Current Bioinformatics Tools to Optimize CRISPR/Cas9 Experiments to Reduce Off-Target Effects von Naeem, Muhammad, Alkhnbashi, Omer S

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SpacerPlacer: ancestral reconstruction of CRISPR arrays reveals the evolutionary dynamics of spacer deletions von Fehrenbach, Axel, Mitrofanov, Alexander, Alkhnbashi, Omer S, Backofen, Rolf, Baumdicker, Franz

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CRISPR-Cas bioinformatics von Alkhnbashi, Omer S., Meier, Tobias, Mitrofanov, Alexander, Backofen, Rolf, Voß, Björn

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Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants von Makarova, Kira S., Wolf, Yuri I., Iranzo, Jaime, Shmakov, Sergey A., Alkhnbashi, Omer S., Brouns, Stan J. J., Charpentier, Emmanuelle, Cheng, David, Haft, Daniel H., Horvath, Philippe, Moineau, Sylvain, Mojica, Francisco J. M., Scott, David, Shah, Shiraz A., Siksnys, Virginijus, Terns, Michael P., Venclovas, Česlovas, White, Malcolm F., Yakunin, Alexander F., Yan, Winston, Zhang, Feng, Garrett, Roger A., Backofen, Rolf, van der Oost, John, Barrangou, Rodolphe, Koonin, Eugene V.

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An updated evolutionary classification of CRISPR–Cas systems von Makarova, Kira S., Wolf, Yuri I., Alkhnbashi, Omer S., Costa, Fabrizio, Shah, Shiraz A., Saunders, Sita J., Barrangou, Rodolphe, Brouns, Stan J. J., Charpentier, Emmanuelle, Haft, Daniel H., Horvath, Philippe, Moineau, Sylvain, Mojica, Francisco J. M., Terns, Rebecca M., Terns, Michael P., White, Malcolm F., Yakunin, Alexander F., Garrett, Roger A., van der Oost, John, Backofen, Rolf, Koonin, Eugene V.

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Interrogating two extensively self-targeting Type I CRISPR-Cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block DNA degradation von Wimmer, Franziska, Englert, Frank, Wandera, Katharina G, Alkhnbashi, Omer S, Collins, Scott P, Backofen, Rolf, Beisel, Chase L

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Gene Expression-Based Cancer Classification for Handling the Class Imbalance Problem and Curse of Dimensionality von Al-Azani, Sadam, Alkhnbashi, Omer S, Ramadan, Emad, Alfarraj, Motaz

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CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems von Lange, Sita J, Alkhnbashi, Omer S, Rose, Dominic, Will, Sebastian, Backofen, Rolf

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Freiburg RNA tools: a central online resource for RNA-focused research and teaching von Raden, Martin, Ali, Syed M, Alkhnbashi, Omer S, Busch, Anke, Costa, Fabrizio, Davis, Jason A, Eggenhofer, Florian, Gelhausen, Rick, Georg, Jens, Heyne, Steffen, Hiller, Michael, Kundu, Kousik, Kleinkauf, Robert, Lott, Steffen C, Mohamed, Mostafa M, Mattheis, Alexander, Miladi, Milad, Richter, Andreas S, Will, Sebastian, Wolff, Joachim, Wright, Patrick R, Backofen, Rolf

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CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection von Mitrofanov, Alexander, Ziemann, Marcus, Alkhnbashi, Omer S, Hess, Wolfgang R, Backofen, Rolf

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CRISPRidentify: identification of CRISPR arrays using machine learning approach von Mitrofanov, Alexander, Alkhnbashi, Omer S, Shmakov, Sergey A, Makarova, Kira S, Koonin, Eugene V, Backofen, Rolf

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Deepdefense: annotation of immune systems in prokaryotes using deep learning von Hauns, Sven, Alkhnbashi, Omer S, Backofen, Rolf

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Characterizing leader sequences of CRISPR loci von Alkhnbashi, Omer S, Shah, Shiraz A, Garrett, Roger A, Saunders, Sita J, Costa, Fabrizio, Backofen, Rolf

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Anti-CRISPR prediction using deep learning reveals an inhibitor of Cas13b nucleases von Wandera, Katharina G, Alkhnbashi, Omer S, Bassett, Harris V I, Mitrofanov, Alexander, Hauns, Sven, Migur, Anzhela, Backofen, Rolf, Beisel, Chase L

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An Integrated Multimodal-Based CAD System for Breast Cancer Diagnosis von Sunba, Amal, AlShammari, Maha, Almuhanna, Afnan, Alkhnbashi, Omer S

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Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-cas gene cassettes reveals 39 new cas gene families von Shah, Shiraz A., Alkhnbashi, Omer S., Behler, Juliane, Han, Wenyuan, She, Qunxin, Hess, Wolfgang R., Garrett, Roger A., Backofen, Rolf

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Aspect-Based Sentiment Analysis of Patient Feedback Using Large Language Models von Alkhnbashi, Omer S., Mohammad, Rasheed, Hammoudeh, Mohammad

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Optimizing Large Language Models for Arabic Healthcare Communication: A Focus on Patient-Centered NLP Applications von Mohammad, Rasheed, Alkhnbashi, Omer S., Hammoudeh, Mohammad

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

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

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