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references.bib
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@article{2002, title={Identification of genes that are associated with DNA repeats in prokaryotes}, volume={43}, ISSN={1365-2958}, url={http://dx.doi.org/10.1046/j.1365-2958.2002.02839.x}, DOI={10.1046/j.1365-2958.2002.02839.x}, number={6}, journal={Molecular Microbiology}, publisher={Wiley}, author={Jansen, Ruud. and Embden, Jan. D. A. van and Gaastra, Wim. and Schouls, Leo. M.}, year={2002}, month={Mar}, pages={1565–1575} }
@article{2005, title={Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin}, volume={151}, ISSN={1465-2080}, url={http://dx.doi.org/10.1099/mic.0.28048-0}, DOI={10.1099/mic.0.28048-0}, number={8}, journal={Microbiology}, publisher={Microbiology Society}, author={Bolotin, Alexander and Quinquis, Benoit and Sorokin, Alexei and Ehrlich, S. Dusko}, year={2005}, month={Aug}, pages={2551–2561} }
@article{2005, title={A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes}, volume={1}, ISSN={1553-7358}, url={http://dx.doi.org/10.1371/journal.pcbi.0010060}, DOI={10.1371/journal.pcbi.0010060}, number={6}, journal={PLoS Computational Biology}, publisher={Public Library of Science (PLoS)}, author={Haft, Daniel H and Selengut, Jeremy and Mongodin, Emmanuel F and Nelson, Karen E}, editor={Eisen, Jonathan A}, year={2005}, month={Nov}, pages={e60} }
@article{2005, title={A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes}, volume={1}, ISSN={1553-7358}, url={http://dx.doi.org/10.1371/journal.pcbi.0010060}, DOI={10.1371/journal.pcbi.0010060}, number={6}, journal={PLoS Computational Biology}, publisher={Public Library of Science (PLoS)}, author={Haft, Daniel H and Selengut, Jeremy and Mongodin, Emmanuel F and Nelson, Karen E}, editor={Eisen, Jonathan A}, year={2005}, month={Nov}, pages={e60} }
@article{2008, title={Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes}, volume={321}, ISSN={1095-9203}, url={http://dx.doi.org/10.1126/science.1159689}, DOI={10.1126/science.1159689}, number={5891}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Brouns, Stan J. J. and Jore, Matthijs M. and Lundgren, Magnus and Westra, Edze R. and Slijkhuis, Rik J. H. and Snijders, Ambrosius P. L. and Dickman, Mark J. and Makarova, Kira S. and Koonin, Eugene V. and van der Oost, John}, year={2008}, month={Aug}, pages={960–964} }
@article{2011, title={Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems}, volume={6}, ISSN={1745-6150}, url={http://dx.doi.org/10.1186/1745-6150-6-38}, DOI={10.1186/1745-6150-6-38}, number={1}, journal={Biology Direct}, publisher={Springer Science and Business Media LLC}, author={Makarova, Kira S and Aravind, L and Wolf, Yuri I and Koonin, Eugene V}, year={2011}, month={Jul} }
@article{2013, title={CRISPR-Cas Systems and Cas Protein Families}, url={http://dx.doi.org/10.1002/9781118743089.ch13}, DOI={10.1002/9781118743089.ch13}, journal={Protein Families}, publisher={John Wiley \& Sons, Inc.}, author={Makarova, Kira S. and Haft, Daniel H. and Koonin, Eugene V.}, year={2013}, month={Nov}, pages={341–381} }
