CRISPR technology

@article{mojica2005intervening,
    author = "Mojica, Francisco J. M. and Díez-Villaseñor, César and García-Martínez, Jesús and Soria, Elena",
    title = "Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements",
    year = "2005",
    journal = "Journal of Molecular Evolution",
    url = "https://doi.org/10.1007/s00239-004-0046-3",
    doi = "10.1007/s00239-004-0046-3",
    number = "2",
    pages = "174--182",
    volume = "60",
    x-summary = "Early evidence that CRISPR spacer sequences derive from foreign genetic elements."
}

@article{barrangou2007crispr,
    author = "Barrangou, Rodolphe and Fremaux, Christophe and Deveau, Hélène and Richards, Melissa and Boyaval, Patrick and Moineau, Sylvain and Romero, Dennis A. and Horvath, Philippe",
    title = "{CRISPR} provides acquired resistance against viruses in prokaryotes",
    year = "2007",
    journal = "Science",
    url = "https://doi.org/10.1126/science.1138140",
    doi = "10.1126/science.1138140",
    number = "5819",
    pages = "1709--1712",
    volume = "315",
    x-summary = "Experimental demonstration that CRISPR loci can provide acquired antiviral resistance in bacteria."
}

@article{gasiunas2012cas9,
    author = "Gasiunas, Giedrius and Barrangou, Rodolphe and Horvath, Philippe and Siksnys, Virginijus",
    title = "Cas9-cr{RNA} ribonucleoprotein complex mediates specific {DNA} cleavage for adaptive immunity in bacteria",
    year = "2012",
    journal = "Proceedings of the National Academy of Sciences",
    url = "https://doi.org/10.1073/pnas.1208507109",
    doi = "10.1073/pnas.1208507109",
    number = "39",
    pages = "E2579--E2586",
    volume = "109",
    x-summary = "Biochemical demonstration of Cas9-crRNA-mediated sequence-specific DNA cleavage."
}

@article{jinek2012programmable,
    author = "Jinek, Martin and Chylinski, Krzysztof and Fonfara, Ines and Hauer, Michael and Doudna, Jennifer A. and Charpentier, Emmanuelle",
    title = "A programmable dual-{RNA}-guided {DNA} endonuclease in adaptive bacterial immunity",
    year = "2012",
    journal = "Science",
    url = "https://doi.org/10.1126/science.1225829",
    doi = "10.1126/science.1225829",
    number = "6096",
    pages = "816--821",
    volume = "337",
    x-summary = "Biochemical foundation for programmable Cas9 DNA targeting with guide RNAs."
}

@article{cho2013targeted,
    author = "Cho, Seung Woo and Kim, Sojung and Kim, Jeong-Sun and Kim, Jin-Soo",
    title = "Targeted genome engineering in human cells with the {Cas9} {RNA}-guided endonuclease",
    year = "2013",
    journal = "Nature Biotechnology",
    url = "https://doi.org/10.1038/nbt.2507",
    doi = "10.1038/nbt.2507",
    number = "3",
    pages = "230--232",
    volume = "31",
    x-summary = "Early report of Cas9-mediated targeted genome engineering in human cells."
}

@article{cong2013multiplex,
    author = "Cong, Le and Ran, F. Ann and Cox, David and Lin, Shuailiang and Barretto, Robert and Habib, Naomi and Hsu, Patrick D. and Wu, Xuebing and Jiang, Wenyan and Marraffini, Luciano A. and Zhang, Feng",
    title = "Multiplex genome engineering using {CRISPR}/{Cas} systems",
    year = "2013",
    journal = "Science",
    url = "https://doi.org/10.1126/science.1231143",
    doi = "10.1126/science.1231143",
    number = "6121",
    pages = "819--823",
    volume = "339",
    x-summary = "Early demonstration of CRISPR/Cas genome engineering in mammalian cells."
}

