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Improved TGIRT-seq methods for comprehensive transcriptome profiling with decreased adapter dimer formation and bias correction.

Xu H, Yao J, Wu DC, Lambowitz AM.

Sci Rep. 2019 May 28;9(1):7953. doi: 10.1038/s41598-019-44457-z.


Group II Intron RNPs and Reverse Transcriptases: From Retroelements to Research Tools.

Belfort M, Lambowitz AM.

Cold Spring Harb Perspect Biol. 2019 Apr 1;11(4). pii: a032375. doi: 10.1101/cshperspect.a032375. Review.


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.


Limitations of alignment-free tools in total RNA-seq quantification.

Wu DC, Yao J, Ho KS, Lambowitz AM, Wilke CO.

BMC Genomics. 2018 Jul 3;19(1):510. doi: 10.1186/s12864-018-4869-5.


A Highly Proliferative Group IIC Intron from Geobacillus stearothermophilus Reveals New Features of Group II Intron Mobility and Splicing.

Mohr G, Kang SY, Park SK, Qin Y, Grohman J, Yao J, Stamos JL, Lambowitz AM.

J Mol Biol. 2018 Aug 17;430(17):2760-2783. doi: 10.1016/j.jmb.2018.06.019. Epub 2018 Jun 15.


Simultaneous sequencing of coding and noncoding RNA reveals a human transcriptome dominated by a small number of highly expressed noncoding genes.

Boivin V, Deschamps-Francoeur G, Couture S, Nottingham RM, Bouchard-Bourelle P, Lambowitz AM, Scott MS, Abou-Elela S.

RNA. 2018 Jul;24(7):950-965. doi: 10.1261/rna.064493.117. Epub 2018 Apr 27.


Structure of a Thermostable Group II Intron Reverse Transcriptase with Template-Primer and Its Functional and Evolutionary Implications.

Stamos JL, Lentzsch AM, Lambowitz AM.

Mol Cell. 2017 Dec 7;68(5):926-939.e4. doi: 10.1016/j.molcel.2017.10.024. Epub 2017 Nov 16.


Broad role for YBX1 in defining the small noncoding RNA composition of exosomes.

Shurtleff MJ, Yao J, Qin Y, Nottingham RM, Temoche-Diaz MM, Schekman R, Lambowitz AM.

Proc Natl Acad Sci U S A. 2017 Oct 24;114(43):E8987-E8995. doi: 10.1073/pnas.1712108114. Epub 2017 Oct 10.


Detection of expanded RNA repeats using thermostable group II intron reverse transcriptase.

Carrell ST, Tang Z, Mohr S, Lambowitz AM, Thornton CA.

Nucleic Acids Res. 2018 Jan 9;46(1):e1. doi: 10.1093/nar/gkx867.


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.


DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo.

Zubradt M, Gupta P, Persad S, Lambowitz AM, Weissman JS, Rouskin S.

Nat Methods. 2017 Jan;14(1):75-82. doi: 10.1038/nmeth.4057. Epub 2016 Nov 7.


Structural Divergence of the Group I Intron Binding Surface in Fungal Mitochondrial Tyrosyl-tRNA Synthetases That Function in RNA Splicing.

Lamech LT, Saoji M, Paukstelis PJ, Lambowitz AM.

J Biol Chem. 2016 May 27;291(22):11911-27. doi: 10.1074/jbc.M116.725390. Epub 2016 Apr 1.


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.


RNA-seq of human reference RNA samples using a thermostable group II intron reverse transcriptase.

Nottingham RM, Wu DC, Qin Y, Yao J, Hunicke-Smith S, Lambowitz AM.

RNA. 2016 Apr;22(4):597-613. doi: 10.1261/rna.055558.115. Epub 2016 Jan 29.


High-throughput sequencing of human plasma RNA by using thermostable group II intron reverse transcriptases.

Qin Y, Yao J, Wu DC, Nottingham RM, Mohr S, Hunicke-Smith S, Lambowitz AM.

RNA. 2016 Jan;22(1):111-28. doi: 10.1261/rna.054809.115. Epub 2015 Nov 9.


Retrohoming of a Mobile Group II Intron in Human Cells Suggests How Eukaryotes Limit Group II Intron Proliferation.

Truong DM, Hewitt FC, Hanson JH, Cui X, Lambowitz AM.

PLoS Genet. 2015 Aug 4;11(8):e1005422. doi: 10.1371/journal.pgen.1005422. eCollection 2015 Aug.


Efficient and quantitative high-throughput tRNA sequencing.

Zheng G, Qin Y, Clark WC, Dai Q, Yi C, He C, Lambowitz AM, Pan T.

Nat Methods. 2015 Sep;12(9):835-837. doi: 10.1038/nmeth.3478. Epub 2015 Jul 27.


Mobile Bacterial Group II Introns at the Crux of Eukaryotic Evolution.

