Multidimensional persistence in biomolecular data
暂无分享,去创建一个
Guo-Wei Wei | Kelin Xia | Kelin Xia | G. Wei
[1] Afra Zomorodian,et al. The Theory of Multidimensional Persistence , 2007, SCG '07.
[2] Shan Zhao,et al. Geometric and potential driving formation and evolution of biomolecular surfaces , 2009, Journal of mathematical biology.
[3] P. Nithiarasu,et al. Flow‐induced ATP release in patient‐specific arterial geometries – a comparative study of computational models , 2013, International journal for numerical methods in biomedical engineering.
[4] Perumal Nithiarasu,et al. Semi‐automatic surface and volume mesh generation for subject‐specific biomedical geometries , 2012, International journal for numerical methods in biomedical engineering.
[5] Zhengmeng Jin,et al. Strong solutions for the generalized Perona–Malik equation for image restoration , 2010 .
[6] Nathan A. Baker,et al. Computational methods for biomolecular electrostatics. , 2008, Methods in cell biology.
[7] Howard Reiss,et al. Further Development of Scaled Particle Theory of Rigid Sphere Fluids , 1970 .
[8] M. Gameiro,et al. A topological measurement of protein compressibility , 2014, Japan Journal of Industrial and Applied Mathematics.
[9] Patrizio Frosini,et al. Size theory as a topological tool for computer vision , 1999 .
[10] Guo-Wei Wei,et al. Multiscale Multiphysics and Multidomain Models I: Basic Theory. , 2013, Journal of theoretical & computational chemistry.
[11] 坂上 貴之. 書評 Computational Homology , 2005 .
[12] D. Ringach,et al. Topological analysis of population activity in visual cortex. , 2008, Journal of vision.
[13] M Tasumi,et al. Normal vibrations of proteins: glucagon. , 1982, Biopolymers.
[14] 林炳承,et al. A microfluidic DNA computing processor for gene expression analysis and gene drug synthesis , 2009 .
[15] Tirion,et al. Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis. , 1996, Physical review letters.
[16] D. Castle. Cannabis and psychosis: what causes what? , 2013, F1000 medicine reports.
[17] Charles L Brooks,et al. Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions. , 2008, Physical chemistry chemical physics : PCCP.
[18] Tamal K. Dey,et al. Reeb Graphs: Approximation and Persistence , 2011, SoCG '11.
[19] R. Rosenfeld. Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.
[20] Rony Granek,et al. Cooperativity in thermal and force-induced protein unfolding: integration of crack propagation and network elasticity models. , 2013, Physical review letters.
[21] Kelin Xia,et al. Persistent homology analysis of protein structure, flexibility, and folding , 2014, International journal for numerical methods in biomedical engineering.
[22] J. van Leeuwen,et al. Algorithms and Computation , 2002, Lecture Notes in Computer Science.
[23] Guo-Wei Wei,et al. Partial differential equation transform—Variational formulation and Fourier analysis , 2011, International journal for numerical methods in biomedical engineering.
[24] E. Alexov,et al. Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins. , 2002, Biophysical journal.
[25] Vin de Silva,et al. On the Local Behavior of Spaces of Natural Images , 2007, International Journal of Computer Vision.
[26] M. Gameiro,et al. Topological Measurement of Protein Compressibility via Persistence Diagrams , 2012 .
[27] David Cohen-Steiner,et al. Computing geometry-aware handle and tunnel loops in 3D models , 2008, ACM Trans. Graph..
[28] Yiying Tong,et al. Multiscale geometric modeling of macromolecules II: Lagrangian representation , 2013, J. Comput. Chem..
[29] Peter Bubenik,et al. A statistical approach to persistent homology , 2006, math/0607634.
[30] Daniela Giorgi,et al. Describing shapes by geometrical-topological properties of real functions , 2008, CSUR.
[31] David Cohen-Steiner,et al. Vines and vineyards by updating persistence in linear time , 2006, SCG '06.
[32] Qiong Zheng,et al. Biomolecular surface construction by PDE transform , 2012, International journal for numerical methods in biomedical engineering.
[33] J Andrew McCammon,et al. Feature-preserving adaptive mesh generation for molecular shape modeling and simulation. , 2008, Journal of molecular graphics & modelling.
[34] Yiying Tong,et al. Multiscale geometric modeling of macromolecules I: Cartesian representation , 2014, J. Comput. Phys..
