BehindThePipette

Basem is a Ph.D. Candidate and National Science Foundation Predoctoral Fellow at the University of California, Berkeley, working in the labs of Dr. Jillian Banfield, Professor in the Departments of Earth and Planetary Science and Environmental Science, Policy, and Management, and Dr. Jennifer DoudnaProfessor in the Departments of Chemistry and Chemical Engineering, and Molecular and Cell Biology.

During his graduate career, Basem has applied computational approaches to the discovery and investigation of viruses and novel tools for biotechnological applications. His Ph.D. research has introduced a paradigm shift in our understanding of bacterial viruses by uncovering new groups of bacteriophages with huge genomes, including the largest documented, equipped with a wide variety of features typically associated with life and cellular organisms. This breakthrough was reported this year in Nature Magazine, and was highlighted as part of the 2020 Nobel Prize in Chemistry Collection, recommended by faculty in f1000 prime, widely covered in the popular press (including the Atlantic, GizmodoarsTechnica, & IFLS), science blogs, and multiple highlights in Nature Reviews and in Nature Reviews Microbiology as "too big to be ignored", among other major scientific journals.

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, 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.

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.

Most recently, he discovered 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 also highlighted by the American Society for Microbiology’s popular podcast, This Week in Microbiology, and featured in Nature Magazine, Science Magazine, The Independent, SYFY, Quanta, The Scientist, C&EN, Futurism, and other news outlets.

EDUCATION
RESEARCH INTERESTS

Geomicrobiology
Genome Editing

Metabolic Engineering

Microbial Physiology and Evolution

Natural Product Biosynthesis
Evolutionary and Rational Protein Design
Biogeochemistry

Microbial 'Immunology' 

Microbial Eukaryotes

Viral Evolution

Planetary Science & Astrobiology
Origin of Life

in situ Resource Utilization

Microbial Electrosynthesis

 

Ph.D. Microbiology (In Progress)

Department of Plant and Microbial Biology

University of California, Berkeley


B.S. Genetics, Cell Biology and Development

B.S. Microbiology

Minor: Philosophy

College of Biological Sciences
University of Minnesota- Twin Cities

 

International General Certificate of Secondary Education

Modern Education Schools, Cairo, Egypt

Evaluations administered by University of Cambridge, UK