Basem also uses data mining to unleash the potential of such mobile elements to revolutionize biotechnology, medicine, crop production, and basic research. The first product of this effort, which was published in Science Magazine in 2020, yielded more compact and more versatile gene-editing technologies that they have shown to edit the DNA of bacteria, plants, and human cell lines, with a higher targeting capacity that also enables molecular diagnostics, and high promise for delivery into human and plant cells. This work was highlighted in the 2020 Nobel Prize in Chemistry Lecture​, in addition to being featured by Nature, Nature Plants, Nature Biotechnology, Cell Molecular Plant, and more. In 2022, Basem expanded upon this line of work, culminating in a manuscript on the discovery, biochemistry, & structural insights of novel CRISPR-Cas systems and their development into gene-editing tools. This effort was published in Cell with features in Nature and Science Magazines. Overall, these inventions are poised to transform agricultural practices and disease treatment by enabling novel editing approaches and delivery options that are difficult to achieve or not even possible with previously described systems, and have been licensed towards biotechnology development deals valued at over $1.5 billion for leading CRISPR-focused companies.

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During the COVID-19 pandemic, Basem has contributed to multiple open-science efforts to develop economical methods for coronavirus surveillance in municipal wastewater, to study the coronaviruses circulating in our communities, and to establish more robust computational pipelines for viral pandemic detection. The latter resulted in a joint first-author publication in Nature Magazine, with a feature in Science.

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Recently, Basem led the discovery of a new type of giant extrachromosomal element, which they named the Borgs, in a number of environments in California, Colorado, and other states. These elements carry numerous genes that were completely unknown to science, till now. Many Borg functionalities impact biogeochemical cycles and potentially play a role in the removal of greenhouse gases from our atmosphere, thereby aiding in climate change mitigation. This work was published in Nature Magazine and featured on the magazine cover. The research was further highlighted by the American Society for Microbiology’s popular podcast, This Week in Microbiology, and featured in Science Magazine, The Independent, SYFY, Quanta, The Scientist, C&EN, Futurism, Nature Magazine and other news outlets prior to publication.