CurrentWork
UNCULTURED MICROBES
UNCULTURED MICROBES
CRISPR-CAS SYSTEMS
CRISPR-CAS SYSTEMS
VIRUSES & MOBILE
ELEMENTS
VIRUSES &
MOBILE
ELEMENTS
METAGENOMICS
METAGENOMICS
SeniorAuthorPublications
* denotes equal co-first-author level contribution
1
Programmable multi-kilobase RNA editing using CRISPR-mediated trans-splicing
BioRxiv
Jacob Borrajo*, Kamyab Javanmardi*, James Griffin, Susan J St. Martin, David Yao, Kaisle Hill, Paul Blainey#, Basem Al-Shayeb#
2023
Highlighted by Forbes Magazine, EndpointsNews, C&EN, GEN Genetic Engineering and Biotechnology News, and other news outlets and blogs.
FirstAuthorPublications
* denotes equal co-first-author level contribution
5
Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors
Cell
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
2022
Highlighted by Nature Magazine & Science Magazine and multiple news outlets and blogs, Wikipedia’s 2022 in Science, 2023 Faces of Cell. Recommended by F1000 Faculty Opinions. Altmetric’s 99th percentile of highly discussed research.
4
Borgs are giant archaeal extrachromosomal elements with the potential to augment methane oxidation
Nature
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 A Doudna, Jillian F Banfield
2022
Featured on the cover of Nature Magazine.
Research highlighted by Science Magazine, Nature Magazine, Science Magazine top stories of 2021, SYFY, Vice, The Independent, C&EN, The Scientist, Innovative Genomics Institute 2020-2021 Impact Report, Quanta Magazine, Live Science, ASM’s This Week in Microbiology, Wikipedia’s 2021 in Science, and 30+ news outlets, blogs, and podcasts. Invited panelist on Phytobiomes Webinars, and the DNA Tie Club on Clubhouse.
Altmetric’s 99th percentile of highly discussed research.
3
Petabase-scale sequence alignment catalyses viral discovery
Nature
Robert C. Edgar*, Jeff Taylor*, Victor Lin*, Tomer Altman*, Pierre Barbera*, Dmitry Meleshko*, Dan Lohr*, Gherman Novakovsky*, Benjamin Buchfink*, Basem Al-Shayeb*, Jillian F. Banfield*, Marcos de la Peña*, Anton Korobeynikov*, Rayan Chikhi*, Artem Babaian*
2022
Research highlighted by Science Magazine, Nature Methods, National Geographic,
El Pais, and 60 other international news outlets. Recommended by F1000 Faculty
Opinions. Altmetric’s 99th percentile of highly discussed research.
2
2020
CRISPR-CasΦ from huge phages is a hypercompact genome editor
Science
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.
Featured in the 2020 Nobel Prize in Chemistry Lecture, Innovative Genomics Institute 2020-2021 Impact Report. Highlighted by Nature, Nature Reviews Microbiology, Nature Biotechnology, Nature Plants, Cell Molecular Plant, Addgene’s Hot Plasmids list, coverage in 30+ news outlets, multiple blogs and podcasts.
Altmetric’s 99th percentile of highly discussed research
1
Featured in the 2020 Nobel Prize in Chemistry Lecture, Nature’s Nobel Prize in Chemistry 2020 collection, recommended in f1000 prime, highlighted several times by Nature Reviews Microbiology as “Too big to be ignored”, coverage in 38+ news outlets (including the Atlantic, Gizmodo, arsTechnica) and multiple science blogs.
Altmetric’s 99th percentile of highly discussed research
2020
Clades of Huge Phages from Across Earth's Ecosystems
Nature
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.
