Articles & Book Chapters

 

Refereed Journal Publications:

89. Y. Li, S. Wang, R. Umarov, B. Xie, M. Fan, L. Li, and X. Gao. DEEPre: sequence-based enzyme EC number prediction by deep learning. Bioinformatics. In press.
88. R. Han, F. Zhang, and X. Gao. A fast fiducial marker tracking model for fully automatic alignment in electron tomography. Bioinformatics. In press.
87. H. Dai, R. Umarov, H. Kuwahara, Y. Li, L. Song, and X. Gao. Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape. Bioinformatics. (2017) 33(22): 3575-3583.
86. T. Rapakoulia, X. Gao, Y. Huang, M. de Hoon, M. Okada-Hatakeyama, H. Suzuki, E. Arner. Genome-scale regression analysis reveals a linear relationship for promoters and enhancers after combinatorial drug treatment. Bioinformatics. In press.
85. M. Alzahrani, H. Kuwahara, W. Wang, and X. Gao. Gracob: a novel graph-based constant-column biclustering method for mi. ning growth phenotype data. Bioinformatics. (2017). 33(16): 2523-2531.
84. P. Yang, P. Zhao, and X. Gao. Robust online multi-task learning with correlative and personalized structures. IEEE Transactions on Knowledge and Data Engineering (TKDE). (2017). 29(11): 2510-2521.
83. S. Wu, D. Wang, J. Liu, Y. Feng, J. Weng, Y. Li, X. Gao, J. Liu, and W. Wang. The dynamic multisite interactions between two intrinsically disordered proteins. Angewandte Chemie. (2017). 56(26): 7515-7519.
82. H. Kuwahara, X. Cui, R. Umarov, R. Grunberg, C. Myers, and X. Gao. SBOLme: a repository of SBOL parts for metabolic engineering. ACS Synthetic Biology. (2017). 6(4): 732-736.
81. J. Wang, I. Tsang, X. Cui, Z. Lu, and X. Gao. Multi-instance dictionary learning via multivariate performance measure optimization. Pattern Recognition. (2017) 66: 448-459.
80. M. Fan, T. He, P. Zhang, H. Cheng, J. Zhang, X. Gao, and L. Li. Diffussion-weighted imaging features of breast tumours and the surrounding stroma reflect intrinsic heterogeneous characteristics of molecular subtypes in breast cancer. NMR in Biomedicine. In press.
79. H. Kuwahara, R. Umarov, I. Almasri, and X. Gao. ACRE: absolute concentration robustness exploration in module-based combinatorial networks. Synthetic Biology. (2017) 2(1): ysx001.
78. R. Han, X. Wan, Z. Wang, Y. Hao, Y. Chen, X. Gao, Z. Liu, F. Ren, F. Sun, and F. Zhang. AuTom: a novel automatic platform for electron tomography reconstruction. Journal of Structural Biology. (2017). 199(3): 196-208. 
77. A. Abdel-Haleem, N. Lewis, N. Jamshidi, K. Mineta, X. Gao, and T. Gojobori. The emerging facets of noncancerous Warburg effect. Frontiers in Endocrinology, section Cellular Endocrinology. In press.
76. J. Wang, X. Cui, G. Yu, L. Guo, and X. Gao. When sparse coding meets ranking: a joint framework for learning sparse coding and ranking scores. Neural Computing and Applications. In press.
75. S. Najibi, M. Maadooliat, L. Zhou, J. Huang, and X. Gao. Protein structure classification and loop modeling using multiple Ramachandran distributions. Computational and Structural Biotechnology Journal. (2017) 15: 243-254.
74. J. Weng, S. Gu, X. Gao, X. Huang, and W. Wang. Maltose binding protein effectively stabilizes the partially closed conformation of the ATP-binding cassette transporter MalFGK2. Physical Chemistry Chemical Physics. (2017). 19: 9366-9373.
73. O. Motwalli, M. Essack, B. Jankovic, B. Ji, X. Liu, H. Rahman, R. Hoehndorf, X. Gao, S. Arold, K. Mineta, J. Archer, T. Gojobori, I. Mijakovic, and V. Bajic. In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria. BMC Genomics. (2017) 18: 33. 
