@article{Koehl:2021a, author = {P. Koehl and H. Orland and M. Delarue}, title = {Parameterizing elastic network models to capture the dynamics of proteins}, journal = {J.\ Chem.\ Phys.}, volume = {43}, pages = {1643}, year = {2021} }
@article{Koehl:2021b, author = {P. Koehl and M. Delarue and H. Orland}, title = {Simultaneous identification of multiple binding sites in proteins: A statistical mechanics approach}, journal = {J.\ Phys.\ Chem.\ B}, volume = {125}, pages = {5052}, year = {2021} }
@article{Koehl:2021c, author = {P. Koehl and H. Orland}, title = {Fast computation of exact solutions of generic and degenerate assignment problems}, journal = {Phys.\ Rev. E}, volume = {103}, pages = {042101}, year = {2021} }
@article{Koehl:2021d, author = {P. Koehl and M. Delarue and H. Orland}, title = {Physics approach to the variable-mass optimal-transport problem}, journal = {Phys.\ Rev. E}, volume = {103}, pages = {012113}, year = {2021} }
@article{Koehl:2019a, author = {P. Koehl and M. Delarue and H. Orland}, title = {Statistical physics approach to the optimal transport problem}, journal = {Phys.\ Rev.\ Lett.}, volume = {123}, pages = {040603}, year = {2019} }
@article{Koehl:2019b, author = {P. Koehl and M. Delarue and H. Orland}, title = {Optimal transport at finite temperature}, journal = {Phys.\ Rev.\ E}, volume = {100}, pages = {013310}, year = {2019} }
@article{Koehl:2019c, author = {P. Koehl and M. Delarue}, title = {Coarse-grained dynamics of supramolecules: Conformational changes in outer shells of Dengue viruses}, journal = {Prog.\ Biophys.\ Molec.\ Biol.}, volume = {143}, pages = {20}, year = {2019} }
@article{Guan:2019, author = {J. Guan and F. Hsieh and P. Koehl}, title = {DCG++: A data-driven metric for geometric pattern recognition}, journal = {{PloS} One}, volume = {14}, pages = {e0217838}, year = {2019} }
@article{Hsieh:2019, author = {F. Hsieh and O. Lee and C. Heitkamp and H. Heymann and S. E. Ebeler and R. B. Boulton and P. Koehl}, title = {Unraveling the regional specificities of Malbec wines from Mendoza, Argentina and from Northern California}, journal = {Agronomy}, volume = {9}, pages = {234}, year = {2019} }
@article{Koehl:2019d, author = {P. Koehl and H. Orland and M. Delarue}, title = {Numerical encodings of amino acids in multivariate Gaussian modeling of protein multiple sequence alignments}, journal = {Molecules}, volume = {24}, pages = {104}, year = {2019} }
@article{Hu:2018, author = {H. Hu and K. Ataka and A. Menny and Z. Fourati and L. Sauguet and P.-J. Corringer and P. Koehl and J. Heberle and M. Delarue}, title = {Electrostatics, proton sensor, and networks governing the gating transition in GLIC, a proton-gated pentameric ion channel}, journal = {Proc.\ Natl.\ Acad.\ Sci.\ (USA)}, volume = {115}, pages = {E12172-E12181}, year = {2018} }
@article{Vaziri:2018, author = {S. Vaziri and P. Koehl and S. Aviran}, title = {Extracting information from RNA SHAPE data: Kalman filtering approach}, journal = {{PloS} One}, volume = {13}, pages = {e0207029}, year = {2018} }
@article{Koehl:2018a, author = {P. Koehl}, title = {Large eigenvalue problems in coarse-grained dynamic analyses of supra molecular systems}, journal = {J.\ Chem.\ Theo.\ Comput.}, volume = {14}, pages = {3903-3919}, year = {2018} }
@article{Koehl:2018b, author = {P. Koehl and M. Delarue}, title = {Combined approaches from physics, statistics, and computer science for ab initio protein structure prediction: ex unitate vires (unity is strength)?}, journal = {F1000 Research}, volume = {7}, pages = {1125}, year = {2018} }