@article{hsu2013dna,
    author = "Hsu, Patrick D. and Scott, David A. and Weinstein, Joshua A. and Ran, F. Ann and Konermann, Silvana and Agarwala, Vineeta and Li, Yinqing and Fine, Eli J. and Wu, Xuebing and Shalem, Ophir and Cradick, Thomas J. and Marraffini, Luciano A. and Bao, Gang and Zhang, Feng",
    title = "{DNA} targeting specificity of {RNA}-guided {Cas9} nucleases",
    year = "2013",
    journal = "Nature Biotechnology",
    url = "https://doi.org/10.1038/nbt.2647",
    doi = "10.1038/nbt.2647",
    number = "9",
    pages = "827--832",
    volume = "31",
    x-summary = "Important early analysis of Cas9 targeting specificity and off-target behavior."
}

@article{hwang2013efficient,
    author = "Hwang, Woong Y. and Fu, Yanfang and Reyon, Deepak and Maeder, Morgan L. and Tsai, Shengdar Q. and Sander, Jeffry D. and Peterson, Randall T. and Yeh, Joung K. and Joung, J. Keith",
    title = "Efficient genome editing in zebrafish using a {CRISPR}-{Cas} system",
    year = "2013",
    journal = "Nature Biotechnology",
    url = "https://doi.org/10.1038/nbt.2501",
    doi = "10.1038/nbt.2501",
    number = "3",
    pages = "227--229",
    volume = "31",
    x-summary = "Early demonstration of CRISPR-Cas genome editing in a vertebrate model organism."
}

@article{mali2013rna,
    author = "Mali, Prashant and Yang, Luhan and Esvelt, Kevin M. and Aach, John and Guell, Marc and DiCarlo, James E. and Norville, Julie E. and Church, George M.",
    title = "{RNA}-guided human genome engineering via {Cas9}",
    year = "2013",
    journal = "Science",
    url = "https://doi.org/10.1126/science.1232033",
    doi = "10.1126/science.1232033",
    number = "6121",
    pages = "823--826",
    volume = "339",
    x-summary = "Early demonstration of RNA-guided Cas9 engineering in human cells."
}

@article{doi101016jcell201405010,
    author = "Hsu, Patrick D. and Lander, Eric S. and Zhang, Feng",
    title = "Development and Applications of CRISPR-Cas9 for Genome Engineering",
    year = "2014",
    journal = "Cell",
    url = "https://doi.org/10.1016/j.cell.2014.05.010",
    doi = "10.1016/j.cell.2014.05.010",
    note = "discovered\_from = {doi101038s4157601901587}",
    number = "6",
    pages = "1262-1278",
    volume = "157"
}

@article{doi101038nature13166,
    author = "Zhou, Yuexin and Zhu, Shiyou and Cai, Changzu and Yuan, Pengfei and Li, Chunmei and Huang, Yanyi and Wei, Wensheng",
    title = "High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells",
    year = "2014",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature13166",
    doi = "10.1038/nature13166",
    note = "discovered\_from = {doi101186s1305901405508}",
    number = "7501",
    pages = "487-491",
    volume = "509"
}

@article{doudna2014new,
    author = "Doudna, Jennifer A. and Charpentier, Emmanuelle",
    title = "The new frontier of genome engineering with {CRISPR}-{Cas9}",
    year = "2014",
    journal = "Science",
    url = "https://doi.org/10.1126/science.1258096",
    doi = "10.1126/science.1258096",
    number = "6213",
    pages = "1258096",
    volume = "346",
    x-summary = "Review of CRISPR-Cas9 genome engineering by key developers of the technology."
}

@article{shalem2014genome,
    author = "Shalem, Ophir and Sanjana, Neville E. and Hartenian, Ella and Shi, Xi and Scott, David A. and Mikkelson, Tarjei and Heckl, Dirk and Ebert, Benjamin L. and Root, David E. and Doench, John G. and Zhang, Feng",
    title = "Genome-scale {CRISPR}-{Cas9} knockout screening in human cells",
    year = "2014",
    journal = "Science",
    url = "https://doi.org/10.1126/science.1247005",
    doi = "10.1126/science.1247005",
    number = "6166",
    pages = "84--87",
    volume = "343",
    x-summary = "Foundational genome-scale CRISPR knockout screening study."
}

@article{wang2014genetic,
    author = "Wang, Tim and Wei, Jenny J. and Sabatini, David M. and Lander, Eric S.",
    title = "Genetic screens in human cells using the {CRISPR}-{Cas9} system",
    year = "2014",
    journal = "Science",
    url = "https://doi.org/10.1126/science.1246981",
    doi = "10.1126/science.1246981",
    number = "6166",
    pages = "80--84",
    volume = "343",
    x-summary = "Foundational CRISPR-Cas9 screening platform paper in human cells."
}

