Gunther H. Weber

Staff Scientist & Adjunct Associate Professor
Deputy Group Leader
Data Analytics & Visualization Group
Data Science & Technology
Email: GHWeber@lbl.gov
Phone: 510-486-5871
Fax: 510-486-4300
One Cyclotron Road, MS 59R3103
Berkeley, California 94720 US

Biographical Sketch

Gunther H. Weber received a Ph.D. in computer science, with a focus on computer graphics and visualization, from the University of Kaiserslautern, Germany in 2003. He is currently a Staff Scientist in the Computational Research Division at the Lawrence Berkeley National Laboratory (LBNL), where he serves as Deputy Group Lead of the Data Analysis and Visualization Group in the Data Science and Technology Department. Gunther Weber is an Adjunct Associate Professor of Computer Science at the University of California, Davis. His research interests include computer graphics, scientific visualization, data analysis with using topological methods, parallel and distributed computing for visualization and data analysis applications, hierarchical data representation methods, and bioinformatics. He has extensive experience in working with researchers from diverse science and engineering fields, including applied numerical computing, combustion simulation, gene expression, medicine, civil engineering, cosmology, climate and particle accelerator modeling. Dr. Weber has authored or co-authored over 80 publications, five of which won best paper awards. He has served as principal investigator (PI) or Co-PI on several Department of Energy (DOE) and National Science Foundation (NSF) projects. He is a reviewer for major funding agencies (DOE, NSF), conference proceedings and journals. Dr. Weber served as co-organizer, co-chair and program committee member of more than 40 internationally recognized conferences.

Publications

Journal Articles

G. H. Weber, M. S. Bandstra, D. Chivers, H. H. Elgammal, V. Hendrix, J. Kua, J. Maltz, K. Muriki, Y. Ong, K. Song, M. Quinlan, L. Ramakrishnan, and B. J. Quiter, “Web-based Visual Data Exploration for Improved Radiological Source Detection,” Concurrency and Computation: Practice and Experience, vol. 29, no. 18, p. e4203, Sep. 2017.

@article{Weber:2017:ARESVis,
  author = {Weber, Gunther H. and Bandstra, Mark S. and Chivers, Daniel and Elgammal, Hamdy H. and Hendrix, Valerie and Kua, John and Maltz, Jonathan and Muriki, Krishna and Ong, Yeongshnn and Song, Kai and Quinlan, Michael and Ramakrishnan, Lavanya and Quiter, Brian J.},
  title = {Web-based Visual Data Exploration for Improved Radiological Source Detection},
  journal = {Concurrency and Computation: Practice and Experience},
  volume = {29},
  number = {18},
  issn = {1532-0634},
  month = sep,
  pages = {e4203},
  year = {2017},
  doi = {10.1002/cpe.4203},
  escholarshipurl = {https://escholarship.org/uc/item/14z1h9gr}
}

B. Friesen, A. Almgren, Z. Lukić, G. H. Weber, D. Morozov, V. Beckner, and M. Day, “In Situ and In-transit Analysis of Cosmological Simulations,” Computational Astrophysics and Cosmology, vol. 3, no. 4, pp. 1–18, Aug. 2016.

@article{Friesen:2016:FISIT,
  author = {Friesen, Brian and Almgren, Ann and Luki{\'c}, Zarija and Weber, Gunther H. and Morozov, Dmitriy and Beckner, Vincent and Day, Marcus},
  title = {\emph{In Situ} and In-transit Analysis of Cosmological Simulations},
  journal = {Computational Astrophysics and Cosmology},
  volume = {3},
  number = {4},
  pages = {1--18},
  month = aug,
  year = {2016},
  doi = {10.1186/s40668-016-0017-2},
  escholarshipurl = {https://escholarship.org/uc/item/2vg3b50m},
  lbnl-number = {LBNL-1006104},
  received = {8 May 2016},
  accepted = {17 August 2016},
  pulished = {24 August 2016}
}

S. Murugesan, K. Bouchard, J. A. Brown, B. Hamann, W. W. Seeley, A. Trujillo, and G. H. Weber, “Brain Modulyzer: Interactive Visual Analysis of Functional Brain Connectivity,” IEEE Transactions on Computational Biology and Bioinformatics, vol. 14, no. 4, pp. 805–818, Jul. 2017.

@article{Murugesan:2017:BrainModulyzer,
  author = {Murugesan, Sugeerth and Bouchard, Kristofer and Brown, Jesse A. and Hamann, Bernd and Seeley, William W. and Trujillo, Andrew and Weber, Gunther H.},
  title = {{B}rain {M}odulyzer: Interactive Visual Analysis of Functional Brain Connectivity},
  journal = {{IEEE} Transactions on Computational Biology and Bioinformatics},
  doi = {10.1109/TCBB.2016.2564970},
  volume = {14},
  number = {4},
  pages = {805--818},
  month = jul,
  year = {2017},
  lbnl-number = {LBNL-1005732},
  escholarshipurl = {https://escholarship.org/uc/item/3xt3702n}
}

T. Liebmann, G. H. Weber, and G. Scheuermann, “Hierarchical Correlation Clustering in Multiple 2D Scalar Fields,” Computer Graphics Forum (Special Issue, Proceedings Eurographics/IEEE Symposium on Visualization), vol. 37, no. 3, Jun. 2018.
```
@article{Liebmann:2018:HCC,
  author = {Liebmann, Tom and Weber, Gunther H. and Scheuermann, Gerik},
  title = {Hierarchical Correlation Clustering in Multiple 2D Scalar Fields},
  journal = {Computer Graphics Forum (Special Issue, Proceedings
               Eurographics/IEEE Symposium on Visualization)},
  year = {2018},
  volume = {37},
  number = {3},
  month = jun,
  doi = {10.1111/cgf.13396}
}
```
H. A. Carr, G. H. Weber, C. M. Sewell, O. Rübel, P. Fasel, and J. P. Ahrens, “Scalable Contour Tree Computation by Data Parallel Peak Pruning,” Transactions on Visualization and Computer Graphics, vol. 27, no. 4, pp. 2437–2454, Apr. 2021. Published online 2019.
```
@article{Carr:2021:DPCT,
  author = {Carr, Hamish A. and Weber, Gunther H. and Sewell, Christopher M. and R{\"u}bel, Oliver and Fasel, Patricia and Ahrens, James P.},
  title = {Scalable Contour Tree Computation by Data Parallel Peak Pruning},
  journal = {Transactions on Visualization and Computer Graphics},
  volume = {27},
  number = {4},
  month = apr,
  pages = {2437--2454},
  year = {2021},
  doi = {10.1109/TVCG.2019.2948616},
  note = {Published online 2019}
}
```

S. Murugesan, K. Bouchard, J. Brown, M. Kiran, D. Lurie, B. Hamann, and G. H. Weber, “State-based Network Similarity Visualization,” Information Visualization, vol. 19, no. 2, pp. 96–113, Apr. 2020. First published online November 2019.

