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@article{Angelelli2011StraighteningTubularFlow,
title={Straightening tubular flow for side-by-side visualization},
author={Angelelli, Paolo and Hauser, Helwig},
journal={Visualization and Computer Graphics, IEEE Transactions on},
volume={17},
number={12},
pages={2063--2070},
year={2011},
publisher={IEEE}
}
@article{Auzinger2013Vessel,
title={Vessel visualization using curved surface reformation},
author={Auzinger, Thomas and Mistelbauer, Gabriel and Baclija, Ivan and Schernthaner, Rudiger and Kochl, Arnold and Wimmer, Manuel and Gr{\"o}ller, M Eduard and Bruckner, Stefan},
journal={Visualization and Computer Graphics, IEEE Transactions on},
volume={19},
number={12},
pages={2858--2867},
year={2013},
publisher={IEEE}
}
@inproceedings{Brambilla2016ComparativeVisTimeSufaces,
title={Comparative visualization of multiple time surfaces by planar surface reformation},
author={Brambilla, Andrea and Angelelli, Paolo and {\O}. Andreassen and Hauser, Helwig},
booktitle={2016 IEEE Pacific Visualization Symposium (PacificVis)},
pages={88--95},
year={2016},
organization={IEEE}
}
@article{Brezovsky2013SoftwareTools,
title = {Software tools for identification, visualization and analysis of protein tunnels and channels},
author = {Jan Brezovsk{\'y} and Eva Chovancov{\'a} and Artur Gora and Antonin Pavelka and Lada Biedermannov{\'a} and Jiri Damborsk{\'y}},
journal = {Biotechnology Advances},
volume = {31},
number = {1},
pages = {38--49},
year = {2013}
}
@ARTICLE{Elzen2016SnapshotsToPoints,
author={S. van den Elzen and D. Holten and J. Blaas and J. J. van Wijk},
journal={IEEE Transactions on Visualization and Computer Graphics},
title={Reducing Snapshots to Points: A Visual Analytics Approach to Dynamic Network Exploration},
year={2016},
volume={22},
number={1},
pages={1-10}
}
@article{Fang2013NaturalImageStatistics,
author={H. Fang and G. K. L. Tam and R. Borgo and A. J. Aubrey and P. W. Grant and P. L. Rosin and C. Wallraven and D. Cunningham and D. Marshall and M. Chen},
journal={IEEE Transactions on Visualization and Computer Graphics},
title={Visualizing Natural Image Statistics},
year={2013},
volume={19},
number={7},
pages={1228-1241},
publisher={IEEE}
}
@incollection{Faraj2012RobustDeformationInVolumetricMedicalImages,
title={Robust and scalable interactive freeform modeling of high definition medical images},
author={Faraj, Noura and Thiery, Jean-Marc and Bloch, Isabelle and Varsier, Nad{\`e}ge and Wiart, Joe and Boubekeur, Tamy},
booktitle={Mesh Processing in Medical Image Analysis 2012},
pages={1--11},
year={2012},
publisher={Springer}
}
@book{Flusser09Moments,
author = {Flusser, Jan and Suk, Tomas and Zitova, Barbara},
publisher = {John Wiley \& Sons, Ltd},
isbn = {9780470684757},
title = {Moments and Moment Invariants in Pattern Recognition},
year = {2009}
}
@article{Gleicher2011VisualComparisonInformationVisualization,
author = {Michael Gleicher and Danielle Albers and Rick Walker and Ilir Jusufi and Charles D. Hansen and Jonathan C. Roberts},
title = {Visual Comparison for Information Visualization},
journal = {Information Visualization},
year = {2011},
volume = {10},
number = {4},
pages = {289--309}
}
@article{Kim2005KPCA,
author={Kwang In Kim and M. O. Franz and B. Scholkopf},
journal={IEEE Transactions on Pattern Analysis and Machine Intelligence},
title={Iterative kernel principal component analysis for image modeling},
year={2005},
volume={27},
number={9},
pages={1351-1366},
publisher={IEEE}
}
@inproceedings {Kozlikova2015VisualizationBiomolecularStructure,