72. S. Lftikhar, S. Khan, A. Bilal, S. Manzoor, M. Abdullah, A. Emwas, S. Sioud, X. Gao, G. Chotana, A. Faisal, and R. Saleem. Synthesis and evaluation of modified chalcone based p53 stabilizing agents. Bioorganic & Medicinal Chemistry Letters. (2017) 27(17):4101-4106.
71. Y. Feng, L. Zhang, S. Wu, Z. Liu, X. Gao, X. Zhang, M. Liu, J. Liu, X. Huang, and W. Wang. Comformational dynamics of apo-GlnBP revealed by experimental and computational analysis. Angewandte Chemie. (2016) 55: 13990-13994.
70. X. Cui, Z. Lu, S. Wang, J. Wang, and X. Gao. CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction. Bioinformatics. (2016) 32(12): 332-340.
69. H. Kuwahara, M. Alazmi, X. Cui, and X. Gao. MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind. Nucleic Acids Research. (2016) 44(W1): W217-25. [Highlighted by PHYS.ORG: https://phys.org/news/2016-07-metabolic-route-explorer-optimize-pathways.html]
68. Z. Lu, Z. Fu, T. Xiang, P. Han, L. Wang, and X. Gao. Learning from weak and noisy labels for semantic segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence (TPAMI). (2016) 39(3): 486-500.
67. L. Da, F. Pardo-Avila, L. Xu, D. Silva, L. Zhang, X. Gao, D. Wang, and X. Huang. Bridge helix bending promoters RNA polymerase II backtracking through a critical and conserved Threonine residue. Nature Communications. (2016) 7:11244. [Highlighted by EurekAlert!: https://www.eurekalert.org/pub_releases/2016-05/hkuo-srh050316.php]
66. A. Salhi, M. Essack, A. Radovanvic, B. Marchand, S. Bougouffa, A. Antunes, M. Simoes, F. Lafi, O. Motwalli, A. Bokhari, T. Malas, S. Al Amoudi, G. Othoum, I. Alam, K. Mineta, X. Gao, R. Hoehndorf, J. Archer, T. Gojobori, and V. Bajic. DESM: Portal for microbial knowledge exploration systems. Nucleic Acids Research. (2016) 44(D1): D624-D633.
65. L. Zhu, H. Jiang, F.K. Sheong, X. Cui, Y. Wang, X. Gao, and X. Huang. Understanding the core of RNA interference: the dynamic aspects of Argonaute-mediated processes. Progress in Biophysics and Molecular Biology. (2017). 128: 39-46.
64. E. Smirnova, J. Kwan, R. Siu, X. Gao, G. Zoidl, B. Demeler, V. Saridakis, and L. Donaldson. A new mode of SAM domain mediated oligomerization observed in the CASKIN2 neuronal scaffolding protein. Cell Communication and Signaling. (2016) 14:17.
63. F. Batool, A. Emwas, X. Gao, M. Munawar, and G. Chotana. Synthesis and Suzuki cross-coupling reactions of 2,6-Bis(trifluoromethyl)pyridine-4-boronic acid pinacol ester. Synthesis. (2017) 49(6): 1327-1334.
62. X. Cui, and X. Gao. K-nearest uphill clustering in the protein structure space. Neurocomputing. (2017) 220: 52-59.
61. L. Zhu, H. Jiang, F. K. Sheong, X. Cui, X. Gao, Y. Wang, and X. Huang. A flexible domain-domain hinge promotes an induced-fit dominant mechanism for the loading of guide-DNA into Argonaute protein in Thermus Thermophilus. Journal of Physical Chemistry B. (2016) 120(10): 2709-2720.
60. C. Fujii, H. Kuwahara, G. Yu, L. Guo, and X. Gao. Learning gene regulatory networks from gene expression data using weighted consensus. Neurocomputing. (2017) 220: 23-33.
59. A. Emwas, R. Roy, R. McKay, D. Ryan, L. Brennan, L. Tenori, C. Luchinat, X. Gao, A. Zeri, N. Gowda, D. Raftery, C. Steinbeck, R. Salek, and D. Wishart. Recommendations and standardization of biomarker quantification using NMR-based metabolomics with particular focus on urinary analysis. Journal of Proteome Research. (2016) 15(2): 360-373.