@article{2015, title={Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System}, volume={163}, ISSN={0092-8674}, url={http://dx.doi.org/10.1016/j.cell.2015.09.038}, DOI={10.1016/j.cell.2015.09.038}, number={3}, journal={Cell}, publisher={Elsevier BV}, author={Zetsche, Bernd and Gootenberg, Jonathan S. and Abudayyeh, Omar O. and Slaymaker, Ian M. and Makarova, Kira S. and Essletzbichler, Patrick and Volz, Sara E. and Joung, Julia and van der Oost, John and Regev, Aviv and Koonin, Eugene V. and Zhang, Feng}, year={2015}, month={Oct}, pages={759–771} }
@article{2017, title={Diversity, classification and evolution of CRISPR-Cas systems}, volume={37}, ISSN={1369-5274}, url={http://dx.doi.org/10.1016/j.mib.2017.05.008}, DOI={10.1016/j.mib.2017.05.008}, journal={Current Opinion in Microbiology}, publisher={Elsevier BV}, author={Koonin, Eugene V and Makarova, Kira S and Zhang, Feng}, year={2017}, month={Jun}, pages={67–78} }
@article{2015, title={Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems}, volume={60}, ISSN={1097-2765}, url={http://dx.doi.org/10.1016/j.molcel.2015.10.008}, DOI={10.1016/j.molcel.2015.10.008}, number={3}, journal={Molecular Cell}, publisher={Elsevier BV}, author={Shmakov, Sergey and Abudayyeh, Omar O. and Makarova, Kira S. and Wolf, Yuri I. and Gootenberg, Jonathan S. and Semenova, Ekaterina and Minakhin, Leonid and Joung, Julia and Konermann, Silvana and Severinov, Konstantin and Zhang, Feng and Koonin, Eugene V.}, year={2015}, month={Nov}, pages={385–397} }
@article{2016, title={New CRISPR–Cas systems from uncultivated microbes}, volume={542}, ISSN={1476-4687}, url={http://dx.doi.org/10.1038/nature21059}, DOI={10.1038/nature21059}, number={7640}, journal={Nature}, publisher={Springer Science and Business Media LLC}, author={Burstein, David and Harrington, Lucas B. and Strutt, Steven C. and Probst, Alexander J. and Anantharaman, Karthik and Thomas, Brian C. and Doudna, Jennifer A. and Banfield, Jillian F.}, year={2016}, month={Dec}, pages={237–241} }
@article{2018, title={Programmed DNA destruction by miniature CRISPR-Cas14 enzymes}, volume={362}, ISSN={1095-9203}, url={http://dx.doi.org/10.1126/science.aav4294}, DOI={10.1126/science.aav4294}, number={6416}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Harrington, Lucas B. and Burstein, David and Chen, Janice S. and Paez-Espino, David and Ma, Enbo and Witte, Isaac P. and Cofsky, Joshua C. and Kyrpides, Nikos C. and Banfield, Jillian F. and Doudna, Jennifer A.}, year={2018}, month={Nov}, pages={839–842} }
@article{2019, title={Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants}, volume={18}, ISSN={1740-1534}, url={http://dx.doi.org/10.1038/s41579-019-0299-x}, DOI={10.1038/s41579-019-0299-x}, number={2}, journal={Nature Reviews Microbiology}, publisher={Springer Science and Business Media LLC}, author={Makarova, Kira S. and Wolf, Yuri I. and Iranzo, Jaime and Shmakov, Sergey A. and Alkhnbashi, Omer S. and Brouns, Stan J. J. and Charpentier, Emmanuelle and Cheng, David and Haft, Daniel H. and Horvath, Philippe and Moineau, Sylvain and Mojica, Francisco J. M. and Scott, David and Shah, Shiraz A. and Siksnys, Virginijus and Terns, Michael P. and Venclovas, Česlovas and White, Malcolm F. and Yakunin, Alexander F. and Yan, Winston and Zhang, Feng and Garrett, Roger A. and Backofen, Rolf and van der Oost, John and Barrangou, Rodolphe and Koonin, Eugene V.}, year={2019}, month={Dec}, pages={67–83} }
