Publications
Selected Journal Articles & Book Chapters
Selected Conference Publications


Selected Journal Articles & Book Chapters:
  • N. Tran and J. Gao, "OpenOmics: A bioinformatics API to integrate multi-omics datasets and interface with public databases." Journal of Open Source Software, 6(61), p.3249, May 9, 2021.
  • N. Than and J. Gao, "Functional Representation of Large-Scale Heterogeneous RNA Sequences with Integration of Diverse Multi-omics, Interactions, and Annotation Data," Pacific Symposium on Biocomputing (PSB), January 2020.
  • N. Tran and J. Gao, "Layer-stacked Attention for Heterogeneous Network Embedding." arXiv preprint arXiv:2009.08072, Sep 17, 2020.
  • B. Alipourfard and J. Gao, "Solving All Regression Models For Learning Gaussian Networks Using Givens Rotations." arXiv:1901.07643 [cs.NA], Jan 22, 2019.
  • B. Alipourfard and J. Gao, "Renormalized Normalized Maximum Likelihood and Three-Part Code Criteria For Learning Gaussian Networks." arXiv:1810.08749 [cs.LG], Oct 20, 2018. (Also submitted to IEEE Transctions on Knowledge and Data Engineering.)
  • N. Tran, V. Abhyankar, KT. Nguyen, J. Weidanz, and J. Gao, "MicroRNA Dysregulational Synergistic Network: Discovering MicroRNA Dysregulatory Modules Across Subtypes in Non-Small Cell Lung Cancers." BMC Bioinformatics, Accepted 2018.
  • A. Biswas, M. Kang, D. Kim, and J. Gao, "Robust Inductive Matrix Completion Strategy to Explore Associations between LincRNAs and Human Disease Phenotypes." IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018.
  • M. Hasan, S. Peri, V. Sabane, N. Mansur, J. Gao, K. Nguyen, J. Weidanz, S. Iqbal, and V. Abhyankar "One-step fabrication of flexible nanotextured PDMS as a substrate for selective cell capture," Biomedical Physics & Engineering Express, vol. 2, no. 2, pp. 025015, 2018.
  • A. Biswas, D. Kim, M. Kang, C. Ding, and J. Gao, "Stable solution to l-2,1-based robust inductive matrix completion and its application in linking long noncoding RNAs to human diseases," BMC medical genomics, vol. 10, no. 5, pp. 77, 2017.
  • M. Kang, J. Park, D. Kim, A. Biswas, C. Liu and J. Gao, "Multi-Block Bipartite Graph for Integrative Genomic Analysis," IEEE/ACM Transactions on Computational Biology and Bioinformatics, doi: 10.1109/TCBB. 2016.2591521, vol. 14, no. 6, pp. 1350-1358, 2017.
  • M. Kang, L. Tang, and J. Gao, "Computational modeling of phagocyte transmigration for foreign body responses to subcutaneous biomaterial implants in mice," BMC Bioinformatics, (impact factor 2.576), Accepted on Feb 15, 2016.
  • S. Hill, L. Heiser, D. Kim, M. Kang, J. Gao, etc, "Inferring causal molecular networks: empirical assessment through a community-based effort," Nature Methods, (impact factor: 32.072), Accepted on Jan 28, 2016.
  • A. Biswas, M. Kang, D. Kim, C. Ding, B. Zhang, X. Wu and J. Gao, "Inferring disease associations of the long non-coding RNAs through non-negative matrix factorization," Network Modeling Analysis in Health Informatics and Bioinformatics (NetMAHIB), Vol. 4, No. 1, pp. 1-17, 2015.
  • S. Li, J. Nyagilo, D. Dave, W. Wang, B. Zhang, and J. Gao, "Probabilistic partial least squares regression for quantitative analysis of Raman spectra," International Journal of Data Mining & Bioinformatics, Vol. 11, No. 2, pp. 223-243, 2015.
  • M. Kang, C. Zhang, H. Chun, C. Ding, C. Liu and J. Gao, "eQTL epistasis: detecting epistatic effects and inferring hierarchical relationships of genes in biological pathway," Bioinformatics, (current 5 year impact facto: 6.968) doi: 10.1093/bioinformatics/btu727, 2014.
