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Welcome!
Welcome to Xia's research group of Molecular Based Mathematical Biology
at the School of Physical and Mathematical Sciences, Nanyang Technological University (NTU), Singapore!
The last century has witnessed the tremendous advancement of Biological Sciences. The availability of massive biological data, high-performance computers, efficient computational algorithms, and mathematical and physical models have paved the way for Biological Sciences to undertake a historic transition from being qualitative, phenomenological, and descriptive to being quantitative, analytical, and predictive. Under this transition, modern Mathematical Biology will be fundamentally changed from macroscale modelings (of species, population, disease, blood fluid, etc) to molecular based analysis (of proteins, DNAs, genes, ligands, etc). A brief introduction of the Molecular Based Mathematical Biology can be found in SIAM news Sep 2016, Dec 2017, Prof Wei's Harvard talk, and D3R news. Our group focuses on Molecular Based Mathematical Biology. We use computational tools from PDE, differential geometry, algebraic topology and statistical learning to study the material, chemical and biomolecular structure, flexibility, dynamics, and functions. In particular, we are interested in topological data analysis (TDA), topology based machine learning/deep learning models and their applications in drug design, biomolecular interactions, and chromosome structures. We sincerely welcome highly motivated students and postdocs to join our group. Principal Investigator
Research Interests - Topological data analysis: Persistent homology analysis of big data in biomolecules; Topology based machine learning models
- Geometric and Variational Modeling: Geometric Modeling of Biomolecules; Flexibility-Rigidity Index(FRI); Variational multiscale models;
- Scientific Computing: Matched interface and boundary (MIB); Adaptive mesh based MIB method; MIB Galerkin method;
(After joining NTU) - PI, Merlion Program, "Machine learning models based on weighted-persistent-homology for structure-based drug design", 2020-2022
- Co-PI,
MOE AcRF Tier 1 Thematic Grant, "Improving photocatalysts that recycle
microplastics to fuels by artificial intelligence", 2020-2022
- PI MOE AcRF Tier 1, "Bipartite-graph-based machine learning models for biomolecular interaction analysis", 2020-2022
- Collaborator, ACE, "Artificial
intelligence for the prediction of alternative splicing from
epigenomics and transcriptomics data in cancer", 2019-2021
- PI, NTU/NUS-JSPS, "Elucidation of dynamic opening and closing mechanism of giant protein cage vault", 2019-2021
- PI, MOE AcRF Tier 2,"Persistent homology based topological approaches for biomolecular data analysis", 2018-2021
- PI, MOE AcRF Tier 1, "Modeling and analyzing environmental effects and self-assembly mechanism of large-sized biomolecules", 2018-2020
- PI, MOE AcRF Tier 1, "A unified framework for multiscale geometric modeling of biomolecular complex", 2017-2019
- Co-PI, ASPIRE League Research Grant, "Functional Design of Protein Cage for Sustainable Bionanomaterial", 2017-2018
- PI, NTU-SUG, "Geometric and topological modeling of biomolecular structure, dynamics and function", 2016-2021
- Co-PI (PI: Guo-Wei Wei), National Science Foundation, DMS-1160352, "FRG: Collaborative research: Variational multiscale approaches to biomolecular structure, dynamics and transport", 09/2012-08/2015.