@article{2019, title={Functionally diverse type V CRISPR-Cas systems}, volume={363}, ISSN={1095-9203}, url={http://dx.doi.org/10.1126/science.aav7271}, DOI={10.1126/science.aav7271}, number={6422}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Yan, Winston X. and Hunnewell, Pratyusha and Alfonse, Lauren E. and Carte, Jason M. and Keston-Smith, Elise and Sothiselvam, Shanmugapriya and Garrity, Anthony J. and Chong, Shaorong and Makarova, Kira S. and Koonin, Eugene V. and Cheng, David R. and Scott, David A.}, year={2019}, month={Jan}, pages={88–91} }
@article{2020, title={Clades of huge phages from across Earth’s ecosystems}, volume={578}, ISSN={1476-4687}, url={http://dx.doi.org/10.1038/s41586-020-2007-4}, DOI={10.1038/s41586-020-2007-4}, number={7795}, journal={Nature}, publisher={Springer Science and Business Media LLC}, author={Al-Shayeb, Basem and Sachdeva, Rohan and Chen, Lin-Xing and Ward, Fred and Munk, Patrick and Devoto, Audra and Castelle, Cindy J. and Olm, Matthew R. and Bouma-Gregson, Keith and Amano, Yuki and He, Christine and Méheust, Raphaël and Brooks, Brandon and Thomas, Alex and Lavy, Adi and Matheus-Carnevali, Paula and Sun, Christine and Goltsman, Daniela S. A. and Borton, Mikayla A. and Sharrar, Allison and Jaffe, Alexander L. and Nelson, Tara C. and Kantor, Rose and Keren, Ray and Lane, Katherine R. and Farag, Ibrahim F. and Lei, Shufei and Finstad, Kari and Amundson, Ronald and Anantharaman, Karthik and Zhou, Jinglie and Probst, Alexander J. and Power, Mary E. and Tringe, Susannah G. and Li, Wen-Jun and Wrighton, Kelly and Harrison, Sue and Morowitz, Michael and Relman, David A. and Doudna, Jennifer A. and Lehours, Anne-Catherine and Warren, Lesley and Cate, Jamie H. D. and Santini, Joanne M. and Banfield, Jillian F.}, year={2020}, month={Feb}, pages={425–431} }
@article{2017, title={Diversity and evolution of class 2 CRISPR–Cas systems}, volume={15}, ISSN={1740-1534}, url={http://dx.doi.org/10.1038/nrmicro.2016.184}, DOI={10.1038/nrmicro.2016.184}, number={3}, journal={Nature Reviews Microbiology}, publisher={Springer Science and Business Media LLC}, author={Shmakov, Sergey and Smargon, Aaron and Scott, David and Cox, David and Pyzocha, Neena and Yan, Winston and Abudayyeh, Omar O. and Gootenberg, Jonathan S. and Makarova, Kira S. and Wolf, Yuri I. and Severinov, Konstantin and Zhang, Feng and Koonin, Eugene V.}, year={2017}, month={Jan}, pages={169–182} }
@article{2019, title={RNA-guided DNA insertion with CRISPR-associated transposases}, volume={365}, ISSN={1095-9203}, url={http://dx.doi.org/10.1126/science.aax9181}, DOI={10.1126/science.aax9181}, number={6448}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Strecker, Jonathan and Ladha, Alim and Gardner, Zachary and Schmid-Burgk, Jonathan L. and Makarova, Kira S. and Koonin, Eugene V. and Zhang, Feng}, year={2019}, month={Jul}, pages={48–53} }
@article{2020, title={Novel Type V-A CRISPR Effectors Are Active Nucleases with Expanded Targeting Capabilities}, volume={3}, ISSN={2573-1602}, url={http://dx.doi.org/10.1089/crispr.2020.0043}, DOI={10.1089/crispr.2020.0043}, number={6}, journal={The CRISPR Journal}, publisher={Mary Ann Liebert Inc}, author={Aliaga Goltsman, Daniela S. and Alexander, Lisa M. and Devoto, Audra E. and Albers, Justine B. and Liu, Jason and Butterfield, Cristina N. and Brown, Christopher T. and Thomas, Brian C.}, year={2020}, month={Dec}, pages={454–461} }
