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Xu P, Saito M, Faure G, Maguire S, Chau-Duy-Tam Vo S, Wilkinson ME, Kuang H, Wang B, Rice WJ, Macrae RK, Zhang F. Structural insights into the diversity and DNA cleavage mechanism of Fanzor. Cell. 2024 Sep 19;187(19):5238-5252.e20. doi: 10.1016/j.cell.2024.07.050. Epub 2024 Aug 28. PubMed PMID: 39208796; PubMed Central PMCID: PMC11423790.
Hirano S, Altae-Tran H, Kannan S, Macrae RK, Zhang F. Structural determinants of DNA cleavage by a CRISPR HNH-Cascade system. Mol Cell. 2024 Aug 22;84(16):3154-3162.e5. doi: 10.1016/j.molcel.2024.07.026. Epub 2024 Aug 6. PubMed PMID: 39111310; PubMed Central PMCID: PMC11459484.
Frangieh CJ, Wilkinson ME, Strebinger D, Strecker J, Walsh ML, Faure G, Yushenova IA, Macrae RK, Arkhipova IR, Zhang F. Internal initiation of reverse transcription in a Penelope-like retrotransposon. Mob DNA. 2024 Jun 11;15(1):12. doi: 10.1186/s13100-024-00322-z. PubMed PMID: 38863000; PubMed Central PMCID: PMC11167929.
Madigan V, Zhang Y, Raghavan R, Wilkinson ME, Faure G, Puccio E, Segel M, Lash B, Macrae RK, Zhang F. Human paraneoplastic antigen Ma2 (PNMA2) forms icosahedral capsids that can be engineered for mRNA delivery. Proc Natl Acad Sci U S A. 2024 Mar 12;121(11):e2307812120. doi: 10.1073/pnas.2307812120. Epub 2024 Mar 4. PubMed PMID: 38437549; PubMed Central PMCID: PMC10945824.
Altae-Tran H, Shmakov SA, Makarova KS, Wolf YI, Kannan S, Zhang F, Koonin EV. Diversity, evolution, and classification of the RNA-guided nucleases TnpB and Cas12. Proc Natl Acad Sci U S A. 2023 Nov 28;120(48):e2308224120. doi: 10.1073/pnas.2308224120. Epub 2023 Nov 20. PubMed PMID: 37983496; PubMed Central PMCID: PMC10691335.
Altae-Tran H, Kannan S, Suberski AJ, Mears KS, Demircioglu FE, Moeller L, Kocalar S, Oshiro R, Makarova KS, Macrae RK, Koonin EV, Zhang F. Uncovering the functional diversity of rare CRISPR-Cas systems with deep terascale clustering. Science. 2023 Nov 24;382(6673):eadi1910. doi: 10.1126/science.adi1910. Epub 2023 Nov 23. PubMed PMID: 37995242; PubMed Central PMCID: PMC10910872.
Madigan V, Zhang F, Dahlman JE. Drug delivery systems for CRISPR-based genome editors. Nat Rev Drug Discov. 2023 Nov;22(11):875-894. doi: 10.1038/s41573-023-00762-x. Epub 2023 Sep 18. Review. PubMed PMID: 37723222.
Strebinger D, Frangieh CJ, Friedrich MJ, Faure G, Macrae RK, Zhang F. Cell type-specific delivery by modular envelope design. Nat Commun. 2023 Aug 23;14(1):5141. doi: 10.1038/s41467-023-40788-8. PubMed PMID: 37612276; PubMed Central PMCID: PMC10447438.
Dolan MJ, Therrien M, Jereb S, Kamath T, Gazestani V, Atkeson T, Marsh SE, Goeva A, Lojek NM, Murphy S, White CM, Joung J, Liu B, Limone F, Eggan K, Hacohen N, Bernstein BE, Glass CK, Leinonen V, Blurton-Jones M, Zhang F, Epstein CB, Macosko EZ, Stevens B. Exposure of iPSC-derived human microglia to brain substrates enables the generation and manipulation of diverse transcriptional states in vitro. Nat Immunol. 2023 Aug;24(8):1382-1390. doi: 10.1038/s41590-023-01558-2. Epub 2023 Jul 27. PubMed PMID: 37500887; PubMed Central PMCID: PMC10382323.