  • D. Kim, J. Wang, C. Liu, and J. Gao, "Inference of SNP-Gene Regulatory Networks by Integrating Gene Expressions and Genetic Perturbations," BioMed Research International (SCI impact factor 2.88), vol. 2014, Article ID 629697, 9 pages, doi:10.1155/2014/629697, 2014.
  • A. Biswas, B. Zhang, X. Wu and J. Gao, "CNCTDiscriminator: Coding and Non-coding Transcript Discriminator-An Excursion through Hypothesis Learning and Ensemble Learning Approaches," Journal of Bioinformatics and Computational Biology, vol. 11, no. 5, id 1342002, 2013.
  • S. Li, J. Nyagilo, D. Dave, and J. Gao, "Models and Methods for Quantitative Analysis of Raman Spectra," IEEE Journal of Biomedical and Health Informatics, vol. 18, no. 2, pp. 525-536, 2014.
  • S. Li, J.O. Nyagilo, D.P. Dave and J. Gao, "Continuous Wavelet Transform based PLS Regression method for Quantitative Analysis of Raman Spectra", IEEE Transactions on Nanobioscience, vol. 12, no. 3, pp. 214-221, 2013
  • S. Li, J. Nyagilo, D. Dave, B. Zhang, and J. Gao, "Eigenspectra, a robust regression method for multiplexed surface enhanced Raman spectra analysis," International Journal of Data Mining & Bioinformatics, vol. 7, no. 4, pp. 358-75, 2012.
  • D. Kim, X. Wang, C. Yang, and J. Gao, "A Framework for Personalized Medicine with Reverse Phase Protein Array and Drug Sensitivity," Proteome Science (impact factor: 2.49), 10(Suppl 1):S13, 2012
  • J.H. Oh and J. Gao, "Fast kernel discriminant analysis for classification of liver cancer mass spectra," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. 6, pp. 1522-1534, 2011.
  • N. Thakoor and J. Gao, "Branch-and-bound for model selection and its computational complexity," IEEE Transactions on Knowledge and Data Engineering, vol. 23, no. 5, pp. 655-668, 2011.
  • D. Kim, X. Wang, C. Yang, and J. Gao, "Learning biological network using mutual information and conditional independence," BMC Bioinformatics, 11(Suppl 3):S9, 2010.
  • N. Thakoor, J. Gao, and V. Devragen, "Multibody structure-and-motion segmentation by branch-and-bound model selection," IEEE Transactions on Image Processing, Volume 19 Issue 6, June 2010.
  • J.H. Oh and J. Gao, "A kernel-based approach for detecting outliers of high-dimensional biological data," BMC Bioinformatics (impact factor: 3.49), 10(Suppl 4): S7, April 2009.
  • J. Oh, P. Gurnani, L. Knowles, J. Schorge, K. Rosenblatt, and J. Gao, "An extended Markov blanket approach to proteomic biomarker detection from high-resolution mass spectrometry data," IEEE Transactions on Information Technology in Biomedicine, vol. 13, Issue 2, pp. 195-206, March 2009.
  • J. Oh, Y. Kim, P. Gurnani, K. Rosenblatt, and J. Gao, "Biomarker selection and sample prediction in multi-category disease on MALDI-TOF data," Bioinformatics, (impact factor: 4.894), vol. 24, no. 16, pp. 1812-1818, 2008.
  • N. Thakoor, J. Gao, and V. Devarajan, "Multi-stage branch-and-bound merging for planar surface segmentation in disparity Space," IEEE Transactions on Image Processing, vol. 17, Issue 11, pp. 2217-2226, Nov. 2008.
  • Q. Wen, K. Luby-Phelps, and J. Gao, "Tracking multiple subcellular structures using a sequential Monte Carlo approach," International Journal of Data Mining & Bioinformatics, vol. 3, no. 3, 2009.