[35] R. Ghrist. Barcodes: The persistent topology of data , 2007 .
[36] 貴之 坂上. T. Kaczynski, K. Mischaikow, M. Mrozek, Computational Homology, Springer Verlag, NY, 2004 , 2005 .
[37] Klaus Schulten,et al. Identifying unfolding intermediates of FN-III(10) by steered molecular dynamics. , 2002, Journal of molecular biology.
[38] Gunnar E. Carlsson,et al. Topology and data , 2009 .
[39] G. Wei. Differential Geometry Based Multiscale Models , 2010, Bulletin of mathematical biology.
[40] Qiang Cui,et al. Combining implicit solvation models with hybrid quantum mechanical/molecular mechanical methods: A critical test with glycine , 2002 .
[41] Valerio Pascucci,et al. Branching and Circular Features in High Dimensional Data , 2011, IEEE Transactions on Visualization and Computer Graphics.
[42] M Karplus,et al. Unfolding proteins by external forces and temperature: the importance of topology and energetics. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[43] Patrizio Frosini,et al. Persistent Betti numbers for a noise tolerant shape-based approach to image retrieval , 2011, Pattern Recognit. Lett..
[44] G. G. Stokes. "J." , 1890, The New Yale Book of Quotations.
[45] Tamal K. Dey,et al. Reeb Graphs: Approximation and Persistence , 2013, Discret. Comput. Geom..
[46] Barry Honig,et al. Extending the Applicability of the Nonlinear Poisson−Boltzmann Equation: Multiple Dielectric Constants and Multivalent Ions† , 2001 .
[47] Guo-Wei Wei. Wavelets generated by using discrete singular convolution kernels , 2000 .
[48] Michael Holst,et al. Multilevel Methods for the Poisson-Boltzmann Equation , 1993 .
[49] Cornelis H. Slump,et al. Flow prediction in cerebral aneurysms based on geometry reconstruction from 3D rotational angiography , 2013, International journal for numerical methods in biomedical engineering.
[50] Kelin Xia,et al. Persistent topology for cryo‐EM data analysis , 2014, International journal for numerical methods in biomedical engineering.
[51] Bung-Nyun Kim,et al. Persistent Brain Network Homology From the Perspective of Dendrogram , 2012, IEEE Transactions on Medical Imaging.
[52] P. Henrard,et al. Measurement of the $\Lambda_b^0$, $\Xi_b^-$ and $\Omega_b^-$ baryon masses , 2013, 1302.1072.
[53] Ming C. Lin,et al. Simulation-Based Joint Estimation of Body Deformation and Elasticity Parameters for Medical Image Analysis , 2012, IEEE Transactions on Medical Imaging.
[54] Herbert Edelsbrunner,et al. Computational Topology - an Introduction , 2009 .
[55] Duan Chen,et al. Modeling and simulation of electronic structure, material interface and random doping in nano-electronic devices , 2010, J. Comput. Phys..
[56] Hubert Mara,et al. Multivariate Data Analysis Using Persistence-Based Filtering and Topological Signatures , 2012, IEEE Transactions on Visualization and Computer Graphics.
[57] A. Atilgan,et al. Vibrational Dynamics of Folded Proteins: Significance of Slow and Fast Motions in Relation to Function and Stability , 1998 .
[58] Joël Janin,et al. Protein flexibility, not disorder, is intrinsic to molecular recognition , 2013, F1000 biology reports.
[59] Guo-Wei Wei,et al. Multiscale molecular dynamics using the matched interface and boundary method , 2011, J. Comput. Phys..
[60] 김삼묘,et al. “Bioinformatics” 특집을 내면서 , 2000 .
[61] Stephen Smale,et al. A Topological View of Unsupervised Learning from Noisy Data , 2011, SIAM J. Comput..
[62] M. Karplus,et al. Dynamics of folded proteins , 1977, Nature.
[63] C. Brooks,et al. Recent advances in the development and application of implicit solvent models in biomolecule simulations. , 2004, Current opinion in structural biology.
[64] Kelin Xia,et al. Multiscale multiphysics and multidomain models--flexibility and rigidity. , 2013, The Journal of chemical physics.
[65] E. Fischer. Einfluss der Configuration auf die Wirkung der Enzyme , 1894 .
