@conference {947,
	title = {Chatbot Explorer: Towards an understanding of knowledge bases of chatbot systems},
	booktitle = {30th International Conference in Central Europe on Computer Graphics, Visualization and Computer Vision 2022},
	year = {2022},
	abstract = {A chatbot can automatically process a user{\textquoteright}s request, e.g. to provide a requested information. In doing so, the user starts a conversation with the chatbot and can specify the request by further inquiry. Due to the developments in the field of NLP in recent years, algorithmic text comprehension has been significantly improved. As a result, chatbots are increasingly used by companies and other institutions for various tasks such as order processes or service requests. Knowledge bases are often used to answer users queries, but these are usually curated manually in various text files, prone to errors. Visual methods can help the expert to identify common problems in the knowledge base and can provide an overview of the chatbot system. In this paper, we present Chatbot Explorer, a system to visually assist the expert to understand, explore, and manage a knowledge base of different chatbot systems. For this purpose, we provide a tree-based visualization of the knowledge base as an overview. For a detailed analysis, the expert can use appropriate visualizations to drill down the analysis to the level of individual elements of a specific story to identify problems within the knowledge base. We support the expert with automatic detection of possible problems, which can be visually highlighted. Additionally, the expert can also change the order of the queries to optimize the conversation lengths and it is possible to add new content. To develop our solution, we have conducted an iterative design process with domain experts and performed two user evaluations. The evaluations and the feedback from our domain experts have shown that our solution can significantly improve the maintainability of chatbot knowledge bases.},
	author = {Alrik Hausdorf and Lydia M{\"u}ller and Gerik Scheuermann and Andreas Niekler and Daniel Wiegreffe}
}
@article {879,
	title = {Masakari: visualization supported statistical analysis of genome segmentations},
	journal = {BMC Bioinformatics},
	volume = {21},
	year = {2020},
	month = {10/2020},
	chapter = {437},
	abstract = {Background

In epigenetics, the change of the combination of histone modifications at the same genomic location during cell differentiation is of great interest for understanding the function of these modifications and their combinations. Besides analyzing them locally for individual genomic locations or globally using correlations between different cells types, intermediate level analyses of these changes are of interest. More specifically, the different distributions of these combinations for different cell types, respectively, are compared to gain new insights.

Results and discussion

We propose a new tool called {\textquoteleft}Masakari{\textquoteright} that allows segmenting genomes based on lists of ranges having a certain property, e.g., peaks describing histone modifications. It provides a graphical user interface allowing to select all data sets and setting all parameters needed for the segmentation process. Moreover, the graphical user interface provides statistical graphics allowing to assess the quality and suitability of the segmentation and the selected data.

Conclusion

Masakari provides statistics based visualizations and thus fosters insights into the combination of histone modification marks on genome ranges, and the differences of the distribution of these combinations between different cell types.},
	doi = {10.1186/s12859-020-03761-6},
	url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03761-6},
	author = {Dirk Zeckzer and Alrik Hausdorf and Nicole Hinzmann and Lydia M{\"u}ller and Daniel Wiegreffe}
}
@article {769,
	title = {Analyzing Histone Modifications Using Tiled Binned Clustering and 3D Scatter Plots},
	journal = {Journal of WSCG},
	volume = {26},
	year = {2018},
	month = {05/2018},
	pages = {1-10},
	chapter = {1},
	issn = {1213-6972},
	doi = {10.24132/JWSCG.2018.26.1.1},
	url = {http://wscg.zcu.cz/DL/wscg_DL.htm},
	author = {Dirk Zeckzer and Daniel Wiegreffe and Lydia M{\"u}ller}
}
@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},
	doi = {https://doi.org/10.1186/s13104-018-3633-x},
	url = {https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-018-3633-x},
	author = {Daniel Wiegreffe and Lydia M{\"u}ller and Jens Steuck and Dirk Zeckzer and Peter F. Stadler}
}
@proceedings {708,
	title = {Analyzing Histone Modifications in iPS Cells Using Tiled Binned 3D Scatter Plots},
	year = {2016},
	month = {11/2016},
	pages = {1--8},
	publisher = {International Symposium on Big Data Visual Analytics},
	address = {Sydney, Australia},
	abstract = {Epigenetics data is very important for understand- ing the differentiation of cells into different cell types. More- over, the amount of epigenetic data available was and still is considerably increasing. To cope with this big amount of data, statistical or visual analysis is used. Usually, biologists analyze epigenetic data using statistical methods like correlations on a high level. However, this does not allow to analyze the fate of histone modifications in detail during cell specification or to compare histone modifications in different cell lines. Tiled binned scatter plot matrices proved to be very useful for this type of analysis showing binary relationships. We adapted the idea of tiling and binning scatter plots from 2D to 3D, such that ternary relationships can be depicted. Comparing tiled binned 3D scatter plots{\textemdash}the new method{\textemdash}to tiled binned 2D scatter plot matrices showed, that many relations that are difficult or impossible to find using tiled binned 2D scatter plot matrices can easily be observed using the new approach. We found that using our approach, changes in the distribution of the marks over time (different cell types) or differences between different replicates of the same cell sample are easy to detect. Tiled binned 3D scatter plots proved superior compared to the previously used method due to the reduced amount of overplotting leading to less interaction necessary for gaining similar insights.},
	doi = {10.1109/BDVA.2016.7787042},
	author = {Dirk Zeckzer and Daniel Wiegreffe and Lydia M{\"u}ller}
}
@article {695,
	title = {Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering},
	journal = {BMC Bioinformatics},
	volume = {17},
	year = {2016},
	month = {09/2016},
	pages = {1--13},
	chapter = {1},
	abstract = {Histone modifications play an important role in gene regulation. Their genomic locations are of great interest. Usually, the location is measured by ChIP-seq and analyzed with a peak-caller. Replicated ChIP-seq experiments become more and more available. However, their analysis is based on single-experiment peak-calling or on tools like PePr which allows peak-calling of replicates but whose underlying model might not be suitable for the conditions under which the experiments are performed.},
	issn = {1471-2105},
	doi = {10.1186/s12859-016-1248-6},
	url = {http://dx.doi.org/10.1186/s12859-016-1248-6},
	author = {Lydia M{\"u}ller and Daniel Wiegreffe and Mariam Farman and Dirk Zeckzer}
}
@proceedings {666,
	title = {ChromatinVis:  a tool for analyzing epigenetic data},
	year = {2014},
	author = {Daniel Wiegreffe and Dirk Zeckzer and Lydia M{\"u}ller and Sonja J. Prohaska}
}