- Co-PI (PI: Guo-Wei Wei), NIH/NIGMS, 3R01GM090208-04S1, "Geometric flow approach to implicit solvation modeling", 07/2014-062015
- Co-organizer (with Prof. Jie Wu and Prof. Jelena Grbic), "Biomolecular Topology: Modelling and Data Analysis", IMS, NUS, April 5-9, 2021
- Co-organizer (with Prof. Jie Wu, Prof. Fei Han, and Prof. Jelena Grbic), "Applied Topology in Frontier Sciences", IMS, NUS, July 11-22, 2022
(After joining NTU) Under Review 54. Kelin Xia, Guowei
Wei, "A review of geometric, topological and graph theory apparatuses
for the modeling and analysis of biomolecular data", arXiv
(2017)
53. Zhenyu Meng, Kelin Xia, "Persistent spectral based machine learning (PerSpect ML) for drug design", arXiv, (2020) (Code) 52. D Vijay Anand, Kelin Xia, Yuguang Mu, "Weighted persistent homology for osmolyte molecular aggregation and hydrogen-bonding network analysis", arXiv, (2019) 51. Liangzhen Zheng, Jingrong Fan, Kelin Xia, Yuguang Mu, "Identification of PR LBD potent ligands using machine learning aided rescoring with low false positive rates", submitted, (2019) 50. D Vijay Anand, Zhenyu Meng, Kelin Xia, "Normal mode analysis of chromosome structures", submitted, (2019) 49. Chi Seng Pun, Kelin Xia, Si Xian Lee, "Persistent Homology based Machine Learning and its Applications – A Survey", arXiv (2019) (SSRN's Top Ten download list (Dec 01, 2019)) 48. Chengyuan Wu, Shiquan Ren, Jie Wu, Kelin Xia,"Weighted fundamental group", arXiv (2019) 47. Jiajie Peng, Jinjin Yang, Kelin Xia, "Flexibility and rigidity index for chromosome packing, ﬂexibility and dynamics analysis", bioRxiv (2019) Published/Accepted 46. Chengyuan Wu, Shiquan Ren, Jie Wu, Kelin Xia, "Discrete Morse Theory for Weighted Simplicial Complexes", Topology and its Applications, 270, 107038, (2020) 45. Zhenyu Meng, D Vijay Anand, Yunpeng Lu, Jie Wu, Kelin Xia, "Weighted persistent homology for biomolecular data analysis", Scientific Report, 10, 2079, (2020) 44. Chengyuan Wu, Shiquan Ren, Jie Wu, Kelin Xia,"Weighted (Co)homology and Weighted Laplacian", Science China Mathematics, https://doi.org/10.1007/s11425-019-1595-1 (2019) 43. Kelin Xia, D Vijay Anand, Shikhar Saxena, Yuguang Mu, "Persistent homology analysis of osmolyte molecular aggregation and their hydrogen-bonding networks", Physical Chemistry Chemical Physics, 21, 21038-21048 (2019) 42. Zhenliang Wu, Yuwei Zhang, John Zenghui Zhang, Kelin Xia, and Fei Xia, "Determining Optimal Coarse-Grained Representation for Biomolecules Using Internal Cluster Validation Indexes", Journal of Computational Chemistry, https://doi.org/10.1002/jcc.26070 (2019) 41. Chengyuan Wu, Shiquan Ren, Jie Wu, Kelin Xia, "Magnus Representation of Genome Sequences", Journal of Theoretical Biology, 480(7), 104-111 (2019) 40. Liangzhen Zheng, Kelin Xia, and Yuguang Mu. "Ligand binding induces agonistic-like conformational adaptations in helix 12 of progesterone receptor ligand binding domain." Frontiers in Chemistry, 7(315) (2019) 39. Yuwei Zhang, Kelin Xia, Zexing Cao, Frauke Grater, and Fei Xia, "A New Multiscale Method for Construction of Coarse-Grained Models of Large Biomolecules from Low Resolution Data of Cryo-Electron Microscopy", Physical Chemistry Chemical Physics, 21, 9720-9727 (2019) (PCCP HOT Articles) 38. Manchugondanahalli S. Krishna, Desiree-Faye Kaixin Toh, Zhenyu Meng, Alan Ann Lerk Ong, Zhenzhang Wang, Yunpeng Lu, Kelin Xia, Mookkan Prabakaran, and Gang Chen, "Sequence- and structure-specific probing of RNAs by short nucleobase-modified dsRNA-binding PNAs (dbPNAs) incorporating a fluorescent light-up