@article{2022, title={A new family of CRISPR‐type V nucleases with C‐rich PAM recognition}, volume={23}, ISSN={1469-3178}, url={http://dx.doi.org/10.15252/embr.202255481}, DOI={10.15252/embr.202255481}, number={12}, journal={EMBO reports}, publisher={EMBO}, author={Urbaitis, Tomas and Gasiunas, Giedrius and Young, Joshua K and Hou, Zhenglin and Paulraj, Sushmitha and Godliauskaite, Egle and Juskeviciene, Mantvyda M and Stitilyte, Migle and Jasnauskaite, Monika and Mabuchi, Megumu and Robb, G Brett and Siksnys, Virginijus}, year={2022}, month={Oct} }
@article{2023, title={The compact Casπ (Cas12l) ‘bracelet’ provides a unique structural platform for DNA manipulation}, volume={33}, ISSN={1748-7838}, url={http://dx.doi.org/10.1038/s41422-022-00771-2}, DOI={10.1038/s41422-022-00771-2}, number={3}, journal={Cell Research}, publisher={Springer Science and Business Media LLC}, author={Sun, Ao and Li, Cheng-Ping and Chen, Zhihang and Zhang, Shouyue and Li, Dan-Yuan and Yang, Yun and Li, Long-Qi and Zhao, Yuqian and Wang, Kaichen and Li, Zhaofu and Liu, Jinxia and Liu, Sitong and Wang, Jia and Liu, Jun-Jie Gogo}, year={2023}, month={Jan}, pages={229–244} }
@article{2022, title={The miniature CRISPR-Cas12m effector binds DNA to block transcription}, volume={82}, ISSN={1097-2765}, url={http://dx.doi.org/10.1016/j.molcel.2022.11.003}, DOI={10.1016/j.molcel.2022.11.003}, number={23}, journal={Molecular Cell}, publisher={Elsevier BV}, author={Wu, Wen Y. and Mohanraju, Prarthana and Liao, Chunyu and Adiego-Pérez, Belén and Creutzburg, Sjoerd C.A. and Makarova, Kira S. and Keessen, Karlijn and Lindeboom, Timon A. and Khan, Tahseen S. and Prinsen, Stijn and Joosten, Rob and Yan, Winston X. and Migur, Anzhela and Laffeber, Charlie and Scott, David A. and Lebbink, Joyce H.G. and Koonin, Eugene V. and Beisel, Chase L. and van der Oost, John}, year={2022}, month={Dec}, pages={4487-4502.e7} }
@article{2018, title={Cas13d Is a Compact RNA-Targeting Type VI CRISPR Effector Positively Modulated by a WYL-Domain-Containing Accessory Protein}, volume={70}, ISSN={1097-2765}, url={http://dx.doi.org/10.1016/j.molcel.2018.02.028}, DOI={10.1016/j.molcel.2018.02.028}, number={2}, journal={Molecular Cell}, publisher={Elsevier BV}, author={Yan, Winston X. and Chong, Shaorong and Zhang, Huaibin and Makarova, Kira S. and Koonin, Eugene V. and Cheng, David R. and Scott, David A.}, year={2018}, month={Apr}, pages={327-339.e5} }
@article{2018, title={Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors}, volume={173}, ISSN={0092-8674}, url={http://dx.doi.org/10.1016/j.cell.2018.02.033}, DOI={10.1016/j.cell.2018.02.033}, number={3}, journal={Cell}, publisher={Elsevier BV}, author={Konermann, Silvana and Lotfy, Peter and Brideau, Nicholas J. and Oki, Jennifer and Shokhirev, Maxim N. and Hsu, Patrick D.}, year={2018}, month={Apr}, pages={665-676.e14} }
@article{2023, title={Cas12n nucleases, early evolutionary intermediates of type V CRISPR, comprise a distinct family of miniature genome editors}, ISSN={1097-2765}, url={http://dx.doi.org/10.1016/j.molcel.2023.06.014}, DOI={10.1016/j.molcel.2023.06.014}, journal={Molecular Cell}, publisher={Elsevier BV}, author={Chen, Weizhong and Ma, Jiacheng and Wu, Zhaowei and Wang, Zhipeng and Zhang, Hongyuan and Fu, Wenhan and Pan, Deng and Shi, Jin and Ji, Quanjiang}, year={2023}, month={Jul} }