@article{10.1093/nar/gkae301,
author = {Philipp, Michelle and Moth, Christopher W and Ristic, Nikola and Tiemann, Johanna K S and Seufert, Florian and Panfilova, Aleksandra and Meiler, Jens and Hildebrand, Peter W and Stein, Amelie and Wiegreffe, Daniel and Staritzbichler, René},
title = "{MutationExplorer: a webserver for mutation of proteins and 3D visualization of energetic impacts}",
journal = {Nucleic Acids Research},
pages = {gkae301},
year = {2024},
month = {04},
abstract = "{The possible effects of mutations on stability and function of a protein can only be understood in the context of protein 3D structure. The MutationExplorer webserver maps sequence changes onto protein structures and allows users to study variation by inputting sequence changes. As the user enters variants, the 3D model evolves, and estimated changes in energy are highlighted. In addition to a basic per-residue input format, MutationExplorer can also upload an entire replacement sequence. Previously the purview of desktop applications, such an upload can back-mutate PDB structures to wildtype sequence in a single step. Another supported variation source is human single nucelotide polymorphisms (SNPs), genomic coordinates input in VCF format. Structures are flexibly colorable, not only by energetic differences, but also by hydrophobicity, sequence conservation, or other biochemical profiling. Coloring by interface score reveals mutation impacts on binding surfaces. MutationExplorer strives for efficiency in user experience. For example, we have prepared 45 000 PDB depositions for instant retrieval and initial display. All modeling steps are performed by Rosetta. Visualizations leverage MDsrv/Mol*. MutationExplorer is available at: http://proteinformatics.org/mutation_explorer/.}",
issn = {0305-1048},
doi = {10.1093/nar/gkae301},
url = {https://doi.org/10.1093/nar/gkae301},
eprint = {https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkae301/57299197/gkae301.pdf},
}
@inproceedings{kaubowski2023,
title={Classification of Large and Heterogeneous LiDAR Data Sets},
author={Kaubowski, Kenn and Nsonga, Baldwin and Kretzschmar, Vanessa and Annanias, Yves and Wiegreffe, Daniel and Hlawitschka, Mario},
booktitle={INFORMATIK 2023},
year={2023},
publisher={Gesellschaft f{\"u}r Informatik, Bonn}
}
@inproceedings{mueller2023,
title={Nachnutzungskonzept für Daten in der Altlastenverwaltung},
author={Müller, Lydia and Wiegreffe, Daniel},
booktitle={INFORMATIK 2023},
year={2023},
publisher={Gesellschaft f{\"u}r Informatik, Bonn}
}
@InProceedings{annanias_et_al:LIPIcs.GIScience.2023.14,
author =  {Annanias, Yves and Wiegreffe, Daniel and Niekler, Andreas and Kuzma, Marta and Harvey, Francis},
title =   {Development of a Semantic Segmentation Approach to Old-Map Comparison},
booktitle =   {12th International Conference on Geographic Information Science (GIScience 2023)},
pages =   {14:1--14:6},
series =  {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN =    {978-3-95977-288-4},
ISSN =    {1868-8969},
year =    {2023},
volume =  {277},
editor =  {Beecham, Roger and Long, Jed A. and Smith, Dianna and Zhao, Qunshan and Wise, Sarah},
publisher =   {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL =     {https://drops.dagstuhl.de/opus/volltexte/2023/18909},
annote =  {Keywords: Geographic/Geospatial Visualization, Visual Knowledge Discovery, Cartographic Analysis}
}
@inproceedings {envirvis,
title = {An Interactive Decision Support System for Analyzing Time Related Restrictions in Renaturation and Redevelopment Planning Projects},
booktitle = {Workshop on Visualisation in Environmental Sciences (EnvirVis)},
editor = {Dutta, Soumya and Feige, Kathrin and Rink, Karsten and Zeckzer, Dirk},
author = {Annanias, Yves and Meinecke, Christofer and Wiegreffe, Daniel},