uracil analog", Analytical Chemistry, 91(8):5331-5338 (2019) 37. Alan Ann Lerk Ong, Desiree-Faye Kaixin Toh, Kiran M. Patil , Zhenyu Meng, Zhen Yuan, Manchugondanahalli S. Krishna, Gitali Devi, Phensinee Haruehanroengra, Yunpeng Lu, Kelin Xia, Katsutomo Okamura, Jia Sheng , and Gang Chen, "General Recognition of U-G, U-A, and C-G Pairs by Double-Stranded RNA-Binding PNAs Incorporated with an Artificial Nucleobase", Biochemistry, 58(10), 1319-1331 (2019) 36. D Vijay Anand, Zhengyu Meng, Kelin Xia "Complex multiscale virtual particle model based elastic network model (CMVP-ENM) for normal mode analysis of biomolecular complexes", Physical Chemistry Chemical Physics, 21, 4359-4366 (2019) 35. Kelin Xia,"Persistent similarity for biomolecular structure comparison", Comunications in information and systems, 18 (4), 251-280 (2018) 34. Kelin Xia, "Persistent homology analysis of ion aggregation and hydrogen-bonding network", Physical Chemistry Chemical Physics, 20, 13448-13460 (2018) 33. Kelin Xia, "Sequence-based Multiscale Modeling for high-throughput Chromosome Conformation Capture (Hi-C) Data Analysis", PLOS ONE, 13(2), 0191899 (2018) 32. Kelin Xia, "Multiscale virtual particle based elastic network model (MVP-ENM) for biomolecular normal mode analysis" , Physical Chemistry Chemical Physics, 20(1), 658-669 (2018) 31. Kelin Xia, Zhiming Li, Lin Mu, "Multiscale persistent functions for biomolecular structure characterization", Bulletin of Mathematical Biology, 80(1),1-31 (2018) 30. Yin Cao, Bao Wang, Kelin Xia and Guo-Wei Wei, "Finite volume formulation of the MIB method for elliptic interface problems", Journal of Computational and Applied Mathematics, 321, 60-77 (2017) 29. Lin Mu,Kelin Xia, Guowei Wei, "Geometric and electrostatic modeling using molecular rigidity functions", Journal of Computational and Applied Mathematics, 313, 18-37 (2017) 28. Duc D Nguyen, Kelin Xia and Guo-Wei Wei, "Generalized flexibility-rigidity index", Journal of Chemical Physics, 144, 234106 (2016). 27. Kristopher Opron, Kelin Xia, Zachary F. Burton and Guo-Wei Wei, "Flexibility-rigidity index for protein-nucleic acid flexibility and fluctuation analysis", Journal of Computational Chemistry, 37, 1283-1295 (2016). (Before joining NTU) 26. Zixuan Cang, Lin Mu, Kedi Wu, Kristopher Opron, Kelin Xia and Guo-Wei Wei, "A topological approach to protein classification", Molecular Based Mathematical Biology, 3, 140-162 (2015). PDF 25. Kelin Xia, Kristopher Opron and Guo-Wei Wei, "Multiscale Gaussian network model (mGNM) and multiscale anisotropic network model (mANM)", Journal of Chemical Physics, 143, 204106(2015). PDF 24. Kelin Xia, Zhixiong Zhao and Guo-Wei Wei, "Multiresolution persistent homology for excessively large biomolecular datasets", Journal of Chemical Physics, 143, 134103(2015).PDF 23. Kelin Xia and Guo-Wei Wei, "Multiresolution topological simplification", Journal of Computational Biology, 22(9), 1-5 (2015).PDF 22. Kelin Xia and Guo-Wei Wei, "Multidimensional persistence in biomolecular data", Journal of Computational Chemistry, 36, 1502-1520(2015).PDF 21. Kelin Xia and Guo-Wei Wei, "Persistent homology for cryo-EM data analysis", International Journal for Numerical Methods in Biomedical Engineering, 31(8), e02719(2015).PDF 20. Jinkyoung Park, Kelin Xia and Guo-Wei Wei, "Atomic scale design and three-dimensional simulations of nanofluidic systems", Microfluidics and Nanofluidics, 19(3), 665-692(2015).PDF 19. Kristopher Opron, Kelin Xia and Guo-Wei Wei, "Communication: Capturing protein multiscale thermal fluctuations", Journal