@article{Saunders:2018, author = {T.E. Saunders and C.Y. He and P. Koehl and L.L.S. Ong and P.T.C. So}, title = {Eleven quick tips for running an interdisciplinary short course for new graduate students}, journal = {{PLoS} Comput.\ Biol.}, volume = {14}, pages = {e1006039}, year = {2018} }
@article{Koehl:2017a, author = {P. Koehl}, title = {Minimum action principle and shape dynamics}, journal = {J.\ R.\ Soc.\ Interface}, volume = {14}, pages = {20170031}, year = {2017} }
@article{Nojoomi:2017, author = {S. Nojoomi and P. Koehl}, title = {A weighted string kernel for protein fold recognition}, journal = {BMC Bioinformatics}, volume = {18}, pages = {378}, year = {2017} }
@article{Hass:2017, author = {J. Hass and P. Koehl}, title = {Comparing shapes of genus-zero surfaces}, journal = {J.\ Applied Comput.\ Topology}, volume = {1}, pages = {57}, year = {2017} }
@article{Delarue:2017, author = {M. Delarue and P. Koehl and H. Orland}, title = {Ab initio sampling of transition paths by conditioned Langevin dynamics}, journal = {J.\ Chem.\ Phys.}, volume = {147}, pages = {152703}, year = {2017} }
@article{Hsieh:2017, author = {Y.-C. Hsieh and F. Poitevin and M. Delarue and P. Koehl}, title = {Comparative Normal Mode Analysis of the Dynamics of DENV and ZIKV Capsids}, journal = {Frontiers Mol.\ Biosci.}, volume = {3}, pages = {85}, year = {2017} }
@article{Koehl:2017b, author = {P. Koehl and F. Poitevin and R. Navaza and M. Delarue}, title = {The Renormalization Group and Its Applications to Generating Coarse-Grained Models of Large Biological Molecular Systems}, journal = {J.\ Chem.\ Theo.\ Comput.}, volume = {13}, pages = {1424}, year = {2017} }
@article{Nojoomi:2017b, author = {S. Nojoomi and P. Koehl}, title = {String kernels for protein sequence comparisons: improved fold recognition}, journal = {BMC Bioinformatics}, volume = {18}, pages = {137}, year = {2017} }
@article{Koehl:2016a, author = {P. Koehl}, title = {Minimum action transition paths connecting minima on an energy surface}, journal = {J.\ Chem.\ Phys.}, volume = {145}, pages = {184111}, year = {2016} }
@article{Fourati:2016, author = {Z. Fourati and R. R. Ruza and D. Laverty and E. Drege and S. Delarue-Cochin and D. Joseph and P. Koehl and T. Smart and M. Delarue}, title = {Barbiturates bind in the GLIC ion channel pore and cause inhibition by stabilizing a closed state}, journal = {J.\ Bio.\ Chem.}, volume = {292}, pages = {1550}, year = {2016} }
@article{Edelsbrunner:2016, author = {H. Edelsbrunner and P. Koehl}, title = {Computational topology for structural molecular biology}, journal = {Handbook of Computational Geometry}, volume = {1}, pages = {}, year = {2016} }
@article{Koehl:2015a, author = {P. Koehl and J. Hass}, title = {Landmark-free geometric methods in biological shape analysis}, journal = {J.\ R.\ Soc.\ Interface}, volume = {12}, pages = {20150795}, year = {2015} }
@article{Fushing:2015, author = {H. Fushing and C.H. Hsieh and C. Heitkamp and M.A. Matthews P. Koehl.}, title = {Unravelling the geometry of data matrices: effects of water stress regimes on winemaking}, journal = {J.\ R.\ Soc.\ Interface}, volume = {12}, pages = {20150753}, year = {2015} }
@article{Hass:2015, author = {J. Hass and P. Koehl}, title = {A metric for genus-zero surfaces}, journal = {arXiv:1507.00798}, pages = {arXiv:1507.00798}, year = {2015} }
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