Alumni
University of California, Berkeley
Ph.D. Microbiology (2017-2022)
University of Minnesota- Twin Cities
B.S. Genetics, Cell Biology, and Development
B.S. Microbiology
Minor in Philosophy
22. Joy Y. Wang*, Owen T. Tuck*, Petr Skopintsev*, Katarzyna M. Soczek, Gary Li, Basem Al-Shayeb, Julia Zhou and Jennifer A. Doudna. "Genome expansion by a CRISPR trimmer-integrase". BioRxiv. (2023)
21. Zheng Li, Zhenhui Zhong, Zhongshou Wu, Patrick Pausch, Basem Al-Shayeb, Jasmine Amerasekera, Jennifer A. Doudna, Steven E. Jacobsen “Genome editing in plants using the compact editor CasΦ”. PNAS. (2023)
20. Basem Al-Shayeb, Petr Skopintsev, Katarzyna M. Soczek, Elizabeth C. Stahl, Zheng Li, Evan Groover, Dylan Smock, Amy R. Eggers, Patrick Pausch, Brady F. Cress, Carolyn J. Huang, Brian Staskawicz, David F. Savage, Steven E. Jacobsen, Jillian F. Banfield, Jennifer A. Doudna. "Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors". Cell. (2022)
19. Basem Al-Shayeb, Marie C Schoelmerich, Jacob West-Roberts, Luis E. Valentin-Alvarado, Rohan Sachdeva, Susan Mullen, Alexander Crits-Christoph, Michael J. Wilkins, Kenneth H. Williams, Jennifer Doudna, Jillian F. Banfield. 2021. "Borgs are giant extrachromosomal elements with the potential to augment methane oxidation". Nature.
18. Robert C. Edgar*, Jeff Taylor*, Tomer Altman*, Pierre Barbera*, Dmitry Meleshko*, Victor Lin*, Dan Lohr*, Gherman Novakovsky*, Basem Al-Shayeb*, Jillian F. Banfield*, Anton Korobeynikov*, Rayan Chikhi*, and Artem Babaian*. 2022. "Petabase-scale sequence alignment catalyses viral discovery". Nature.
17. Adair L Borges, Yue Clare Lou, Rohan Sachdeva, Basem Al-Shayeb, Alexander L. Jaffe, Shufei Lei, Joanne M. Santini, Jillian F. Banfield. 2022. "Stop codon recoding is widespread in diverse phage lineages and has the potential to regulate translation of late stage and lytic genes". Nature Microbiology.
16. Jacob A. West-Roberts, Paula B. Matheus-Carnevali, Basem Al-Shayeb, Marie Charlotte Schoelmerich, Alex D. Thomas, Allison Sharrar, Christine He, Lin-Xing Chen, Adi Lavy, Ray Keren, Yuki Amano, Jillian F Banfield. “The Chloroflexi supergroup is metabolically diverse and representatives have novel genes for non-photosynthesis based CO2 fixation”. BioRxiv.
15. Alexander Crits-Christoph, Spencer Diamond, Basem Al-Shayeb, Luis Valentin-Alvarado, and Jillian F. Banfield. 2022. “A widely distributed genus of soil Acidobacteria genomically enriched in biosynthetic gene clusters”. ISME Communications.
14. Hannah D. Greenwald, Lauren L. Kennedy, Adrian Hinkle, Oscar Whitney, Vinson Fan, Alexander Crits-Christoph, Sasha Harris-Lovett, Avi Flamholz, Basem Al-Shayeb, L. Liao, M. Beyers, D. Brown, A. Chakrabarti, J. Dow, D. Frost, M. Koekemer, C. Lynch, P. Sarkar, E. White, R. Kantor, Kara L. Nelson. 2021. “Interpretation of spatial and temporal trends of SARS-CoV-2 RNA in San Francisco Bay Area wastewater”. Water Research X.
13. Patrick Pausch*, Kasia M. Soczek*, D. A. Herbst, Basem Al-Shayeb, Jillian F. Banfield, Eva Nogales, Jennifer A. Doudna. “DNA interference states of the hypercompact CRISPR-CasΦ effector”. 2021. Nature Structural & Molecular Biology.