of Chemical Physics, 142, 211101(2015).PDF 18. Bao Wang, Kelin Xia and Guo-Wei Wei, "Second order method for solving 3D elasticity equations with complex interfaces", J. Comput. Phys., 294, 405-438(2015).PDF 17. Kelin Xia, Xin Feng, Yiying Tong and Guo-Wei Wei, "Persistent homology for the quantitative prediction of fullerene stability", Journal of Computational Chemistry, 36, 408-422(2015).PDF 16. Bao Wang, Kelin Xia and Guo-Wei Wei, "Matched interface and boundary method for elasticity interface problems", Journal of Computational and Applied Mathematics, 285, 203-225(2015).PDF 15. Kelin Xia and Guo-Wei Wei, "A Galerkin formulation of the MIB method for three dimensional elliptic interface problems", Computers and Mathematics with Applications, 68, 719-745(2014).PDF 14. Kelin Xia and Guo-Wei Wei, "Persistent homology analysis of protein structure, flexibility and folding", International Journal for Numerical Methods in Biomedical Engineering, 30(8):814-844(2014).PDF 13. Kristopher Opron, Kelin Xia and Guo-Wei Wei, "Fast and anisotropic flexibility-rigidity index for protein flexibility and fluctuation analysis", J. Chem. Phys., 140, 234105(2014) .PDF 12. Kelin Xia, Meng Zhan and Guo-Wei Wei, "MIB Galerkin method for elliptic interface problem", Journal of Computational and Applied Mathematics, 272, 195-220(2014).PDF 11. Kelin Xia and Guo-Wei Wei, "Molecular nonlinear dynamics and protein thermal uncertainty quantification", Chaos: 24, 013103(2014).PDF 10. Kelin Xia and Guo-Wei Wei, "Stochastic model for protein flexibility analysis", Physical Review E, 88, 062709(2013).PDF 9. Kelin Xia, Kristopher Opron and Guo-Wei Wei, "Multiscale multiphysics and multidomain models-Flexibility and rigidity", Journal of Chemical Physics, 139, 194109(2013).PDF 8. Kelin Xia, Xin Feng, Zhan Chen, Yiying Tong and Guo-Wei Wei, "Multiscale geometric modeling of macromolecules I: Cartesian representation", J. Comput. Phys., 257, 912-936(2014).PDF 7. Xin Feng, Kelin Xia, Zhan Chen, Yiying Tong and Guo-Wei Wei, "Multiscale geometric modeling of macromolecules II: Lagrangian representation", Journal of Computational Chemistry, 34, 2100-2120(2013).PDF 6. Xin Feng, Kelin Xia, Yiying Tong and Guo-Wei Wei, "Geometric modeling of organelles, subcellular structures and multiprotein complexes", International Journal for Numerical Methods in Biomedical Engineering, 28(12), 1198-1223(2012). PDF 5. Guo-Wei Wei, Qiong Zheng, Zhan Chen and Kelin Xia, "Variational multiscale models for charge transport", SIAM Review, 54(4), 699-754(2012).PDF 4. Kelin Xia, Meng Zhan, Decheng Wan and Guo-Wei Wei, "Adaptively deformed mesh based matched interface and boundary (MIB) method for elliptic interface problems", J. Comput. Phys., 231(4), 1440-1461(2012).PDF 3. Kelin Xia, Meng Zhan and Guo-Wei Wei, "MIB method for elliptic equations with multimaterial interfaces", J. Comput. Phys., 230(12), 4588-4615(2011).PDF 2. Ming Yi, Kelin Xia and Meng Zhan, "Theoretical study for regulatory property of scaffold protein on MAPK cascade: a qualitative modeling", Biophysical Chemistry, 147(3), 130-139(2010).PDF 1. Qi Zhao, Ming Yi, Kelin Xia and Meng Zhan, "Information propagation from IP3 to target protein: A combined model for encoding and decoding of Ca2+ signal", Physica A, 388, 4105-4114(2009).PDF Presentations (After joining NTU) (Invited speaker) Symposium "Graph Theory Underpinning New Domains of Physical Chemistry" at Spring 2020 National Meeting of the American Chemical Society, Philadelphia, USA, March 22 – 26, 2020 (Invited speaker, workshop