  • S. Pan, J. Rush, E. R. Peskind, D. Galasko, K. Chung, J. Quinn, J. Jankovic, J. B. Leverenz, C. Zabetian, C. Pan, Y. Wang, J. Oh, J. Gao, J. Zhang, T. Montine and J. Zhang, "Application of targeted quantitative proteomics analysis in human cerebrospinal fluid using an LC MALDI TOF/TOF platform," Journal of Proteome Research, (impact factor: 5.151), vol. 7, Issue 2, pp. 720-730, Feb. 2008.
  • S. Gopinath, Q. Wen, N. Thakoor, K. Luby-Phelps, J. Gao, "A statistical approach for intensity loss compensation of confocal microscopy images," Journal of Microscopy (Blackwell publishing), vol. 230, pp. 143-159, 2008.
  • N. Thakoor, J. Gao and S. Jung, "Hidden Markov model based weighted likelihood discriminant for 2D shape classification," IEEE Transactions on Image Processing, vol. 16, Issue 11, pp. 2707 - 2719, Nov. 2007.
  • J. Xue, G. Arbique, D. Hatef, S. Brown, M. Saint-Cyr, J. Gao, "Four-dimensional vascular tree reconstruction using moving grid deformation,"  Academic Radiology, vol. 14, Issue 12, pp. 1540-1553, Dec. 2007.
  • H. Shu, Q. Liang, and J. Gao, "Wireless sensor network lifetime analysis using interval type-2 fuzzy logic systems," IEEE Transactions on Fuzzy Systems, vol. 16, no. 2, pp. 416-427, 2008.
  • P. Machalak, Y. Kim, and J. Gao, "Computational challenges of microarray analysis," in Computational Genomics: Current Methods, Horizon Scientific Press, Hethersett, UK, 2007.
  • J. Oh, A. Nandi, P. Gurnani, L. Knowles, and J. Schorge, K. Rosenblatt, and J. Gao, "Identifying biomarkers to predict early relapse in ovarian cancer," Journal of Bioinformatics and Computational Biology (JBCB), vol.4, no.6, 2006. 
  • J. Gao, "New discoveries of image display size on observer performance," Academic Radiology (Elsevier), vol.13, no.4, pp.407-408, 2006.
  • J. Oh and J. Gao, "A two-way parallel searching for peptide identification via tandem mass spectrometry," Special Issue on Bioinformatics, Engineering Letters, (invited paper) accepted in June 2006.
  • J. Gao, A. Kosaka, and A. Kak, "A multi-Kalman filtering approach for video tracking of human-delineated objects in cluttered environments," Computer Vision and Image Understanding, vol. 99, no. 1, pp. 1-57, 2005.
  • K. Nojima, S. Brown, C. Acikel, J. Janis, G, Arbique, T. Abulezz, J. Gao, Q. Wen, K. Kurihara, R. Rohrich, "Defining vascular supply and territory of thinned perforator flaps: Part II. superior gluteal artery perforator flap," Plastic and Reconstructive Surgery, vol. 118, no. 6, pp. 1338-1348, 2006.
  • J. Oh, J. Gao, A. Nandi, P. Gurnani, L. Knowles, J. Schorge, and K. Rosenblatt, "Diagnosis of early relapse in ovarian cancer using serum proteomic profiling," Genome Informatics, vol.16, no. 2, pp.195-204, 2005.
  • N. Thakoor and J. Gao, "Occlusion resistant shape classifier based on warped optimal path matching," International Transactions on Communication and Signal Processing, vol. 9, no. 1, 2006.
  • J. Gao, A. Kosaka, and A. Kak, "A deformable model for human CT liver extraction," Academic Radiology (Elsevier), vol. 12, no.9, pp. 1178-1189, 2005
  • J. Gao and L. Waite, "Patellofemoral joint study via image processing," Biomedical Sciences Instrumentation, pp. 151-160, vol. 32, 1996.

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Selected Conference Publications:
  • B. Alipourfard and J. Gao, "Inference of Direct Causal Influences for Biomedical Data," 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (19.9 % regular paper acceptance rate), Dec 7-8, 2022.
  • F. Khoshghalbvash and J. Gao, "Integrative Feature Ranking by Applying Deep Learning on Multi Source Genomic Data," ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), Sept 7-10. 2019.," Proceedings of IEEE International Conference on Bioinformatics & Biomedicine (IEEE BIBM 2015)(regular paper acceptance rate 19%, 68/346), Washington D.C., USA, Nov. 9-12, 2015.