Saito M, Xu P, Faure G, Maguire S, Kannan S, Altae-Tran H, Vo S, Desimone A, Macrae RK, Zhang F. Fanzor is a eukaryotic programmable RNA-guided endonuclease. Nature. 2023 Aug;620(7974):660-668. doi: 10.1038/s41586-023-06356-2. Epub 2023 Jun 28. PubMed PMID: 37380027; PubMed Central PMCID: PMC10432273.
Cain A, Taga M, McCabe C, Green GS, Hekselman I, White CC, Lee DI, Gaur P, Rozenblatt-Rosen O, Zhang F, Yeger-Lotem E, Bennett DA, Yang HS, Regev A, Menon V, Habib N, De Jager PL. Multicellular communities are perturbed in the aging human brain and Alzheimer's disease. Nat Neurosci. 2023 Jul;26(7):1267-1280. doi: 10.1038/s41593-023-01356-x. Epub 2023 Jun 19. PubMed PMID: 37336975; PubMed Central PMCID: PMC10789499.
Faure G, Saito M, Benler S, Peng I, Wolf YI, Strecker J, Altae-Tran H, Neumann E, Li D, Makarova KS, Macrae RK, Koonin EV, Zhang F. Modularity and diversity of target selectors in Tn7 transposons. Mol Cell. 2023 Jun 15;83(12):2122-2136.e10. doi: 10.1016/j.molcel.2023.05.013. Epub 2023 Jun 1. PubMed PMID: 37267947; PubMed Central PMCID: PMC10293859.
Nety SP, Altae-Tran H, Kannan S, Demircioglu FE, Faure G, Hirano S, Mears K, Zhang Y, Macrae RK, Zhang F. The Transposon-Encoded Protein TnpB Processes Its Own mRNA into ωRNA for Guided Nuclease Activity. CRISPR J. 2023 Jun;6(3):232-242. doi: 10.1089/crispr.2023.0015. PubMed PMID: 37272862; PubMed Central PMCID: PMC10278001.
Wilkinson ME, Frangieh CJ, Macrae RK, Zhang F. Structure of the R2 non-LTR retrotransposon initiating target-primed reverse transcription. Science. 2023 Apr 21;380(6642):301-308. doi: 10.1126/science.adg7883. Epub 2023 Apr 6. PubMed PMID: 37023171; PubMed Central PMCID: PMC10499050.
Nakagawa R, Hirano H, Omura SN, Nety S, Kannan S, Altae-Tran H, Yao X, Sakaguchi Y, Ohira T, Wu WY, Nakayama H, Shuto Y, Tanaka T, Sano FK, Kusakizako T, Kise Y, Itoh Y, Dohmae N, van der Oost J, Suzuki T, Zhang F, Nureki O. Cryo-EM structure of the transposon-associated TnpB enzyme. Nature. 2023 Apr;616(7956):390-397. doi: 10.1038/s41586-023-05933-9. Epub 2023 Apr 5. PubMed PMID: 37020030; PubMed Central PMCID: PMC10097598.
Kreitz J, Friedrich MJ, Guru A, Lash B, Saito M, Macrae RK, Zhang F. Programmable protein delivery with a bacterial contractile injection system. Nature. 2023 Apr;616(7956):357-364. doi: 10.1038/s41586-023-05870-7. Epub 2023 Mar 29. PubMed PMID: 36991127; PubMed Central PMCID: PMC10097599.
