@article{uzsoy_zareiesfandabadi_jennings_kemper_elting_2021, title={Automated tracking of S. pombe spindle elongation dynamics}, volume={6}, ISSN={["1365-2818"]}, url={https://doi.org/10.1111/jmi.13044}, DOI={10.1111/jmi.13044}, abstractNote={AbstractThe mitotic spindle is a microtubule‐based machine that pulls the two identical sets of chromosomes to opposite ends of the cell during cell division. The fission yeast Schizosaccharomyces pombe is an important model organism for studying mitosis due to its simple, stereotyped spindle structure and well‐established genetic toolset. S. pombe spindle length is a useful metric for mitotic progression, but manually tracking spindle ends in each frame to measure spindle length over time is laborious and can limit experimental throughput. We have developed an ImageJ plugin that can automatically track S. pombe spindle length over time and replace manual or semi‐automated tracking of spindle elongation dynamics. Using an algorithm that detects the principal axis of the spindle and then finds its ends, we reliably track the length of the spindle as the cell divides. The plugin integrates with existing ImageJ features, exports its data for further analysis outside of ImageJ and does not require any programming by the user. Thus, the plugin provides an accessible tool for quantification of S. pombe spindle length that will allow automatic analysis of large microscopy data sets and facilitate screening for effects of cell biological perturbations on mitotic progression.}, journal={JOURNAL OF MICROSCOPY}, publisher={Wiley}, author={Uzsoy, Ana Sofia M. and Zareiesfandabadi, Parsa and Jennings, Jamie and Kemper, Alexander F. and Elting, Mary Williard}, year={2021}, month={Jul} }
 @article{wang_brown_jennings_stolee_2022, title={Demystifying regular expression bugs A comprehensive study on regular expression bug causes, fixes, and testing}, volume={27}, ISSN={["1573-7616"]}, DOI={10.1007/s10664-021-10033-1}, abstractNote={Regular expressions cause string-related bugs and open security vulnerabilities for DOS attacks. However, beyond ReDoS (Regular expression Denial of Service), little is known about the extent to which regular expression issues affect software development and how these issues are addressed in practice. We conduct an empirical study of 356 regex-related bugs from merged pull requests in Apache, Mozilla, Facebook, and Google GitHub repositories. We identify and classify the nature of the regular expression problems, the fixes, and the related changes in the test code. The most important findings in this paper are as follows: 1) incorrect regular expression semantics is the dominant root cause of regular expression bugs (165/356, 46.3%). The remaining root causes are incorrect API usage (9.3%) and other code issues that require regular expression changes in the fix (29.5%), 2) fixing regular expression bugs is nontrivial as it takes more time and more lines of code to fix them compared to the general pull requests, 3) most (51%) of the regex-related pull requests do not contain test code changes. Certain regex bug types (e.g., compile error, performance issues, regex representation) are less likely to include test code changes than others, and 4) the dominant type of test code changes in regex-related pull requests is test case addition (75%). The results of this study contribute to a broader understanding of the practical problems faced by developers when using, fixing, and testing regular expressions.}, number={1}, journal={EMPIRICAL SOFTWARE ENGINEERING}, author={Wang, Peipei and Brown, Chris and Jennings, Jamie A. and Stolee, Kathryn T.}, year={2022}, month={Jan} }