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Items: 1 to 50 of 160

1.

A Reverse Transcriptase-Cas1 Fusion Protein Contains a Cas6 Domain Required for Both CRISPR RNA Biogenesis and RNA Spacer Acquisition.

Mohr G, Silas S, Stamos JL, Makarova KS, Markham LM, Yao J, Lucas-Elío P, Sanchez-Amat A, Fire AZ, Koonin EV, Lambowitz AM.

Mol Cell. 2018 Nov 15;72(4):700-714.e8. doi: 10.1016/j.molcel.2018.09.013. Epub 2018 Oct 18.

PMID:
30344094
2.

Correction: Type III CRISPR-Cas systems can provide redundancy to counteract viral escape from type I systems.

Silas S, Lucas-Elio P, Jackson SA, Aroca-Crevillén A, Hansen LL, Fineran PC, Fire AZ, Sánchez-Amat A.

Elife. 2018 Apr 4;7. pii: e36853. doi: 10.7554/eLife.36853. No abstract available.

3.

A Small RNA Isolation and Sequencing Protocol and Its Application to Assay CRISPR RNA Biogenesis in Bacteria.

Silas S, Jain N, Stadler M, Fu BXH, Sánchez-Amat A, Fire AZ, Arribere J.

Bio Protoc. 2018 Feb 20;8(4). pii: e2727. doi: 10.21769/BioProtoc.2727.

4.

Nonsense mRNA suppression via nonstop decay.

Arribere JA, Fire AZ.

Elife. 2018 Jan 8;7. pii: e33292. doi: 10.7554/eLife.33292.

5.

A novel TRIP11-FLT3 fusion in a patient with a myeloid/lymphoid neoplasm with eosinophilia.

Chung A, Hou Y, Ohgami RS, Von Gehr A, Fisk DG, Roskin KM, Li X, Gojenola L, Bangs CD, Arber DA, Fire AZ, Cherry AM, Zehnder JL, Gotlib J, Merker JD.

Cancer Genet. 2017 Oct;216-217:10-15. doi: 10.1016/j.cancergen.2017.05.001. Epub 2017 May 10.

PMID:
29025582
6.

Type III CRISPR-Cas systems can provide redundancy to counteract viral escape from type I systems.

Silas S, Lucas-Elio P, Jackson SA, Aroca-Crevillén A, Hansen LL, Fineran PC, Fire AZ, Sánchez-Amat A.

Elife. 2017 Aug 17;6. pii: e27601. doi: 10.7554/eLife.27601. Erratum in: Elife. 2018 Apr 04;7:.

7.

Intricate and Cell Type-Specific Populations of Endogenous Circular DNA (eccDNA) in Caenorhabditis elegans and Homo sapiens.

Shoura MJ, Gabdank I, Hansen L, Merker J, Gotlib J, Levene SD, Fire AZ.

G3 (Bethesda). 2017 Oct 5;7(10):3295-3303. doi: 10.1534/g3.117.300141.

8.

On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires.

Silas S, Makarova KS, Shmakov S, Páez-Espino D, Mohr G, Liu Y, Davison M, Roux S, Krishnamurthy SR, Fu BXH, Hansen LL, Wang D, Sullivan MB, Millard A, Clokie MR, Bhaya D, Lambowitz AM, Kyrpides NC, Koonin EV, Fire AZ.

MBio. 2017 Jul 11;8(4). pii: e00897-17. doi: 10.1128/mBio.00897-17.

9.

High-Throughput Characterization of Cascade type I-E CRISPR Guide Efficacy Reveals Unexpected PAM Diversity and Target Sequence Preferences.

Fu BX, Wainberg M, Kundaje A, Fire AZ.

Genetics. 2017 Aug;206(4):1727-1738. doi: 10.1534/genetics.117.202580. Epub 2017 Jun 20.

10.

Sequence-Modified Antibiotic Resistance Genes Provide Sustained Plasmid-Mediated Transgene Expression in Mammals.

Lu J, Zhang F, Fire AZ, Kay MA.

Mol Ther. 2017 May 3;25(5):1187-1198. doi: 10.1016/j.ymthe.2017.03.003. Epub 2017 Mar 30.

11.

An Abundant Class of Non-coding DNA Can Prevent Stochastic Gene Silencing in the C. elegans Germline.

Frøkjær-Jensen C, Jain N, Hansen L, Davis MW, Li Y, Zhao D, Rebora K, Millet JRM, Liu X, Kim SK, Dupuy D, Jorgensen EM, Fire AZ.