@article{Murugesan:2020:SNSV,
  author = {Murugesan, Sugeerth and Bouchard, Kristofer and Brown, Jesse and Kiran, Mariam and Lurie, Dan and Hamann, Bernd and Weber, Gunther H.},
  title = {State-based Network Similarity Visualization},
  journal = {Information Visualization},
  volume = {19},
  number = {2},
  pages = {96--113},
  month = apr,
  year = {2020},
  publisher = {SAGE Publishing},
  doi = {10.1177/1473871619882019},
  escholarshipurl = {https://escholarship.org/uc/item/304277z3},
  note = {First published online {November} 2019}
}

K. Beketayev, D. Yeliussizov, D. Morozov, G. H. Weber, and B. Hamann, “Measuring the Error in Approximating the Sub-level Set Topology of Sampled Scalar Data,” International Journal of Computational Geometry & Applications, vol. 28, no. 1, pp. 57–77, Mar. 2018.
```
@article{Beketayev:2018:MEAT,
  author = {Beketayev, Kenes and Yeliussizov, Damir and Morozov, Dmitriy and Weber, Gunther H. and Hamann, Bernd},
  title = {Measuring the Error in Approximating the Sub-level Set Topology of Sampled Scalar Data},
  journal = {International Journal of Computational Geometry {\&} Applications},
  volume = {28},
  number = {1},
  month = mar,
  year = {2018},
  pages = {57--77},
  doi = {10.1142/S0218195918500036}
}
```
R. Sadre, C. Ophus, A. Butko, and G. H. Weber, “Deep Learning Segmentation of Complex Features in Atomic-Resolution Phase Contrast Transmission Electron Microscopy Images,” Microscopy and Microanalysis, 2021. In press, preprint available at \urlhttps://arxiv.org/abs/2012.05322.
```
@article{Sadre:2021:DLSC,
  author = {Sadre, Robbie and Ophus, Colin and Butko, Anstasiia and Weber, Gunther H},
  title = {Deep Learning Segmentation of Complex Features in Atomic-Resolution Phase Contrast Transmission Electron Microscopy Images},
  journal = {Microscopy and Microanalysis},
  year = {2021},
  doi = {10.1017/S1431927621000167},
  note = {In press, preprint available at \url{https://arxiv.org/abs/2012.05322}}
}
```
H. Carr, O. Rübel, G. H. Weber, and J. Ahrens, “Optimization and Augmentation for Data Parallel Contour Trees,” IEEE Transactions on Visualization and Computer Graphics, 2021. In press.
```
@article{Carr:2021:OADPCT,
  author = {Carr, Hamish and R{\"u}bel, Oliver and Weber, Gunther H. and Ahrens, James},
  title = {Optimization and Augmentation for Data Parallel Contour Trees},
  journal = {IEEE Transactions on Visualization and Computer Graphics},
  year = {2021},
  doi = {10.1109/TVCG.2021.3064385},
  note = {In press}
}
```

H. Childs, S. Ahern, J. Ahrens, A. C. Bauer, J. Bennett, E. W. Bethel, P.-T. Bremer, E. Brugger, J. Cottam, M. Dorier, S. Dutta, J. Favre, T. Fogal, S. Frey, C. Garth, B. Geveci, W. F. Godoy, C. D. Hansen, C. Harrison, B. Hentschel, J. Insley, C. Johnson, S. Klasky, A. Knoll, J. Kress, M. Larsen, J. Lofstead, K.-L. Ma, P. Malakar, J. Meredith, K. Moreland, P. Navratil, P. O’Leary, M. Parashar, V. Pascucci, J. Patchett, T. Peterka, S. Petruzza, N. Podhorszki, D. Pugmire, M. Rasquin, S. Rizzi, D. H. Rogers, S. Sane, F. Sauer, R. Sisneros, H.-W. Shen, W. Usher, R. Vickery, V. Vishwanath, I. Wald, R. Wang, G. H. Weber, B. Whitlock, M. Wolf, H. Yu, and S. B. Ziegler, “A Terminology for In Situ Visualization and Analysis Systems,” International Journal of High Performance Computing Applications, vol. 34, no. 6, pp. 676–691, 2020.

@article{Childs:2020:ISTP,
  author = {Childs, H. and Ahern, S. and Ahrens, J. and Bauer, A. C. and Bennett, J. and Bethel, E. W. and Bremer, P.-T. and Brugger, E. and Cottam, J. and Dorier, M. and Dutta, S. and Favre, J. and Fogal, T. and Frey, S. and Garth, C. and Geveci, B. and Godoy, W. F. and Hansen, C. D. and Harrison, C. and Hentschel, B. and Insley, J. and Johnson, C. and Klasky, S. and Knoll, A. and Kress, J. and Larsen, M. and Lofstead, J. and Ma, K.-L. and Malakar, P. and Meredith, J. and Moreland, K. and Navratil, P. and O'Leary, P. and Parashar, M. and Pascucci, V. and Patchett, J. and Peterka, T. and Petruzza, S. and Podhorszki, N. and Pugmire, D. and Rasquin, M. and Rizzi, S. and Rogers, D. H. and Sane, S. and Sauer, F. and Sisneros, R. and Shen, H.-W. and Usher, W. and Vickery, R. and Vishwanath, V. and Wald, I. and Wang, R. and Weber, G. H. and Whitlock, B. and Wolf, M. and Yu, H. and Ziegler, S. B.},
  title = {A Terminology for In Situ Visualization and Analysis Systems},
  journal = {International Journal of High Performance Computing Applications},
  volume = {34},
  number = {6},
  pages = {676--691},
  year = {2020},
  doi = {10.1177/1094342020935991},
  escholarshipurl = {https://escholarship.org/uc/item/20q1s49z}
}

A.-P. Lohfink, F. Wetzels, J. Lukasczyk, G. H. Weber, and C. Garth, “Fuzzy Contour Trees: Alignment and Joint Layout of Multiple Contour Trees,” Computer Graphics Forum (Special Issue, Proceedings Eurographics/IEEE Symposium on Visualization), vol. 39, no. 3, pp. 343–355, 2020.
```
@article{Lohfink:2020:FCT,
  author = {Lohfink, Anna-Pia and Wetzels, Florian and Lukasczyk, Jonas and Weber, Gunther H. and Garth, Christoph},
  title = {Fuzzy Contour Trees: Alignment and Joint Layout of Multiple Contour Trees},
  journal = {Computer Graphics Forum (Special Issue, Proceedings Eurographics/IEEE Symposium on Visualization)},
  volume = {39},
  number = {3},
  pages = {343--355},
  year = {2020},
  doi = {10.1111/cgf.13985}
}
```
J. Lukasczyk, C. Garth, G. H. Weber, T. Biedert, R. Maciejewski, and H. Leitte, “Dynamic Nested Tracking Graphs,” IEEE Transactions on Visualization and Computer Graphics (Proceedings IEEE VIS 2019), vol. 26, no. 1, pp. 249–258, 2020.
```
@article{Lukasczyk:2020:DNTG,
  author = {Lukasczyk, Jonas and Garth, Christoph and Weber, Gunther H. and Biedert, Tim and Maciejewski, Ross and Leitte, Heike},
  title = {Dynamic Nested Tracking Graphs},
  journal = {IEEE Transactions on Visualization and Computer Graphics (Proceedings IEEE VIS 2019)},
  volume = {26},
  number = {1},
  pages = {249--258},
  year = {2020},
  doi = {10.1109/TVCG.2019.2934368}
}
```

J. Lukasczyk, R. Maciejewski, G. H. Weber, C. Garth, and H. Leitte, “Nested Tracking Graphs,” Computer Graphics Forum (Special Issue, Proceedings Eurographics/IEEE Symposium on Visualization), vol. 36, no. 3, pp. 12–22, 2017. Best paper award.

@article{Lukasczyk:2017:NTG,
  author = {Lukasczyk, Jonas and Maciejewski, Ross and Weber, Gunther H. and Garth, Christoph and Leitte, Heike},
  title = {Nested Tracking Graphs},
  journal = {Computer Graphics Forum (Special Issue, Proceedings
               Eurographics/IEEE Symposium on Visualization)},
  publisher = {European Assiciation for Computer Graphics},
  volume = {36},
  number = {3},
  pages = {12--22},
  year = {2017},
  note = {Best paper award},
  doi = {10.1111/cgf.13164},
  escholarshipurl = {https://escholarship.org/uc/item/1b51k20d}
}