58. T. Ryu, L. Seridi, L. Moitinho-Silva, M. Otates, Y. Liew, H. Marvromatis, X. Wang, A. Haywood, F. Lafi, M. Kupresanin, R. Sougrat, M. Alzahrani, E. Giles, Y. Ghoseh, C. Schunter, S. Baumgarten, M. Berumen, X. Gao, M. Aranda, S. Foret, J. Gough, C. Voolstra, U. Hentschel, and T. Ravasi. Hologenome analysis of two marine sponges with different microbiomes. BMC Genomics. (2016) 17:158.
57. H. Naveed, U. Hameed, D. Harrus, W. Bourguet, S. Arold, and X. Gao. An integrated structure- and system-based framework to identify new targets of metabolites and known drugs. Bioinformatics. (2015) 31(24): 3922-3929. [Highlighted by Nature Middle East: http://www.natureasia.com/en/nmiddleeast/article/10.1038/nmiddleeast.2015.153]
56. H. Kuwahara, S. Arold, and X. Gao. Beyond initiation-limited translational bursting: the effects of burst size distributions on the stability of gene expression. Integrative Biology. (2015) 7:1622-1632. 
55. M. Maadooliat, L. Zhou, S. Najibi, X. Gao, and J. Huang. Collective estimation of multiple bivariate density functions with application to angular-sampling-based protein loop modeling. Journal of the American Statistical Association (JASA). (2015) 111(513): 43-56.
54. H. Jiang, F. K. Sheong, L. Zhu, X. Gao, J. Bernauer, and X. Huang. Markov state models reveal a two-step mechanism of miRNA loading into the human Argonaute protein: selective binding followed by structural re-arrangement. PLOS Computational Biology. (2015) 11(7): e1004404.
53. X. Cui, H. Naveed, and X. Gao. Finding optimal interaction interface alignments between biological complexes. Bioinformatics. (2015) 31(12): i133-i141.
52. M. Fan, H. Kuwahara, X. Wang, S. Wang, and X. Gao. Parameter estimation methods for gene circuit modeling from time-series mRNA data: a comprative study. Briefings in Bioinformatics. (2015) 16(6): 987-999.
51. I. Alabdulmohsin, M. Cisse, X. Gao, and X. Zhang. Large margin classification with indefinite similarities. Machine Learning. (2016) 103(2): 215-237.
50. P. Chen, B. Wang, J. Zhang, X. Gao, J. Li, and J. Xia. A sequence-based dynamic ensemble learning system for protein ligand-binding site prediction. IEEE/ACM Transactions on Computational Biology and Bioinformatics. (2015) 13(5): 901-912.
49. F. Batool, S. Perveen, A. Emwas, S. Sioud, X. Gao, M. Munawar, and G. Chotana. Synthesis of fluoroalkoxy substituted aryl boronic esters by iridium catalyzed aromatic C-H borylation. Organic Letters. (2015) 17(17): 4256-9.
48. S. Sun, X. Wang, X. Gao, L. Ren, X. Sun, D. Bu, and K. Ning. Preprocess and condensation of Raman spectrum for single-cell phenotype analysis. BMC Bioinformatics. (2015) 16(S18): S15.
47. C. Cannistraci, A. Abbas, and X. Gao. Median modified Wiener filter for nonlinear adaptive spatial denoising of protein NMR multidimensional spectra. Scientific Reports. (2015) 5:8017.
46. A. Khamis, M. Essack, X. Gao, and V. Bajic. Distinct profiling of antimicrobial peptide families. Bioinformatics. (2015) 31(6): 849-856.
45. J. Wang, and X. Gao. Max-min distance nonnegative matrix factorization. Neural Networks. (2015) 61: 75-84.
44. J. Wang, Y. Wang, B.-Y. Jing, and X. Gao. Regularized maximum correntropy machine. Neurocomputing. (2015) 160: 85-92.
43. J. Wang, Y. Wang, S. Zhao, and X. Gao. Maximum mutual information regularized classification. Engineering Applications of Artificial Intelligence. (2015). 37: 1-8.