Cell. 2016 Jul 14;166(2):343-357. doi: 10.1016/j.cell.2016.05.072. Epub 2016 Jun 30.

12.

Translation readthrough mitigation.

Arribere JA, Cenik ES, Jain N, Hess GT, Lee CH, Bassik MC, Fire AZ.

Nature. 2016 Jun 30;534(7609):719-23. Epub 2016 Jun 1.

13.

Distinct patterns of Cas9 mismatch tolerance in vitro and in vivo.

Fu BX, St Onge RP, Fire AZ, Smith JD.

Nucleic Acids Res. 2016 Jun 20;44(11):5365-77. doi: 10.1093/nar/gkw417. Epub 2016 May 19.

14.

A streamlined tethered chromosome conformation capture protocol.

Gabdank I, Ramakrishnan S, Villeneuve AM, Fire AZ.

BMC Genomics. 2016 Apr 1;17:274. doi: 10.1186/s12864-016-2596-3.

15.

Maturation Pathway from Germline to Broad HIV-1 Neutralizer of a CD4-Mimic Antibody.

Bonsignori M, Zhou T, Sheng Z, Chen L, Gao F, Joyce MG, Ozorowski G, Chuang GY, Schramm CA, Wiehe K, Alam SM, Bradley T, Gladden MA, Hwang KK, Iyengar S, Kumar A, Lu X, Luo K, Mangiapani MC, Parks RJ, Song H, Acharya P, Bailer RT, Cao A, Druz A, Georgiev IS, Kwon YD, Louder MK, Zhang B, Zheng A, Hill BJ, Kong R, Soto C; NISC Comparative Sequencing Program, Mullikin JC, Douek DC, Montefiori DC, Moody MA, Shaw GM, Hahn BH, Kelsoe G, Hraber PT, Korber BT, Boyd SD, Fire AZ, Kepler TB, Shapiro L, Ward AB, Mascola JR, Liao HX, Kwong PD, Haynes BF.

Cell. 2016 Apr 7;165(2):449-63. doi: 10.1016/j.cell.2016.02.022. Epub 2016 Mar 3.

16.

Direct CRISPR spacer acquisition from RNA by a natural reverse transcriptase-Cas1 fusion protein.

Silas S, Mohr G, Sidote DJ, Markham LM, Sanchez-Amat A, Bhaya D, Lambowitz AM, Fire AZ.

Science. 2016 Feb 26;351(6276):aad4234. doi: 10.1126/science.aad4234.

17.

Cas9 Variants Expand the Target Repertoire in Caenorhabditis elegans.

Bell RT, Fu BX, Fire AZ.

Genetics. 2016 Feb;202(2):381-8. doi: 10.1534/genetics.115.185041. Epub 2015 Dec 17. Erratum in: Genetics. 2016 Jun;203(2):999.

18.

Chikungunya Virus Sequences Across the First Epidemic in Nicaragua, 2014-2015.

Wang C, Saborio S, Gresh L, Eswarappa M, Wu D, Fire A, Parameswaran P, Balmaseda A, Harris E.

Am J Trop Med Hyg. 2016 Feb;94(2):400-3. doi: 10.4269/ajtmh.15-0497. Epub 2015 Dec 7.

19.

Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species.

Nakatani Y, Mello CC, Hashimoto S, Shimada A, Nakamura R, Tsukahara T, Qu W, Yoshimura J, Suzuki Y, Sugano S, Takeda H, Fire A, Morishita S.

BMC Genomics. 2015 Nov 19;16:978. doi: 10.1186/s12864-015-2198-5.

20.

Persistence and evolution of allergen-specific IgE repertoires during subcutaneous specific immunotherapy.

Levin M, King JJ, Glanville J, Jackson KJ, Looney TJ, Hoh RA, Mari A, Andersson M, Greiff L, Fire AZ, Boyd SD, Ohlin M.

J Allergy Clin Immunol. 2016 May;137(5):1535-44. doi: 10.1016/j.jaci.2015.09.027. Epub 2015 Nov 11.

21.

Functional relevance of "seed" and "non-seed" sequences in microRNA-mediated promotion of C. elegans developmental progression.

Zhang H, Artiles KL, Fire AZ.

RNA. 2015 Nov;21(11):1980-92. doi: 10.1261/rna.053793.115. Epub 2015 Sep 18.