title = {Visualization of Biomolecular Structures: State of the Art},
author = {Kozlikova, Barbora and Krone, Michael and Lindow, Norbert and Falk, Martin and Baaden, Marc and Baum, Daniel and Viola, Ivan and Parulek, Julius and Hege, Hans-Christian},
booktitle = {Eurographics Conference on Visualization (EuroVis) - STARs},
pages = {061--081},
year = {2015},
publisher = {The Eurographics Association}
}
@article{Kretschmer2014AnatomyDriveReformation,
title={{ADR}-anatomy-driven reformation},
author={Kretschmer, Jan and Soza, Grzegorz and Tietjen, Christian and Suehling, Michael and Preim, Bernhard and Stamminger, Marc},
journal={Visualization and Computer Graphics, IEEE Transactions on},
volume={20},
number={12},
pages={2496--2505},
year={2014},
publisher={IEEE}
}
@article {Krone2016VisualAnalysisBiomolecularCavities,
title = {Visual Analysis of Biomolecular Cavities: State of the Art},
author = {Krone, Michael and Kozl{\'i}kova, Barbora and Lindow, Norbert and Baaden, Marc and Baum, Daniel and Parulek, Julius and Hege, Hans-Christian and Viola, Ivan},
journal = {Computer Graphics Forum},
volume = {35},
number = {3},
year = {2016}
}
@inproceedings{Liu2008LocalGlobalMeshParametrization,
title={A local/global approach to mesh parameterization},
author={Liu, Ligang and Zhang, Lei and Xu, Yin and Gotsman, Craig and Gortler, Steven J},
booktitle={Computer Graphics Forum},
volume={27},
number={5},
pages={1495--1504},
year={2008},
organization={Wiley Online Library}
}
@article{Masood2015CHEXVIS,
title = {{CHEXVIS}: a tool for molecular channel extraction and visualization},
author = {Masood, Talha Bin and Sandhya, Sankaran and Chandra, Nagasuma and Natarajan, Vijay},
journal = {BMC Bioinformatics},
volume = {16},
number = {1},
pages = {1--19},
year = {2015}
}
@inproceedings{Macqueen1967KMeans,
author = {MacQueen, J.},
title = {Some methods for classification and analysis of multivariate observations},
booktitle = {Proceedings of the Fifth Berkeley Symposium on Mathematical Statistics and Probability, Volume 1: Statistics},
pages = {281--297},
year = {1967},
publisher = {University of California Press}
}
@article{mateen2008tsne,
title={Visualizing High-Dimensional Data Using t-SNE},
author={L.J.P. van der Maaten and G.E. Hinton},
journal={Journal of Machine Learning Research},
volume={9},
pages={2579--2605},
year={2008}
}
@inproceedings{Mistelbauer2012CP,
title={Centerline reformations of complex vascular structures},
author={Mistelbauer, Gabriel and Varchola, Andrej and Bouzari, Hamed and Starinsky, Juraj and K{\"o}chl, Arnold and Schernthaner, R{\"u}diger and Fleischmann, Dominik and Gr{\"o}ller, Meister Eduard and {\v{S}}r{\'a}mek, Milos},
booktitle={Visualization Symposium (PacificVis), 2012 IEEE Pacific},
pages={233--240},
year={2012},
organization={IEEE}
}
@article{Oeltze2007IVAPerfusionData,
title = {Interactive Visual Analysis of Perfusion Data},
author = {S. Oeltze and H. Doleisch and H. Hauser and P. Muigg and B. Preim},
journal = {IEEE Transactions on Visualization and Computer Graphics},
volume = {13},
number = {6},
pages = {1392--1399},
year = {2007},
publisher = {IEEE}
}
@article{Olshausen1997ICA,
title = {Sparse coding with an overcomplete basis set: A strategy employed by V1?},
author = {Bruno A. Olshausen and David J. Field},
journal = {Vision Research},
volume = {37},
number = {23},
pages = {3311 -- 3325},
year = {1997},
publisher={Elsevier}
}
@article{Gurijala2013Colon,
title={Colon Flattening Using Heat Diffusion Riemannian Metric},
author={Gurijala, Krishna Chaitanya and Shi, Rui and Zeng, Wei and Gu, Xianfeng and Kaufman, Arie},