AllPublications&Preprints
24
2023
Programmable multi-kilobase RNA editing using CRISPR-mediated trans-splicing
BioRxiv
Jacob Borrajo*, Kamyab Javanmardi*, James Griffin, Susan J St. Martin, David Yao, Kaisle Hill, Paul Blainey#, Basem Al-Shayeb#
22
2023
Genome expansion by a CRISPR trimmer-integrase
Nature
Joy Y. Wang*, Owen T. Tuck*, Petr Skopintsev*, Katarzyna M. Soczek, Gary Li, Basem Al-Shayeb, Julia Zhou and Jennifer A. Doudna
23
2023
Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires.
BioRxiv
Marie C. Schoelmerich, Lynn Ly, Jacob West-Roberts, LingDong Shi, Cong Shen, Nikhil S. Malvankar, Najwa Taib, Simonetta Gribaldo, Ben J. Woodcroft, Christopher W. Schadt, Basem Al-Shayeb, Xiaoguang Dai, Christopher Mozsary, Scott Hickey, Christine He, John Beaulaurier, Sissel Juul, Rohan Sachdeva, Jillian F. Banfield
21
Genome editing in plants using the compact editor CasΦ
PNAS
Zheng Li, Zhenhui Zhong, Zhongshou Wu, Patrick Pausch, Basem Al-Shayeb, Jasmine Amerasekera, Jennifer A. Doudna, Steven E. Jacobsen
2023
20
Diverse virus-encoded CRISPR-Cas systems include streamlined genome editorsCell
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
2022
19
Borgs are giant archaeal extrachromosomal elements with the potential to augment methane oxidation
Nature
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 A Doudna, Jillian F Banfield
2022
18
Petabase-scale sequence alignment catalyses viral discovery
Nature
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
17
A widely distributed genus of soil Acidobacteria genomically enriched in biosynthetic gene clusters
ISME Communications
Alexander Crits-Christoph, Spencer Diamond, Basem Al-Shayeb, Luis Valentin-Alvarado, Jillian F Banfield
2022
16
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
Adair L. Borges, Yue Clare Lou, Rohan Sachdeva, Basem Al-Shayeb, Alexander L. Jaffe, Shufei Lei, Joanne M. Santini, Jillian F. Banfield
The Chloroflexi supergroup is metabolically diverse and representatives have novel genes for non-photosynthesis based CO2 fixation
BioRxiv
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
2021
15
14
2021
DNA interference states of the hypercompact CRISPR-CasΦ effector
Nature Structural & Molecular Biology
Patrick Pausch*, Katarzyna M. Soczek*, Dominik A. Herbst, Basem Al-Shayeb, Jillian F. Banfield, Eva Nogales, Jennifer A. Doudna
2021
Tools for interpretation of wastewater SARS-CoV-2 temporal and spatial trends demonstrated with data collected in the San Francisco Bay Area
Water Research X
Hannah D Greenwald, Lauren C Kennedy, Adrian Hinkle, Oscar N Whitney, Vinson B Fan, Alexander Crits-Christoph, Sasha Harris-Lovett, Avi I Flamholz, Basem Al-Shayeb, Lauren D Liao, Matt Beyers, Daniel Brown, Alicia R Chakrabarti, Jason Dow, Dan Frost, Mark Koekemoer, Chris Lynch, Payal Sarkar, Eileen White, Rose Kantor, Kara L Nelson
13
12
2021
Structural coordination between active sites of a Cas6-reverse transcriptase-Cas1—Cas2 CRISPR integrase complex
Nature Communications
Joy Y. Wang, Christopher M. Hoel, Basem Al-Shayeb, Jillian F. Banfield, Stephen G. Brohawn, Jennifer A. Doudna.
2021
The NIH Somatic Cell Genome Editing program
Nature
K. Saha, E. J. Sontheimer, P. J. Brooks, ... , & The SCGE Consortium.
11
10
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
Oscar N. Whitney, Lauren Kennedy, Vinson Fan, Adrian Hinkle, Rose Kantor, Hannah Greenwald, Alex Crits-Christoph, Basem Al-Shayeb, Mira Chaplin, Anna Maurer, Robert Tjian, Kara L. Nelson.
