterogeneous label propagation algorithm for disease gene discovery, , Proceedings of the 2010 SIAM International Conference on Data Mining, 583-594, SIAM, 2010
- Network propagation models for gene selection, , 2010 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 1-4, IEEE, 2010
- Launching: university partnership for health informatics, , Proceedings of the 1st ACM International Health Informatics Symposium, 521-525, 2010
- Subspace differential coexpression analysis: problem definition and a general approach, , Biocomputing 2010, 145-156, World Scientific, 2010
- Integrative classification and analysis of multiple arrayCGH datasets with probe alignment, , Bioinformatics, 26, 18, 2313-2320, Oxford University Press, 2010
- A hypergraph-based learning algorithm for classifying arraycgh data with spatial prior, , 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, 1-4, IEEE, 2009
- Learning random-walk kernels for protein remote homology identification and motif discovery, , Proceedings of the 2009 SIAM International Conference on Data Mining, 133-144, SIAM, 2009
- Improved prediction of malaria degradomes by supervised learning with SVM and profile kernel, , Genetica, 136, 189-209, Springer, 2009
- Partial profile alignment kernels for protein classification, , 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, 1-4, IEEE, 2009
- A hypergraph-based learning algorithm for classifying gene expression and arrayCGH data with prior knowledge, , Bioinformatics, 25, 21, 2831-2838, Oxford University Press, 2009
- Integrative biomarker discovery for breast cancer metastasis from gene expression and protein interaction data using error-tolerant pattern mining, , 2009
- Robust and efficient identification of biomarkers by classifying features on graphs, , Bioinformatics, 24, 18, 2023-2029, Oxford University Press, 2008
- Learning on weighted hypergraphs to integrate protein interactions and gene expressions for cancer outcome prediction, , 2008 Eighth IEEE international conference on data mining, 293-302, IEEE, 2008
- SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition, , BMC bioinformatics, 8, 1-15, Springer, 2007
- Protein ranking by semi-supervised network propagation, , BMC bioinformatics, 7, 1-9, Springer, 2006
- Identifying remote protein homologs by network propagation, , The FEBS journal, 272, 20, 5119-5128, Wiley Online Library, 2005
- Profile-based string kernels for remote homology detection and motif extraction, , Journal of bioinformatics and computational biology, 3, 03, 527-550, World Scientific, 2005
- Motif-based protein ranking by network propagation, , Bioinformatics, 21, 19, 3711-3718, Oxford University Press, 2005
- Fast string kernels using inexact matching for protein sequences, , Journal of Machine Learning Research, 5, Nov, 1435-1455, 2004
- Inexact matching string kernels for protein classification, , Kernel Methods in Computational Biology, 95-112, MIT Press, Cambridge, MA, 2004
- Protein backbone angle prediction with machine learning approaches, , Bioinformatics, 20, 10, 1612-1621, Oxford University Press, 2004
- Fast kernels for inexact string matching, , Learning Theory and Kernel Machines: 16th Annual Conference on Learning Theory and 7th Kernel Workshop, COLT/Kernel 2003, Washington, DC, USA, August 24-27, 2003. Proceedings, 114-128, Springer, 2003