G. H. Weber, S. Carpendale, D. Ebert, B. Fisher, H. Hagen, B. Shneiderman, and A. Ynnerman, “Apply or Die: On the Role and Assessment of Application Papers in Visualization,” IEEE Computer Graphics & Applications, vol. 37, no. 3, pp. 96–104, 2017.
```
@article{Weber:2017:Apply,
  author = {Weber, Gunther H. and Carpendale, Sheelagh and Ebert, David and Fisher, Brian and Hagen, Hans and Shneiderman, Ben and Ynnerman, Anders},
  title = {Apply or Die:  On the Role and Assessment of Application Papers in
             Visualization},
  journal = {{IEEE} Computer Graphics \& Applications},
  volume = {37},
  number = {3},
  pages = {96--104},
  year = {2017},
  doi = {10.1109/MCG.2017.51},
  escholarshipurl = {https://escholarship.org/uc/item/9bd62631}
}
```
S. Murugesan, K. Bouchard, E. Chang, M. Dougherty, B. Hamann, and G. H. Weber, “Multi-scale Visual Analysis of Time-varying Electrocorticography Data via Clustering of Brain Regions,” BMC Bioinformatics, vol. 18, no. Suppl 6, p. 236, 2017.
```
@article{Murugesan:2017:MSVA,
  author = {Murugesan, Sugeerth and Bouchard, Kristofer and Chang, Edward and Dougherty, Max and Hamann, Bernd and Weber, Gunther H.},
  title = {Multi-scale Visual Analysis of Time-varying Electrocorticography Data
              via Clustering of Brain Regions},
  journal = {BMC Bioinformatics},
  volume = {18},
  number = {Suppl 6},
  pages = {236},
  year = {2017},
  doi = {10.1186/s12859-017-1633-9},
  escholarshipurl = {https://escholarship.org/uc/item/8d86w21r}
}
```
P. Oesterling, C. Heine, G. H. Weber, and G. Scheuermann, “Visualizing nD Point Clouds as Topological Landscape Profiles to Guide Local Data Analysis,” IEEE Transactions on Visualization and Computer Graphics, vol. 19, no. 3, pp. 514–526, 2013.
```
@article{Oesterling:2013:VGSPC,
  author = {Oesterling, Patrick and Heine, Christian and Weber, Gunther H. and Scheuermann, Gerik},
  title = {Visualizing n{D} Point Clouds as Topological Landscape Profiles to Guide
             Local Data Analysis},
  journal = {{IEEE} Transactions on Visualization and Computer Graphics},
  volume = {19},
  number = {3},
  pages = {514--526},
  year = {2013},
  doi = {10.1109/TVCG.2012.120},
  lbnl-number = {LBNL-5694E}
}
```
D. M. Ushizima, D. Morozov, G. H. Weber, A. G. C. Bianchi, J. A. Sethian, and E. W. Bethel, “Augmented Topological Descriptors of Pore Networks for Material Science,” IEEE Transactions on Visualization and Computer Graphics (Proceedings IEEE Vis 2012), vol. 18, no. 12, pp. 2041–2050, 2012.
```
@article{Ushizima:2012:ATD,
  author = {Ushizima, Daniela M. and Morozov, Dmitriy and Weber, Gunther H. and Bianchi, Andrea G.C. and Sethian, James A. and Bethel, E. Wes},
  title = {Augmented Topological Descriptors of Pore Networks for Material Science},
  journal = {{IEEE} Transactions on Visualization and Computer Graphics (Proceedings IEEE Vis 2012)},
  volume = {18},
  number = {12},
  pages = {2041--2050},
  year = {2012},
  doi = {10.1109/TVCG.2012.200},
  lbnl-number = {LBNL-5964E}
}
```

K. Beketayev, G. H. Weber, M. Haranczyk, P.-T. Bremer, M. Hlawitschka, and B. Hamann, “Topology-based Visualization of Transformation Pathways in Complex Chemical Systems,” Computer Graphics Forum (Special Issue, Proceedings Eurographics/IEEE Symposium on Visualization), vol. 30, no. 3, pp. 663–672, 2011.

@article{Beketayev:2011:VTTP,
  author = {Beketayev, Kenes and Weber, Gunther H. and Haranczyk, Maciej and Bremer, Peer-Timo and Hlawitschka, Mario and Hamann, Bernd},
  title = {Topology-based Visualization of Transformation Pathways in Complex Chemical Systems},
  journal = {Computer Graphics Forum (Special Issue, Proceedings
               Eurographics/IEEE Symposium on Visualization)},
  publisher = {European Assiciation for Computer Graphics},
  volume = {30},
  number = {3},
  year = {2011},
  pages = {663--672},
  doi = {10.1111/j.1467-8659.2011.01915.x},
  lbnl-number = {LBNL-5242E}
}

P.-T. Bremer, G. H. Weber, J. Tierny, V. Pascucci, M. S. Day, and J. B. Bell, “Interactive Exploration and Analysis of Large Scale Turbulent Combustion Using Topology-based Data Segmentation,” IEEE Transactions on Visualization and Computer Graphics, vol. 17, no. 9, pp. 1307–1324, 2011.
```
@article{Bremer:2011:IEA,
  author = {Bremer, Peer-Timo and Weber, Gunther H. and Tierny, Julien and Pascucci, Valerio and Day, Marcus S. and Bell, John B.},
  title = {Interactive Exploration and Analysis of Large Scale Turbulent Combustion
             Using Topology-based Data Segmentation},
  journal = {IEEE Transactions on Visualization and Computer Graphics},
  volume = {17},
  number = {9},
  pages = {1307--1324},
  year = {2011},
  doi = {10.1109/TVCG.2010.80},
  lbnl-number = {LBNL-5921E}
}
```
H. Childs, D. Pugmire, S. Ahern, B. Whitlock, M. Howison, Prabhat, G. H. Weber, and E. W. Bethel, “Extreme Scaling of Production Visualization Software on Diverse Architectures,” IEEE Computer Graphics and Applications, vol. 30, no. 3, pp. 22–31, 2010.
```
@article{Childs:2010:ESPV,
  author = {Childs, Hank and Pugmire, David and Ahern, Sean and Whitlock, Brad and Howison, Mark and Prabhat and Weber, Gunther H. and Bethel, E. Wes},
  title = {Extreme Scaling of Production Visualization Software on Diverse Architectures},
  journal = {IEEE Computer Graphics and Applications},
  volume = {30},
  number = {3},
  pages = {22--31},
  year = {2010},
  doi = {10.1109/MCG.2010.51},
  lbnl-number = {LBNL-3403E}
}
```

O. Rübel, G. H. Weber, M.-Y. Huang, E. W. Bethel, M. D. Biggin, C. C. Fowlkes, C. L. Hendriks, S. V. E. Keränen, M. B. Eisen, D. W. Knowles, J. Malik, H. Hagen, and B. Hamann, “Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data,” IEEE Transactions on Computational Biology and Bioinformatics, vol. 7, no. 1, pp. 64–79, 2010.

@article{Ruebel:2010:IDCV,
  author = {R{\"u}bel, Oliver and Weber, Gunther H. and Huang, Min-Yu and Bethel, E. Wes and Biggin, Mark D. and Fowlkes, Charless. C. and Hendriks, C. Luengo and Ker{\"a}nen, Soile. V. E. and Eisen, Michael B. and Knowles, David W. and Malik, Jitendra and Hagen, Hans and Hamann, Bernd},
  title = {Integrating Data Clustering and Visualization for the Analysis of 3D Gene
             Expression Data},
  journal = {IEEE Transactions on Computational Biology and Bioinformatics},
  volume = {7},
  number = {1},
  pages = {64--79},
  year = {2010},
  doi = {10.1109/TCBB.2008.49},
  lbnl-nunber = {LBNL-382E}
}

