Mathematical Biophysics/Mathematical Molecular
Biosciences
(235) Kelin Xia and Guo-Wei Wei, A
review of geometric, topological and graph theory apparatuses for the modeling
and analysis of biomolecular data (2016) arXiv:1612.01735.
(234) Qing Zhu, Yuzhe
Du, Yoshiko Nomura, Rong Gao, Zixuan
Cang, Guo-Wei Wei, Dalia
Gordon, Michael Gurevitz, James Groome
and Ke Dong, The voltage-sensing module of domain III
in an insect sodium channel modulates the action of both α and β
toxins, (2018).
(233)
Duc D. Nguyen and Guo-Wei
Wei, Manifold learning of activity ligands and decoys (2018)
(232) Duc D Nguyen and Guo-Wei Wei, Multiscale weighted colored algebraic graphs
(2018).
(231) Menglun Wang, Z. X. Cang, R. Q. Guo, Heedeok Hong and Guo-Wei Wei, Prediction of membrane protein
stability changes upon mutation, (2018).
(230)
Zixuan Cang and Guo-Wei Wei, Persistent cohomology
for datasets with heterogeneous information (2018). arXiv:1807.11120
(229)
Zixuan Cang, Elizabeth
Munch, and Guo-Wei Wei, Evolutionary homology on a
dynamical system (2018). arXiv:1802.04677
(228)
Duc D. Nguyen and Guo-Wei
Wei, DG-GL: Differential geometry based geometric learning of molecular
datasets (2018). arXiv:1806.03765
(227)
Rundong Zhao, Menglun Wang,
Yiying Tong and Guo-Wei
Wei, A divide-and-conquer strategy for large-scale Eulerian solvent excluded
surface, (2018)
(226) David Bramer and G. W. Wei,
Blind prediction of protein B-factor and flexibility, Journal of Chemical
Physics, (2018).
(225)
Duc Duy Nguyen, Zixuan Cang, Kedi
Wu, Menglun Wang, Yin Cao and Guo-Wei
Wei, Mathematical deep learning for pose and binding affinity prediction and
ranking in D3R Grand Challenges, Journal
of Computer Aided Molecular Design,
https://doi.org/10.1007/s10822-018-0146-6 (2018).
(224)
Rundong Zhao, Zixuan Cang, Yiying Tong and Guo-Wei Wei, Protein Pocket Detection via Convex Hull Surface Evolution
and Associated Reeb Graph, Bioinformatics,
https://doi:10.1093/bioinformatics/bty598 (2018).
(223)
Kedi Wu, Zhixiong Zhao, Renxiao Wang and Guo-Wei
Wei, TopP–S: Persistent Homology-Based Multi-Task Deep Neural
Networks for Simultaneous Predictions of Partition Coefficient and Aqueous
Solubility, Journal of
Computational Chemistry, 39, 1444-1454 (2018).
(222)
Kedi Wu and Guo-Wei Wei,
Quantitative toxicity prediction using topology based multi-task deep neural
networks, Journal of Chemical
Information and Modeling, 58, 520-531
(2018).
(221) David Bramer and G. W. Wei, Multiscale weighted colored graphs for protein flexibility and rigidity analysis, Journal of
Chemical Physics, 148, 054103 (2018). (This work
was featured in AIP
Scilight)
(219) Z.
X. Cang, Lin Mu and Guo-Wei
Wei, Representability of
algebraic topology for biomolecules in machine learning based scoring and
virtual screening, PLOS Computational Biology, 14(1), e100592 (2018).
(218) Yuri A. Nedialkov,
Kristopher Opron, Hailey L. Caudill1, Fadi Assaf, Amanda J. Anderson,
Robert I. Cukier, Guo-Wei
Wei and Zachary F. Burton, Hinge action
versus grip in translocation by RNA polymerase, Transcription, 9,1-16 (2018)
(216) Bao Wang, Chengzhang Wang, Kedi Wu and Guo-Wei Wei, Breaking the polar-nonpolar division in
solvation free energy prediction, Journal of Computational Chemistry, 39, 217–232
(2018).
(215) Z. X. Cang and Guo-Wei Wei, Integration of element specific persistent
homology and machine learning for protein-ligand binding affinity prediction, International Journal for Numerical Methods in Biomedical Engineering,
34 (2), e2914 (2018).
(214) Guo-Wei Wei,
Mathematics at the eve of a historic transition in biology, Molecular Based Mathematical
Biology, 5, 138-141 (2017).
(213)
Guo-Wei Wei, Persistent homology analysis of biomolecular data, SIAM News, 50 (10) December (2017).