22.

A requirement for ERK-dependent Dicer phosphorylation in coordinating oocyte-to-embryo transition in C. elegans.

Drake M, Furuta T, Suen KM, Gonzalez G, Liu B, Kalia A, Ladbury JE, Fire AZ, Skeath JB, Arur S.

Dev Cell. 2014 Dec 8;31(5):614-28. doi: 10.1016/j.devcel.2014.11.004.

23.

Landscape of target:guide homology effects on Cas9-mediated cleavage.

Fu BX, Hansen LL, Artiles KL, Nonet ML, Fire AZ.

Nucleic Acids Res. 2014 Dec 16;42(22):13778-87. doi: 10.1093/nar/gku1102. Epub 2014 Nov 15.

24.

Immunoglobulin gene insertions and deletions in the affinity maturation of HIV-1 broadly reactive neutralizing antibodies.

Kepler TB, Liao HX, Alam SM, Bhaskarabhatla R, Zhang R, Yandava C, Stewart S, Anasti K, Kelsoe G, Parks R, Lloyd KE, Stolarchuk C, Pritchett J, Solomon E, Friberg E, Morris L, Karim SS, Cohen MS, Walter E, Moody MA, Wu X, Altae-Tran HR, Georgiev IS, Kwong PD, Boyd SD, Fire AZ, Mascola JR, Haynes BF.

Cell Host Microbe. 2014 Sep 10;16(3):304-13. doi: 10.1016/j.chom.2014.08.006.

25.

Efficient marker-free recovery of custom genetic modifications with CRISPR/Cas9 in Caenorhabditis elegans.

Arribere JA, Bell RT, Fu BX, Artiles KL, Hartman PS, Fire AZ.

Genetics. 2014 Nov;198(3):837-46. doi: 10.1534/genetics.114.169730. Epub 2014 Aug 26.

26.

Human responses to influenza vaccination show seroconversion signatures and convergent antibody rearrangements.

Jackson KJ, Liu Y, Roskin KM, Glanville J, Hoh RA, Seo K, Marshall EL, Gurley TC, Moody MA, Haynes BF, Walter EB, Liao HX, Albrecht RA, García-Sastre A, Chaparro-Riggers J, Rajpal A, Pons J, Simen BB, Hanczaruk B, Dekker CL, Laserson J, Koller D, Davis MM, Fire AZ, Boyd SD.

Cell Host Microbe. 2014 Jul 9;16(1):105-14. doi: 10.1016/j.chom.2014.05.013. Epub 2014 Jun 26.

27.

Effects of aging, cytomegalovirus infection, and EBV infection on human B cell repertoires.

Wang C, Liu Y, Xu LT, Jackson KJ, Roskin KM, Pham TD, Laserson J, Marshall EL, Seo K, Lee JY, Furman D, Koller D, Dekker CL, Davis MM, Fire AZ, Boyd SD.

J Immunol. 2014 Jan 15;192(2):603-11. doi: 10.4049/jimmunol.1301384. Epub 2013 Dec 11.

28.

Unusual DNA packaging characteristics in endoreduplicated Caenorhabditis elegans oocytes defined by in vivo accessibility to an endogenous nuclease activity.

Gu S, Goszczynski B, McGhee JD, Fire AZ.

Epigenetics Chromatin. 2013 Nov 1;6(1):37. doi: 10.1186/1756-8935-6-37.

29.

Gamete-type dependent crossover interference levels in a defined region of Caenorhabditis elegans chromosome V.

Gabdank I, Fire AZ.

G3 (Bethesda). 2014 Jan 10;4(1):117-20. doi: 10.1534/g3.113.008672.

30.

Conserved translatome remodeling in nematode species executing a shared developmental transition.

Stadler M, Fire A.

PLoS Genet. 2013;9(10):e1003739. doi: 10.1371/journal.pgen.1003739. Epub 2013 Oct 3.

31.

Comprehensive whole-genome sequencing of an early-stage primary myelofibrosis patient defines low mutational burden and non-recurrent candidate genes.

Merker JD, Roskin KM, Ng D, Pan C, Fisk DG, King JJ, Hoh R, Stadler M, Okumoto LM, Abidi P, Hewitt R, Jones CD, Gojenola L, Clark MJ, Zhang B, Cherry AM, George TI, Snyder M, Boyd SD, Zehnder JL, Fire AZ, Gotlib J.