[66] Afra Zomorodian,et al. Computing Persistent Homology , 2005, Discret. Comput. Geom..
[67] Guo-Wei Wei,et al. Mode Decomposition Evolution Equations , 2012, J. Sci. Comput..
[68] Guo-Wei Wei,et al. Variational Multiscale Models for Charge Transport , 2012, SIAM Rev..
[69] E. Nogales,et al. Structural intermediates in microtubule assembly and disassembly: how and why? , 2006, Current opinion in cell biology.
[70] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[71] I. Holopainen. Riemannian Geometry , 1927, Nature.
[72] Konstantin Mischaikow,et al. Morse Theory for Filtrations and Efficient Computation of Persistent Homology , 2013, Discret. Comput. Geom..
[73] K. Sharp,et al. Electrostatic interactions in macromolecules: theory and applications. , 1990, Annual review of biophysics and biophysical chemistry.
[74] Michele Vendruscolo,et al. Validity of Gō models: comparison with a solvent-shielded empirical energy decomposition. , 2002, Biophysical journal.
[75] Abubakr Muhammad,et al. Blind Swarms for Coverage in 2-D , 2005, Robotics: Science and Systems.
[76] P. Flory,et al. Statistical thermodynamics of random networks , 1976, Proceedings of the Royal Society of London. A. Mathematical and Physical Sciences.
[77] A. Bertozzi,et al. $H^1$ Solutions of a class of fourth order nonlinear equations for image processing , 2003 .
[78] Afra Zomorodian,et al. Computing Multidimensional Persistence , 2009, J. Comput. Geom..
[79] Afra Zomorodian,et al. Localized Homology , 2007, IEEE International Conference on Shape Modeling and Applications 2007 (SMI '07).
[80] J. Rogers. Chaos , 1876 .
[81] N. Go,et al. Dynamics of a small globular protein in terms of low-frequency vibrational modes. , 1983, Proceedings of the National Academy of Sciences of the United States of America.
[82] Mikael Vejdemo-Johansson,et al. javaPlex: A Research Software Package for Persistent (Co)Homology , 2014, ICMS.
[83] Guo-Wei Wei,et al. Objective-oriented Persistent Homology , 2014, 1412.2368.
[84] C. Hall,et al. α‐Helix formation: Discontinuous molecular dynamics on an intermediate‐resolution protein model , 2001, Proteins.
[85] Moo K. Chung,et al. Topology-Based Kernels With Application to Inference Problems in Alzheimer's Disease , 2011, IEEE Transactions on Medical Imaging.
[86] Yuri Dabaghian,et al. A Topological Paradigm for Hippocampal Spatial Map Formation Using Persistent Homology , 2012, PLoS Comput. Biol..
[87] Marcia O. Fenley,et al. Hybrid boundary element and finite difference method for solving the nonlinear Poisson–Boltzmann equation , 2004, J. Comput. Chem..
[88] A. Warshel,et al. Electrostatic effects in macromolecules: fundamental concepts and practical modeling. , 1998, Current opinion in structural biology.
[89] Guo-Wei Wei,et al. Synchronization-based image edge detection , 2002 .
[90] N. Sochen,et al. Image Sharpening by Flows Based on Triple Well Potentials , 2004 .
[91] Nathan A. Baker,et al. Differential geometry based solvation model I: Eulerian formulation , 2010, J. Comput. Phys..
[92] J. Sethian,et al. Fronts propagating with curvature-dependent speed: algorithms based on Hamilton-Jacobi formulations , 1988 .
[93] Guo-Wei Wei,et al. Molecular nonlinear dynamics and protein thermal uncertainty quantification. , 2014, Chaos.
[94] Shulin Zhou,et al. Existence and uniqueness of weak solutions for a fourth-order nonlinear parabolic equation , 2007 .
[95] Herbert Edelsbrunner,et al. Computing Robustness and Persistence for Images , 2010, IEEE Transactions on Visualization and Computer Graphics.
[96] Y. Tong,et al. Geometric modeling of subcellular structures, organelles, and multiprotein complexes , 2012, International journal for numerical methods in biomedical engineering.
[97] R. Jernigan,et al. Anisotropy of fluctuation dynamics of proteins with an elastic network model. , 2001, Biophysical journal.
[98] Emil Alexov,et al. Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies. , 2007, Biophysical journal.