(212) Z. X. Cang and Guo-Wei Wei, TopologyNet: Topology based deep
convolutional and multi-task neural networks for biomolecular
property predictions
,
PLOS Computational Biology, 13(7), e1005690 (2017).
(211) Z. X. Cang and Guo-Wei Wei, Element specific persistent homology for the
analysis and prediction of protein folding stability upon mutation,
Bioinformatics, 33, 3549-3557 (2017).
(210)
Duc D Nguyen, Tian Xiao, Menglun
Wang and Guo-Wei Wei, Rigidity strengthening: A mechanism for protein-ligand binding, Journal
of Chemical Information and Modeling, 57, 1715-1721 (2017).
(209) Bao Wang, Zhixiong Zhao, Duc Nguyen and Guo-Wei Wei, Feature functional theory - binding predictor
(FFT-BP) for the blind prediction of binding free energy, Theoretical Chemistry
Account, 136, 55 (2017).
(207) Duc D Nguyen, Bao Wang and Guo-Wei Wei,
Accurate, robust
and reliable calculations of Poisson-Boltzmann binding
energies, Journal of Computational
Chemistry, 38, 941-948 (2017).
(206) Duan Chen and Guo-Wei Wei, A Review of Mathematical Modeling,
Simulation and Analysis of Membrane Channel Charge Transport, Reference Module in Life
Sciences, https://doi.org/10.1016/B978-0-12-809633-8.12044-8
(2017).
(205) Yongcheng Zhou and Guo-Wei
Wei, Variational Methods for Biomolecular Modeling, in Variational
Methods in Molecular Modeling, Edited by Jianzhong
Wu, Springer Science+Business Media Singapore,
181-221, (2017).
(204) Beibei Liu, Bao Wang, Rundong Zhao, Yiying Tong and Guo-Wei Wei, ESES:
software for Eulerian solvent excluded surface, Journal of
Computational Chemistry, 38, 446-466 (2017).
(203)
Lin Mu, Kelin Xia and Guo-Wei
Wei, Geometric and electrostatic
modeling using molecular rigidity functions, Journal of Computational
and Applied Mathematics, 313, 18-37
(2017).
(202) Duc D Nguyen and Guo-Wei Wei, The impact of surface area, volume, curvature and Lennard-Jones potential to solvation modeling, Journal of Computational Chemistry, 38, 24–36 (2017).
(200) Guo-Wei Wei, Mathematical Molecular Bioscience and Biophysics, SIAM News, 49 (7), (2016).
(199) Bao Wang, Zhixiong Zhao and Guo-Wei Wei, Automatic parametrization of non-polar implicit solvent models for the blind prediction of solvation free energies, Journal of Chemical Physics, 145, 124110 (2016).
(198) Duc D Nguyen, Kelin Xia and Guo-Wei Wei, Generalized flexibility-rigidity index, Journal of Chemical Physics, 144, 234106 (2016).
(197)
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).
(196) Zachary F. Burton, Kristopher Opron, Guowei Wei and James H. Geiger, A model for genesis of transcription systems, Transcription, 7, 1-13 (2016).
(195) Bao Wang and Guo-Wei Wei, Object-oriented persistent homology, Journal of Computational Physics, 305, 276-299 (2016).
(194) Zixuan Cang, Lin Mu, Kedi Wu, Kris Opron, Kelin Xia and Guo-Wei Wei, A topological approach to protein classification, Molecular based Mathematical Biology, 3, 140-162 (2015)
(193) 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).
(192) Bao Wang and Guo-Wei Wei, Parameter optimization in differential geometry based solvation models, Journal of Chemical Physics, 143, 134119 (2015).
(191) Kelin Xia, Zhixiong Zhao
and Guo-Wei
Wei, Multiresolution persistent homology
for excessively large biomolecular datasets, Journal of Chemical Physics, 143, 134103 (2015).
(190) Kristopher Opron, Kelin Xia, and Guo-Wei Wei,
Communication: Capturing protein multiscale thermal fluctuations, Journal of
Chemical Physics, 142, 211101 (2015).
(189) Jinkyoung Park, Kelin Xia and G.W. Wei, Atomic scale design and three-dimensional simulations of nanofluidic systems, Microfluidics and Nanofluidics, 19, 665-692 (2015).
(188) Kelin Xia and Guo-Wei Wei, Multidimensional persistence in biomolecular data, Journal of Computational Chemistry, 36, 1502-1520 (2015).
(187) Kelin Xia, Zhixiong Zhao and Guo-Wei Wei, Multiresolution topological simplification, Journal of Computational Biology, 22, 9, 1-5 (2015).