  • D. Kim, M. Kang, A. Biswas, C. Liu, and J. Gao, "Integrative approach for inference of gene regulatory networks using lasso-based random featuring and application to Psychiatric disorders," Proceedings of IEEE International Conference on Bioinformatics & Biomedicine (IEEE BIBM 2015)(regular paper acceptance rate 19%, 68/346), Washington D.C., USA, Nov. 9-12, 2015.
  • M. Kang, J. Park, D. Kim, A. Biswas, C. Liu, and J. Gao, "An Integrative Genomic Study for Multimodal Genomic Data Using Multi-Block Bipartite Graph," Proceedings of IEEE International Conference on Bioinformatics & Biomedicine (IEEE BIBM 2015)(regular paper acceptance rate 19%, 68/346), Washington D.C., USA, Nov. 9-12, 2015.
  • D. Kim, M. Kang, C. Liu, and J. Gao, "Integration of DNA Methylation, Copy Number Variation, and Gene Expression for Gene Regulatory Network Inference and Application to Psychiatric Disorders," Proceedings of IEEE 14th International Conference on BioInformatics and BioEngineering (IEEE BIBE 2014), Boca Raton, USA, Nov. 10-12, 2014.
  • M. Kang, D. Kim, C. Liu, and J. Gao, "Multi-Block and Multi-Task Learning for Integrative Genomic Study," Proceedings of IEEE 14th International Conference on BioInformatics and BioEngineering (IEEE BIBE 2014), Boca Raton, USA, Nov. 10-12, 2014.
  • A. Biswas, J. Gao, B. Zhang and X. Wu, "NMF-based LncRNA-Disease Association Inference and Bi-clustering," Proceedings of IEEE 14th International Conference on BioInformatics and BioEngineering (IEEE BIBE 2014), Boca Raton, USA, Nov. 10-12, 2014. (Received the best paper award in the Bioinformatics category)
  • M. Kang, S. Li, C. Liu, and J. Gao, "eQTL Epistasis: Detecting Complex Interaction Effects between Multiple Loci from eQTL Data," IEEE International Conference on Bioinformatics & Biomedicine (IEEE BIBM) (regular paper acceptance rate 19.6%), Shanghai, China, Dec. 18-21, 2013.
  • D. Kim, C. Liu, and J. Gao, "Inference of gene regulatory networks by integrating gene expression and genetic perturbations," IEEE International Conference on Bioinformatics and Biomedicine 2013 (IEEE BIBM) (regular paper acceptance rate 19.6%), Shanghai, China, Dec 18-21, 2013.
  • A. Biswas, B. Zhang, X. Wu and J. Gao, "QLZCClust: Quaternary Lempel-Ziv Complexity based Clustering of the RNA-seq Read Block Segments," The 13th IEEE International Conference on Bioinformatics and Bioengineering (IEEE BIBE 2013), Chania, Greece, 10-13 November 2013.
  • M. Kang, S. Li, D. Kim, C. Liu, and J. Gao, "eQTL Mapping Study via Regularized Sparse Canonical Correlation Analysis," IEEE International Conference on Machine Learning and Applications (IEEE ICMLA) (regular paper acceptance rate 27%), Miami, FL, Dec. 4-7, 2013.
  • S. Li, J. Gao, J.O. Nyagilo and D.P. Dave, "Probabilistic Partial Least Square Regression: A Robust Model for Quantitative Analysis of Raman Spectroscopy Data," IEEE International Conference on Bioinformatics & Biomedicine (IEEE BIBM) (regular paper acceptance rate 19.4%), Atlanta, GA, Nov 12-15, 2011.
  • D. Kim, X. Wang, C. Yang, and J. Gao, "A Framework for Personalized Medicine with Reverse Phase Protein Array and Drug Sensitivity and Drug Sensitivity," IEEE International Conference on Bioinformatics & Biomedicine (IEEE BIBM), (19.7 % short paper acceptance rate), Atlanta, GA, Nov 12-15, 2011.