cancelled) Workshop on Geometry of Metric Spaces, Tsinghua Sanya International Mathematics Forum (TSIMF), Sanya, China, March 16-20, 2020 (Invited speaker) Winter School on Topological Data Analysis, Novosibirsk State University, Russia, February 3-8, 2020 (Invited speaker) Conference on "Algebraic Topology and Applied Topology", Chongqing, China, Jan 3-8, 2020 (Invited speaker) The second conference on "Computational and Mathematical Bioinformatics and Biophysics", Tsinghua Sanya International Mathematics Forum (TSIMF), Sanya, China, December 9-13, 2019 (Invited speaker) Singapore University of Technology and Design, Singapore, Sep 27 2019 (Invited speaker) Workshop on Computational Topology at Dalian, Dalian University of Technology, July 21-31, 2019 (Invited speaker) School of Mathematics, South China University of Technology, Guangzhou, June 11, 2019 (Invited speaker, declined due to Visa issue) TGDA@OSU TRIPODS workshop on Structure in the Micro-world, Ohio State University, May 28-31, 2019. (Invited speaker, declined due to Visa issue) NSF-CBMS Regional Research Conference: Mathematical Molecular Bioscience and Biophysics, The University of Alabama, May 13 - 17, 2019. (Invited speaker) "Computational and Mathematical Approaches for Bioinformatics and Biophysics" workshop at Tsinghua Sanya International Mathematics Forum (TSIMF), Sanya, China, Dec 10-14, 2018 (Academic Committee, Speaker) The First National Conference on Molecular Biology and Topology, Shijiazhuang, Hebei, China, Oct 26-29, 2018 (Invited speaker) Mini-symposium "Applied and Computational Topology" at the SIAM Central States Section Meeting, Norman, Oklahoma, USA, Oct 5-7, 2018 (Invited speaker) Complexity community Share session, NTU, Singapore, Sep 25, 2018 (Invited speaker) Strategic Partnership with IIT Madras, IISc and IIT Bombay and Joint Workshops, India, Sep 17-20, 2018 (Invited speaker) Workshop on Algebraic Topology and Geometric Topology, Dalian, China, Aug 9-13, 2018 (Invited speaker, declines due to time conflict) Mathematics of Drug Design/Discovery, The Fields Institute for Research in Mathematical Sciences, Toronto, Canada, June 4 - 7, 2018 (Invited speaker) Workshop on Algebraic Topology and Applied Topology, NUS, Singapore, Jan 23, 2018 (Invited speaker) ASPIRE League Research Workshop, School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan, Nov 24, 2017 (Invited speaker) Mini-symposium "Molecular Bioscience and Biophysics: Modeling and Computation" at the 3rd SIAM CSS annual meeting, Fort Collins, Colorado, Sep 29 - Oct 1, 2017 (Invited speaker) NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, September 7, 2017 (Invited speaker) Workshop on "Topology of the Biomolecular World", American Institute of Mathematics, San Jose, CA, July 24-28, 2017 (Invited speaker) International Symposium on Computational Mathematics, Optimization, and Computational Intelligence (CMOCI 2017), IIT Indore, India, July 17 - 19, 2017 (Invited speaker) "Mathematics Biophysics and Molecular Biosciences" Workshop at Tsinghua Sanya International Mathematics Forum (TSIMF), Sanya, China, Dec 19-23, 2016 (Poster) "Topological, Geometric, and Statistical Techniques in Biological Data Analysis", Mathematical Biosciences Institute, September 12-September 16, 2016 (Invited speaker) Department of Mathematics, National University of Singapore, Singapore, August 31, 2016 (Invited speaker) Bioinformatics Institute, A*STAR, Singapore, August 23, 2016 (Invited speaker) School of Biological Science, Nanyang Technological University, Singapore, August 