@article{zetsche2015cpf1,
    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, J. Keith and van der Oost, John and Regev, Aviv and Koonin, Eugene V. and Zhang, Feng",
    title = "{Cpf1} is a single {RNA}-guided endonuclease of a class 2 {CRISPR}-{Cas} system",
    year = "2015",
    journal = "Cell",
    url = "https://doi.org/10.1016/j.cell.2015.09.038",
    doi = "10.1016/j.cell.2015.09.038",
    number = "3",
    pages = "759--771",
    volume = "163",
    x-summary = "Introduces Cpf1/Cas12a as a class 2 CRISPR-Cas genome-editing nuclease."
}

@article{abudayyeh2016c2c2,
    author = "Abudayyeh, Omar O. and Gootenberg, Jonathan S. and Konermann, Silvana and Joung, Julia and Slaymaker, Ian M. and Cox, David B. T. and Shmakov, Sergey and Makarova, Kira S. and Semenova, Ekaterina and Minakhin, Leonid and Severinov, Konstantin and Regev, Aviv and Lander, Eric S. and Koonin, Eugene V. and Zhang, Feng",
    title = "{C2c2} is a single-component programmable {RNA}-guided {RNA}-targeting {CRISPR} effector",
    year = "2016",
    journal = "Science",
    url = "https://doi.org/10.1126/science.aaf5573",
    doi = "10.1126/science.aaf5573",
    number = "6299",
    pages = "aaf5573",
    volume = "353",
    x-summary = "Introduces Cas13/C2c2 as an RNA-targeting CRISPR effector."
}

@article{komor2016programmable,
    author = "Komor, Alexis C. and Kim, Yongjoo B. and Packer, Michael S. and Zuris, John A. and Liu, David R.",
    title = "Programmable editing of a target base in genomic {DNA} without double-stranded {DNA} cleavage",
    year = "2016",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature17946",
    doi = "10.1038/nature17946",
    number = "7603",
    pages = "420--424",
    volume = "533",
    x-summary = "Introduces cytosine base editing without double-strand DNA breaks."
}

@article{doi101038nature24049,
    author = "Abudayyeh, Omar O. and Gootenberg, Jonathan S. and Essletzbichler, Patrick and Han, Shuo and Joung, Julia and Belanto, Joseph J. and Verdine, Vanessa and Cox, David B. T. and Kellner, Max J. and Regev, Aviv and Lander, Eric S. and Voytas, Daniel F. and Ting, Alice Y. and Zhang, Feng",
    title = "RNA targeting with CRISPR–Cas13",
    year = "2017",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature24049",
    doi = "10.1038/nature24049",
    note = "discovered\_from = {doi101038s4157601901587}",
    number = "7675",
    pages = "280-284",
    volume = "550"
}

@article{gaudelli2017programmable,
    author = "Gaudelli, Nicole M. and Komor, Alexis C. and Rees, Holly A. and Packer, Michael S. and Badran, Ahmed H. and Bryson, David I. and Liu, David R.",
    title = "Programmable base editing of {A}•{T} to {G}•{C} in genomic {DNA} without {DNA} cleavage",
    year = "2017",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature24644",
    doi = "10.1038/nature24644",
    number = "7681",
    pages = "464--471",
    volume = "551",
    x-summary = "Introduces adenine base editing."
}

@article{gootenberg2017nucleic,
    author = "Gootenberg, Jonathan S. and Abudayyeh, Omar O. and Lee, Jeong Wook and Essletzbichler, Patrick and Dy, Amy J. and Joung, Julia and Verdine, Vanessa and Donghia, Nina and Daringer, Nichole M. and Freije, Catherine A. and Myhrvold, Cameron and Bhattacharyya, Rumi P. and Livny, Jonathan and Regev, Aviv and Koonin, Eugene V. and Hung, Deborah T. and Sabeti, Pardis C. and Collins, James J. and Zhang, Feng",
    title = "Nucleic acid detection with {CRISPR}-{Cas13a}/{C2c2}",
    year = "2017",
    journal = "Science",
    url = "https://doi.org/10.1126/science.aam9321",
    doi = "10.1126/science.aam9321",
    number = "6336",
    pages = "438--442",
    volume = "356",
    x-summary = "Introduces SHERLOCK-style CRISPR-Cas13 nucleic acid detection."
}

