CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci. - Omer S. Alkhnbashi; Fabrizio Costa; Shiraz A. Shah; Roger A. Garrett; Sita J. Saunders; Rolf Backofen (Bioinform., 2014)

Characterizing leader sequences of CRISPR loci. - Omer S. Alkhnbashi; Shiraz A. Shah; Roger A. Garrett; Sita J. Saunders; Fabrizio Costa; Rolf Backofen (Bioinform., 2016)

Computational characterisation of genomic CRISPR-Cas systems in archaea and bacteria - Omer S. Alkhnbashi (2017)

Freiburg RNA tools: a central online resource for RNA-focused research and teaching. - Martin Raden; Syed M. Ali; Omer S. Alkhnbashi; Anke Busch; Fabrizio Costa; Jason A. Davis; Florian Eggenhofer; Rick Gelhausen; Jens Georg; Steffen Heyne; Michael Hiller; Kousik Kundu; et al. (Nucleic Acids Res., 2018)

Casboundary: automated definition of integral Cas cassettes. - Victor Alexandre Padilha; Omer S. Alkhnbashi; Van Dinh Tran; Shiraz A. Shah; André C. P. L. F. de Carvalho; Rolf Backofen (Bioinform., 2021)

CRISPRloci: comprehensive and accurate annotation of CRISPR-Cas systems. - Omer S. Alkhnbashi; Alexander Mitrofanov; Robson Bonidia; Martin Raden; Van Dinh Tran; Florian Eggenhofer; Shiraz A. Shah; Ekrem Öztürk; Victor Alexandre Padilha; Danilo Sipoli Sanches; André C. P. L. F. de Carvalho; Rolf Backofen (Nucleic Acids Res., 2021)

RiboReport - benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria. - Rick Gelhausen; Teresa Müller; Sarah L. Svensson; Omer S. Alkhnbashi; Cynthia M. Sharma; Florian Eggenhofer; Rolf Backofen (Briefings Bioinform., 2022)

CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection. - Alexander Mitrofanov; Marcus Ziemann; Omer S. Alkhnbashi; Wolfgang R. Hess; Rolf Backofen (Bioinform., 2022)

Aspect-Based Sentiment Analysis of Patient Feedback Using Large Language Models. - Omer S. Alkhnbashi; Rasheed Mohammad 001; Mohammad Hammoudeh (Big Data Cogn. Comput., 2024)

Optimizing Large Language Models for Arabic Healthcare Communication: A Focus on Patient-Centered NLP Applications. - Rasheed Mohammad 001; Omer S. Alkhnbashi; Mohammad Hammoudeh (Big Data Cogn. Comput., 2024)

Education in Transition: Adapting and Thriving in a Post-COVID World. - Omer S. Alkhnbashi; Rasheed Mohammad 001; Doaa M. Bamasoud (Syst., 2024)