12. Joy Y. Wang, Christopher M. Hoel, Basem Al-Shayeb, Jillian F. Banfield, Stephen G. Brohawn, Jennifer A. Doudna. “Structural coordination between active sites of a Cas6-reverse transcriptase-Cas1—Cas2 CRISPR integrase complex”. 2021. Nature Communications
11. Kris Saha, Erik J. Sontheimer, P. J. Brooks, ... , & The SCGE Consortium. 2021. “The NIH Somatic Cell Genome Editing program”. Nature.
10. Oscar N. Whitney, Lauren Kennedy, Vinson Fan, Adrian Hinkle, Rose Kantor, Hannah Greenwald, Alexander Crits-Christoph, Basem Al-Shayeb, Mira Chaplin, Anna Maurer, Robert Tjian, Kara L. Nelson. 2021. "Sewage, Salt, Silica and SARS-CoV-2 (4S): An economical kit-free method for direct capture of SARS-CoV-2 RNA from wastewater". Environmental Science & Technology.
9. Alexander Crits-Christoph, Rose S. Kantor, Matthew R. Olm, Oscar N. Whitney, Basem Al-Shayeb, Yue C. Lou, Avi Flamholz, Lauren C. Kennedy, Hannah Greenwald, Adrian Hinkle, Jonathan Hetzel, Sara Spitzer, Jeffery Koble, Asako Tan, Fred Hyde, Gary Schroth, Scott Kuersten, Jillian F. Banfield, and Kara L. Nelson. 2021. "Genome sequencing of sewage detects regionally prevalent SARS-CoV-2 variants". mBio.
8. Patrick Pausch*, Basem Al-Shayeb*, Ezra Bisom-Rapp, Connor A. Tsuchida, Zheng Li, Brady F. Cress, Gavin J. Knott, Steven E. Jacobsen, Jillian F. Banfield, Jennifer. A. Doudna. 2020. "CRISPR-CasΦ from huge phages is a hypercompact genome editor". Science. https://doi.org/10.1126/science.abb1400
7. Lucas B. Harrington*, Enbo Ma*, Janice S. Chen, Isaac P. Witte, Dov Gertz, David Paez-Espino, Basem Al-Shayeb, Nikos C. Krypides, David Burstein, Jillian F. Banfield, Jennifer A. Doudna. 2020. "A scoutRNA Is Required for Some Type V CRISPR-Cas Systems." Molecular Cell. https://doi.org/10.1016/j.molcel.2020.06.022
6. Basem Al-Shayeb*, Rohan Sachdeva*, Lin-Xing Chen, Fred Ward, Patrick Munk, Audra Devoto, Cindy J. Castelle, Matthew R. Olm, Keith Bouma-Gregson, Yuki Amano, Christine He, Raphaël Méheust, Brandon Brooks, Alex Thomas, Adi Lavy, Paula Matheus-Carnevali, Christine Sun, Daniela S. A. Goltsman, Mikayla A. Borton, Allison Sharrar, Alexander L. Jaffe, Tara C. Nelson, Rose Kantor, Ray Keren, Katherine R. Lane, Ibrahim F. Farag, Shufei Lei, Kari Finstad, Ronald Amundson, Karthik Anantharaman, Jinglie Zhou, Alexander J. Probst, Mary E. Power, Susannah G. Tringe, Wen-Jun Li, Kelly Wrighton, Sue Harrison, Michael Morowitz, David A. Relman, Jennifer A. Doudna, Anne-Catherine Lehours, Lesley Warren, Jamie H. D. Cate, Joanne M. Santini, & Jillian F. Banfield. 2020. “Clades of Huge Phages from across Earth’s Ecosystems.” Nature, February. https://doi.org/10.1038/s41586-020-2007-4.