P.-T. Bremer, G. H. Weber, V. Pascucci, M. S. Day, and J. B. Bell, “Analyzing and Tracking Burning Structures in Lean Premixed Hydrogen Flames,” IEEE Transactions on Visualization and Computer Graphics, vol. 16, no. 2, pp. 248–260, 2010.
```
@article{Bremer:2010:ATBS,
  author = {Bremer, Peer-Timo and Weber, Gunther H. and Pascucci, Valerio and Day, Marcus S. and Bell, John B.},
  title = {Analyzing and Tracking Burning Structures in Lean Premixed Hydrogen Flames},
  journal = {IEEE Transactions on Visualization and Computer Graphics},
  volume = {16},
  number = {2},
  year = {2010},
  pages = {248--260},
  doi = {10.1109/TVCG.2009.69},
  lbnl-number = {LBNL-2276E}
}
```
O. Rübel, C. G. R. Geddes, E. Cormier-Michel, K. Wu, Prabhat, G. H. Weber, D. M. Ushizima, P. Messmer, H. Hagen, B. Hamann, and E. W. Bethel, “Automatic beam path analysis of laser wakefield particle acceleration data,” Computational Science & Discovery, vol. 2, no. 1, p. 015005, 2009.
```
@article{Ruebel:2009:ABPA,
  author = {R{\"u}bel, Oliver and Geddes, Cameron G. R. and Cormier-Michel, Estelle and Wu, Kesheng and Prabhat and Weber, Gunther H. and Ushizima, Daniela M. and Messmer, Peter and Hagen, Hans and Hamann, Bernd and Bethel, E. Wes},
  title = {Automatic beam path analysis of laser wakefield particle acceleration data},
  journal = {Computational Science \& Discovery},
  volume = {2},
  number = {1},
  year = {2009},
  pages = {015005},
  doi = {10.1088/1749-4699/2/1/015005}
}
```
G. H. Weber, O. Rübel, M.-Y. Huang, A. DePace, C. C. Fowlkes, S. V. E. Keränen, C. L. Luengo Hendriks, H. Hagen, D. W. Knowles, J. Malik, M. D. Biggin, and B. Hamann, “Visual exploration of three-dimensional gene expression using physical views and linked abstract views,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, no. 2, pp. 296–309, 2009.
```
@article{Weber:2009:VEGE,
  author = {Weber, Gunther H. and R{\"u}bel, Oliver and Huang, Min-Yu and DePace, Angela and Fowlkes, Charless C. and Ker{\"a}nen, Soile V. E. and Luengo Hendriks, Cris L. and Hagen, Hans and Knowles, David W. and Malik, Jitendra and Biggin, Mark D. and Hamann, Bernd},
  title = {Visual exploration of three-dimensional gene expression using physical views
              and linked abstract views},
  journal = {{IEEE}/{ACM} Transactions on Computational Biology and Bioinformatics},
  volume = {6},
  number = {2},
  pages = {296--309},
  doi = {10.1109/TCBB.2007.70249},
  year = {2009}
}
```
S. E. Dillard, V. Natarajan, G. H. Weber, V. Pascucci, and B. Hamann, “Topology-guided tessellation of quadratic elements,” International Journal of Computational Geometry & Applications, vol. 19, no. 2, pp. 195–211, 2009.
```
@article{Dillard:2009:TGT,
  author = {Dillard, Scott E. and Natarajan, Vijay and Weber, Gunther H. and Pascucci, Valerio and Hamann, Bernd},
  title = {Topology-guided tessellation of quadratic elements},
  journal = {International Journal of Computational Geometry \& Applications},
  volume = {19},
  number = {2},
  pages = {195--211},
  doi = {10.1142/S0218195909002903},
  year = {2009}
}
```

C. C. Fowlkes, C. L. Luengo Hendriks, S. V. E. Keränen, G. H. Weber, O. Rübel, M.-Y. Huang, S. Chatoor, A. H. DePace, L. Simirenko, C. Henriquez, A. Beaton, R. Weiszmann, S. Celniker, B. Hamann, D. W. Knowles, M. D. Biggin, M. B. Eisen, and J. Malik, “A Quantitative Spatiotemporal Atlas of Gene Expression in the \textslDrosophila Blastoderm,” Cell, vol. 133, no. 2, pp. 364–374, 2008.

@article{Fowlkes:2008:ATLAS,
  author = {Fowlkes, Charless C. and Luengo Hendriks, Cris L. and Ker{\"a}nen, Soile V.E. and Weber, Gunther H. and R{\"u}bel, Oliver and Huang, Min-Yu and Chatoor, Sohail and DePace, Angela H. and Simirenko, Lisa and Henriquez, Clara and Beaton, Amy and Weiszmann, Richard and Celniker, Susan and Hamann, Bernd and Knowles, David W. and Biggin, Mark D. and Eisen, Michael B. and Malik, Jitendra},
  title = {A Quantitative Spatiotemporal Atlas of Gene Expression in the \textsl{{Drosophila}} Blastoderm},
  journal = {Cell},
  volume = {133},
  number = {2},
  pages = {364--374},
  year = {2008},
  doi = {10.1016/j.cell.2008.01.053}
}

G. H. Weber, P.-T. Bremer, and V. Pascucci, “Topological Landscapes: A Terrain Metaphor for Scientific Data,” IEEE Transactions on Visualization and Computer Graphics (Special Issue: Proceedings of IEEE Visualization 2007), vol. 13, no. 6, pp. 1416–1423, 2007.
```
@article{Weber:2007:TL,
  title = {Topological Landscapes: A Terrain Metaphor for Scientific Data},
  author = {Weber, Gunther H. and Bremer, Peer-Timo and Pascucci, Valerio},
  journal = {{IEEE} Transactions on Visualization and Computer Graphics
                 (Special Issue: Proceedings of {IEEE} Visualization 2007)},
  year = {2007},
  volume = {13},
  number = {6},
  pages = {1416--1423},
  doi = {10.1109/TVCG.2007.70601},
  lbnl-number = {LBNL-63763}
}
```

O. G. Staadt, V. Natarjan, G. H. Weber, D. F. Wiley, and B. Hamann, “Interactive Processing and Visualization of Image Data for Biomedical and Life Science Applications,” BMC Cell Biology, vol. 8, no. Suppl 1, p. S10, 2007.

@article{Staadt:2007:IPV,
  author = {Staadt, Oliver G. and Natarjan, Vijay and Weber, Gunther H. and Wiley, David F. and Hamann, B.},
  title = {Interactive Processing and Visualization of Image Data for Biomedical and
              Life Science Applications},
  journal = {{BMC} Cell Biology},
  editor = {Auer, M. and Peng, H. and Singh, A.},
  pages = {S10},
  volume = {8},
  number = {Suppl 1},
  year = {2007},
  doi = {10.1186/1471-2121-8-S1-S10},
  publisher = {BioMed Central Ltd.},
  lbnl-number = {LBNL-63127}
}

G. H. Weber, S. E. Dillard, H. Carr, V. Pascucci, and B. Hamann, “Topology-Controlled Volume Rendering,” IEEE Transactions on Visualization and Computer Graphics, vol. 13, no. 2, pp. 330–341, 2007.
```
@article{Weber:2007:TCVR,
  title = {Topology-Controlled Volume Rendering},
  author = {Weber, Gunther H. and Dillard, Scott E. and Carr, Hamish and Pascucci, Valerio and Hamann, Bernd},
  journal = {{IEEE} Transactions on Visualization and Computer Graphics},
  year = {2007},
  volume = {13},
  number = {2},
  pages = {330--341},
  doi = {10.1109/TVCG.2007.47},
  lbnl-number = {LBNL-63120}
}
```
S. Gu, I. Anderson, V. Kunin, M. Cipriano, S. Minovitsky, G. H. Weber, N. Amenta, B. Hamann, and I. Dubchak, “TreeQ-VISTA: An Interactive Tree Visualization Tool with Functional Annotation Query Capabilities,” Bioinformatics, vol. 23, no. 6, pp. 764–766, 2007.
```
@article{Gu:2007:TreeQ-VISTA,
  author = {Gu, Shengyin and Anderson, Iain and Kunin, Victor and Cipriano, Michael and Minovitsky, Simon and Weber, Gunther H. and Amenta, Nina and Hamann, Bernd and Dubchak, Inna},
  title = {{TreeQ-VISTA}: An Interactive Tree Visualization Tool with Functional
             Annotation Query Capabilities},
  journal = {Bioinformatics},
  volume = {23},
  number = {6},
  pages = {764--766},
  year = {2007},
  doi = {10.1093/bioinformatics/btl643}
}
```
C. L. Luengo Hendriks, S. V. E. Keränen, C. C. Fowlkes, L. Simirenko, G. H. Weber, A. H. DePace, C. Henriquez, D. W. Kaszuba, B. Hamann, M. B. Eisen, J. Malik, D. Sudar, M. D. Biggin, and D. W. Knowles, “Three-dimensional Morphology and Gene Expression in the \textslDrosophila Blastoderm at Cellular Resolution I: Data Acquisition Pipeline,” Genome Biology, vol. 7, no. 12, p. R123, 2006.
```
@article{Luengo:2006:3DGE,
  author = {Luengo Hendriks, Cris L. and Ker{\"a}nen, Soile V. E. and Fowlkes, Charless C. and Simirenko, Lisa and Weber, Gunther H. and DePace, Angela H. and Henriquez, Clara and Kaszuba, David W. and Hamann, Bernd and Eisen, Michael B. and Malik, Jitendra and Sudar, Damir and Biggin, Mark D. and Knowles, David W.},
  title = {Three-dimensional Morphology and Gene Expression in the \textsl{{Drosophila}}
              Blastoderm at Cellular Resolution {I}: Data Acquisition Pipeline},
  journal = {Genome Biology},
  volume = {7},
  number = {12},
  pages = {R123},
  doi = {10.1186/gb-2006-7-12-r123},
  year = {2006}
}
```