Lambowitz AM, Belfort M.

Microbiol Spectr. 2015 Feb;3(1):MDNA3-0050-2014. doi: 10.1128/microbiolspec.MDNA3-0050-2014. Review.


Lester Reed: A "complex" man who loved science.

Hackert ML, Appling DR, Lambowitz AM.

Proc Natl Acad Sci U S A. 2015 May 19;112(20):6247. doi: 10.1073/pnas.1505119112. Epub 2015 Apr 21. No abstract available.


Protein synthesis. Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains.

Shen PS, Park J, Qin Y, Li X, Parsawar K, Larson MH, Cox J, Cheng Y, Lambowitz AM, Weissman JS, Brandman O, Frost A.

Science. 2015 Jan 2;347(6217):75-8. doi: 10.1126/science.1259724.


Evolution of RNA-protein interactions: non-specific binding led to RNA splicing activity of fungal mitochondrial tyrosyl-tRNA synthetases.

Lamech LT, Mallam AL, Lambowitz AM.

PLoS Biol. 2014 Dec 23;12(12):e1002028. doi: 10.1371/journal.pbio.1002028. eCollection 2014 Dec.


Molecular insights into RNA and DNA helicase evolution from the determinants of specificity for a DEAD-box RNA helicase.

Mallam AL, Sidote DJ, Lambowitz AM.

Elife. 2014 Dec 12;3:e04630. doi: 10.7554/eLife.04630.


Broad and adaptable RNA structure recognition by the human interferon-induced tetratricopeptide repeat protein IFIT5.

Katibah GE, Qin Y, Sidote DJ, Yao J, Lambowitz AM, Collins K.

Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):12025-30. doi: 10.1073/pnas.1412842111. Epub 2014 Aug 4.


The contribution of cellulosomal scaffoldins to cellulose hydrolysis by Clostridium thermocellum analyzed by using thermotargetrons.

Hong W, Zhang J, Feng Y, Mohr G, Lambowitz AM, Cui GZ, Liu YJ, Cui Q.

Biotechnol Biofuels. 2014 May 29;7:80. doi: 10.1186/1754-6834-7-80. eCollection 2014.


Biotechnological applications of mobile group II introns and their reverse transcriptases: gene targeting, RNA-seq, and non-coding RNA analysis.

Enyeart PJ, Mohr G, Ellington AD, Lambowitz AM.

Mob DNA. 2014 Jan 13;5(1):2. doi: 10.1186/1759-8753-5-2.


Rapid targeted gene disruption in Bacillus anthracis.

Saldanha RJ, Pemberton A, Shiflett P, Perutka J, Whitt JT, Ellington A, Lambowitz AM, Kramer R, Taylor D, Lamkin TJ.

BMC Biotechnol. 2013 Sep 18;13:72. doi: 10.1186/1472-6750-13-72.


Enhanced group II intron retrohoming in magnesium-deficient Escherichia coli via selection of mutations in the ribozyme core.

Truong DM, Sidote DJ, Russell R, Lambowitz AM.

Proc Natl Acad Sci U S A. 2013 Oct 1;110(40):E3800-9. doi: 10.1073/pnas.1315742110. Epub 2013 Sep 16.


Generalized bacterial genome editing using mobile group II introns and Cre-lox.

Enyeart PJ, Chirieleison SM, Dao MN, Perutka J, Quandt EM, Yao J, Whitt JT, Keatinge-Clay AT, Lambowitz AM, Ellington AD.

Mol Syst Biol. 2013;9:685. doi: 10.1038/msb.2013.41.


A targetron system for gene targeting in thermophiles and its application in Clostridium thermocellum.

Mohr G, Hong W, Zhang J, Cui GZ, Yang Y, Cui Q, Liu YJ, Lambowitz AM.

PLoS One. 2013 Jul 9;8(7):e69032. doi: 10.1371/journal.pone.0069032. Print 2013.


Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing.

Mohr S, Ghanem E, Smith W, Sheeter D, Qin Y, King O, Polioudakis D, Iyer VR, Hunicke-Smith S, Swamy S, Kuersten S, Lambowitz AM.

RNA. 2013 Jul;19(7):958-70. doi: 10.1261/rna.039743.113. Epub 2013 May 22.


Genetic and biochemical assays reveal a key role for replication restart proteins in group II intron retrohoming.

Yao J, Truong DM, Lambowitz AM.

PLoS Genet. 2013 Apr;9(4):e1003469. doi: 10.1371/journal.pgen.1003469. Epub 2013 Apr 25.


Toward a molecular understanding of RNA remodeling by DEAD-box proteins.

Russell R, Jarmoskaite I, Lambowitz AM.

RNA Biol. 2013 Jan;10(1):44-55. doi: 10.4161/rna.22210. Epub 2012 Sep 20. Review.