42. J. Wang, J. Huang, Y. Sun, and X. Gao. Feature selection and multi-kernel learning for adaptive graph regularized nonnegative matrix factorization. Expert Systems with Applications. (2015). 42(3): 1278-1286.
41. X. Hou, Y. Liu, H. Liu, X. Chen, M. Liu, H. Che, F. Guo, C. Wang, D. Zhang, J. Wu, X. Chen, C. Shen, C. Li, F. Peng, Y. Bi, Z. Yang, G. Yang, J. Ai, X. Gao, and S. Zhao. PERK silence inhibits glioma cell growth under low glucose stress by blockage of p-AKT and subsequent HK2's mitochondria translocation. Scientific Reports. (2015) 5:9065.
40. P. Chen, J. Huang, and X. Gao. LigandRFs: random forest ensemble to identify ligand-binding residues from sequence information alone. BMC Bioinformatics. (2015) S15: S4.
39. X. Wang, H. Kuwahara, and X. Gao. Modeling DNA affinity landscape through two-round support vector regression with weighted degree kernels. BMC Systems Biology. (2014). 8(S5): S5. 
38. G. Yang, C. Li, X. Chen, Y. Liu, D. Han, X. Gao, K. Kawamoto, and S. Zhao. Large capillary hemangioma of the temporal bone with a dural tail sign: A case report. Oncology Letters. (2014). 8(1): 183-186.
37. A. Abbas, X. Guo, B. Jing, and X. Gao. An automated framework for NMR resonance assignment through simultaneous slice picking and spin system forming. Journal of Biomolecular NMR. (2014). 59(2): 75-86.
36. T. Alam, M. Alazmi, X. Gao, and S. Arold. How to find a Leucine in a Haystack? Structure, ligand recognition and regulation of Leucine-Aspartic acid (LD) motifs. Biochemical Journal. (2014). 460(3): 317-329.
35. J. Wang, Y. Sun and X. Gao. Sparse structure regularized ranking. Multimedia Tools and Applications. (2015) 74(2): 635-654.
34. D. Zhang, G. Yang, X. Chen, C. Li, L. Wang, Y. Liu, D. Han, H. Liu, X. Hou, W. Zhang, C. Li, Z. Han, X. Gao, and S. Zhao. mir-300 promotes self-renewal and inhibits the differentiation of glioma stem-like cells. Journal of Molecular Nueroscience. (2014). 53(4): 637-644.
33. J. Wang, H. Bensmail, and X. Gao. Feature selection and multi-kernel learning for sparse representation on manifold. Neural Networks. (2014). 51: 9-16.
32. Y. Cheng, X. Gao, and F. Liang. Bayesian peak picking for NMR spectra. Genomics, Proteomics, and Bioinformatics. (2014). 12(1): 39-47.
31. J. Wang, and X. Gao. Beyond cross-domain learning: multiple-domain nonnegative matrix factorization. Engineering Applications of Artificial Intelligence. (2014). 28:181-189.
30. J. Wang, Y. Shi, and X. Gao. Semi-supervised transductive hot spot predictor working on multiple assumptions. Current Bioinformatics. (2014). 9(3): 258-267.
29. G. Yang, D. Han, X. Chen, D. Zhang, L. Wang, C. Shi, W. Zhang, C. Li, X. Chen, H. Liu, D. Zhang, J. Kang, F. Peng, Z. Liu, J. Qi, X. Gao, J. Ai, C. Shi, and S. Zhao. MiR-196a exerts its oncogenic effect in glioblastoma multiforme by inhibition of IkBa both in vitro and in vivo. Neuro-Oncology. (2014). 16(5): 652-661.
28. H. Kuwahara, and X. Gao. Stochastic effects as a force to increase the complexity of signaling networks. Scientific Reports. (2013). 3:2297. doi: 10.1038/srep02297.
27. H. Kuwahara, M. Fan, S. Wang, and X. Gao. A framework for scalable parameter estimation of gene circuit models using structural information. Bioinformatics. (2013). 29(13): i98-i107. [Highlighted by Nature Middle East: http://www.nature.com/nmiddleeast/2013/130731/full/nmiddleeast.2013.118.html]
26. B. Xie, B. Jankovic, V. Bajic, L. Song, and X. Gao. Poly(A) motif prediction using spectral latent features from human DNA sequences. Bioinformatics. (2013). 29(13): i316-i325.