  • S. Li, K. Luby-Phelps, B. Zhang, X. Wu, and J. Gao, "Subcellular Particles Tracking in Time-lapse Confocal Microscopy Images," Proceedings of IEEE Engineering in Medicine and Biology Society (IEEE EMBC), Boston, MA, Aug 30-Sept 3, 2011.
  • D. Kim, C. Yang, X. Wang, B. Zhang, X. Wu, and J. Gao, "Discovery of Lung Cancer Pathways using Reverse Phase Protein Microarray and Prior-Knowledge based Bayesian Networks," Proceedings of IEEE Engineering in Medicine and Biology Society (IEEE EMBC), Boston, MA, Aug 30-Sept 3, 2011.
  • M. Kang, J. Gao, and L. Tang, "Nonlinear RANSAC Optimization for Parameter Estimation with Applications to Phagocyte Transmigration," Proceedings of IEEE International Conference on Machine Larning and Applications (IEEE ICMLA), Honolulu, HI, Dec 18-21 2011.
  • M. Kang, J. Gao, L. Tang, "Computational modeling of phagocyte transmigration during biomaterial-mediated foreign body responses," IEEE International Conference on Bioinformatics & Biomedicine (IEEE BIBM), pp. 609-612, Hong Kong, Dec 18-21, 2010.
  • S. Li, J. Gao, J.O. Nyagilo and D.P. Dave, "Eigenspectra, A Robust Regression Method For Multiplexed Raman Spectra Analysis", IEEE International Conference on Bioinformatics & Biomedicine (IEEE BIBM) (regular paper acceptance rate 17.2%), pp. 525-530, , Hong Kong, Dec 18-21,2010.
  • D. Kim, J. Gao, C. Yang, "Learning Proteomic Network Structure by a New Hill Climbing Algorithm" Proceedings of IEEE Symposium of Bioinformatics and Bioengineering (IEEE BIBE), pp. 191-196, Philadelphia, PA, May 31-Jun 3, 2010.
  • H. Iwaki, A. Kosaka, S. Li, J. Gao, "Motion detection for subcellular structure trafficking," Proceedings of IEEE Engineering in Medicine and Biology Society (IEEE EMBC), pp. 6722-6725, Minneapolis, MN, Sept 2-6, 2009.
  • N. Thakoor and J. Gao, "Branch-and-bound hypothesis selection for two-view multiple structure and motion segmentation," Proceedings of IEEE International Conference on Computer Vision and Pattern Recognition (IEEE CVPR), Anchorage, AK, June 23-28, 2008.
  • Q. Wen and J. Gao, "Tracking interacting subcellular structures by sequential Monte Carlo method," Proceedings of IEEE Engineering in Medicine and Biology Society (IEEE EMBC), pp. 4185-4188, Lyon, France, Aug 22-26, 2007.
  • J. Xue, J. Gao, and L. Tang, "Phagocyte transmigration modeling using system dynamic controls," Proceedings of IEEE Symposium of Bioinformatics and Bioengineering (IEEE BIBE)(full paper acceptance rate < 12%, 60/500+), pp. 480-485, Boston, MA, Oct 14-17, 2007
  • J. Oh, Y. Kim, P. Gurnani, K. Rosenblatt, and J. Gao, "Biomarker selection for predicting Alzheimer disease using high-resolution MALDI-TOF data," Proceedings of IEEE Symposium of Bioinformatics and Bioengineering (IEEE BIBE) (full paper acceptance rate < 12%, 60/500+), pp. 464-471, Boston, MA, Oct 14-17, 2007.
  • J. Xue, J. Gao, G. Arbique, S. Brown, and M. Cyr-Saint, "Three dimensional analysis of the vascular perfusion for anterolateral thigh perforator flaps," Proc. of SPIE Medical Imaging, San Jose, CA, Feb 11-16, 2007.
  • Y. Kim and J. Gao, "Unsupervised gene selection for high dimensional data," Proceedings of IEEE Symposium of Bioinformatics and Bioengineering (IEEE BIBE) (38.8% regular paper acceptance rate), pp. 227-232, Washington DC, Oct 16-18, 2006.