Haematologica. 2013 Nov;98(11):1689-96. doi: 10.3324/haematol.2013.092379. Epub 2013 Jul 19.

32.

Convergent antibody signatures in human dengue.

Parameswaran P, Liu Y, Roskin KM, Jackson KK, Dixit VP, Lee JY, Artiles KL, Zompi S, Vargas MJ, Simen BB, Hanczaruk B, McGowan KR, Tariq MA, Pourmand N, Koller D, Balmaseda A, Boyd SD, Harris E, Fire AZ.

Cell Host Microbe. 2013 Jun 12;13(6):691-700. doi: 10.1016/j.chom.2013.05.008.

33.

The transcription start site landscape of C. elegans.

Saito TL, Hashimoto S, Gu SG, Morton JJ, Stadler M, Blumenthal T, Fire A, Morishita S.

Genome Res. 2013 Aug;23(8):1348-61. doi: 10.1101/gr.151571.112. Epub 2013 May 1.

34.

Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus.

Liao HX, Lynch R, Zhou T, Gao F, Alam SM, Boyd SD, Fire AZ, Roskin KM, Schramm CA, Zhang Z, Zhu J, Shapiro L; NISC Comparative Sequencing Program, Mullikin JC, Gnanakaran S, Hraber P, Wiehe K, Kelsoe G, Yang G, Xia SM, Montefiori DC, Parks R, Lloyd KE, Scearce RM, Soderberg KA, Cohen M, Kamanga G, Louder MK, Tran LM, Chen Y, Cai F, Chen S, Moquin S, Du X, Joyce MG, Srivatsan S, Zhang B, Zheng A, Shaw GM, Hahn BH, Kepler TB, Korber BT, Kwong PD, Mascola JR, Haynes BF.

Nature. 2013 Apr 25;496(7446):469-76. doi: 10.1038/nature12053. Epub 2013 Apr 3.

35.

Minicircle DNA vectors achieve sustained expression reflected by active chromatin and transcriptional level.

Gracey Maniar LE, Maniar JM, Chen ZY, Lu J, Fire AZ, Kay MA.

Mol Ther. 2013 Jan;21(1):131-8. doi: 10.1038/mt.2012.244. Epub 2012 Nov 27.

36.

Protection from feed-forward amplification in an amplified RNAi mechanism.

Pak J, Maniar JM, Mello CC, Fire A.

Cell. 2012 Nov 9;151(4):885-899. doi: 10.1016/j.cell.2012.10.022.

37.

Contributions of mRNA abundance, ribosome loading, and post- or peri-translational effects to temporal repression of C. elegans heterochronic miRNA targets.

Stadler M, Artiles K, Pak J, Fire A.

Genome Res. 2012 Dec;22(12):2418-26. doi: 10.1101/gr.136515.111. Epub 2012 Aug 1.

38.

A nuclear Argonaute promotes multigenerational epigenetic inheritance and germline immortality.

Buckley BA, Burkhart KB, Gu SG, Spracklin G, Kershner A, Fritz H, Kimble J, Fire A, Kennedy S.

Nature. 2012 Sep 20;489(7416):447-51. doi: 10.1038/nature11352. Epub 2012 Jul 18.

39.

The extragenic spacer length between the 5' and 3' ends of the transgene expression cassette affects transgene silencing from plasmid-based vectors.

Lu J, Zhang F, Xu S, Fire AZ, Kay MA.

Mol Ther. 2012 Nov;20(11):2111-9. doi: 10.1038/mt.2012.65. Epub 2012 May 8.

40.

Davos declaration: allergy as a global problem.

Ring J, Akdis C, Behrendt H, Lauener RP, Schäppi G, Akdis M, Ammann W, de Beaumont O, Bieber T, Bienenstock J, Blaser K, Bochner B, Bousquet J, Crameri R, Custovic A, Czerkinsky C, Darsow U, Denburg J, Drazen J, de Villiers EM, Fire A, Galli S, Haahtela T, zur Hausen H, Hildemann S, Holgate S, Holt P, Jakob T, Jung A, Kemeny M, Koren H, Leung D, Lockey R, Marone G, Mempel M, Menné B, Menz G, Mueller U, von Mutius E, Ollert M, O'Mahony L, Pawankar R, Renz H, Platts-Mills T, Roduit C, Schmidt-Weber C, Traidl-Hoffmann C, Wahn U, Rietschel E.