15, 2016 (Organizer) Mini-symposium "Molecular Biosciences and Biophysics: Topological and Geometic methods" at SIAM Conference on Life Sciences, Boston, Masschusetts, July 13, 2016 (Co-organizer: Prof. Natasha Jonoska) (Before joining NTU) (Invited speaker) Department of Mathematics and Statistics, University of North Carolina Charlotte, April 25, 2016 (Invited speaker) School of Mathematical Science, Monash University, April 21, 2016 (Invited speaker) School of Physical and Mathematical Science, Nanyang Technological University, March 8, 2016 (Invited speaker) Department of Mathematics, The university of Tennessee at Chattanooga, February 30, 2016 (Invited speaker) Department of Mathematical Science, Georgia Sourthern University, February 22, 2016 (Invited speaker) Department of Mathematics, North Carolina State University, January 21, 2016 (Invited speaker) Geometric and Topological Modeling of Biomolecules, Mathematical Biosciences Institute, September 28-October 2, 2015 (Video) (Invited speaker) IMA hot topic workshop on "Mathematics of Biological Charge Transport: Molecular and Beyond", IMA, Twin Cities, July 20-24, 2015 (Poster) Advanced Numerical Methods in the Mathematical Sciences, Texas A&M, College Station, TX, May 4-7, 2015 (Invited speaker) "Modeling, Numerics and Analysis of Electrodiffusion Phenomena" at AMS Central Spring Sectional Meeting, Michigan State University, East Lansing, Michigan, March 14-15, 2015 (Organizer) Workshop on persistent homology for biosciences, East Lansing, October 18, 2014 (With Prof.Guowei Wei and Prof. Yiying Tong) (Organizer) Mini-symposium "Molecular Biosciences: Topological modeling of biomolecules" at SIAM Conference on Life Sciences, Charlotte, North Carolina, August 4-7, 2014(Co-organizer: Prof.Yuanan Diao) (Invited speaker) Mini-symposium "Modeling and computation of problems in mathematical biology" at the 38th annual meeting of the SIAM Southeastern Atlantic Section, Florida Institute of Technology in Melbourne, Florida, March 28-30, 2014 (Poster) IMA Annual Program Year Workshop Topological Structures in Computational Biology, December 9-13, 2013 (Poster) 2013 Great Lakes SIAM Conference on "Computational Mathematics: Modeling, Algorithms and Applications", Central Michigan University, April 20, 2013 (Invited speaker) Mathematical Challenges in Biomolecular/Biomedical Imaging and Visualization, Mathematical Biosciences Institute, February 18-22, 2013 (Invited speaker) 12th International Symposium on Mathematical and Computational Biology, Tempe, Arizona, November 7-10, 2012 (Speaker) SMB Annual Meeting and Conference, Knoxville, Tennessee, July 25-28, 2012 (Participation) 2nd Midwest Conference on "Mathematical Methods for Images and Surfaces", East Lansing, August 27-28, 2011 (Traveling award) Modeling and Computation of Biomolecular Structure and Dynamics, Mathematical Biosciences Institute, Ohio State University, April 25-29, 2011 (Poster,traveling award) Fluid Motion Driven by Immersed Structures, University of Toronto, August 9-13, 2010 (Participation) Workshop on Nano-Bio Mathematics and Mechanics, Michigan State University, August 5, 2010 (Participation) Modeling and Numerical PDEs in Mathematical Biology and Applications, Oakland University, April 16, 2011 (Participation) Frontiers in Mathematical Biology: NSF-NIH PIs Meeting 2010, University of Maryland, College Park, April 26-27, 2010 (Participation) SIAM Great Lakes Conference: Modeling and numerical PDEs in Mathematical Biology, University of Michigan at Dearborn, April 17, 2010 |