@article{doi101038nbt4061,
    author = "Kim, Hui Kwon and Min, Seonwoo and Song, Myungjae and Jung, Soobin and Choi, Jae Woo and Kim, Younggwang and Lee, Sangeun and Yoon, Sungroh and Kim, Hyongbum (Henry)",
    title = "Deep learning improves prediction of CRISPR–Cpf1 guide RNA activity",
    year = "2018",
    journal = "Nature Biotechnology",
    url = "https://doi.org/10.1038/nbt.4061",
    doi = "10.1038/nbt.4061",
    note = "discovered\_from = {doi101038s4159101803007}",
    number = "3",
    pages = "239-241",
    volume = "36"
}

@article{doi101038s4155101701786,
    author = "Listgarten, Jennifer and Weinstein, Michael and Kleinstiver, Benjamin P. and Sousa, Alexander A. and Joung, J. Keith and Crawford, Jake and Gao, Kevin and Hoang, Luong and Elibol, Melih and Doench, John G. and Fusi, Nicolo",
    title = "Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs",
    year = "2018",
    journal = "Nature Biomedical Engineering",
    url = "https://doi.org/10.1038/s41551-017-0178-6",
    doi = "10.1038/s41551-017-0178-6",
    note = "discovered\_from = {doi101038s4159101803007}",
    number = "1",
    pages = "38-47",
    volume = "2"
}

@article{doi101038s4155101803187,
    author = "Zhu, Haibao and Zhang, Linlin and Tong, Sheng and Lee, Ciaran M. and Deshmukh, Harshavardhan and Bao, Gang",
    title = "Spatial control of in vivo CRISPR–Cas9 genome editing via nanomagnets",
    year = "2018",
    journal = "Nature Biomedical Engineering",
    url = "https://doi.org/10.1038/s41551-018-0318-7",
    doi = "10.1038/s41551-018-0318-7",
    note = "discovered\_from = {doi101038s4157801901486}",
    number = "2",
    pages = "126-136",
    volume = "3"
}

Taking CRISPR technology further CRISPR techniques are allowing the development of technologies for nucleic acid detection (see the Perspective by Chertow). Taking advantages of the distinctive enzymatic properties of CRISPR enzymes, Gootenberg et al. developed an improved nucleic acid detection technology for multiplexed quantitative and highly sensitive detection, combined with lateral flow for visual readout. Myhrvold et al. added a sample preparation protocol to create a field-deployable viral diagnostic platform for rapid detection of specific strains of pathogens in clinical samples. Cas12a (also known as Cpf1), a type V CRISPR protein, cleaves double-stranded DNA and has been adapted for genome editing. Chen et al. discovered that Cas12a also processes single-stranded DNA threading activity. A technology platform based on this activity detected human papillomavirus in patient samples with high sensitivity. Science, this issue p. 439, p. 444, p. 436; see also p. 381

@article{doi101126scienceaas8836,
    author = "Myhrvold, Cameron and Freije, Catherine A. and Gootenberg, Jonathan S. and Abudayyeh, Omar O. and Metsky, Hayden C. and Durbin, Ann F. and Kellner, Max J. and Tan, Amanda L. and Paul, Lauren M. and Parham, Leda A. and Garcia, Kimberly F. and Barnes, Kayla G. and Chak, Bridget and Mondini, Adriano and Nogueira, Mauricio L. and Isern, Sharon and Michael, Scott F. and Lorenzana, Ivette and Yozwiak, Nathan L. and MacInnis, Bronwyn L. and Bosch, Irene and Gehrke, Lee and Zhang, Feng and Sabeti, Pardis C.",
    title = "Field-deployable viral diagnostics using CRISPR-Cas13",
    year = "2018",
    journal = "Science",
    abstract = "Taking CRISPR technology further CRISPR techniques are allowing the development of technologies for nucleic acid detection (see the Perspective by Chertow). Taking advantages of the distinctive enzymatic properties of CRISPR enzymes, Gootenberg et al. developed an improved nucleic acid detection technology for multiplexed quantitative and highly sensitive detection, combined with lateral flow for visual readout. Myhrvold et al. added a sample preparation protocol to create a field-deployable viral diagnostic platform for rapid detection of specific strains of pathogens in clinical samples. Cas12a (also known as Cpf1), a type V CRISPR protein, cleaves double-stranded DNA and has been adapted for genome editing. Chen et al. discovered that Cas12a also processes single-stranded DNA threading activity. A technology platform based on this activity detected human papillomavirus in patient samples with high sensitivity. Science, this issue p. 439, p. 444, p. 436; see also p. 381",
    url = "https://doi.org/10.1126/science.aas8836",
    doi = "10.1126/science.aas8836",
    note = "discovered\_from = {doi103390v12040372}",
    number = "6387",
    pages = "444-448",
    volume = "360"
}