Conference Articles

G. H. Weber, C. Ophus, and L. Ramakrishnan, “Automated Labeling of Electron Microscopy Images Using Deep Learning,” in Proc. IEEE/ACM Machine Learning in HPC Environments (MLHPC), pp. 26–36, Nov. 2018.
```
@inproceedings{Weber:2018:ALEM,
  author = {Weber, Gunther H. and Ophus, Colin and Ramakrishnan, Lavanya},
  title = {Automated Labeling of Electron Microscopy Images Using Deep Learning},
  booktitle = {Proc. IEEE/ACM Machine Learning in HPC Environments (MLHPC)},
  pages = {26--36},
  year = {2018},
  month = nov,
  doi = {10.1109/MLHPC.2018.8638633},
  escholarshipurl = {https://escholarship.org/uc/item/8m19p87t}
}
```
A. Ovsyannikov, M. Romanus, B. Van Straalen, G. H. Weber, and D. Trebotich, “Scientific Workflows at DataWarp-Speed: Accelerated Data-Intensive Science using NERSC’s Burst Buffer,” in Proceedings of the 1st Joint International Workshop on Parallel Data Storage & Data Intensive Scalable Computing Systems, pp. 1–6, Nov. 2016.
```
@inproceedings{Ovsyannikov:2016:EAWC,
  author = {Ovsyannikov, Andrey and Romanus, Melissa and Van Straalen, Brian and Weber, Gunther H. and Trebotich, David},
  title = {Scientific Workflows at {DataWarp}-Speed: Accelerated Data-Intensive Science using {NERSC}'s Burst Buffer},
  booktitle = {Proceedings of the 1st Joint International Workshop on Parallel Data Storage \& Data Intensive Scalable Computing Systems},
  year = {2016},
  month = nov,
  pages = {1--6},
  doi = {10.1109/PDSW-DISCS.2016.005},
  publisher = {{IEEE} Press}
}
```
P. Hristov, G. H. Weber, H. A. Carr, O. Rübel, and J. P. Ahrens, “Data Parallel Hypersweeps for In Situ Topological Analysis,” in Proceedings of the 10th IEEE Symposium on Large Data Analysis and Visualization (LDAV), pp. 12–21, Oct. 2020.
```
@inproceedings{Hristov:2020:DPH,
  author = {Hristov, Petar and Weber, Gunther H. and Carr, Hamish A. and R{\"u}bel, Oliver and Ahrens, James P.},
  title = {Data Parallel Hypersweeps for In Situ Topological Analysis},
  booktitle = {Proceedings of the 10th IEEE Symposium on Large Data Analysis and Visualization (LDAV)},
  year = {2020},
  month = oct,
  pages = {12--21},
  doi = {10.1109/LDAV51489.2020.00008}
}
```
G. P. Rodrigo, M. Henderson, G. H. Weber, C. Ophus, K. Antypas, and L. Ramakrishnan, “ScienceSearch: Enabling Search through Automatic Metadata Generation,” in Proceedings IEEE 14th International Conference on e-Science (e-Science) 2018, pp. 93–104, Oct. 2018.
```
@inproceedings{Rodrigo:2018:ScienceSearch,
  author = {Rodrigo, Gonzalo P. and Henderson, Matt and Weber, Gunther H. and Ophus, Colin and Antypas, Katie and Ramakrishnan, Lavanya},
  title = {{S}cience{S}earch: Enabling Search through Automatic Metadata Generation},
  booktitle = {Proceedings IEEE 14th International Conference on e-Science (e-Science) 2018},
  year = {2018},
  month = oct,
  pages = {93--104},
  doi = {10.1109/eScience.2018.00025}
}
```
H. A. Carr, G. H. Weber, C. M. Sewell, and J. P. Ahrens, “Parallel Peak Pruning for Scalable SMP Contour Tree Computation,” in Proceedings of the 6th IEEE Symposium on Large Data Analysis and Visualization (LDAV), pp. 75–84, Oct. 2016. Best paper award.
```
@inproceedings{Carr:2016:PPP,
  author = {Carr, Hamish A. and Weber, Gunther H. and Sewell, Christopher M. and Ahrens, James P.},
  title = {Parallel Peak Pruning for Scalable {SMP} Contour Tree Computation},
  booktitle = {Proceedings of the 6th IEEE Symposium on Large Data Analysis and Visualization (LDAV)},
  pages = {75--84},
  year = {2016},
  month = oct,
  doi = {10.1109/LDAV.2016.7874312},
  note = {Best paper award}
}
```
G. H. Weber, H. Childs, and J. S. Meredith, “Efficient Parallel Extraction of Crack-free Isosurfaces from Adaptive Mesh Refinement (AMR) Data,” in Proceedings of IEEE Symposium on Large Data Analysis and Visualization (LDAV), pp. 31–38, Oct. 2012.
```
@inproceedings{Weber:2012:EPCI,
  author = {Weber, Gunther H. and Childs, Hank and Meredith, Jeremy S.},
  title = {Efficient Parallel Extraction of Crack-free Isosurfaces from Adaptive Mesh Refinement ({AMR}) Data},
  booktitle = {Proceedings of IEEE Symposium on Large Data Analysis and Visualization (LDAV)},
  month = oct,
  year = {2012},
  pages = {31--38},
  doi = {10.1109/LDAV.2012.6378973},
  lbnl-number = {LBNL-5799E}
}
```

A. R. Sanderson, B. Whitlock, O. Rübel, H. Childs, G. H. Weber, Prabhat, and K. Wu, “A System for Query Based Analysis and Visualization,” in Third International EuroVis Workshop on Visual Analytics EuroVA 2012, Vienna, Austria, pp. 25–29, Jun. 2012.

@inproceedings{Sanderson:2012:QBAV,
  author = {Sanderson, Allen R. and Whitlock, Brad and R{\"u}bel, Oliver and Childs, Hank and Weber, Gunther H. and Prabhat and Wu, Kesheng},
  title = {A System for Query Based Analysis and Visualization},
  editor = {Matkovic, Kresimir and Santucci, Giuseppe},
  booktitle = {Third International EuroVis Workshop on Visual Analytics EuroVA 2012},
  pages = {25--29},
  year = {2012},
  address = {Vienna, Austria},
  month = jun,
  doi = {10.2312/PE/EuroVAST/EuroVA12/025-029},
  lbnl-number = {LBNL-5507E}
}

S. Murugesan, K. Bouchard, E. Chang, M. Dougherty, B. Hamann, and G. H. Weber, “Hierarchical Spatio-temporal Visual Analysis of Cluster Evolution in Electrocorticography Data,” in Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, New York, NY, USA, pp. 630–639, 2016. Best paper award.
```
@inproceedings{Murugesan:2016:ECoGClusterFlow,
  author = {Murugesan, Sugeerth and Bouchard, Kristofer and Chang, Edward and Dougherty, Max and Hamann, Bernd and Weber, Gunther H.},
  title = {Hierarchical Spatio-temporal Visual Analysis of Cluster Evolution in
                Electrocorticography Data},
  booktitle = {Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics},
  series = {BCB '16},
  pages = {630--639},
  year = {2016},
  doi = {10.1145/2975167.2985688},
  publisher = {ACM},
  address = {New York, NY, USA},
  note = {Best paper award}
}
```

U. Ayachit, A. Bauer, E. P. N. Duque, G. Eisenhauer, N. Ferrier, J. Gu, K. E. Jansen, B. Loring, Z. Lukić, S. Menon, D. Morozov, P. O’Leary, R. Ranjan, M. Rasquin, C. P. Stone, V. Vishwanath, G. H. Weber, B. Whitlock, M. Wolf, K. J. Wu, and E. W. Bethel, “Performance Analysis, Design Considerations, and Applications of Extreme-scale In Situ Infrastructures,” in SC ’16: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, 2016.