25. J. Wang, H. Bensmail, and X. Gao. Joint learning and weighting of visual vocabulary for bag-of-feature based tissue classification. Pattern Recognition. (2013). 46(12): 3249-3255. [Highlighted by Advances in Engineering: http://advanceseng.com/electrical-engineering/joint-learning-weighting-visual-vocabulary-bag-feature-based-tissue-classification/]
24. J. Wang, H. Bensmail, and X. Gao. Multiple graph regularized nonnegative matrix factorization. Pattern Recognition (2013). 46(10): 2840-2847.
23. P. Chen, J. Li, L. Wong, H. Kuwahara, J. Huang, and X. Gao. Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences. PROTEINS. (2013). 81(8): 1351-1362.
22. J. Wang, X. Wang, and X. Gao. Non-negative matrix factorization by maximizing correntropy for cancer clustering. BMC Bioinformatics (2013). 14:107.
21. X. Gao. Recent advances in computational methods for nuclear magnetic resonance data processing. Genomics, Proteomics, and Bioinformatics (2013). 11(1):29-33. doi: 10.1016/j.gpb.2012.12.003.
20. A. Abbas, X. Kong, Z. Liu, B. Jing, and X. Gao. Automatic peak selection by a Benjamini-Hochberg-based algorithm. PLOS ONE (2013). 8(1): e53112. doi:10.1371/journal.pone.0053112.
19. J. Wang, H. Bensmail, N. Yao, and X. Gao. Discriminative Sparse Coding on Multi-Manifolds. Knowledge-Based Systems. (2013). 54: 199-206.
18. L. Dai, X. Gao, Y. Guo, J. Xiao and Z. Zhang. Bioinformatics clouds for big data manipulation. Biology Direct (2012). 7: 43. doi:10.1186/1745-6150-7-43.
17. M. Maadooliat, X. Gao, and J. Huang. Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles. Briefings in Bioinformatics (2012). 14(6): 724-736.
16. M. Fan, K. Wong, T. Ryu, T. Ravasi, and X. Gao. SECOM: a novel hash seed and community detection-based approach for genome-scale protein domain identification. PLOS ONE (2012), 7(6): e39475. doi:10.1371/journal.pone.0039475. [Source code]
15. M. Messih, M. Chitale, V. Bajic, D. Kihara and X. Gao. Protein domain recurrence and order can enhance prediction of protein functions. Bioinformatics (2012), 28(18): i444-i450.
14. X. Gao. Mathematical approaches to the NMR peak-picking problem. Journal of Applied and Computational Mathematics. (2012), 1:1.
13. Z. Liu, A. Abbas, B. Jing, and X. Gao. WaVPeak: picking NMR peaks through wavelet transform and volume-based filtering. Bioinformatics (2012), 28(7): 914-920. [PDF] [Source code]
12. J. Wang, Y. Li, Q. Wang, J. Zhang, X. You, J. Man, C. Wang, and X. Gao. ProClusEnsem: predicting membrane protein types by fusing different models of pseudo amino acid composition. Computers in Biology and Medicine (2012), 42(5): 564-574. [PDF]
11. J. Wang, X. Gao, Q. Wang, Q. Wang, and Y. Li. ProDis-ContSHC: learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrieval. BMC Bioinformatics (2012), 13(S7): S2. [PDF]
10. J. Wang, H. Bensmail, and X. Gao. Multiple graph regularized protein domain ranking. BMC Bioinformatics (2012). 13:307. doi:10.1186/1471-2105-13-307.