  • Q. Wen, J. Gao, and K. Luby-Phelps, "Markov chain Monte Carlo data association for protein clusters tracking," Proceedings of IEEE International Conference on Pattern Recognition (IEEE ICPR), (15% oral acceptance rate), vol. 1, pp. 1030-1033, Hong Kong, Aug. 20-24, 2006.
  • J. Oh, A. Nandi, P. Gurnani, L. Knowles, J. Schorge, K. Rosenblatt, and J. Gao, "A hybrid feature selection for MALDI-TOF mass spectrometry data analysis," Proceedings of IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (IEEE CIBCB), pp. 36-43, Toronto, Canada, Sept 28-29, 2006.
  • N. Thakoor, J. Gao, Q. Wen, and S. Jung, "Occlusion resistant shape classifier based on warped optimal path matching," Proceedings of IEEE International Conference on Pattern Recognition (IEEE ICPR) (15% oral acceptance rate), vol. 2, pp. 60-63, Hong Kong, Aug. 20-24, 2006.
  • Q. Wen, J. Gao, and K. Luby-Phelps, "Feature selection, matching, and evaluation for subcellular structure tracking," Proceedings of IEEE Engineering in Medicine and Biology Society (IEEE EMBC), pp. 3013-3016, New York, USA, Aug. 30-Sept. 3, 2006.
  • Y. Kim, J. Gao, and P. Michalak, "A new maximum-relevance criterion for significant gene selection," Lecture Notes in Bioinformatics, (IEEE Workshop on Pattern Recognition in Bioinformatics, Hong Kong, Aug 20, 2006), vol.4146, pp. 71-80, Springer Verlag, 2006.
  • Q. Wen, J. Gao, A. Kosaka, H. Iwaki, K. Luby-Phelps, and D. Mundy, "A particle filter framework using optimal importance function for protein molecules tracking," Proc. IEEE International Conference on Image Processing (IEEE ICIP) (acceptance rate 46%), vol.1, pp.1161-1164, Genova, Sept 11-14, 2005.
  • J. Oh and J. Gao, "Peptide identification by tandem mass spectra: an efficient parallel searching," Proceedings of IEEE Symposium on Bioinformatics and Bioengineering (IEEE BIBE) (full paper acceptance rate 18%, 30 out of 164,), pp.161-168, Minneapolis, MN, Oct 19-21, 2005.
  • N. Thakoor and J. Gao, "Shape classification based on generalized Gaussian descent method with hidden Markov model descriptor," Proceedings of IEEE International Conference on Computer Vision (IEEE ICCV) (blind review, acceptance rate: 20.4%, 245 out of 1200), vol.1, pp.495-502, Beijing, China, Oct 15-21, 2005.
  • J. Oh, J. Gao, A. Nandi, P. Gurnani, L. Knowles, J. Schorge, and K. Rosenblatt, "Multicategory classification using extended SVM-RFE and Markov blanket on SELD I-TOF mass Spectrometry data,"Proceedings of IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (IEEE CIBCB), pp. 1-7, San Diego, CA, Nov 14-15, 2005.
  • N. Thakoor and J. Gao, "Automatic video object shape extraction and its classification with camera in motion," Proc. IEEE International Conference on Image Processing (IEEE ICIP), (acceptance rate 46%), vol.3, pp.437-440, Genova, Sept 11-14, 2005.
  • Q. Wen and J. Gao, "Shape-based 3D vascular tree extraction for perforator flaps," Proc. of SPIE Medical Imaging, vol. 5747, pp.1855-1863, San Diego, CA, Feb 12-17, 2005.
  • Y. B. Kim, J. H. Oh, and J. Gao, "Emerging pattern based subspace clustering of microarray gene expression using mixture models," Proceedings of International Conference on Bioinformatics and its Applications (ICBA) (acceptance rate 28%), pp. 13-24, Fort Lauderdale, FL, Dec 16-19, 2004.
  • J. H. Oh, Y.B. Kim, and J. Gao, "A two-way searching algorithm for De Novo peptide sequencing via tandem mass spectrometry," Proceedings of International Conference on Bioinformatics and its Applications (ICBA) (acceptance rate 28%), pp. 402-413, Fort Lauderdale, FL, Dec 16-19, 2004.

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