Allergy. 2012 Feb;67(2):141-3. doi: 10.1111/j.1398-9995.2011.02770.x. No abstract available. Erratum in: Allergy. 2012 May;67(5):712. multiple author names added.

PMID:
22235793
41.

Amplification of siRNA in Caenorhabditis elegans generates a transgenerational sequence-targeted histone H3 lysine 9 methylation footprint.

Gu SG, Pak J, Guang S, Maniar JM, Kennedy S, Fire A.

Nat Genet. 2012 Jan 8;44(2):157-64. doi: 10.1038/ng.1039.

42.

The inference of phased haplotypes for the immunoglobulin H chain V region gene loci by analysis of VDJ gene rearrangements.

Kidd MJ, Chen Z, Wang Y, Jackson KJ, Zhang L, Boyd SD, Fire AZ, Tanaka MM, Gaëta BA, Collins AM.

J Immunol. 2012 Feb 1;188(3):1333-40. doi: 10.4049/jimmunol.1102097. Epub 2011 Dec 28.

43.

High-throughput VDJ sequencing for quantification of minimal residual disease in chronic lymphocytic leukemia and immune reconstitution assessment.

Logan AC, Gao H, Wang C, Sahaf B, Jones CD, Marshall EL, Buño I, Armstrong R, Fire AZ, Weinberg KI, Mindrinos M, Zehnder JL, Boyd SD, Xiao W, Davis RW, Miklos DB.

Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):21194-9. doi: 10.1073/pnas.1118357109. Epub 2011 Dec 12.

44.

Wobble base-pairing slows in vivo translation elongation in metazoans.

Stadler M, Fire A.

RNA. 2011 Dec;17(12):2063-73. doi: 10.1261/rna.02890211. Epub 2011 Nov 1.

45.

Initial antibodies binding to HIV-1 gp41 in acutely infected subjects are polyreactive and highly mutated.

Liao HX, Chen X, Munshaw S, Zhang R, Marshall DJ, Vandergrift N, Whitesides JF, Lu X, Yu JS, Hwang KK, Gao F, Markowitz M, Heath SL, Bar KJ, Goepfert PA, Montefiori DC, Shaw GC, Alam SM, Margolis DM, Denny TN, Boyd SD, Marshal E, Egholm M, Simen BB, Hanczaruk B, Fire AZ, Voss G, Kelsoe G, Tomaras GD, Moody MA, Kepler TB, Haynes BF.

J Exp Med. 2011 Oct 24;208(11):2237-49. doi: 10.1084/jem.20110363. Epub 2011 Oct 10.

46.

Human leukocyte antigen I knockdown human embryonic stem cells induce host ignorance and achieve prolonged xenogeneic survival.

Deuse T, Seifert M, Phillips N, Fire A, Tyan D, Kay M, Tsao PS, Hua X, Velden J, Eiermann T, Volk HD, Reichenspurner H, Robbins RC, Schrepfer S.

Circulation. 2011 Sep 13;124(11 Suppl):S3-9. doi: 10.1161/CIRCULATIONAHA.111.020727.

PMID:
21911816
47.

Competition between ADAR and RNAi pathways for an extensive class of RNA targets.

Wu D, Lamm AT, Fire AZ.

Nat Struct Mol Biol. 2011 Sep 11;18(10):1094-101. doi: 10.1038/nsmb.2129.

48.

Immunobiology of naïve and genetically modified HLA-class-I-knockdown human embryonic stem cells.

Deuse T, Seifert M, Tyan D, Tsao PS, Hua X, Velden J, Eiermann T, Volk HD, Reichenspurner H, Robbins RC, Schrepfer S.

J Cell Sci. 2011 Sep 1;124(Pt 17):3029-37. doi: 10.1242/jcs.087718. Erratum in: J Cell Sci. 2011 Dec 1;124(Pt 23):4127-8. Phillips, Neil [removed]; Fire, Andrew [removed]; Kay, Mark [removed].

49.

'Inc-miRs': functional intron-interrupted miRNA genes.

Zhang H, Maniar JM, Fire AZ.

Genes Dev. 2011 Aug 1;25(15):1589-94. doi: 10.1101/gad.2058711.

50.

Up-regulated Dicer expression in patients with cutaneous melanoma.

Ma Z, Swede H, Cassarino D, Fleming E, Fire A, Dadras SS.

PLoS One. 2011;6(6):e20494. doi: 10.1371/journal.pone.0020494. Epub 2011 Jun 17.

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