Patchsung M, Homchan A, Aphicho K, Suraritdechachai S, Wanitchanon T, Pattama A, Sappakhaw K, Meesawat P, Wongsatit T, Athipanyasilp A, Jantarug K, Athipanyasilp N, Buahom J, Visanpattanasin S, Niljianskul N, Chaiyen P, Tinikul R, Wichukchinda N, Mahasirimongkol S, Sirijatuphat R, Angkasekwinai N, Crone MA, Freemont PS, Joung J, Ladha A, Abudayyeh O, Gootenberg J, Zhang F, Chewapreecha C, Chanarat S, Horthongkham N, Pakotiprapha D, Uttamapinant C. A Multiplexed Cas13-Based Assay with Point-of-Care Attributes for Simultaneous COVID-19 Diagnosis and Variant Surveillance. CRISPR J. 2023 Apr;6(2):99-115. doi: 10.1089/crispr.2022.0048. Epub 2022 Nov 11. PubMed PMID: 36367987; PubMed Central PMCID: PMC7614457.
Joung J, Ma S, Tay T, Geiger-Schuller KR, Kirchgatterer PC, Verdine VK, Guo B, Arias-Garcia MA, Allen WE, Singh A, Kuksenko O, Abudayyeh OO, Gootenberg JS, Fu Z, Macrae RK, Buenrostro JD, Regev A, Zhang F. A transcription factor atlas of directed differentiation. Cell. 2023 Jan 5;186(1):209-229.e26. doi: 10.1016/j.cell.2022.11.026. PubMed PMID: 36608654; PubMed Central PMCID: PMC10344468.
Strecker J, Demircioglu FE, Li D, Faure G, Wilkinson ME, Gootenberg JS, Abudayyeh OO, Nishimasu H, Macrae RK, Zhang F. RNA-activated protein cleavage with a CRISPR-associated endopeptidase. Science. 2022 Nov 25;378(6622):874-881. doi: 10.1126/science.add7450. Epub 2022 Nov 3. PubMed PMID: 36423276; PubMed Central PMCID: PMC10028731.
Kato K, Okazaki S, Kannan S, Altae-Tran H, Esra Demircioglu F, Isayama Y, Ishikawa J, Fukuda M, Macrae RK, Nishizawa T, Makarova KS, Koonin EV, Zhang F, Nishimasu H. Structure of the IscB-ωRNA ribonucleoprotein complex, the likely ancestor of CRISPR-Cas9. Nat Commun. 2022 Nov 7;13(1):6719. doi: 10.1038/s41467-022-34378-3. PubMed PMID: 36344504; PubMed Central PMCID: PMC9640706.
Hirano S, Kappel K, Altae-Tran H, Faure G, Wilkinson ME, Kannan S, Demircioglu FE, Yan R, Shiozaki M, Yu Z, Makarova KS, Koonin EV, Macrae RK, Zhang F. Structure of the OMEGA nickase IsrB in complex with ωRNA and target DNA. Nature. 2022 Oct;610(7932):575-581. doi: 10.1038/s41586-022-05324-6. Epub 2022 Oct 12. PubMed PMID: 36224386; PubMed Central PMCID: PMC9581776.
Cui N, Faure G, Singh A, Macrae R, Zhang F. Microfluidic Enrichment and Computational Analysis of Rare Sequences from Mixed Genomic Samples for Metagenomic Mining. CRISPR J. 2022 Oct;5(5):677-684. doi: 10.1089/crispr.2022.0054. Epub 2022 Oct 7. PubMed PMID: 36206017; PubMed Central PMCID: PMC9595627.
Nakagawa R, Kannan S, Altae-Tran H, Takeda SN, Tomita A, Hirano H, Kusakizako T, Nishizawa T, Yamashita K, Zhang F, Nishimasu H, Nureki O. Structure and engineering of the minimal type VI CRISPR-Cas13bt3. Mol Cell. 2022 Sep 1;82(17):3178-3192.e5. doi: 10.1016/j.molcel.2022.08.001. Epub 2022 Aug 25. PubMed PMID: 36027912; PubMed Central PMCID: PMC7613696.