(185) Kelin Xia and Guo-Wei Wei, Persistent topology for cryo-EM data analysis, International Journal for Numerical Methods in Biomedical Engineering, 31, e02719 (2015).
(182) Kelin Xia, X. Feng, Yiying Tong and Guo-Wei Wei, Persistent homology for the quantitative prediction of fullerene stability, Journal of Computational Chemistry, 36, 408-422 (2015).
(178) Kelin Xia and Guo-Wei Wei, Persistent homology analysis of protein structure, flexibility and folding, International Journal for Numerical Methods in Biomedical Engineering, 30, 814-844 (2014).
(177) Kristopher Opron, Kelin Xia, and Guo-Wei Wei, Fast and anisotropic flexibility-rigidity index for protein flexibility and fluctuation analysis, Journal of Chemical Physics, 140(23), (2014).
(176) Kelin Xia and Guo-Wei Wei, Molecular nonlinear dynamics and protein thermal uncertainty quantification, Chaos, 24, 013103 (2014).
(174) Kelin Xia, Xin Feng, Zhan Chen, Yiying Tong and Guo-Wei Wei, Multiscale geometric modeling of macromolecules I: Cartesian representation, Journal of Computational Physics, 257, 912-936 (2014).
(173) Kelin Xia, and Guo-Wei Wei, A stochastic model for protein flexibility analysis, Physical Review E, 88, 062709 (2013).
(172)
X. 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).
(171) Kelin Xia, Kristopher Opron and Guo-Wei Wei, Multiscale multiphysics and multidomain models — Flexibility and rigidity, Journal of Chemical Physics, 139, 194109 (2013).
(169) Michael Daily, Jaehun Chun, Alejandro Heredia-Langner, Guo-Wei Wei, and Nathan Baker, Origin of parameter degeneracy and molecular shape relationships in geometric-flow calculations of solvation free energies. Journal of Chemical Physics, 139, 204108 (2013).
(168) Guo-Wei Wei, Multiscale multiphysics and multidomain models I: Basic theory, Journal of Theoretical and Computational Chemistry, 12(8), 1341006, (2013)
(167) Jinkyoung Park and G.W. Wei, A molecular level prototype for mechanoelectrical transducers in mammalian hair cells, Journal of Computational Neuroscience, 35, 231-241, (2013).
(166) Dennis G. Thomas, Jaehun Chun, Zhan Chen, Guo-Wei Wei, Nathan A. Baker, Parameterization of a geometric flow implicit solvation model, Journal of Computational Chemistry, 24, 687-695 (2013)
(165) Emil Alexov and Guo-Wei Wei, Preface:
Special issue on modeling electrostatics
in molecular biology (MEMB),
Commun. Comput. Phys., 13(1) 1-5, (2013).
(164) Duan Chen and Guo-Wei Wei, Quantum dynamics in continuum models for proton transport I: Basic formulation, Communication in Computational Physics, 13, 285-324 (2013)
(163) Langhua Hu, Duan Chen and Guo-Wei Wei, High-order fractional partial differential equations for molecular surface construction, Molecular Based Mathematical Biology, 1-25 (2012).
(162) X. 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, 1198-1223 (2012).
(161) Zhan Chen, Shan Zhao, Jaehun Chun, Dennis G. Thomas, Nathan Baker, Peter Bates and Guo-Wei Wei, Variational approach for nonpolar solvation analysis, Journal of Chemical Physics, 137, 084101 (2012).
(160) Anita T. Layton and Guo-Wei Wei, Editorials: Interface methods for biological and biomedical problems, International Journal for Numerical Methods in Biomedical Engineering, 28, 289–290, (2012)
(159) Duan Chen and Guo-Wei Wei, Quantum dynamics in continuum models for proton transport --- Generalized correlation, Journal of Chemical Physics, 136, 134109 (2012)
(158) Guo-Wei Wei, Qiong Zheng, Zhan Chen, and Kelin Xia, Variational multiscale models for charge transport, SIAM Review. 54(4), 699-754 (2012)
(157) Yang Wang, Guo-Wei Wei and Siyang Yang, Selective extraction of entangled textures via adaptive PDE transform, Int. J. Biomed Imaging, Volume 2012 (2012), Article ID 958142 (2012).
(156) Langhua Hu and Guo-Wei Wei, Nonlinear Poisson equation for inhomogeneous media. Biophysical Journal, 103, 758–766 (2012).