Structural basis for RNA-duplex recognition and unwinding by the DEAD-box helicase Mss116p.

Mallam AL, Del Campo M, Gilman B, Sidote DJ, Lambowitz AM.

Nature. 2012 Oct 4;490(7418):121-5. doi: 10.1038/nature11402. Epub 2012 Sep 2.


The retrohoming of linear group II intron RNAs in Drosophila melanogaster occurs by both DNA ligase 4-dependent and -independent mechanisms.

White TB, Lambowitz AM.

PLoS Genet. 2012;8(2):e1002534. doi: 10.1371/journal.pgen.1002534. Epub 2012 Feb 16.


High-throughput genetic identification of functionally important regions of the yeast DEAD-box protein Mss116p.

Mohr G, Del Campo M, Turner KG, Gilman B, Wolf RZ, Lambowitz AM.

J Mol Biol. 2011 Nov 11;413(5):952-72. doi: 10.1016/j.jmb.2011.09.015. Epub 2011 Sep 16.


Solution structures of DEAD-box RNA chaperones reveal conformational changes and nucleic acid tethering by a basic tail.

Mallam AL, Jarmoskaite I, Tijerina P, Del Campo M, Seifert S, Guo L, Russell R, Lambowitz AM.

Proc Natl Acad Sci U S A. 2011 Jul 26;108(30):12254-9. doi: 10.1073/pnas.1109566108. Epub 2011 Jul 11.


ATP-dependent roles of the DEAD-box protein Mss116p in group II intron splicing in vitro and in vivo.

Potratz JP, Del Campo M, Wolf RZ, Lambowitz AM, Russell R.

J Mol Biol. 2011 Aug 19;411(3):661-79. doi: 10.1016/j.jmb.2011.05.047. Epub 2011 Jun 7.


NMR Structure of the C-terminal domain of a tyrosyl-tRNA synthetase that functions in group I intron splicing.

Paukstelis PJ, Chari N, Lambowitz AM, Hoffman D.

Biochemistry. 2011 May 10;50(18):3816-26. doi: 10.1021/bi200189u. Epub 2011 Apr 12.


Mechanisms used for genomic proliferation by thermophilic group II introns.

Mohr G, Ghanem E, Lambowitz AM.

PLoS Biol. 2010 Jun 8;8(6):e1000391. doi: 10.1371/journal.pbio.1000391.


Group II introns: mobile ribozymes that invade DNA.

Lambowitz AM, Zimmerly S.

Cold Spring Harb Perspect Biol. 2011 Aug 1;3(8):a003616. doi: 10.1101/cshperspect.a003616. Review.


Genetic identification of potential RNA-binding regions in a group II intron-encoded reverse transcriptase.

Gu SQ, Cui X, Mou S, Mohr S, Yao J, Lambowitz AM.

RNA. 2010 Apr;16(4):732-47. doi: 10.1261/rna.2007310. Epub 2010 Feb 23.


Linear group II intron RNAs can retrohome in eukaryotes and may use nonhomologous end-joining for cDNA ligation.

Zhuang F, Mastroianni M, White TB, Lambowitz AM.

Proc Natl Acad Sci U S A. 2009 Oct 27;106(43):18189-94. doi: 10.1073/pnas.0910277106. Epub 2009 Oct 15.


Structure of the Yeast DEAD box protein Mss116p reveals two wedges that crimp RNA.

Del Campo M, Lambowitz AM.

Mol Cell. 2009 Sep 11;35(5):598-609. doi: 10.1016/j.molcel.2009.07.032.


Crystallization and preliminary X-ray diffraction of the DEAD-box protein Mss116p complexed with an RNA oligonucleotide and AMP-PNP.

Del Campo M, Lambowitz AM.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Aug 1;65(Pt 8):832-5. doi: 10.1107/S1744309109027225. Epub 2009 Jul 30.


Identification of proteins associated with the yeast mitochondrial RNA polymerase by tandem affinity purification.

Markov DA, Savkina M, Anikin M, Del Campo M, Ecker K, Lambowitz AM, De Gnore JP, McAllister WT.

Yeast. 2009 Aug;26(8):423-40. doi: 10.1002/yea.1672.


Unwinding by local strand separation is critical for the function of DEAD-box proteins as RNA chaperones.

Del Campo M, Mohr S, Jiang Y, Jia H, Jankowsky E, Lambowitz AM.

J Mol Biol. 2009 Jun 19;389(4):674-93. doi: 10.1016/j.jmb.2009.04.043. Epub 2009 Apr 23.


EcI5, a group IIB intron with high retrohoming frequency: DNA target site recognition and use in gene targeting.

Zhuang F, Karberg M, Perutka J, Lambowitz AM.

RNA. 2009 Mar;15(3):432-49. doi: 10.1261/rna.1378909. Epub 2009 Jan 20.

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