9. R. Jang, X. Gao, and M. Li. Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from 15N-NOESY. BMC Bioinformatics (2012), 12(S3):S4. [PDF]
8. Md. S. Bhuyan, and X. Gao. A protein-dependent side-chain rotamer library. BMC Bioinformatics (2011), 12(S14): S10. [PDF]
7. R. Jang, X. Gao, and M. Li. Towards fully automated structure-based NMR resonance assignment of 15N-labeled proteins from automatically picked peaks, Journal of Computational Biology, vol. 18(3), (2011), pp 347-363. Equally Contributed First Author. [PDF]
6. B. Alipanahi, X. Gao, E. Karakoc, F. Balbach, S. Li, G. Feng, L. Donaldson, and M. Li. Error tolerant NMR backbone resonance assignment for automated structure generation. Journal of Bioinformatics and Computational Biology, vol. 9, (2011), pp 15-41. Equally Contributed First Author. [PDF]
5. X. Gao, J. Xu, S. C. Li, and M. Li. Predicting local quality of a sequence-structure alignment. Journal of Bioinformatics and Computational Biology, vol. 7, (2009), pp. 789-810. [PDF]
4. X. Gao, D. Bu, J. Xu, and M. Li. Improving consensus contact prediction via server correlation reduction. BMC Structural Biology, 2009, 9:28. [PDF]
Bioinformatics, vol. 25, no. 12, (2009), pp. i268-i275. Equally Contributed First Author. [PDF]
2. S. C. Li, D. Bu, X. Gao, J. Xu, and M. Li. Designing succinct structural alphabets. Bioinformatics, vol. 24, no. 13, (2008), pp. i182-i189. [PDF]
1. X. Gao, D. Bu, S. C. Li, J. Xu, and M. Li. FragQA: predicting local fragment quality of a sequence-structure alignment. Genome Informatics, vol. 19, no. 1, (2007), pp. 27-39. [PDF]
 

Refereed Conference Publications:

34. L. Ding, S. Liao, Y. Liu, P. Yang, and X. Gao. Randomized kernel selection with spectra of multilevel circulant matrices. The Thirtieth-Second AAAI Conference on Artificial Intelligence (AAAI-18), New Orleans, U.S., February 2018. (Acceptance rate 25%).
33. Z. Xu, Y. Ke, and X. Gao. A fast algorithm for matrix eigen-decomposition. The 33rd Conference on Uncertainty in Artificial Intelligence (UAI2017), Sydney, Australia, August 2017. (Acceptance rate 31%).
32. Y. Niu, Z. Lu, S. Huang, X. Gao, J. Wen, and A. Zhao. FeaBoost: Joint feature and label refinement for semantic segmentation.
The Thirtieth-First AAAI Conference on Artificial Intelligence (AAAI-17), San Francisco, U.S., February 2017. (Acceptance rate 24.63%).
31. X. Cui, Z. Lu, S. Wang, J. Wang, and X. Gao. CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction.
The 24th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2016), Orlando, U.S., July 2016. (Acceptance rate 21%).
30. J. Wang, I. Tsang, and X. Gao. Optimizing multivariate performance measures from multi-view data. The Thirtieth AAAI Conference on Artificial Intelligence (AAAI-16), Phoenix, U.S., February 2016. (Acceptance rate 25.75%).
29. J. Wang, and X. Gao. Partially labeled data tuple can optimize multivariate performance measures. ACM International Conference on Information and Kowledge Management (CIKM2015). Melbourne, Australia, October 2015. (Acceptance rate 25.6%).
28. X. Cui, H. Kuwahara, S. Li, and X. Gao. Compare local pocket and global protein structure models by small structure patterns. ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2015 (ACM-BCB2015). Atlanta, U.S., September 2015. (Acceptance rate 34%).
27. S. Sun, X. Wang, X. Gao, L. Ren, X. Sun, D. Bu, and K. Ning. Preprocess and condensation of Raman spectrum for single-cell phenotype analysis. The 26th International Conference on Genome Informatics (GIW2015). Tokyo, Japan, September 2015.
26. Z. Lu, X. Gao, L. Wang, S. Huang, and J. Wen. Social image parsing by cross-modal data refinement. The International Joint Conference on Artificial Intelligence (IJCAI-15), Buenos Aires, Argentina, July 2015. (Acceptance rate 28.8%).
25. X. Cui, H. Naveed, and X. Gao. Finding optimal interaction interface alignments between biological complexes. The 23rd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2015), Dublin, Ireland, July 2015. (Acceptance rate 20%).
24. I. Alabdulmohsin, X. Gao, and X. Zhang. Efficient active learning of halfspaces via query synthesis.
The Twenty-Ninth AAAI Conference on Artificial Intelligence (AAAI-15), Austin, U.S., January 2015. (Acceptance rate 26.67%).