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated genes (Cas) system has been rapidly harnessed to perform various genomic engineering tasks. Recently, it has been demonstrated that a novel RNA-targeting CRISPR effector protein, called Cas13, binds and cleaves RNA rather than DNA substrates analogously to the eukaryotic RNA interference system. The known Cas13a–Cas13d effectors are able to efficiently cleave complementary target single-stranded RNAs, which represent a potentially safer alternative to deoxyribonuclease Cas9, because it induces loss-of-function phenotypes without genomic loss of the targeted gene. Furthermore, through the improvement in Cas13 effector functionalities, a system called REPAIR has been developed to edit full-length transcripts containing pathogenic mutations, thus providing a promising opportunity for precise base editing. Moreover, advanced engineering of this CRISPR effector also permits nucleic acid detection, allowing the identification of mutations in cell-free tumor DNA through a platform termed Specific High Sensitivity Enzymatic Reporter Unlocking. All of these properties give us a glimpse about the potential of the CRISPR toolkit for precise transcriptome engineering, possibly leading to an expansion of CRISPR technologies for cancer therapeutics and diagnostics. Here, we examine previously unaddressed aspects of the CRISPR-based RNA-targeting approach as a feasible strategy for globally interrogating gene function in cancer in a programmable manner. Cancer Res; 78(15); 4107–13. ©2018 AACR.

@article{doi10115800085472can180785,
    author = "Granados-Riveron, Javier T. and Aquino-Jarquin, Guillermo",
    title = "CRISPR–Cas13 Precision Transcriptome Engineering in Cancer",
    year = "2018",
    journal = "Cancer Research",
    abstract = "The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated genes (Cas) system has been rapidly harnessed to perform various genomic engineering tasks. Recently, it has been demonstrated that a novel RNA-targeting CRISPR effector protein, called Cas13, binds and cleaves RNA rather than DNA substrates analogously to the eukaryotic RNA interference system. The known Cas13a–Cas13d effectors are able to efficiently cleave complementary target single-stranded RNAs, which represent a potentially safer alternative to deoxyribonuclease Cas9, because it induces loss-of-function phenotypes without genomic loss of the targeted gene. Furthermore, through the improvement in Cas13 effector functionalities, a system called REPAIR has been developed to edit full-length transcripts containing pathogenic mutations, thus providing a promising opportunity for precise base editing. Moreover, advanced engineering of this CRISPR effector also permits nucleic acid detection, allowing the identification of mutations in cell-free tumor DNA through a platform termed Specific High Sensitivity Enzymatic Reporter Unlocking. All of these properties give us a glimpse about the potential of the CRISPR toolkit for precise transcriptome engineering, possibly leading to an expansion of CRISPR technologies for cancer therapeutics and diagnostics. Here, we examine previously unaddressed aspects of the CRISPR-based RNA-targeting approach as a feasible strategy for globally interrogating gene function in cancer in a programmable manner. Cancer Res; 78(15); 4107–13. ©2018 AACR.",
    url = "https://doi.org/10.1158/0008-5472.can-18-0785",
    doi = "10.1158/0008-5472.can-18-0785",
    note = "discovered\_from = {doi101038s4157601901587}",
    number = "15",
    pages = "4107-4113",
    volume = "78"
}

