CurrentWork
UNCULTURED MICROBES
UNCULTURED MICROBES
CRISPR-CAS SYSTEMS
CRISPR-CAS SYSTEMS
VIRUSES 
VIRUSES &
MOBILE ELEMENTS
METAGENOMICS
METAGENOMICS

Publications&Preprints

 

* denotes equal first-author level contribution

19

2021

Stop codon recoding is widespread in diverse phage lineages and has the potential to regulate translation of late stage and lytic genes
BioRxiv

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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18

2021

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

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2021

Borgs are giant archaeal extrachromosomal elements with the potential to augment methane oxidation
BioRxiv

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

17

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Research highlighted by Nature Magazine, Science Magazine, SYFY, Vice, The Independent, C&EN, The Scientist, Quanta Magazine, Live Science, and dozens of news outlets and podcasts.

Invited panelist on Phytobiomes Webinars, and the DNA Tie Club on Clubhouse

16

2021

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A widely distributed genus of soil Acidobacteria genomically enriched in biosynthetic gene clusters
BioRxiv

Alexander Crits-Christoph, Spencer Diamond, Basem Al-Shayeb, Luis Valentin-Alvarado, Jillian F Banfield

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

15

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14

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

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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.

13

12

2021

The NIH Somatic Cell Genome Editing program
Nature

K. Saha, E. J. Sontheimer, P. J. Brooks, ... , & The SCGE Consortium.

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.

11

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2021

10

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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.

2020

Petabase-scale sequence alignment catalyses viral discovery
BioRxiv Preprint

Robert C. Edgar*, Jeff Taylor*, Tomer Altman*, Pierre Barbera*, Dmitry Meleshko*, Victor Lin*, Dan Lohr*, Gherman Novakovsky*, Basem Al-Shayeb*, Jillian F. Banfield*, AntonKorobeynikov*, Rayan Chikhi*, and Artem Babaian*. 

9

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8

Research highlighted by Nature, Nature Plants, Nature Biotechnology, and more 

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.

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

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 

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.

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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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  * denotes presenter
Conference Talks, invited or selected from abstract
2021        American Museum of Natural History Seminar Series, New York City, USA.
2021        Phages for Health & Energy Symposium, Virtual.
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.
CRISPR Conference 2019
CRISPR Conference 2019

Selected from among hundreds of scientists to present a research talk at the 2019 Annual CRISPR Conference in Quebec

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20th Microbiology Student Symposium
20th Microbiology Student Symposium

Selected to present a research talk at the 20th Annual Microbiology Student Symposium in California, 2019

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2020 Genome Editing Symposium, Texas A&M
2020 Genome Editing Symposium, Texas A&M

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CRISPR Conference 2019
CRISPR Conference 2019

Selected from among hundreds of scientists to present a research talk at the 2019 Annual CRISPR Conference in Quebec

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1/4
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

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 

Undergraduate Research