23. Z. Lu, X. Gao, L. Wang, J. Wen, and S. Huang. Noise-robust semi-supervised learning by large-scale sparse coding. The Twenty-Ninth AAAI Conference on Artificial Intelligence (AAAI-15), Austin, U.S., January 2015. (Acceptance rate 26.67%).

22. I. Alabdulmohsin, X. Gao, and X. Zhang. Support vector machines with indefinite kernels. The 6th Asian Conference on Machine Learning (ACML2014). Nha Trang City, Vietnam, November 2014.
21. J. Wang, and X. Gao. Minimum information loss based multi-kernel for Flagellar protein recognition in Trypanosoma brucei. ICDM 2014 Workshop on Biological Data Mining and Its Applications in Healthcare (BioDM2014). Shenzhen, China, December 2014.
20. I. Almasri, X. Gao, and N. Fedoroff. Quick mining of isomorphic exact large patterns from large graphs. ICDM 2014 Workshop on Data Mining in Networks (DaMNet2014). Shenzhen, China, December 2014.
19. X. Wang, H. Kuwahara, and X. Gao. Modeling DNA affinity landscape through two-round support vector regression with weighted degree kernels. The 25th International Conference on Genome Informatics (GIW / ISCB-Asia 2014). Tokyo, Japan, December 2014.
18. I. Alabdulmohsin, X. Gao, and X. Zhang. Adding robustness to support vector machines against adversarial reverse engineering. ACM International Conference on Information and Knowledge Management (CIKM 2014). Shanghai, China, November 2014. (Acceptance rate 20.8%).
17. M. Al-Shedivat, J. Wang, M. Alzahrani, J. Huang, and X. Gao. Supervised transfer sparse coding. The Twenty-Eighth AAAI Conference on Artificial Intelligence (AAAI-14), Quebec City, Canada, July 2014. (Acceptance rate 28%)
16. J. Wang, M. Alzahrani, and X. Gao. Large margin image set representation and classification. The 2014 International Joint Conference on Neural Networks (IJCNN2014), Beijing, China, July 2014.
15. J. Wang, and X. Gao. Semi-supervised sparse coding. The 2014 International Joint Conference on Neural Networks (IJCNN2014), Beijing, China, July 2014.
14. H. Kuwahara, M. Fan, S. Wang, and X. Gao. A framework for scalable parameter estimation of gene circuit models using structural information. The 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2013), Berlin, Germany, July 2013. (Acceptance rate 16%)
13. B. Xie, B. Jankovic, V. Bajic, L. Song, and X. Gao. Poly(A) motif prediction using spectral latent features from human DNA sequences. The 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2013), Berlin, Germany, July 2013. (Acceptance rate 16%)
12. J. Wang, I. Almasri, and X. Gao. Adaptive graph regularized nonnegative matrix factorization via feature selection. The 21st International Conference on Pattern Recognition (ICPR2012). Tsukuba, Japan. November 2012.
11. M. Messih, M. Chitale, V. Bajic, D. Kihara and X. Gao. Protein domain recurrence and order can enhance prediction of protein functions. The 11th European Conference on Computational Biology (ECCB2012). Basel, Switzerland, September 2012. (Acceptance rate 14%).
10. Md. S. Bhuyan, and X. Gao. A protein-dependent side-chain rotamer library. The 22nd International Conference on Genome Informatics (GIW2011). Busan, Korea, December 2011.
9. H. Kuwahara, and X. Gao. An efficient parallel stochastic simulation method for analysis of nonviral gene delivery systems. The 9th International Conference on Computational Methods in Systems Biology (CMSB2011). Paris, France, September 2011. [PDF]
8. R. Jang, X. Gao, and M. Li. Combined structure-based backbone and NOE assignment from N-HSQC chemical shift mapping and N-NOESY NMR spectra. ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2011 (ACM-BCB2011). Chicago, U.S., August 2011. (Acceptance rate 19%).