@article{gootenberg2018multiplexed,
    author = "Gootenberg, Jonathan S. and Abudayyeh, Omar O. and Kellner, Max J. and Joung, Julia and Collins, James J. and Zhang, Feng",
    title = "Multiplexed and portable nucleic acid detection platform with {Cas13}, {Cas12a}, and {Csm6}",
    year = "2018",
    journal = "Science",
    url = "https://doi.org/10.1126/science.aaq0179",
    doi = "10.1126/science.aaq0179",
    number = "6387",
    pages = "439--444",
    volume = "360",
    x-summary = "Extends CRISPR diagnostics to multiplexed and portable detection."
}

@article{knott2018crispr,
    author = "Knott, Gavin J. and Doudna, Jennifer A.",
    title = "{CRISPR}-{Cas} guides the future of genetic engineering",
    year = "2018",
    journal = "Science",
    url = "https://doi.org/10.1126/science.aat5011",
    doi = "10.1126/science.aat5011",
    number = "6405",
    pages = "866--869",
    volume = "361",
    x-summary = "Accessible review of CRISPR-Cas technology and applications."
}

@article{anzalone2019search,
    author = "Anzalone, Andrew V. and Randolph, Peyton B. and Davis, Jessie R. and Sousa, Alexander A. and Koblan, Luke W. and Levy, Jonathan M. and Chen, Peter J. and Wilson, Christopher and Newby, Gregory A. and Raguram, Aditya and Liu, David R.",
    title = "Search-and-replace genome editing without double-strand breaks or donor {DNA}",
    year = "2019",
    journal = "Nature",
    url = "https://doi.org/10.1038/s41586-019-1711-4",
    doi = "10.1038/s41586-019-1711-4",
    number = "7785",
    pages = "149--157",
    volume = "576",
    x-summary = "Introduces prime editing."
}

@article{doi101038s4159101803386,
    author = "Santiago-Fernández, Olaya and Osorio, Fernando G. and Quesada, Víctor and Rodríguez, Francisco and Basso, Sammy and Maeso, Daniel and Rolas, Loïc and Barkaway, Anna and Nourshargh, Sussan and Folgueras, Alicia R. and Freije, José M. P. and López-Otín, Carlos",
    title = "Development of a CRISPR/Cas9-based therapy for Hutchinson–Gilford progeria syndrome",
    year = "2019",
    journal = "Nature Medicine",
    url = "https://doi.org/10.1038/s41591-018-0338-6",
    doi = "10.1038/s41591-018-0338-6",
    note = "discovered\_from = {doi101016jcell202211001}",
    number = "3",
    pages = "423-426",
    volume = "25"
}

We report the first application of CRISPR‐Cas technology to single species detection from environmental DNA (eDNA). Organisms shed and excrete DNA into their environment such as in skin cells and faeces, referred to as environmental DNA (eDNA). Utilising eDNA allows noninvasive monitoring with increased specificity and sensitivity. Current methods primarily employ PCR‐based techniques to detect a given species from eDNA samples, posing a logistical challenge for on‐site monitoring and potential adaptation to biosensor devices. We have developed an alternative method; coupling isothermal amplification to a CRISPR‐Cas12a detection system. This utilises the collateral cleavage activity of Cas12a, a ribonuclease guided by a highly specific single CRISPR RNA. We used the target species Salmo salar as a proof‐of‐concept test of the specificity of the assay among closely related species and to show the assay is successful at a single temperature of 37°C with signal detection at 535 nM. The specific assay, detects at attomolar sensitivity with rapid detection rates (

