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CurrentWork
UNCULTURED MICROBES
UNCULTURED MICROBES
CRISPR-CAS SYSTEMS
CRISPR-CAS SYSTEMS
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.
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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.
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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

Nature DNA Borgs
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.
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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

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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
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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 
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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#

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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

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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

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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

PNAS

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

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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

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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

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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

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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

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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

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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

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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

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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

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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.

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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

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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

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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

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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

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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

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Abstracts&Posters

 

Graduate Research and Beyond  * denotes presenter
Conference Talks, invited or selected from abstract
2024        Mayo Clinic Genetic Counselors Lecture Series
2024        5th RNA Editing Summit, Boston, MA (invited; presented by co-author)
2024        American Society for Gene and Cell Therapy Invited Speaker (declined)
2024        Investing in Cures Summit, Scottsdale, AZ.

2024        Damon Runyon Cancer Foundation: Bridging the Gap, Boston, MA.
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.
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 

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