5. Gavin J. Knott, Brady F. Cress, Jun-Jie Liu, Brittney W. Thornton, Rachel J. Lew, Basem Al-Shayeb, Daniel J. Rosenberg, Michal Hammel, Benjamin A Adler, Marco J Lobba, Michael Xu, Adam P Arkin, Christof Fellmann, Jennifer A Doudna. 2019. “Structural Basis for AcrVA4 Inhibition of Specific CRISPR-Cas12a.” eLife 8 (August): e49110. http://doi.org/10.7554/eLife.49110
4. Lin-Xing Chen, Basem Al-Shayeb, Raphaël Méheust, Wen-Jun Li, Jennifer A. Doudna, & Jillian F. Banfield. 2019. “Candidate Phyla Radiation Roizmanbacteria From Hot Springs Have Novel and Unexpectedly Abundant CRISPR-Cas Systems.” Frontiers in Microbiology 10: 928. https://doi.org/10.3389/fmicb.2019.00928
3. Gavin J. Knott, Brittney W. Thornton, Marco J. Lobba, Jun-Jie Liu, Basem Al-Shayeb, Kyle E. Watters, and Jennifer A. Doudna. 2019. “Broad-Spectrum Enzymatic Inhibition of CRISPR-Cas12a.” Nature Structural & Molecular Biology, April, 1. https://doi.org/10.1038/s41594-019-0208-z
2. Jun-Jie Liu*, Natalia Orlova*, Benjamin L. Oakes*, Enbo Ma, Hannah B. Spinner, Katherine L. M. Baney, Jonathan Chuck, Dan Tan, Gavin J. Knott, Lucas B. Harrington, Basem Al-Shayeb, Alexander Wagner, Julian Brötzmann, Brett T. Staahl, Kian L. Taylor, John Desmarais, Eva Nogales & Jennifer A. Doudna. (2019). “CasX Enzymes Comprise a Distinct Family of RNA-Guided Genome Editors.” Nature, February, 1. https://doi.org/10.1038/s41586-019-0908-x
1. Aunica L Kane, Basem Al-Shayeb, Patrick V Holec, Srijay Rajan, Nicholas E Le Mieux, Stephen C Heinsch, Sona Psarska, Kelly G Aukema, Casim A Sarkar, Edward A Nater, Jeffrey A Gralnick (2016). "Toward Bioremediation of Methylmercury Using Silica Encapsulated Escherichia coli Harboring the mer Operon." Plos One 11,1. https://doi.org/10.1371/journal.pone.0147036
Protocols
2. Oscar N Whitney, Basem Al-Shayeb, Alex Crits-Cristoph, Mira Chaplin, Vinson Fan, Hannah Greenwald, Adrian Hinkle, Rose Kantor, Lauren Kennedy, Anna Maurer, Robert Tjian, Kara L. Nelson, UC Berkeley Wastewater-based epidemiology consortium 2020. Direct wastewater RNA extraction via the "Milk of Silica (MoS)" method - A companion method to "Sewage, Salt, Silica and SARS-CoV-2 (4S)". protocols.io
https://dx.doi.org/10.17504/protocols.io.biwfkfbn
1. Oscar N Whitney, Basem Al-Shayeb, Alex Crits-Cristoph, Mira Chaplin, Vinson Fan, Hannah Greenwald, Adrian Hinkle, Rose Kantor, Lauren Kennedy, Anna Maurer, Robert Tjian, Kara L. Nelson, UC Berkeley Wastewater-based epidemiology consortium 2020. V.2 - Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method. protocols.io
https://dx.doi.org/10.17504/protocols.io.bjr9km96
2017-2022 NSF Graduate Research Fellowship
2021 Forbes 30 Under 30 in Science, Forbes Magazine
2021 Stanford-Berkeley-UCSF Next Generation Faculty Symposium Fellow
2021 Blue Flame Award, Addgene
2021 Chancellor’s Award for Public Service, UC Berkeley,
Awarded to the COVID-WEB team for surveillance of SARS-CoV-2 in municipal wastewater
2020 Mildred E. Mathias Graduate Student Research Grant, UC Natural Reserve System
2020 First Prize, Texas A&M University Genome Editing Symposium
2015 NASA Space Life Sciences Training Award
2014 iGEM Giant Jamboree Best Environment Project
2014 iGEM Giant Jamboree Gold Medal
2014 President's Student Leadership and Service Award
2014 BioTechnology Institute Undergraduate Research Fellowship
2014 Golden Key International Honour Society
2013 HHMI Undergraduate Research Fellowship
2013 College of Biological Sciences Annual Scholarship
2013 Michael Loveless Scholarship
Basem Al-Shayeb
Berkeley, CA 94720