Merge pull request #169 from markovmodel/revision-fn

revision fn

Author: cwehmeyer

manuscript/figures/figure_1.pdf

@@ -31,18 +31,6 @@ @article{hmm-tutorial
     URL = {https://doi.org/10.1109/5.18626},
     DOI = {10.1109/5.18626}
 }
-@article{kunsch-bootstrap,
-    Author = {Hans R. Kunsch},
-    Title = {The Jackknife and the Bootstrap for General Stationary Observations},
-    Journal = {Ann. Stat.},
-    Year = {1989},
-    Volume = {17},
-    Number = {3},
-    Pages = {1217--1241},
-    Month = {sep},
-    URL = {https://doi.org/10.1214/aos/1176347265},
-    DOI = {10.1214/aos/1176347265}
-}
 @article{tica2,
     Author = {Molgedey, L. and Schuster, H. G.},
     Title = {Separation of a mixture of independent signals using time delayed correlations},
@@ -88,7 +76,7 @@ @misc{scipy
 @inproceedings{aggarwal_surprising_2001,
     Author = {Aggarwal, Charu C. and Hinneburg, Alexander and Keim, Daniel A.},
     Title = {On the {Surprising} {Behavior} of {Distance} {Metrics} in {High} {Dimensional} {Space}},
-    Booktitle = {Database {Theory} — {ICDT} 2001},
+    Booktitle = {Database {Theory} --- {ICDT} 2001},
     Year = {2001},
     Editor = {Van den Bussche, Jan and Vianu, Victor},
     Pages = {420--434},
@@ -290,6 +278,14 @@ @article{noe-fingerprints
     URL = {https://doi.org/10.1073/pnas.1004646108},
     DOI = {10.1073/pnas.1004646108}
 }
+@article{bhmm-preprint,
+    Author = {{Chodera}, J.~D. and {Elms}, P. and {Noé}, F. and {Keller}, B. and {Kaiser}, C.~M. and {Ewall-Wice}, A. and {Marqusee}, S. and {Bustamante}, C. and {Singhal Hinrichs}, N.},
+    Title = {{Bayesian hidden Markov model analysis of single-molecule force spectroscopy: Characterizing kinetics under measurement uncertainty}},
+    Journal = {arXiv preprint arXiv:1108.1430},
+    Year = 2011,
+    Month = aug,
+    URL = {https://arxiv.org/pdf/1108.1430.pdf},
+}
 @article{dror2012biomolecular,
     Author = {Ron O. Dror and Robert M. Dirks and J.P. Grossman and Huafeng Xu and David E. Shaw},
     Title = {Biomolecular Simulation: A Computational Microscope for Molecular Biology},
@@ -390,6 +386,17 @@ @book{msm-book
     URL = {https://doi.org/10.1007%2F978-94-007-7606-7},
     DOI = {10.1007/978-94-007-7606-7}
 }
+@article{jhp-spectral-rate-theory,
+    Author = {Jan-Hendrik Prinz and John D. Chodera and Frank No{\'{e}}},
+    Title = {Spectral Rate Theory for Two-State Kinetics},
+    Journal = {Phys. Rev. X},
+    Year = {2014},
+    Volume = {4},
+    Number = {1},
+    Month = {feb},
+    URL = {https://doi.org/10.1103/physrevx.4.011020},
+    DOI = {10.1103/physrevx.4.011020}
+}
 @article{nueske-vamk,
     Author = {Feliks N\"{u}ske and Bettina G. Keller and Guillermo P{\'{e}}rez-Hern{\'{a}}ndez and Antonia S. J. S. Mey and Frank No{\'{e}}},
     Title = {Variational Approach to Molecular Kinetics},
@@ -570,6 +577,18 @@ @article{oom-feliks
     URL = {https://doi.org/10.1063/1.4976518},
     DOI = {10.1063/1.4976518}
 }
+@article{hao-variational-koopman-models,
+    Author = {Hao Wu and Feliks N\"{u}ske and Fabian Paul and Stefan Klus and P{\'{e}}ter Koltai and Frank No{\'{e}}},
+    Title = {Variational Koopman models: Slow collective variables and molecular kinetics from short off-equilibrium simulations},
+    Journal = {J. Chem. Phys.},
+    Year = {2017},
+    Volume = {146},
+    Number = {15},
+    Pages = {154104},
+    Month = {apr},
+    URL = {https://doi.org/10.1063/1.4979344},
+    DOI = {10.1063/1.4979344}
+}
 @article{NoeClementiReview,
     Author = {Frank No{\'{e}} and Cecilia Clementi},
     Title = {Collective variables for the study of long-time kinetics from molecular trajectories: theory and methods},
@@ -587,6 +606,7 @@ @article{vamp-preprint
     Journal = {arXiv preprint arXiv:1707.04659},
     Year = 2017,
     Month = jul,
+    URL = {https://arxiv.org/pdf/1707.04659.pdf},
 }
 @article{simon-amm,
     Author = {Simon Olsson and Hao Wu and Fabian Paul and Cecilia Clementi and Frank No{\'{e}}},
@@ -613,7 +633,7 @@ @article{trammbar
 }
 @article{plattner_complete_2017,
     Author = {Plattner, Nuria and Doerr, Stefan and Fabritiis, Gianni De and Noé, Frank},
-    Title = {Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and {Markov} modelling},
+    Title = {Complete protein--protein association kinetics in atomic detail revealed by molecular dynamics simulations and {Markov} modelling},
     Journal = {Nat. Chem.},
     Year = {2017},
     Volume = {9},
@@ -699,6 +719,7 @@ @article{deep-gen-msm-preprint
     Journal = {arXiv preprint arXiv:1805.07601},
     Year = 2018,
     Month = may,
+    URL = {https://arxiv.org/pdf/1805.07601.pdf},
 }
 @article{hernandez-vde,
     Author = {Carlos X. Hern{\'{a}}ndez and Hannah K. Wayment-Steele and Mohammad M. Sultan and Brooke E. Husic and Vijay S. Pande},