@inproceedings{Bethel:2016:PADC,
  author = {Ayachit, Utkarsh and Bauer, Andy and Duque, Earl P. N. and Eisenhauer, Greg and Ferrier, Nicola and Gu, Junmin and Jansen, Kenneth E. and Loring, Burlen and Luki{\'c}, Zarija and Menon, Suresh and Morozov, Dmitriy and O'Leary, Patrick and Ranjan, Reetesh and Rasquin, Michel and Stone, Christopher P. and Vishwanath, Venkat and Weber, Gunther H. and Whitlock, Brad and Wolf, Matthew and Wu, K. John and Bethel, E. Wes},
  title = {Performance Analysis, Design Considerations, and Applications of
                  Extreme-scale \emph{In Situ} Infrastructures},
  booktitle = {SC '16: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis},
  doi = {10.1109/SC.2016.78},
  year = {2016},
  publisher = {IEEE},
  location = {Salt Lake City, UT}
}

W. Bhimji, D. Bard, M. Romanus, D. Paul, A. Ovsyannikov, B. Friesen, M. Bryson, J. Correa, G. K. Lockwood, V. Tsulaia, S. Byna, S. Farrell, D. Gursoy, C. Daley, V. Beckner, B. Van Straalen, D. Trebotich, C. Tull, G. H. Weber, N. J. Wright, K. Antypas, and Prabhat, “Accelerating Science with the NERSC Burst Buffer Early User Program,” in CUG2016 Proceedings, 2016. Best paper award, in press.

@inproceedings{Bhimji:2106:ASBB,
  author = {Bhimji, Wahid and Bard, Debbie and Romanus, Melissa and Paul, David and Ovsyannikov, Andrey and Friesen, Brian and Bryson, Matt and Correa, Joaquin and Lockwood, Glenn K. and Tsulaia, Vakho and Byna, Suren and Farrell, Steve and Gursoy, Doga and Daley, Chris and Beckner, Vince and Van Straalen, Brian and Trebotich, David and Tull, Craig and Weber, Gunther H. and Wright, Nicholas J. and Antypas, Katie and Prabhat},
  title = {Accelerating Science with the {NERSC} Burst Buffer Early User Program},
  booktitle = {CUG2016 Proceedings},
  year = {2016},
  note = {Best paper award, in press},
  lbnl-number = {LBNL-1005736}
}

G. H. Weber, H. Johansen, D. T. Graves, and T. J. Ligocki, “Simulating Urban Environments for Energy Analysis,” in Proceedings Visualization in Environmental Sciences (EnvirVis), 2014.
```
@inproceedings{Weber:2014:UEM,
  author = {Weber, Gunther H. and Johansen, Hans and Graves, Daniel T. and Ligocki, Terry J.},
  title = {Simulating Urban Environments for Energy Analysis},
  booktitle = {Proceedings Visualization in Environmental Sciences (EnvirVis)},
  year = {2014},
  lbnl-number = {LBNL-6652E}
}
```
G. H. Weber, H. Childs, and J. S. Meredith, “Recent Advances in VisIt: Parallel Crack-free Isosurface Extraction,” in Numerical Modeling of Space Plasma Flows: Astronum-2012 (Astronomical Society of the Pacific Conference Series), 2013.
```
@inproceedings{Weber:2013:PCI,
  author = {Weber, Gunther H. and Childs, Hank and Meredith, Jeremy S.},
  title = {Recent Advances in {VisIt}: Parallel Crack-free Isosurface Extraction},
  booktitle = {Numerical Modeling of Space Plasma Flows: Astronum-2012 (Astronomical Society of the Pacific Conference Series)},
  year = {2013},
  lbnl-number = {LBNL-6314E}
}
```

D. Morozov and G. H. Weber, “Distributed Merge Trees,” in Proceedings of the 18th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP’13), New York, NY, USA, pp. 93–102, 2013.

@inproceedings{Morozov:2013:DMT,
  author = {Morozov, Dmitriy and Weber, Gunther H.},
  title = {Distributed Merge Trees},
  booktitle = {Proceedings of the 18th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP'13)},
  pages = {93--102},
  year = {2013},
  doi = {10.1145/2442516.2442526},
  isbn = {978-1-4503-1922-5},
  location = {Shenzhen, China},
  publisher = {ACM},
  address = {New York, NY, USA},
  lbnl-number = {LBNL-6137E}
}

K. Beketayev, G. H. Weber, D. Morozov, A. Abzhanov, and B. Hamann, “Geometry-Preserving Topological Landscapes,” in Proceedings of the Workshop at SIGGRAPH Asia 2012, New York, NY, USA, pp. 155–160, 2012.

@inproceedings{Beketayev:2012:GPTL,
  author = {Beketayev, Kenes and Weber, Gunther H. and Morozov, Dmitriy and Abzhanov, Aidos and Hamann, Bernd},
  title = {Geometry-Preserving Topological Landscapes},
  booktitle = {Proceedings of the Workshop at SIGGRAPH Asia 2012},
  pages = {155--160},
  year = {2012},
  isbn = {978-1-4503-1835-8},
  doi = {10.1145/2425296.2425324},
  location = {Singapore, Singapore},
  publisher = {ACM},
  address = {New York, NY, USA},
  lbnl-number = {LBNL-6082E}
}

D. Demir, K. Beketayev, G. H. Weber, P.-T. Bremer, V. Pascucci, and B. Hamann, “Topology Exploration with Hierarchical Landscapes,” in Proceedings of the Workshop at SIGGRAPH Asia 2012, New York, NY, USA, pp. 147–154, 2012.

@inproceedings{Demir:2012:TEHL,
  author = {Demir, Dogan and Beketayev, Kenes and Weber, Gunther H. and Bremer, Peer-Timo and Pascucci, Valerio and Hamann, Bernd},
  title = {Topology Exploration with Hierarchical Landscapes},
  booktitle = {Proceedings of the Workshop at SIGGRAPH Asia 2012},
  pages = {147--154},
  year = {2012},
  isbn = {978-1-4503-1835-8},
  doi = {10.1145/2425296.2425323},
  location = {Singapore, Singapore},
  publisher = {ACM},
  address = {New York, NY, USA},
  lbnl-number = {LBNL-6083E}
}

Book Chapters

H. A. Carr, J. Tierney, and G. H. Weber, “Pathological and Test Cases For Reeb Analysis,” in Topological Methods in Data Analysis and Visualization V: Theory, Algorithms, and Applications, H. Carr, I. Fujishiro, F. Sadlo, and S. Takahashi, Eds. Springer International Publishing, pp. 103–120, Dec. 2020.

@incollection{Carr:2019:PTCRA,
  author = {Carr, Hamish A. and Tierney, Julien and Weber, Gunther H.},
  title = {Pathological and Test Cases For {R}eeb Analysis},
  booktitle = {Topological Methods in Data Analysis and Visualization {V}: Theory, Algorithms, and Applications},
  series = {Mathematics and Visualization},
  editor = {Carr, Hamish and Fujishiro, Issei and Sadlo, Filip and Takahashi, Shigeo},
  publisher = {Springer International Publishing},
  pages = {103--120},
  year = {2020},
  month = dec,
  doi = {10.1007/978-3-030-43036-8_7}
}

P. Oesterling, C. Heine, G. H. Weber, D. Morozov, and G. Scheuermann, “Computing and Visualizing Time-Varying Merge Trees for High-Dimensional Data,” in Topological Methods in Data Analysis and Visualization IV: Theory, Algorithms, and Applications, H. Carr, C. Garth, and T. Weinkauf, Eds. Springer International Publishing, pp. 87–101, May 2017. Best paper award.