year = {2023},
publisher = {The Eurographics Association},
DOI = {10.2312/envirvis.20231107}
}
@inproceedings{borst22,
title={A demonstration system towards NLP and knowledge driven data
platforms for Civil Engineering},
author={Borst, Janos and Meinecke, Christofer and Wiegreffe, Daniel and Niekler, Andreas},
booktitle={INFORMATIK 2022},
year={2022},
publisher={Gesellschaft f{\"u}r Informatik, Bonn}
}
@inproceedings{Levia2022a,
author = {Christofer Meinecke and Jeremias Schebera and Jakob Eschrich and Daniel Wiegreffe},
title = {Visualizing Similarities between American Rap-Artists based on Text Reuse},
booktitle = {LEVIA 2022: Leipzig Symposium on Visualization in Applications},
year={2022}
}
@inproceedings{Levia2022b,
author = {Yves Annanias and Jonah Windolph and Robert Wehlitz and Daniel Wiegreffe},
title = {An Interactive Decision Support System for Analyzing and Linkage of Weather-Related Restrictions of Opencast Lignite Mines},
booktitle = {LEVIA 2022: Leipzig Symposium on Visualization in Applications},
year={2022}
}
@inproceedings {rapvis,
booktitle = {EuroVis 2022 - Posters},
editor = {Krone, Michael and Lenti, Simone and Schmidt, Johanna},
title = {Visualizing Similarities between American Rap-Artists},
author = {Meinecke, Christofer and Schebera, Jeremias and Eschrich, Jakob and Wiegreffe, Daniel},
year = {2022},
publisher = {The Eurographics Association},
ISBN = {978-3-03868-185-4},
DOI = {10.2312/evp.20221129}
}
@inproceedings{chatbotexplorer,
title={Chatbot Explorer: Towards an understanding of knowledge bases of chatbot systems},
author={Hausdorf,A. and Mueller,L. and Scheuermann,G. and Niekler,A. and Wiegreffe,D.},
booktitle={30th International Conference in Central Europe on
Computer Graphics, Visualization and Computer Vision 2022},
year={2022},
organization={WSCG}
}
@ARTICLE {9779582,
author = {Y. Annanias and D. Zeckzer and G. Scheuermann and D. Wiegreffe},
journal = {IEEE Computer Graphics and Applications},
title = {An Interactive Decision Support System for Land Reuse Tasks},
year = {2022},
volume = {},
number = {01},
issn = {1558-1756},
pages = {1-1},
keywords = {task analysis;geographic information systems;data visualization;signal processing;planning;licenses;visualization},
doi = {10.1109/MCG.2022.3175604},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
month = {may}
}
@article{10.1093/nar/gkac398,
author = {Kampfrath, Michelle and Staritzbichler, René and Hernández, Guillermo Pérez and Rose, Alexander S and Tiemann, Johanna K S and Scheuermann, Gerik and Wiegreffe, Daniel and Hildebrand, Peter W},
title = "{MDsrv: visual sharing and analysis of molecular dynamics simulations}",
journal = {Nucleic Acids Research},
year = {2022},
month = {05},
abstract = "{Molecular dynamics simulation is a proven technique for computing and visualizing the time-resolved motion of macromolecules at atomic resolution. The MDsrv is a tool that streams MD trajectories and displays them interactively in web browsers without requiring advanced skills, facilitating interactive exploration and collaborative visual analysis. We have now enhanced the MDsrv to further simplify the upload and sharing of MD trajectories and improve their online viewing and analysis. With the new instance, the MDsrv simplifies the creation of sessions, which allows the exchange of MD trajectories with preset representations and perspectives. An important innovation is that the MDsrv can now access and visualize trajectories from remote datasets, which greatly expands its applicability and use, as the data no longer needs to be accessible on a local server. In addition, initial analyses such as sequence or structure alignments, distance measurements, or RMSD calculations have been implemented, which optionally support visual analysis. Finally, based on Mol*, MDsrv now provides faster and more efficient visualization of even large trajectories compared to its predecessor tool NGL.}",