@article{doi1011111755099813045,
    author = "Williams, Molly‐Ann and O'Grady, Joyce and Ball, Bernard and Carlsson, Jens and de Eyto, Elvira and McGinnity, Philip and Jennings, Eleanor and Regan, Fiona and Parle‐McDermott, Anne",
    title = "The application of CRISPR‐Cas for single species identification from environmental DNA",
    year = "2019",
    journal = "Molecular Ecology Resources",
    abstract = "We report the first application of CRISPR‐Cas technology to single species detection from environmental DNA (eDNA). Organisms shed and excrete DNA into their environment such as in skin cells and faeces, referred to as environmental DNA (eDNA). Utilising eDNA allows noninvasive monitoring with increased specificity and sensitivity. Current methods primarily employ PCR‐based techniques to detect a given species from eDNA samples, posing a logistical challenge for on‐site monitoring and potential adaptation to biosensor devices. We have developed an alternative method; coupling isothermal amplification to a CRISPR‐Cas12a detection system. This utilises the collateral cleavage activity of Cas12a, a ribonuclease guided by a highly specific single CRISPR RNA. We used the target species Salmo salar as a proof‐of‐concept test of the specificity of the assay among closely related species and to show the assay is successful at a single temperature of 37°C with signal detection at 535 nM. The specific assay, detects at attomolar sensitivity with rapid detection rates (",
    url = "https://doi.org/10.1111/1755-0998.13045",
    doi = "10.1111/1755-0998.13045",
    note = "discovered\_from = {doi101002ece373386}",
    number = "5",
    pages = "1106-1114",
    volume = "19"
}

@article{pickar2019crispr,
    author = "Pickar-Oliver, Adrian and Gersbach, Charles A.",
    title = "{CRISPR}-{Cas9} genome editing technology and applications",
    year = "2019",
    journal = "Nature Reviews Molecular Cell Biology",
    url = "https://doi.org/10.1038/s41580-019-0131-5",
    doi = "10.1038/s41580-019-0131-5",
    number = "8",
    pages = "490--507",
    volume = "20",
    x-summary = "Broad review of CRISPR-Cas9 genome editing technology and applications."
}

Inactivation of the histone acetyltransferase gene KAT7 prolongs survival in naturally aged mice and progeroid mice that age prematurely.

@article{doi101126scitranslmedabd2655,
    author = "Wang, Wei and Zheng, Yuxuan and Sun, Shuhui and Li, Wei and Song, Moshi and Ji, Qianzhao and Wu, Zeming and Liu, Zunpeng and Fan, Yanling and Liu, Feifei and Li, Jingyi and Esteban, Concepcion Rodriguez and Wang, Si and Zhou, Qi and Belmonte, Juan Carlos Izpisua and Zhang, Weiqi and Qu, Jing and Tang, Fuchou and Liu, Guang-Hui",
    title = "A genome-wide CRISPR-based screen identifies KAT7 as a driver of cellular senescence",
    year = "2021",
    journal = "Science Translational Medicine",
    abstract = "Inactivation of the histone acetyltransferase gene KAT7 prolongs survival in naturally aged mice and progeroid mice that age prematurely.",
    url = "https://doi.org/10.1126/scitranslmed.abd2655",
    doi = "10.1126/scitranslmed.abd2655",
    note = "discovered\_from = {doi101016jcell202211001}",
    number = "575",
    volume = "13"
}

Molecular methods are rapidly evolving to enable nucleic acid diagnostics outside a laboratory setting. Such techniques are primarily utilizing isothermal amplification such as Recombinase Polymerase Amplification (RPA) and Loop‐Mediated Isothermal Amplification (LAMP) but are yet to be fully explored for monitoring using environmental DNA (eDNA). We previously presented an RPA‐CRISPR‐Cas approach for detection of Atlantic salmon in Ireland and Canada and in this manuscript we present a further application of this technique for monitoring of brown trout and Arctic char in the Burrishoole Catchment, Co. Mayo, Ireland. In developing these assays, we offer an alternative approach to the PCR‐based assays previously published and have evolved a streamlined approach to single‐species monitoring using RPA‐CRISPR‐Cas, reducing the fluorescence acquisition time from 2 h to 30 min. This demonstrates the applicability of using RPA‐CRISPR‐Cas assays for eDNA‐based detection beyond Atlantic salmon with the added benefit of a faster assay time without compromising detection sensitivity.