[99] Claudia Landi,et al. A Mayer–Vietoris Formula for Persistent Homology with an Application to Shape Recognition in the Presence of Occlusions , 2011, Found. Comput. Math..
[100] X. Liu,et al. A fast algorithm for constructing topological structure in large data , 2012 .
[101] S. Zhao,et al. A fast alternating direction implicit algorithm for geometric flow equations in biomolecular surface generation , 2014, International journal for numerical methods in biomedical engineering.
[102] Nathan A. Baker,et al. Poisson-Boltzmann Methods for Biomolecular Electrostatics , 2004, Numerical Computer Methods, Part D.
[103] TongYiying,et al. Multiscale geometric modeling of macromolecules I , 2014 .
[104] G. W. Wei,et al. Generalized Perona-Malik equation for image restoration , 1999, IEEE Signal Processing Letters.
[105] Yiying Tong,et al. Persistent homology for the quantitative prediction of fullerene stability , 2014, J. Comput. Chem..
[106] Otfried Cheong,et al. Proceedings of the twenty-second annual symposium on Computational geometry , 2006, SoCG 2006.
[107] Shan Zhao,et al. Minimal molecular surfaces and their applications , 2008, J. Comput. Chem..
[108] Andrzej J. Rzepiela,et al. Reconstruction of atomistic details from coarse‐grained structures , 2010, J. Comput. Chem..
[109] Andrea Cerri,et al. The Persistence Space in Multidimensional Persistent Homology , 2013, DGCI.
[110] John B. Greer,et al. Traveling Wave Solutions of Fourth Order PDEs for Image Processing , 2004, SIAM J. Math. Anal..
[111] K. Schulten,et al. Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. , 1998, Biophysical journal.
[112] D. Mumford,et al. Optimal approximations by piecewise smooth functions and associated variational problems , 1989 .
[113] Herbert Edelsbrunner,et al. Topological Persistence and Simplification , 2000, Proceedings 41st Annual Symposium on Foundations of Computer Science.
[114] Joshua D. Reiss,et al. Construction of symbolic dynamics from experimental time series , 1999 .
[115] Zhan Chen,et al. Differential geometry based solvation model II: Lagrangian formulation , 2011, Journal of mathematical biology.
[116] M. Ferri,et al. Betti numbers in multidimensional persistent homology are stable functions , 2013 .
[117] Rocio Gonzalez-Diaz,et al. Discrete Geometry for Computer Imagery , 2013, Lecture Notes in Computer Science.
[118] Guo-Wei Wei,et al. Highly accurate biomolecular electrostatics in continuum dielectric environments , 2008, J. Comput. Chem..
[119] A. Atilgan,et al. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. , 1997, Folding & design.
[120] Shin'ichi Oishi,et al. Japan Journal of Industrial and Applied Mathematics: Guest editors' preface , 2009 .
[121] C. Anfinsen. Principles that govern the folding of protein chains. , 1973, Science.
[122] S. Osher,et al. Algorithms Based on Hamilton-Jacobi Formulations , 1988 .
[123] Kelin Xia,et al. Fast and anisotropic flexibility-rigidity index for protein flexibility and fluctuation analysis. , 2014, The Journal of chemical physics.
[124] Guo-Wei Wei,et al. Selective Extraction of Entangled Textures via Adaptive PDE Transform , 2012, Int. J. Biomed. Imaging.
[125] Lee-Wei Yang,et al. Coarse-Grained Models Reveal Functional Dynamics - I. Elastic Network Models – Theories, Comparisons and Perspectives , 2008, Bioinformatics and biology insights.
[126] Guo-Wei Wei,et al. Quantum dynamics in continuum for proton transport II: Variational solvent–solute interface , 2012, International journal for numerical methods in biomedical engineering.
[127] Arvid Lundervold,et al. Noise removal using fourth-order partial differential equation with applications to medical magnetic resonance images in space and time , 2003, IEEE Trans. Image Process..
[128] Danijela Horak,et al. Persistent homology of complex networks , 2008, 0811.2203.
[129] Shan Zhao,et al. Variational approach for nonpolar solvation analysis. , 2012, The Journal of chemical physics.
[130] M. Levitt,et al. Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. , 1985, Journal of molecular biology.
[131] Leonidas J. Guibas,et al. BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm250 Structural bioinformatics Persistent voids: a new structural metric for membrane fusion , 2022 .