Gao LA, Wilkinson ME, Strecker J, Makarova KS, Macrae RK, Koonin EV, Zhang F. Prokaryotic innate immunity through pattern recognition of conserved viral proteins. Science. 2022 Aug 12;377(6607):eabm4096. doi: 10.1126/science.abm4096. Epub 2022 Aug 12. PubMed PMID: 35951700; PubMed Central PMCID: PMC10028730.
Li H, Namburi P, Olson JM, Borio M, Lemieux ME, Beyeler A, Calhoon GG, Hitora-Imamura N, Coley AA, Libster A, Bal A, Jin X, Wang H, Jia C, Choudhury SR, Shi X, Felix-Ortiz AC, de la Fuente V, Barth VP, King HO, Izadmehr EM, Revanna JS, Batra K, Fischer KB, Keyes LR, Padilla-Coreano N, Siciliano CA, McCullough KM, Wichmann R, Ressler KJ, Fiete IR, Zhang F, Li Y, Tye KM. Neurotensin orchestrates valence assignment in the amygdala. Nature. 2022 Aug;608(7923):586-592. doi: 10.1038/s41586-022-04964-y. Epub 2022 Jul 20. PubMed PMID: 35859170; PubMed Central PMCID: PMC9583860.
Mestre MR, Gao LA, Shah SA, López-Beltrán A, González-Delgado A, Martínez-Abarca F, Iranzo J, Redrejo-Rodríguez M, Zhang F, Toro N. UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions. Nucleic Acids Res. 2022 Jun 24;50(11):6084-6101. doi: 10.1093/nar/gkac467. PubMed PMID: 35648479; PubMed Central PMCID: PMC9226505.
Mutz P, Rochman ND, Wolf YI, Faure G, Zhang F, Koonin EV. Human pathogenic RNA viruses establish noncompeting lineages by occupying independent niches. Proc Natl Acad Sci U S A. 2022 Jun 7;119(23):e2121335119. doi: 10.1073/pnas.2121335119. Epub 2022 May 31. PubMed PMID: 35639694; PubMed Central PMCID: PMC9191635.
Rochman ND, Faure G, Wolf YI, Freddolino PL, Zhang F, Koonin EV. Epistasis at the SARS-CoV-2 Receptor-Binding Domain Interface and the Propitiously Boring Implications for Vaccine Escape. mBio. 2022 Apr 26;13(2):e0013522. doi: 10.1128/mbio.00135-22. Epub 2022 Mar 15. PubMed PMID: 35289643; PubMed Central PMCID: PMC9040817.
Joung J, Kirchgatterer PC, Singh A, Cho JH, Nety SP, Larson RC, Macrae RK, Deasy R, Tseng YY, Maus MV, Zhang F. CRISPR activation screen identifies BCL-2 proteins and B3GNT2 as drivers of cancer resistance to T cell-mediated cytotoxicity. Nat Commun. 2022 Mar 25;13(1):1606. doi: 10.1038/s41467-022-29205-8. PubMed PMID: 35338135; PubMed Central PMCID: PMC8956604.
Kannan S, Altae-Tran H, Jin X, Madigan VJ, Oshiro R, Makarova KS, Koonin EV, Zhang F. Compact RNA editors with small Cas13 proteins. Nat Biotechnol. 2022 Feb;40(2):194-197. doi: 10.1038/s41587-021-01030-2. Epub 2021 Aug 30. PubMed PMID: 34462587; PubMed Central PMCID: PMC8929162.
Benler S, Faure G, Altae-Tran H, Shmakov S, Zheng F, Koonin E. Cargo Genes of Tn7-Like Transposons Comprise an Enormous Diversity of Defense Systems, Mobile Genetic Elements, and Antibiotic Resistance Genes. mBio. 2021 Dec 21;12(6):e0293821. doi: 10.1128/mBio.02938-21. Epub 2021 Dec 7. PubMed PMID: 34872347; PubMed Central PMCID: PMC8649781.