@article{doi101002edn3384,
    author = "Williams, Molly Ann and de Eyto, Elvira and Caestecker, Silke and Regan, Fiona and Parle‐McDermott, Anne",
    title = "Development and field validation of RPA‐CRISPR‐Cas environmental DNA assays for the detection of brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus)",
    year = "2023",
    journal = "Environmental DNA",
    abstract = "Molecular methods are rapidly evolving to enable nucleic acid diagnostics outside a laboratory setting. Such techniques are primarily utilizing isothermal amplification such as Recombinase Polymerase Amplification (RPA) and Loop‐Mediated Isothermal Amplification (LAMP) but are yet to be fully explored for monitoring using environmental DNA (eDNA). We previously presented an RPA‐CRISPR‐Cas approach for detection of Atlantic salmon in Ireland and Canada and in this manuscript we present a further application of this technique for monitoring of brown trout and Arctic char in the Burrishoole Catchment, Co. Mayo, Ireland. In developing these assays, we offer an alternative approach to the PCR‐based assays previously published and have evolved a streamlined approach to single‐species monitoring using RPA‐CRISPR‐Cas, reducing the fluorescence acquisition time from 2 h to 30 min. This demonstrates the applicability of using RPA‐CRISPR‐Cas assays for eDNA‐based detection beyond Atlantic salmon with the added benefit of a faster assay time without compromising detection sensitivity.",
    url = "https://doi.org/10.1002/edn3.384",
    doi = "10.1002/edn3.384",
    note = "discovered\_from = {doi101002ece373386}",
    number = "2",
    pages = "240-250",
    volume = "5"
}

The known diversity of CRISPR–Cas systems continues to expand. To encompass new discoveries, here we present an updated evolutionary classification of CRISPR–Cas systems. The updated CRISPR–Cas classification includes 2 classes, 7 types and 46 subtypes, compared with the 6 types and 33 subtypes in our previous survey 5 years ago. In addition, a classification of the cyclic oligoadenylate-dependent signalling pathway in type III systems is presented. We also discuss recently characterized alternative CRISPR–Cas functionalities, notably, type IV variants that cleave the target DNA and type V variants that inhibit the target replication without cleavage. Analysis of the abundance of CRISPR–Cas variants in genomes and metagenomes shows that the previously defined systems are relatively common, whereas the more recently characterized variants are comparatively rare. These low abundance variants comprise the long tail of the CRISPR–Cas distribution in prokaryotes and their viruses, and remain to be characterized experimentally.

@article{doi101038s41564025021808,
    author = "Makarova, Kira S. and Shmakov, Sergey A. and Wolf, Yuri I. and Mutz, Pascal and Altae-Tran, Han and Beisel, Chase L. and Brouns, Stan J. J. and Charpentier, Emmanuelle and Cheng, David and Doudna, Jennifer and Haft, Daniel H. and Horvath, Philippe and Moineau, Sylvain and Mojica, Francisco J. M. and Pausch, Patrick and Pinilla-Redondo, Rafael and Shah, Shiraz A. and Siksnys, Virginijus and Terns, Michael P. and Tordoff, Jesse and Venclovas, Česlovas and White, Malcolm F. and Yakunin, Alexander F. and Zhang, Feng and Garrett, Roger A. and Backofen, Rolf and van der Oost, John and Barrangou, Rodolphe and Koonin, Eugene V.",
    title = "An updated evolutionary classification of CRISPR–Cas systems including rare variants",
    year = "2025",
    journal = "Nature Microbiology",
    abstract = "The known diversity of CRISPR–Cas systems continues to expand. To encompass new discoveries, here we present an updated evolutionary classification of CRISPR–Cas systems. The updated CRISPR–Cas classification includes 2 classes, 7 types and 46 subtypes, compared with the 6 types and 33 subtypes in our previous survey 5 years ago. In addition, a classification of the cyclic oligoadenylate-dependent signalling pathway in type III systems is presented. We also discuss recently characterized alternative CRISPR–Cas functionalities, notably, type IV variants that cleave the target DNA and type V variants that inhibit the target replication without cleavage. Analysis of the abundance of CRISPR–Cas variants in genomes and metagenomes shows that the previously defined systems are relatively common, whereas the more recently characterized variants are comparatively rare. These low abundance variants comprise the long tail of the CRISPR–Cas distribution in prokaryotes and their viruses, and remain to be characterized experimentally.",
    url = "https://doi.org/10.1038/s41564-025-02180-8",
    doi = "10.1038/s41564-025-02180-8",
    note = "discovered\_from = {doi101038s41467026710966}",
    number = "12",
    pages = "3346-3361",
    volume = "10"
}