2021
Genome sequencing of sewage detects regionally prevalent SARS-CoV-2 variants
mBio
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.
9
8
CRISPR-CasΦ from huge phages is a hypercompact genome editor
Science
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
Research highlighted by Nature, Nature Plants, Nature Biotechnology, and more
2020
A scoutRNA Is Required for Some Type V CRISPR-Cas Systems
Molecular Cell
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
7
6
2020
Clades of Huge Phages from Across Earth's Ecosystems
Nature
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.
Research recommended by f1000 Prime, coverage in 30+ news outlets (including the Atlantic, Gizmodo, arsTechnica) and 8 science blogs, reviewed in Nature Reviews Microbiology and more
2019
Structural Basis for AcrVA4 Inhibition of Specific CRISPR-Cas12a
eLife
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
5
4
2019
Candidate Phyla Radiation Roizmanbacteria From Hot Springs Have Novel and Unexpectedly Abundant CRISPR-Cas Systems
Frontiers in Microbiology
Lin-Xing Chen, Basem Al-Shayeb, Raphaël Méheust, Wen-Jun Li, Jennifer A. Doudna, and Jillian F. Banfield
2019
Broad-spectrum enzymatic inhibition of CRISPR-Cas12a
Nature Structural and Molecular Biology
Gavin Knott, Brittney Thornton, Marco Lobba, Jun-Jie Liu, Basem Al-Shayeb, Kyle Watters, Jennifer A Doudna
3
2
2019
CasX enzymes comprise a distinct family of RNA-guided genome editors
Nature
Jun-Jie Liu, Natalia Orlova, Benjamin L Oakes, Enbo Ma, Hannah B Spinner, Katherine LM 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
2016
Bioremediation of Methylmercury Using Silica Encapsulated Escherichia coli Harboring the mer Operon
PLOS One
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
1
Abstracts&Posters
Graduate Research and Beyond * denotes presenter
Conference Talks, invited or selected from abstract
2024 Damon Runyon Cancer Foundation: Bridging the Gap, Boston, MA.
2024 Investing in Cures Summit, Scottsdale, AZ.
2023 International Conference on CRISPR Technologies, Boston, MA.
2023 University of Minnesota Seminar Series, Minneapolis, MN.
2022 Cold Spring Harbor Laboratory Genome Engineering: CRISPR Frontiers Conference, NY.
2022 International Society for Microbial Ecology, Lausanne, Switzerland.
2021 Phytobiomes Alliance Webinar Series, Virtual.
2021 Next Generation Faculty Symposium, Stanford-UCSF-UC Berkeley, Virtual.
2021 The Arab Scientists Forum (ASF), Virtual.
2021 American Museum of Natural History Seminar Series, New York City, USA.
2021 Phages for Health & Energy Symposium, Virtual.
2021 Scribe Therapeutics, CA, USA
2020 NIH Somatic Cell Genome Editing Conference, Virtual.
2020 Cold Spring Harbor Laboratory Genome Engineering: CRISPR Frontiers Conference, Virtual.
2020 Texas A&M Genome Editing Symposium (& First Prize winner)
2020 21st Annual Microbiology Student Symposium. University of California, Berkeley, USA. (Invited, COVID-impacted)
2019 CRISPR Conference. Québec City, Canada.
2019 20th Annual Microbiology Student Symposium. University of California, Berkeley, USA.