Ludwig KU, Schmithausen RM, Li D, Jacobs ML, Hollstein R, Blumenstock K, Liebing J, Słabicki M, Ben-Shmuel A, Israeli O, Weiss S, Ebert TS, Paran N, Rüdiger W, Wilbring G, Feldman D, Lippke B, Ishorst N, Hochfeld LM, Beins EC, Kaltheuner IH, Schmitz M, Wöhler A, Döhla M, Sib E, Jentzsch M, Moench EC, Borrajo JD, Strecker J, Reinhardt J, Cleary B, Geyer M, Hölzel M, Macrae R, Nöthen MM, Hoffmann P, Exner M, Regev A, Zhang F, Schmid-Burgk JL. LAMP-Seq enables sensitive, multiplexed COVID-19 diagnostics using molecular barcoding. Nat Biotechnol. 2021 Dec;39(12):1556-1562. doi: 10.1038/s41587-021-00966-9. Epub 2021 Jun 29. PubMed PMID: 34188222; PubMed Central PMCID: PMC8678193.
Altae-Tran H, Kannan S, Demircioglu FE, Oshiro R, Nety SP, McKay LJ, Dlakić M, Inskeep WP, Makarova KS, Macrae RK, Koonin EV, Zhang F. The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases. Science. 2021 Oct;374(6563):57-65. doi: 10.1126/science.abj6856. Epub 2021 Sep 9. PubMed PMID: 34591643; PubMed Central PMCID: PMC8929163.
Segel M, Lash B, Song J, Ladha A, Liu CC, Jin X, Mekhedov SL, Macrae RK, Koonin EV, Zhang F. Mammalian retrovirus-like protein PEG10 packages its own mRNA and can be pseudotyped for mRNA delivery. Science. 2021 Aug 20;373(6557):882-889. doi: 10.1126/science.abg6155. PubMed PMID: 34413232; PubMed Central PMCID: PMC8431961.
Rochman ND, Wolf YI, Faure G, Mutz P, Zhang F, Koonin EV. Ongoing global and regional adaptive evolution of SARS-CoV-2. Proc Natl Acad Sci U S A. 2021 Jul 20;118(29). doi: 10.1073/pnas.2104241118. Epub 2021 Jul 2. PubMed PMID: 34292871; PubMed Central PMCID: PMC8307621.
Dani N, Herbst RH, McCabe C, Green GS, Kaiser K, Head JP, Cui J, Shipley FB, Jang A, Dionne D, Nguyen L, Rodman C, Riesenfeld SJ, Prochazka J, Prochazkova M, Sedlacek R, Zhang F, Bryja V, Rozenblatt-Rosen O, Habib N, Regev A, Lehtinen MK. A cellular and spatial map of the choroid plexus across brain ventricles and ages. Cell. 2021 May 27;184(11):3056-3074.e21. doi: 10.1016/j.cell.2021.04.003. Epub 2021 Apr 30. PubMed PMID: 33932339; PubMed Central PMCID: PMC8214809.
Saito M, Ladha A, Strecker J, Faure G, Neumann E, Altae-Tran H, Macrae RK, Zhang F. Dual modes of CRISPR-associated transposon homing. Cell. 2021 Apr 29;184(9):2441-2453.e18. doi: 10.1016/j.cell.2021.03.006. Epub 2021 Mar 25. PubMed PMID: 33770501; PubMed Central PMCID: PMC8276595.
Nie M, Du L, Ren W, Joung J, Ye X, Shi X, Ciftci S, Liu D, Wu K, Zhang F, Pan-Hammarström Q. Genome-wide CRISPR screens reveal synthetic lethal interaction between CREBBP and EP300 in diffuse large B-cell lymphoma. Cell Death Dis. 2021 Apr 28;12(5):419. doi: 10.1038/s41419-021-03695-8. PubMed PMID: 33911074; PubMed Central PMCID: PMC8080727.