7. R. Jang, X. Gao, and M. Li. Towards automated structure-based NMR resonance assignment, The Fourteenth Annual International Conference on Research in Computational Molecular Biology (RECOMB2010). Lisbon, Portugal, April 2010. (Acceptance rate 20%). Equally Contributed First Author. [PDF]
6. B. Alipanahi, X. Gao, E. Karakoc, L. Donaldson, A. Gutmanas, C. Arrowsmith, and M. Li. PICKY: a novel SVD-based NMR spectra peak picking method. The Seventeenth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2009). Stockholm, Sweden, June 2009. (Acceptance rate 18%). Equally Contributed First Author. [PDF]
5. S. C. Li, D. Bu, X. Gao, J. Xu, and M. Li. Designing succinct structural alphabets. The Sixteenth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2008), Toronto, Canada, July 2008. (Acceptance rate 15%). [PDF]
4. J. Zhang, X. Gao, J. Xu, and M. Li. Rapid and accurate protein side chain prediction with local backbone information. The Twelfth Annual International Conference on Research in Computational Molecular Biology (RECOMB2008), Singapore, April 2008. (Acceptance rate 15%). Equally Contributed First Author. [PDF]
3. X. Gao, D. Bu, S. C. Li, J. Xu, and M. Li. FragQA: predicting local fragment quality of a sequence-structure alignment. The Eighteenth International Conference on Genome Informatics (GIW 2007), Singapore, December 2007. (Acceptance rate 29%). Best Paper Award. [PDF]
2. X. Gao, D. Bu, S. C. Li, J. Xu, and M. Li. Consensus contact prediction by linear programming, in Proceedings of the Sixth Annual International Conference on Computational Systems Bioinformatics (CSB 2007), pp. 323-334, San Diego, U.S., August 2007. (Acceptance rate 22%). [PDF]
1. X. Gao, S. C. Li, and Y. Lu. New algorithms for the spaced seeds. International Frontiers of Algorithmics Workshop 2007 (FAW 2007), LanZhou, P.R. China, August 2007. (Acceptance rate 23%). Lecture Notes in Computer Science, vol. 4613, (2007), pp. 50-61. [PDF]
 
Book Chapters:

3. H. Jiang, L. Zhu, A. Heliou, X. Gao, J. Bernauer, and X. Huang. Elucidating mechanisms of molecular recognition between human Argonaute and miRNA using computational approaches. In Methods in Molecular Biology, Eds: Marco F. Schmidt, Vol. 1517, Springer, 2016.
2. R. Chowdhary, B. Jankovic, R. Stankowski, J. Archer, X. Zhang, X. Gao, and V. Bajic. Automated mining of disease-specific protein interaction networks based on biomedical literature. Invited book chapter, in Biological Data Mining and Its Applications in Healthcare, Eds: Xiao-Li Li, See-Kiong Ng, and Jason Wang, 2013.
1. D. Bu, S. C. Li, X. Gao, L. Yu, J. Xu, and M. Li. Consensus approaches to protein structure prediction. Invited book chapter, in Machine Learning in Bioinformatics, Chapter 8, Eds: Yanqing Zhang and Jagath C. Rajapakse, John Wiley & Sons, 2007.
 
Non-refereed Conference Publications:
 
 
5. H.
Kuwahara, and X. Gao. A hybrid model decomposition framework for parameter estimation of gene circuit models. The 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC'15). Milano, Italy, August 2015.
4. X. Gao. Automated protein structure determination from NMR multidimensional spectra. The 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC'15). Milano, Italy, August 2015.
3. H. Kuwahara, M. Fan, S. Wang and X. Gao. A scalable approach to parameter estimation for statistical thermodynamic-based models of gene regulation using structural information. The First Annual Winter q-bio Meeting. Hawaii, USA, February 2013.
2. X. Gao, M. Li, and J. Xu. RAPTORESS: an atom-level refinement approach for protein structure prediction. The 7th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP7), pp. 96-97. Long abstract, Pacific Grove, USA, November 2007.
1. L. Yu, D. Bu, S. C. Li, X. Gao, J. Xu, and M. Li. RAPTOR-ACE: an integer linear programming based consensus fold recognition method, The 7th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP7), pp. 94-95. Long abstract, Pacific Grove, USA, November 2007.

 
Thesis:

1. X. Gao. Towards automating protein structure determination from NMR data. Ph.D. Thesis, University of Waterloo, Waterloo, Canada. September, 2009.
 
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