journal={Visualization and Computer Graphics, IEEE Transactions on},
volume={19},
number={12},
pages={2848--2857},
year={2013},
publisher={IEEE}
}
@article{Weisel2007PocketPicker,
title={PocketPicker: analysis of ligand binding-sites with shape descriptors},
author={Weisel, Martin and Proschak, Ewgenij and Schneider, Gisbert},
journal={Chemistry Central Journal},
volume={1},
number={1},
pages={1},
year={2007},
publisher={Springer International Publishing}
}
%%%%% JB: LIST OF ALPHABETICALLY SORTED REFERENCES FOR FUTURE USE --- PLEASE DO NOT INSERT ANYTHING NEW BELOW THIS COMMENT
%%%%% JB: I'LL FIX MY PERSONAL NAMING CONVENTIONS AND SORT THE REFERENCES LATER
%%%%% JB: FIXES, IMPROVEMENTS, ETC. ARE, ON THE OTHER HAND, ALLOWED AND WELCOME! :)
@article{Agre1995AquaporinWaterChannels,
title = {Aquaporin water channels: unanswered questions and unresolved controversies},
author = {Agre, Peter and Brown, Dennis and Nielsen, S{\o}ren},
journal = {Current Opinion in Cell Biology},
volume = {7},
number = {4},
pages = {472--483},
year = {1995},
publisher = {Elsevier}
}
@article{Ahn2004ConnectivityTransformation,
author = {M. Ahn and S. Lee and H. Seidel},
journal = {Proceedings of the 2004 Eurographics/ACM SIGGRAPH Symposium on Geometry Processing},
pages = {75-82},
title = {Connectivity transformation for mesh metamorphosis},
year = {2004}
}
@article{Alard1991Cavities,
title = {Detection of cavities in a set of interpenetrating spheres},
author = {Alard, Philippe and Wodak, Shoshana J},
journal = {Journal of Computational Chemistry},
volume = {12},
number = {8},
pages = {918--922},
year = {1991},
publisher = {Wiley Online Library}
}
@article{An2005Pocketome,
title = {Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes},
author = {An, Jianghong and Totrov, Maxim and Abagyan, Ruben},
journal = {Molecular \& Cellular Proteomics},
volume = {4},
number = {6},
pages = {752--761},
year = {2005},
publisher = {ASBMB}
}
@book{Averill2007PrinciplesGeneralChemistry,
title = {Principles of General Chemistry},
author = {Averill, Bruce and Eldredge, Patricia},
publisher = {2012 Book Archive by Andy Schmitz}
}
@article{Bartek2001G1S,
title = {Pathways governing {G1/S} transition and their response to {DNA} damage},
author = {Bartek, Jiri and Lukas, Jiri},
journal = {FEBS Letters},
volume = {490},
number = {3},
pages = {117--122},
year = {2001},
publisher = {Elsevier}
}
@inproceedings{Benes2010TrackingSingleChannel,
title = {Tracking single channel in protein dynamics},
author = {Bene{\v{s}}, Petr and Medek, Petr and Sochor, Ji{\v{r}}{\'\i}},
booktitle = {WSCG 2010: Communication Papers Proceedings},
volume = {2},
editor = {Skala, Václav},
pages = {109--114},
year = {2010},
isbn = {978-80-86943-94-7}
}
@inproceedings{Benes2011DynamicTunnel,
title = {Computation of channels in protein dynamics},
author = {Bene\v{s}, Petr and Medek, Peter and Sochor, Ji{\v{r}}{\'\i}},
booktitle = {Proceedings of the IADIS International Conference Applied Computing},
pages = {251--258},
month = {November},
year = {2009},
address = {Rome, Italy},
editor = {Weghorn, Hans and Isa{\'\i}as, Pedro}
}
@inproceedings{Benes2011ConstrainedDynamicTunnels,
title = {New path planning method for computation of constrained dynamic channels in proteins},
author = {Bene{\v{s}}, Petr and Strnad, Ond{\v{r}}ej and Sochor, Ji{\v{r}}{\'\i}},
year = {2011},
pages = {81--88},
booktitle = {WSCG 2011: Full Papers Proceedings},
publisher = {V{\'a}clav Skala-UNION Agency}
}
@article{Benkaidali2013CavitiesChannelsPoresPocketsNonSphericalLigandModels,
title = {Computing cavities, channels, pores and pockets in proteins from non-spherical ligands models},