issn = {0305-1048},
doi = {10.1093/nar/gkac398},
url = {https://doi.org/10.1093/nar/gkac398},
note = {gkac398},
eprint = {https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkac398/43848493/gkac398.pdf},
}
@inproceedings{annanias2021report,
title={Report on the Correction of Erroneous Geometry Data in Land Reuse Projects},
author={Annanias, Yves and Wahsner, Marc and Scheuermann, Gerik and Wiegreffe, Daniel},
booktitle={INFORMATIK 2021},
year={2021},
publisher={Gesellschaft f{\"u}r Informatik, Bonn}
}
@inproceedings{schroder2021mining,
title={Supporting Land Reuse of Former Open Pit Mining Sitesusing Text Classification and Active Learning},
author={Schröder, Christopher and Bürgl, Kim and Annanias, Yves and Niekler, Andreas and Müller, Lydia and Wiegreffe, Daniel and Bender, Christian and Mengs, Christoph and Scheuermann, Gerik and Heyer, Gerhard},
booktitle={ACL-IJCNLP 2021},
year={2021}
}
@article{Zeckzer_2020,
DOI = {10.1186/s12859-020-03761-6},
author = {Dirk Zeckzer and Alrik Hausdorf and Nicole Hinzmann and Lydia Müller and Daniel Wiegreffe},
title = {Masakari: visualization supported statistical analysis of genome segmentations},
journal = {BMC Bioinformatics},
URL = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03761-6},
year={2020}
}
@inproceedings{HNWLevia2019,
author = {Alrik Hausdorf and Andreas Niekler and Daniel Wiegreffe},
title = {LocalCompanies: Visual Analytics of spatial aligned regional companies},
booktitle = {LEVIA 2019: Leipzig Symposium on Visualization in Applications},
DOI={10.31219/osf.io/tsdfh},
url={https://osf.io/tsdfh},
year={2019}
}
@article{wasserbau:2020,
title={Einsatz von Künstlicher Intelligenz (KI) für die Optimierung von Planungsprozessen im Wasserbau},
author={Sankowska, P. and Kumbruck, N. and Möller, T. R. and Leyh, C. and Niekler, A. and  Wiegreffe, D. },
journal={Wasserbauliche Mitteilungen 63},
pages={31--40},
publisher={Technische Universit\"at Dresden},
year={2020},
ISBN = {978-3-86780-627-5}
}
@phdthesis{thesis,
author       = {Daniel Wiegreffe},
title        = {Visual Analysis of Form and Function in Computational Biology},
school       = {Leipzig University},
year         = 2019,
URL          = {https://nbn-resolving.org/urn:nbn:de:bsz:15-qucosa2-344026},
}
@article{scads,
title={Big Data Competence Center ScaDS Dresden/Leipzig: Overview and selected research activities},
author={Rahm, Erhard and Nagel, Wolfgang E and Peukert, Eric and J{\"a}kel, Ren{\'e} and G{\"a}rtner, Fabian and Stadler, Peter F and Wiegreffe, Daniel and Zeckzer, Dirk and Lehner, Wolfgang},
journal={Datenbank-Spektrum},
pages={1--12},
publisher={Springer},
year={2018},
URL = {https://doi.org/10.1007/s13222-018-00303-6}
}
@article{doi:10.1093/bioinformatics/bty817,
author = {Wiegreffe, Daniel and Alexander, Daniel and Stadler, Peter F and Zeckzer, Dirk},
title = {RNApuzzler: Efficient Outerplanar Drawing of RNA-Secondary Structures},
journal = {Bioinformatics},
volume = {},
number = {},
pages = {bty817},
year = {2018},
doi = {10.1093/bioinformatics/bty817},
URL = {http://dx.doi.org/10.1093/bioinformatics/bty817},
eprint = {/oup/backfile/content_public/journal/bioinformatics/pap/10.1093_bioinformatics_bty817/2/bty817.pdf}
}
@article {771,
title = {The Sierra Platinum Service for generating peak-calls for replicated ChIP-seq experiments},
journal = {BMC Research Notes},
year = {2018},
month = {07/2018},
type = {Research Note},
abstract = {
Objective
Sierra Platinum is a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering. The required computing resources are optimized but still may exceed the resources available to researchers at biological research institutes.