Selected from among hundreds of scientists to present a research talk at the 2019 Annual CRISPR Conference in Quebec
Selected to present a research talk at the 20th Annual Microbiology Student Symposium in California, 2019
Selected from among hundreds of scientists to present a research talk at the 2019 Annual CRISPR Conference in Quebec
Conference Lightning Talks
Fighting Fire with Fire: CRISPR-CasΦ from huge phages is a hypercompact genome editor. 2020 Genome Editing Symposium, Texas A&M University. Virtual. **First Prize Winner
Posters
Al-Shayeb B*, Pausch P, Bisom-Rapp E, Tsuchida CA, Li Z, Cress BF, Knott GJ, Jacobsen SE, Banfield JF, Doudna JA. CRISPR-CasΦ from huge phages is a hypercompact genome editor. CRISPR 2021. Paris (virtual). June 2021
Wang J., Hoel C., Al-Shayeb B, Banfield JF, Brohawn S, Doudna JA. “Biochemical and structural insights into a reverse transcriptase-Cas1 CRISPR integrase”. Nature Communications. (2021)
Al-Shayeb B*, Pausch P*, Banfield JF, Doudna JA. Novel hypercompact proteins for genome editing applications. NIH Somatic Cell Genome Editing Consortium. Washington DC. December 2019
Knott G*, Thornton B, Lobba M, Liu J-J, Al-Shayeb B, Watters K, Doudna JA. Anti-CRISPR mechanisms for inhibiting CRISPR-Cas12a. CRISPR 2019. Québec City, Canada. June 2019
Al-Shayeb B*, Sachdeva R, Chen L-X, Ward F, Doudna JA, Cate JHD, Banfield JF. Clades of huge phages from across Earth's ecosystems. 20th Annual Microbiology Student Symposium. University of California, Berkeley, USA. April 2019
Undergraduate Research
Moyer EL*, Al-Shayeb B, Baer LA, Ronca AE. Unpredictable Variable Prenatal Stress Programs Expression of Genes Involved in Appetite Control and Energy Expenditure. American Society for Gravitational and Space Research, Cleveland, OH. November 2016.
Al-Shayeb B, A Fish By Any Other Name Would Taste As Sweet: Applied Ethics of Transgenic Fish Commercialization.
Critical Reflections Philosophy Conference, University of Windsor, Ontario. March 2016.
Al-Shayeb B*, Rael V, Lowman J, Hayden A, Sosa J, DeMatteo C, Baas-Thomas M, Vu A, Choi C, Quach V, Berrios D, Fogle H, Marcu O, Rask J, Smith J. GeneLab Resource Expansion And Tools: a Design for Collection, Analysis, and Presentation of Spaceflight Experimental Data. American Society for Gravitational and Space Research, Alexandria, VA. November 2015.
Al-Shayeb B*, Moyer EL, Baer LA, Ronca AE. Effects of Prenatal Stress on Appetite Control and Energy Expenditure Pathways in Adult Male Offspring. American Society for Gravitational and Space Research, Alexandria, VA. November 2015.
NASA Ames Summer Research Symposium. Mountain View, CA. August 2015.
Silica- encapsulated Recombinant Bacteria for Heavy Metal Bioremediation. Cargill R&D Group and Project Sponsors, September 2014. BioTechnology Institute Seminar Series, December 2014. MnDrive Research Symposium, January 2015. Ecolab R&D Group and Project Sponsors, January 2015. UMN Microbiology Club, February 2015. UMN Synthetic Biology Society, February 2015.
Al-Shayeb B*, Holec PV*, Rajan S, Le Mieux NE, Heinsch SC, Sarkar CA, Gralnick JA. MNtallica: Cleaning Up Heavy Metal! International Genetically Engineered Machines Giant Jamboree. Boston, MA. October 2014.
Al-Shayeb B*, Kane AL, Gralnick JA. Silica- encapsulated Recombinant Escherichia coli for Mercury Bioremediation. Minnesota Undergraduate Research Symposium. Minneapolis, MN. August 2014.
Al-Shayeb B*, Tarnowski J*, Heinsch, SC*, Schmidt-Dannert C, Gralnick JA. PichiParts: A Toolkit Approach for Engineering Pichia pastoris. International Genetically Engineered Machine Competition. Toronto, ON, CA. September 2013.
Al-Shayeb B*, Hudson HM, Baker KB, Vitek JL. Quantitative Analysis of Gait Changes Associated with Parkinson’s Disease and Dopamine Replacement Therapy. Howard Hughes Medical Institute Undergraduate Research Symposium. St Paul, MN. May 2013