author = {Benkaidali, Lydia and Andr{\'e}, Fran{\c{c}}ois and Maouche, Boubekeur and Siregar, Pridi and Benyettou, Mohamed and Maurel, Fran{\c{c}}ois and Petitjean, Michel},
journal = {Bioinformatics},
pages = {btt644},
year = {2013},
publisher = {Oxford University Press}
}
@article{Berman2000PDB,
author = {Berman, Helen M. and Westbrook, John and Feng, Zukang and Gilliland, Gary and Bhat, T. N. and Weissig, Helge and Shindyalov, Ilya N. and Bourne, Philip E.},
title = {The Protein Data Bank},
volume = {28},
number = {1},
pages = {235-242},
year = {2000},
journal = {Nucleic Acids Res.}
}
@article {Bidmon2008SolventPathlines,
author = {Bidmon, Katrin and Grottel, Sebastian and B\"{o}s, Fabian and Pleiss, J\"{u}rgen and Ertl, Thomas},
title = {Visual Abstractions of Solvent Pathlines near Protein Cavities},
journal = {Computer Graphics Forum},
volume = {27},
number = {3},
publisher = {Blackwell Publishing Ltd},
issn = {1467-8659},
url = {http://dx.doi.org/10.1111/j.1467-8659.2008.01227.x},
doi = {10.1111/j.1467-8659.2008.01227.x},
pages = {935--942},
year = {2008},
}
@article{Billeter2001HydrideTransferInLiver,
title = {Hydride Transfer in Liver Alcohol Dehydrogenase: Quantum Dynamics, Kinetic Isotope Effects, and Role of Enzyme Motion},
author = {Billeter, Salomon~R. and Webb, Simon~P. and Agarwal, Pratul~K. and Iordanov, Tzvetelin and Hammes-Schiffer, Sharon},
journal = {Journal of the American Chemical Society},
volume = {123},
number = {45},
pages = {11262--11272},
year = {2001},
publisher = {ACS Publications}
}
@misc{Blausen2016TransmembraneImage,
title = {Blausen gallery},
author = {Blausen.com~staff},
journal = {Wikiversity Journal of Medicine},
doi = {10.15347/wjm/2014.010},
issn = {20018762},
year = {2014}
}
@article{Blinn1982Surface,
title = {A Generalization of Algebraic Surface Drawing},
author = {Blinn, James~F.},
journal = {ACM Transactions on Graphics},
volume = {1},
number = {3},
pages = {235--256},
year = {1982},
publisher = {ACM}
}
@book{Bohr1913ConstitutionAtomsMolecules,
title={On the constitution of atoms and molecules: papers of 1913 reprinted from the {P}hilosophical magazine},
author={Bohr, Niels},
volume={1},
year={1963},
publisher={Munksgaard}
}
@article{Bornemann1996QuantumClassicalMD,
title = {Quantum--classical molecular dynamics as an approximation to full quantum dynamics},
author = {Bornemann, Folkmar~A. and Nettesheim, Peter and Sch{\"u}tte, Christof},
journal = {The Journal of Chemical Physics},
volume = {105},
number = {3},
pages = {1074--1083},
year = {1996},
publisher = {AIP Publishing}
}
@book{Branden1998Proteins,
title = {Introduction to Protein Structure: Second Edition},
author = {Branden, Carl and Tooze, John},
year = {1998},
publisher = {Garland Publishing, Inc.},
address = {19 Union Square West, New York},
isbn = {0--8153--2305--0}
}
@article{Brezovsky2013Tunnels,
title = {Software tools for identification, visualization and analysis of protein tunnels and channels},
author = {Brezovsk{\'y}, Jan and Chovancov{\'a}, Eva and Gora, Artur~W. and Pavelka, Anton{\'\i}n and Biedermannov{\'a}, Lada and Damborsk{\'y}, Ji{\v{r}}{\'\i}},
journal = {Biotechnology Advances},
volume = {31},
number = {1},
pages = {38--49},
year = {2013},
publisher = {Elsevier},
}
@inproceedings{Byska2012CESCG,
title = {Discovering molecules: Pass planning through a gap},
author = {By{\v{s}}ka, Jan and Sochor, Ji{\v{r}}{\'\i}},
editor = {Wimmer, Michael and Il{\v{c}}\'ik, Martin},
booktitle = {Proceedings of the 16th Central European Seminar on Computer Graphics},
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