@incollection{Oesterling:2016:TVMT,
  author = {Oesterling, Patrick and Heine, Christian and Weber, Gunther H. and Morozov, Dmitriy and Scheuermann, Gerik},
  title = {Computing and Visualizing Time-Varying Merge Trees for High-Dimensional Data},
  booktitle = {Topological Methods in Data Analysis and Visualization {IV}: Theory, Algorithms, and Applications},
  series = {Mathematics and Visualization},
  editor = {Carr, Hamish and Garth, Christoph and Weinkauf, Tino},
  publisher = {Springer International Publishing},
  month = may,
  year = {2017},
  pages = {87--101},
  doi = {10.1007/978-3-319-44684-4_5},
  note = {Best paper award},
  isbn = {978-3-319-44684-4},
  lbnl-number = {LBNL-1005735}
}

J.-T. Sohns, G. H. Weber, and C. Garth, “Distributed Task-Parallel Topology-Controlled Volume Rendering,” in Topological Methods in Data Analysis and Visualization VI: Theory, Algorithms, and Applications, I. Hotz, T. B. Masood, F. Sadlo, and J. Tierny, Eds. Springer International Publishing, 2021. In press.
```
@incollection{Sohns:2021:DTPT,
  author = {Sohns, Jan-Tobias and Weber, Gunther H. and Garth, Christoph},
  title = {Distributed Task-Parallel Topology-Controlled Volume Rendering},
  booktitle = {Topological Methods in Data Analysis and Visualization {VI}: Theory, Algorithms, and Applications},
  series = {Mathematics and Visualization},
  editor = {Hotz, Ingrid and Masood, Talha Bin and Sadlo, Filip and Tierny, Julien},
  publisher = {Springer International Publishing},
  year = {2021},
  note = {In press}
}
```

P. Oesterling, C. Heine, G. H. Weber, and G. Scheuermann, “A Topology-Based Approach to Visualize the Thematic Composition of Document Collections,” in Text Mining, C. Biemann and A. Mehler, Eds. Springer International Publishing, pp. 63–85, 2014.

@incollection{Oesterling:2014:TBTC,
  author = {Oesterling, Patrick and Heine, Christian and Weber, Gunther H. and Scheuermann, Gerik},
  title = {A Topology-Based Approach to Visualize the Thematic Composition of Document Collections},
  booktitle = {Text Mining},
  series = {Theory and Applications of Natural Language Processing},
  editor = {Biemann, Chris and Mehler, Alexander},
  publisher = {Springer International Publishing},
  year = {2014},
  pages = {63--85},
  isbn = {978-3-319-12654-8},
  doi = {10.1007/978-3-319-12655-5_4},
  lbnl-number = {N/A}
}

K. Beketayev, D. Yeliussizov, D. Morozov, G. H. Weber, and B. Hamann, “Measuring the Distance Between Merge Trees,” in Topological Methods in Data Analysis and Visualization III: Theory, Algorithms, and Applications, P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Springer-Verlag, pp. 151–166, 2014.

@incollection{Beketayev:2014:MDMT,
  author = {Beketayev, Kenes and Yeliussizov, Damir and Morozov, Dmitriy and Weber, Gunther H. and Hamann, Bernd},
  title = {Measuring the Distance Between Merge Trees},
  booktitle = {Topological Methods in Data Analysis and Visualization {III}: Theory, Algorithms, and Applications},
  series = {Mathematics and Visualization},
  editor = {Bremer, Peer-Timo and Hotz, Ingrid and Pascucci, Valerio and Peikert, Ronald},
  publisher = {Springer-Verlag},
  year = {2014},
  pages = {151--166},
  isbn = {978-3-319-04098-1},
  doi = {10.1007/978-3-319-04099-8_10},
  lbnl-number = {LBNL-6629E}
}

D. Morozov and G. H. Weber, “Distributed Contour Trees,” in Topological Methods in Data Analysis and Visualization III: Theory, Algorithms, and Applications, P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Springer-Verlag, pp. 89–102, 2014.

@incollection{Morozov:2014:DCT,
  author = {Morozov, Dmitriy and Weber, Gunther H.},
  title = {Distributed Contour Trees},
  booktitle = {Topological Methods in Data Analysis and Visualization {III}: Theory, Algorithms, and Applications},
  series = {Mathematics and Visualization},
  editor = {Bremer, Peer-Timo and Hotz, Ingrid and Pascucci, Valerio and Peikert, Ronald},
  publisher = {Springer-Verlag},
  year = {2014},
  pages = {89--102},
  doi = {10.1007/978-3-319-04099-8_6},
  isbn = {978-3-319-04098-1},
  lbnl-number = {LBNL-6654E}
}

G. H. Weber and H. Hauser, “Interactive Visual Exploration and Analysis,” in Scientific Visualization: Uncertainty, Multifield, Bio-Medical and Scalable Visualization, C. D. Hansen, M. Chen, C. R. Johnson, A. E. Kaufman, and H. Hagen, Eds. Springer-Verlag, pp. 161–174, 2014.

@incollection{Weber:2014:IVEA,
  author = {Weber, Gunther H. and Hauser, Helwig},
  title = {Interactive Visual Exploration and Analysis},
  booktitle = {Scientific Visualization: Uncertainty, Multifield, Bio-Medical and Scalable Visualization},
  series = {Mathematics and Visualization},
  editor = {Hansen, Charles D. and Chen, Min and Johnson, Chris R. and Kaufman, Arie E. and Hagen, Hans},
  publisher = {Springer-Verlag},
  year = {2014},
  pages = {161--174},
  isbn = {978-1-4471-6496-8},
  doi = {10.1007/978-1-4471-6497-5_15},
  lbnl-number = {LBNL-6655E}
}

H. Childs, E. Brugger, B. Whitlock, J. Meredith, S. Ahern, D. Pugmire, K. Biagas, M. Miller, C. Harrison, G. H. Weber, H. Krishnan, T. Fogal, A. Sanderson, C. Garth, E. W. Bethel, D. Camp, O. Rübel, M. Durant, J. M. Favre, and P. Navratil, “VisIt: An End-User Tool for Visualizing and Analyzing Very Large Data,” in High Performance Visualization: Enabling Extreme-Scale Scientific Insight, E. W. Bethel, H. Childs, and C. Hansen, Eds. Boca Raton, FL: CRC Press, pp. 357–371, 2012.

@incollection{Childs:2012:VISIT,
  author = {Childs, Hank and Brugger, Eric and Whitlock, Brad and Meredith, Jeremy and Ahern, Sean and Pugmire, David and Biagas, Kathleen and Miller, Mark and Harrison, Cyrus and Weber, Gunther H. and Krishnan, Hari and Fogal, Thomas and Sanderson, Allen and Garth, Christoph and Bethel, E. Wes and Camp, David and R{\"u}bel, Oliver and Durant, Marc and Favre, Jean M. and Navratil, Paul},
  title = {{VisIt}: An End-User Tool for Visualizing and Analyzing Very Large Data},
  booktitle = {High Performance Visualization: Enabling Extreme-Scale Scientific Insight},
  editor = {Bethel, E. Wes and Childs, Hank and Hansen, Charles},
  pages = {357--371},
  year = {2012},
  isbn = {978-1-439-87572-8},
  publisher = {CRC Press},
  address = {Boca Raton, FL}
}