(155) Duan Chen, Zhan Chen and Guo-Wei Wei, Quantum dynamics in continuum models for proton transport II: Variational solvent-solute interface, International Journal for Numerical Methods in Biomedical Engineering, 28, 25-51 (2012)
(154) Qiong Zheng, Siyang Yang and Guo-Wei Wei, Molecular surface generation using PDE transform. International Journal for Numerical Methods in Biomedical Engineering, 28, 291-316 (2012)
(150) Zhan Chen and G. W. Wei, Differential geometry based salvation model III: Quantum formulation, Journal of Chemical Physics, 135, 194108 (2011).
(149) Qiong Zheng and Guo-Wei Wei, Poisson-Boltzmann-Nernst-Planck model.
Journal of Chemical
Physics, 134 (19),
194101, (2011) (It was
the most downloaded
in JCP in
May 2011)
(146) Qiong Zheng, Duan Chen and Guo-Wei Wei, Second-order Poisson-Nernst-Planck solver for ion transport. Journal of Computational Physics, 230, 5239-5262 (2011)
(145) Zhan Chen, Nathan Baker and G. W. Wei, Differential geometry based salvation model II: Lagrangian formulation (62 pages), Journal of Mathematical Biology, 63, 1139–1200, (2011).
(144) Weihua Geng and G.W. Wei, Multiscale molecular dynamics via the matched interface and boundary (MIB) method, Journal of Computational Physics, 230, 435-457 (2011).
(143) Duan Chen, Zhan Chen, Changjun Chen, Weihua Geng and Guo-Wei Wei, MIBPB: A software package for electrostatic analysis, Journal of Computational Chemistry, 32, 756–770 (2011).
(141) Zhan Chen, Nathan Baker and G. W. Wei, Differential geometry based solvation model I: Eulerian formulation, Journal of Computational Physics, 229, 8231-8258 (2010).
(140) Duan Chen and Guo-Wei Wei, Modeling and simulation of nano-electronic devices (44 pages), Journal of Computational Physics, 229, 4431-4460, (2010).
(139) Changjun Chen, Rishu Saxena, and Guo-Wei Wei, Differential geometry based multiscale model for virus capsid dynamics, Int. J. Biomed Imaging, Volume 2010, Article ID 308627, 9 pages (2010).
(138) Guo-Wei, Wei, Differential geometry based multiscale models, Bulletin of Mathematical Biology, volume 72, 1562-1622, (2010).
(136) G.W. Wei and G.
Wang, Editoral: Special
issue on recent
advances in computational
techniques for biomedical
imaging, Commun. Numer. Methods Engng, 25,
581-582 (2009)
(135) P.
Bates, Z. Chen, Y.H.
Sun, G.W. Wei and
S. Zhao, Geometric and
potential driving formation
and evolution of
biomolecular surfaces, J.
Math. Biol. 59, 193-231 (2009)
(133) Duan Chen, G.W.
Wei, X. Cong
and Ge Wang,
Computational methods for
optical molecular imaging,
Commun.
Numer. Methods Engng,
25,
1137-1161(2008).
(130) W.H. Geng,
S.N. Yu and
G.W. Wei, Treatment of
charge singularities in
implicit solvent models,
J. Chem. Phys., 127,
114106 (20 pages)
(2007). Also available
at the Virtual
Journal of Biological
Physics Research October
1, 2007
(129) P.
Bates, G.W. Wei and
S. Zhao, Minimal molecular
surfaces and their
applications, J. Comput. Chem., .,
29, 380-391 (2008).
(128) S.
N. Yu, W.
H. Geng and
G.W. Wei, Treatment of
geometric singularities in
implicit solvent models,
J. Chem. Phys.,
126, 244108 (13
pages) (2007). ). Also available at
the Virtual Journal
of Biological Physics
Research July 1,
2007
(127) Y.C.
Zhou, M. Feig and
G.W. Wei, Highly
accurate biomolecular electrostatics in
continuum dielectric environments, J. Comput. Chem. 29, 87-97
(2008).
(124) G.W.
Wei, Editoral: Recent
advances in mathematical
methods for the
analysis of biomedical
image, International Journal
of Biomedical Imaging,
vol. 2006, 70578,
1, (2006).
(121) Ge
Wang, Haiou Shen Wenxiang Cong, Shan
Zhao and G.W.
Wei,
Temperature
modulated bioluminescence tomography,
Optics Express, 14
(17) 7852-7871 (2006).
(MB2) P. W.
Bates, G.W. Wei and Shan Zhao, The minimal molecular surface, arXiv:q-bio/0610038 [q-bio.BM] (2006).
(MB1) G. W. Wei, Yuhui Sun, Yongcheng Zhou and Michael Feig, Molecular multiresolution surfaces, arXiv:math-ph/0511001v1 1 Nov 2005.