Qiu M, Glass Z, Chen J, Haas M, Jin X, Zhao X, Rui X, Ye Z, Li Y, Zhang F, Xu Q. Lipid nanoparticle-mediated codelivery of Cas9 mRNA and single-guide RNA achieves liver-specific in vivo genome editing of Angptl3. Proc Natl Acad Sci U S A. 2021 Mar 9;118(10). doi: 10.1073/pnas.2020401118. PubMed PMID: 33649229; PubMed Central PMCID: PMC7958351.
Sorek M, Oweis W, Nissim-Rafinia M, Maman M, Simon S, Hession CC, Adiconis X, Simmons SK, Sanjana NE, Shi X, Lu C, Pan JQ, Xu X, Pouladi MA, Ellerby LM, Zhang F, Levin JZ, Meshorer E. Pluripotent stem cell-derived models of neurological diseases reveal early transcriptional heterogeneity. Genome Biol. 2021 Mar 4;22(1):73. doi: 10.1186/s13059-021-02301-6. PubMed PMID: 33663567; PubMed Central PMCID: PMC7934477.
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Joung J, Ladha A, Saito M, Kim NG, Woolley AE, Segel M, Barretto RPJ, Ranu A, Macrae RK, Faure G, Ioannidi EI, Krajeski RN, Bruneau R, Huang MW, Yu XG, Li JZ, Walker BD, Hung DT, Greninger AL, Jerome KR, Gootenberg JS, Abudayyeh OO, Zhang F. Detection of SARS-CoV-2 with SHERLOCK One-Pot Testing. N Engl J Med. 2020 Oct 8;383(15):1492-1494. doi: 10.1056/NEJMc2026172. Epub 2020 Sep 16. PubMed PMID: 32937062; PubMed Central PMCID: PMC7510942.
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Allen WE, Altae-Tran H, Briggs J, Jin X, McGee G, Shi A, Raghavan R, Kamariza M, Nova N, Pereta A, Danford C, Kamel A, Gothe P, Milam E, Aurambault J, Primke T, Li W, Inkenbrandt J, Huynh T, Chen E, Lee C, Croatto M, Bentley H, Lu W, Murray R, Travassos M, Coull BA, Openshaw J, Greene CS, Shalem O, King G, Probasco R, Cheng DR, Silbermann B, Zhang F, Lin X. Population-scale longitudinal mapping of COVID-19 symptoms, behaviour and testing. Nat Hum Behav. 2020 Sep;4(9):972-982. doi: 10.1038/s41562-020-00944-2. Epub 2020 Aug 26. PubMed PMID: 32848231; PubMed Central PMCID: PMC7501153.
Gao L, Altae-Tran H, Böhning F, Makarova KS, Segel M, Schmid-Burgk JL, Koob J, Wolf YI, Koonin EV, Zhang F. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science. 2020 Aug 28;369(6507):1077-1084. doi: 10.1126/science.aba0372. PubMed PMID: 32855333; PubMed Central PMCID: PMC7985843.
Segal E, Zhang F, Lin X, King G, Shalem O, Shilo S, Allen WE, Alquaddoomi F, Altae-Tran H, Anders S, Balicer R, Bauman T, Bonilla X, Booman G, Chan AT, Cohen O, Coletti S, Davidson N, Dor Y, Drew DA, Elemento O, Evans G, Ewels P, Gale J, Gavrieli A, Geiger B, Grad YH, Greene CS, Hajirasouliha I, Jerala R, Kahles A, Kallioniemi O, Keshet A, Kocarev L, Landua G, Meir T, Muller A, Nguyen LH, Oresic M, Ovchinnikova S, Peterson H, Prodanova J, Rajagopal J, Rätsch G, Rossman H, Rung J, Sboner A, Sigaras A, Spector T, Steinherz R, Stevens I, Vilo J, Wilmes P. Building an international consortium for tracking coronavirus health status. Nat Med. 2020 Aug;26(8):1161-1165. doi: 10.1038/s41591-020-0929-x. PubMed PMID: 32488218.
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