H. Childs, D. Pugmire, S. Ahern, B. Whitlock, M. Howison, Prabhat, G. H. Weber, and E. W. Bethel, “Visualization at Extreme-Scale Concurrency,” in High Performance Visualization: Enabling Extreme-Scale Scientific Insight, E. W. Bethel, H. Childs, and C. Hansen, Eds. Boca Raton, FL: CRC Press, pp. 291–306, 2012.
```
@incollection{Childs:2012:VESC,
  author = {Childs, Hank and Pugmire, David and Ahern, Sean and Whitlock, Brad and Howison, Mark and Prabhat and Weber, Gunther H. and Bethel, E. Wes},
  title = {Visualization at Extreme-Scale Concurrency},
  booktitle = {High Performance Visualization: Enabling Extreme-Scale Scientific Insight},
  editor = {Bethel, E. Wes and Childs, Hank and Hansen, Charles},
  pages = {291--306},
  year = {2012},
  isbn = {978-1-439-87572-8},
  publisher = {CRC Press},
  address = {Boca Raton, FL}
}
```
G. H. Weber, P.-T. Bremer, and V. Pascucci, “ Topological Cacti: Visualizing Contour-based Statistics,” in Topological Methods in Data Analysis and Visualization II: Theory, Algorithms, and Applications, R. Peikert, H. Hauser, H. Carr, and R. Fuchs, Eds. Heidelberg, Germany: Springer-Verlag, pp. 63–76, 2012.
```
@incollection{Weber:2012:TC,
  author = {Weber, Gunther H. and Bremer, Peer-Timo and Pascucci, Valerio},
  title = { Topological Cacti: Visualizing Contour-based Statistics},
  editor = {Peikert, Ronald and Hauser, Helwig and Carr, Hamish and Fuchs, Raphael},
  booktitle = {Topological Methods in Data Analysis and Visualization {II}: Theory, Algorithms, and Applications},
  pages = {63--76},
  publisher = {Springer-Verlag},
  address = {Heidelberg, Germany},
  year = {2012},
  isbn = {978-3-642-23174-2},
  lbnl-number = {LBNL-5018E}
}
```

O. Rübel, S. V. E. Keränen, M. D. Biggin, D. W. Knowles, G. H. Weber, H. Hagen, B. Hamann, and E. W. Bethel, “Linking Advanced Visualization and MATLAB for the Analysis of 3D Gene Expression Data,” in Mathematical Methods for Visualization in Medicine and Life Sciences II, L. Linsen, H. Hagen, B. Hamann, and H.-C. Hege, Eds. Heidelberg, Germany: Springer-Verlag, pp. 267–286, 2012.

@incollection{Ruebel:2012:LAVM,
  author = {R{\"u}bel, Oliver and Ker{\"a}nen, Soile V. E. and Biggin, Mark D. and Knowles, David W. and Weber, Gunther H. and Hagen, Hans and Hamann, Bernd and Bethel, E. Wes},
  title = {Linking Advanced Visualization and MATLAB for the Analysis of 3{D} Gene Expression Data},
  editor = {Linsen, Lars and Hagen, Hans and Hamann, Bernd and Hege, Hans-Christian},
  booktitle = {Mathematical Methods for Visualization in Medicine and Life Sciences {II}},
  pages = {267--286},
  year = {2012},
  publisher = {Springer-Verlag},
  address = {Heidelberg, Germany},
  isbn = {978-3-642-21608-4},
  lbnl-number = {LBNL-5964E}
}

G. H. Weber, P.-T. Bremer, M. S. Day, J. B. Bell, and V. Pascucci, “Feature Tracking Using Reeb Graphs,” in Topological Methods in Data Analysis and Visualization: Theory, Algorithms, and Applications, V. Pascucci, X. Tricoche, H. Hagen, and J. Tierny, Eds. Heidelberg, Germany: Springer-Verlag, pp. 241–253, 2011.
```
@incollection{Weber:2011:FTRG,
  author = {Weber, Gunther H. and Bremer, Peer-Timo and Day, Marcus S. and Bell, John B. and Pascucci, Valerio},
  title = {Feature Tracking Using {Reeb} Graphs},
  booktitle = {Topological Methods in Data Analysis and Visualization: Theory, Algorithms, and Applications},
  editor = {Pascucci, Valerio and Tricoche, Xavier and Hagen, Hans and Tierny, Julien},
  pages = {241--253},
  publisher = {Springer-Verlag},
  year = {2011},
  address = {Heidelberg, Germany},
  lbnl-number = {LBNL-4226E},
  isbn = {978-3-642-15014-2}
}
```

Technical Reports

E. W. Bethel, D. Camp, H. Childs, M. Howison, H. Krishnan, B. Loring, J. Meyer, Prabhat, O. Rübel, D. Ushizima, and G. Weber, “Towards Exascale: High Performance Visualization and Analytics – Project Status Report,” Lawrence Berkeley National Laboratory, Berkeley, CA, USA, 94720, LBNL-5767E, Apr. 2012. Status report for DOE Exascale Research Conference in Portland, OR.
```
@techreport{LBNL-5767E,
  author = {Bethel, E. Wes and Camp, David and Childs, Hank and Howison, Mark and Krishnan, Hari and Loring, Burlen and Meyer, J\"{o}rg and Prabhat and R\"{u}bel, Oliver and Ushizima, Daniela and Weber, Gunther},
  title = {Towards Exascale: High Performance Visualization and Analytics -- Project Status Report},
  institution = {Lawrence Berkeley National Laboratory},
  address = {Berkeley, CA, USA, 94720},
  month = apr,
  year = {2012},
  number = {LBNL-5767E},
  note = {Status report for {DOE Exascale Research Conference} in {Portland, OR}}
}
```
G. H. Weber and P.-T. Bremer, “In-situ Analysis: Challenges and Opportunities,” Lawrence Berkeley National Laboratory, Berkeley, CA, USA, 94720, LBNL-5692E, Apr. 2012. Position paper for DOE Exascale Research Conference in Portland, OR.
```
@techreport{LBNL-5692E,
  author = {Weber, Gunther H. and Bremer, Peer-Timo},
  title = {In-situ Analysis: Challenges and Opportunities},
  institution = {Lawrence Berkeley National Laboratory},
  address = {Berkeley, CA, USA, 94720},
  month = apr,
  year = {2012},
  number = {LBNL-5692E},
  note = {Position paper for {DOE Exascale Research Conference} in {Portland, OR}}
}
```
G. H. Weber, K. Beketayev, P.-T. Bremer, B. Hamann, M. Haranczyk, M. Hlawitschka, and V. Pascucci, “Comprehensible Presentation of Topological Information,” Lawrence Berkeley National Laboratory, Berkeley, CA, USA, 94720, LBNL-5693E, Apr. 2012. Status report for DOE Exascale Research Conference in Portland, OR.
```
@techreport{LBNL-5693E,
  author = {Weber, Gunther H. and Beketayev, Kenes and Bremer, Peer-Timo and Hamann, Bernd and Haranczyk, Maciej and Hlawitschka, Mario and Pascucci, Valerio},
  title = {Comprehensible Presentation of Topological Information},
  institution = {Lawrence Berkeley National Laboratory},
  address = {Berkeley, CA, USA, 94720},
  month = apr,
  year = {2012},
  number = {LBNL-5693E},
  note = {Status report for {DOE Exascale Research Conference} in {Portland, OR}}
}
```
B. MacCarthy, H. Carr, and G. H. Weber, “Topological Galleries: A High Level User Interface for Topology Controlled Volume Rendering,” Lawerence Berkeley National Laboratory, Berkeley, California, U.S.A., LBNL-5019E, 2011.
```
@techreport{LBNL-5019E,
  author = {MacCarthy, Brian and Carr, Hamish and Weber, Gunther H.},
  title = {Topological Galleries: A High Level User Interface for Topology Controlled Volume Rendering},
  institution = {Lawerence Berkeley National Laboratory},
  address = {Berkeley, California, U.S.A.},
  year = {2011},
  number = {LBNL-5019E}
}
```
O. Kreylos, G. H. Weber, E. W. Bethel, J. M. Shalf, B. Hamann, and K. I. Joy, “Remote Interactive Direct Volume Rendering of AMR Data,” Lawerence Berkeley National Laboratory, Berkeley, California, U.S.A., LBNL-49954, 2006.
```
@techreport{LBNL-49954,
  author = {Kreylos, Oliver and Weber, Gunther H. and Bethel, E. Wes and Shalf, John M. and Hamann, Bernd and Joy, Kenneth I.},
  title = {Remote Interactive Direct Volume Rendering of {AMR} Data},
  institution = {Lawerence Berkeley National Laboratory},
  address = {Berkeley, California, U.S.A.},
  year = {2006},
  number = {LBNL-49954}
}
```