Visualizing errors in object oriented programs. - Hani Z. Girgis; Bharat Jayaraman; Paul V. Gestwicki (OOPSLA Companion, 2005)

JavaTA: A Logic-based Debugger for Java - Hani Z. Girgis; Bharat Jayaraman (CoRR, 2007)

A Meta Registration Framework for Lesion Matching. - Sharmishtaa Seshamani; Purnima Rajan; Rajesh Kumar 001; Hani Z. Girgis; Themos Dassopoulos; Gerard Mullin; Gregory D. Hager (MICCAI (1), 2009)

An intelligent system to detect Crohn's disease inflammation in wireless capsule endoscopy videos. - Hani Z. Girgis; Benjamin R. Mitchell; Themistocles Dassopoulos; Gerard Mullin; Gregory D. Hager (ISBI, 2010)

Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs. - Hani Z. Girgis; Ivan Ovcharenko (BMC Bioinform., 2012)

Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale. - Hani Z. Girgis (BMC Bioinform., 2015)

HebbPlot: an intelligent tool for learning and visualizing chromatin mark signatures. - Hani Z. Girgis; Alfredo Velasco II; Zachary E. Reyes (BMC Bioinform., 2018)

A survey and evaluations of histogram-based statistics in alignment-free sequence comparison. - Brian B. Luczak; Benjamin T. James; Hani Z. Girgis (Briefings Bioinform., 2019)

Look4TRs: a de novo tool for detecting simple tandem repeats using self-supervised hidden Markov models. - Alfredo Velasco II; Benjamin T. James; Vincent D. Wells; Hani Z. Girgis (Bioinform., 2020)