Results
Sierra Platinum Service provides the full functionality of Sierra Platinum: using a web interface, a new instance of the service can be generated. Then experimental data is uploaded and the computation of the peaks is started. Upon completion, the results can be inspected interactively and then downloaded for further analysis, at which point the service terminates.
},
keywords = {ChIP-seq, Histone modifications, Peak-caller, Replicate analysis},
URL = {https://doi.org/10.1186/s13104-018-3633-x},
author = {Daniel Wiegreffe and Lydia Müller and Jens Steuck and Dirk Zeckzer and Peter F. Stadler}
}
@article{zeckzer2018tibind,
title={Analyzing Histone Modifications Using
Tiled Binned Clustering and 3D Scatter Plots},
author={Dirk Zeckzer and Daniel Wiegreffe and Lydia Müller},
journal={Journal of WSCG},
volume={26},
year={2018},
URL = {https://doi.org/10.24132/JWSCG.2018.26.1.1},
publisher={Computer Science Research Notes}
}
@inproceedings{gerighausen2017idotter,
title={iDotter - an interactive dot plot viewer},
author={Daniel Gerighausen and Alrik Hausdorf and Sebastian Zänker and Dirk Zeckzer},
booktitle={25th International Conference in Central Europe on
Computer Graphics, Visualization and Computer Vision 2017},
year={2017},
organization={WSCG}
}
@article{berto2016consensus,
title={A consensus network of gene regulatory factors in the human frontal lobe},
author={Stefano Berto and Alvaro Perdomo-Sabogal and Daniel Gerighausen and Jing Qin and Katja Nowick},
journal={Frontiers in genetics},
volume={7},
year={2016},
publisher={Frontiers Media SA},
URL = {https://doi.org/10.3389/fgene.2016.00031}
}
@article{zeckzer2014analyzing,
title={Analyzing Chromatin Using Tiled Binned Scatterplot Matrices},
author={Dirk Zeckzer and Daniel Gerighausen and Lydia Steiner and Sonja J. Prohaska},
journal={IEEE BioVis 2014},
year={2014}
}
@inproceedings{zeckzer2016analyzing,
title={Analyzing Histone Modifications in iPS Cells Using Tiled Binned 3D Scatter Plots},
author={Dirk Zeckzer and Daniel Gerighausen and Lydia Müller},
booktitle={Big Data Visual Analytics (BDVA), 2016},
pages={1--8},
year={2016},
organization={IEEE},
URL = {https://doi.org/10.1109/BDVA.2016.7787042}
}
@article{muller2016sierra,
title={Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and-steering},
author={Lydia Müller and Daniel Gerighausen and Mariam Farman and Dirk Zeckzer},
journal={BMC Bioinformatics},
volume={17},
number={1},
pages={377},
year={2016},
publisher={BioMed Central},
URL = {https://doi.org/10.1186/s12859-016-1248-6}
}
@article{feist2014using,
title={Using Significant Word Co-occurences for the Lexical Access Problem},
author={Rico Feist and Daniel Gerighausen and Manuel Konrad and Georg Richter and Thomas Eckart and Dirk Goldhahn and Uwe Quasthoff},
journal={COLING 2014},
pages={46},
year={2014},
URL = {http://dx.doi.org/10.3115/v1/W14-4706},
publisher={Citeseer}
}
@book{gerighausen2013kombination,
title={Kombination von K-means++ Clustering und PCA zur Analyse von Chromatin-Daten},
author={Daniel Gerighausen},
year={2013},
URL = {https://nbn-resolving.org/urn:nbn:de:bsz:15-qucosa2-171486}
}
@book{gerighausen2015tibi3d,
title={TiBi-3D – a Guide through the World of Epigenetics},
author={Daniel Gerighausen},
year={2015},
URL = {https://nbn-resolving.org/urn:nbn:de:bsz:15-qucosa2-172276}
}