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Todd Lowe - Publications

Affiliations: 
University of California, Santa Cruz, Santa Cruz, CA, United States 
Area:
Microbiology Biology, Molecular Biology, Biogeochemistry
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54 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Manning AC, Bashir MM, Jimenez AR, Upton HE, Collins K, Lowe TM, Tucker JM. Gammaherpesvirus infection triggers the formation of tRNA fragments from premature tRNAs. Biorxiv : the Preprint Server For Biology. PMID 38746336 DOI: 10.1101/2024.05.01.592122  0.308
2024 Manning AC, Bashir MM, Jimenez AR, Upton HE, Collins K, Lowe TM, Tucker JM. Gammaherpesvirus infection alters transfer RNA splicing and triggers tRNA cleavage. Biorxiv : the Preprint Server For Biology. PMID 38405876 DOI: 10.1101/2024.02.16.580780  0.319
2023 Holmes AD, Chan PP, Chen Q, Ivanov P, Drouard L, Polacek N, Kay MA, Lowe TM. A standardized ontology for naming tRNA-derived RNAs based on molecular origin. Nature Methods. PMID 36869120 DOI: 10.1038/s41592-023-01813-2  0.443
2022 Marygold SJ, Chan PP, Lowe TM. Systematic identification of tRNA genes in . Micropublication Biology. 2022. PMID 35789696 DOI: 10.17912/micropub.biology.000560  0.479
2022 Li G, Manning AC, Bagi A, Yang X, Gokulnath P, Spanos M, Howard J, Chan PP, Sweeney T, Kitchen R, Li H, Laurent BD, Aranki SF, Kontaridis MI, Laurent LC, ... ... Lowe TM, et al. Distinct Stress-Dependent Signatures of Cellular and Extracellular tRNA-Derived Small RNAs. Advanced Science (Weinheim, Baden-Wurttemberg, Germany). e2200829. PMID 35373532 DOI: 10.1002/advs.202200829  0.325
2021 Chan PP, Lin BY, Mak AJ, Lowe TM. tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Research. PMID 34417604 DOI: 10.1093/nar/gkab688  0.361
2021 Sweeney BA, Hoksza D, Nawrocki EP, Ribas CE, Madeira F, Cannone JJ, Gutell R, Maddala A, Meade CD, Williams LD, Petrov AS, Chan PP, Lowe TM, Finn RD, Petrov AI. R2DT is a framework for predicting and visualising RNA secondary structure using templates. Nature Communications. 12: 3494. PMID 34108470 DOI: 10.1038/s41467-021-23555-5  0.435
2020 Seal RL, Chen LL, Griffiths-Jones S, Lowe TM, Mathews MB, O'Reilly D, Pierce AJ, Stadler PF, Ulitsky I, Wolin SL, Bruford EA. A guide to naming human non-coding RNA genes. The Embo Journal. e103777. PMID 32090359 DOI: 10.15252/Embj.2019103777  0.375
2019 Thornlow BP, Armstrong J, Holmes AD, Howard JM, Corbett-Detig RB, Lowe TM. Predicting transfer RNA gene activity from sequence and genome context. Genome Research. PMID 31857444 DOI: 10.1101/gr.256164.119  0.455
2019 Lin BY, Chan PP, Lowe TM. tRNAviz: explore and visualize tRNA sequence features. Nucleic Acids Research. PMID 31127306 DOI: 10.1093/nar/gkz438  0.334
2019 Chan PP, Lowe TM. tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences. Methods in Molecular Biology (Clifton, N.J.). 1962: 1-14. PMID 31020551 DOI: 10.1007/978-1-4939-9173-0_1  0.472
2019 Crecy-Lagard Vd, Limbach P, Yu N, Ross R, Boccaletto P, Lowe T, Sharma P, Leidel S, Bujnicki J. Annotation of tRNA modifications genes in model organisms F1000research. 8. DOI: 10.7490/F1000Research.1116578.1  0.354
2018 Thornlow BP, Hough J, Roger JM, Gong H, Lowe TM, Corbett-Detig RB. Transfer RNA genes experience exceptionally elevated mutation rates. Proceedings of the National Academy of Sciences of the United States of America. PMID 30127029 DOI: 10.1073/Pnas.1801240115  0.345
2018 Lui LM, Uzilov AV, Bernick DL, Corredor A, Lowe TM, Dennis PP. Methylation guide RNA evolution in archaea: structure, function and genomic organization of 110 C/D box sRNA families across six Pyrobaculum species. Nucleic Acids Research. PMID 29771354 DOI: 10.1093/Nar/Gky284  0.797
2017 Hrabeta-Robinson E, Marcus E, Cozen AE, Phizicky EM, Lowe TM. High-Throughput Small RNA Sequencing Enhanced by AlkB-Facilitated RNA de-Methylation (ARM-Seq). Methods in Molecular Biology (Clifton, N.J.). 1562: 231-243. PMID 28349464 DOI: 10.1007/978-1-4939-6807-7_15  0.803
2017 Petrov AI, Kay SJE, Kalvari I, Howe KL, Gray KA, Bruford EA, Kersey PJ, Cochrane G, Finn RD, Bateman A, Kozomara A, Griffiths-Jones S, Frankish A, Zwieb CW, ... ... Lowe TM, et al. RNAcentral: a comprehensive database of non-coding RNA sequences. Nucleic Acids Research. 45: D128-D134. PMID 27794554 DOI: 10.1093/Nar/Gkw1008  0.454
2016 Zhang X, Cozen AE, Liu Y, Chen Q, Lowe TM. Small RNA Modifications: Integral to Function and Disease. Trends in Molecular Medicine. PMID 27840066 DOI: 10.1016/J.Molmed.2016.10.009  0.803
2016 Lowe TM, Chan PP. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Research. PMID 27174935 DOI: 10.1093/nar/gkw413  0.444
2016 Chan PP, Lowe TM. GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes. Nucleic Acids Research. 44: D184-9. PMID 26673694 DOI: 10.1093/nar/gkv1309  0.45
2015 Dennis PP, Tripp V, Lui L, Lowe T, Randau L. C/D box sRNA-guided 2'-O-methylation patterns of archaeal rRNA molecules. Bmc Genomics. 16: 632. PMID 26296872 DOI: 10.1186/S12864-015-1839-Z  0.495
2015 Cozen AE, Quartley E, Holmes AD, Hrabeta-Robinson E, Phizicky EM, Lowe TM. ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments. Nature Methods. 12: 879-84. PMID 26237225 DOI: 10.1038/Nmeth.3508  0.813
2015 Petrov AI, Kay SJE, Gibson R, Kulesha E, Staines D, Bruford EA, Wright MW, Burge S, Finn RD, Kersey PJ, Cochrane G, Bateman A, Griffiths-Jones S, Harrow J, ... ... Lowe TM, et al. RNAcentral: an international database of ncRNA sequences. Nucleic Acids Research. 43: D123-9. PMID 25352543 DOI: 10.1093/Nar/Gku991  0.442
2014 Miller HK, Kwuan L, Schwiesow L, Bernick DL, Mettert E, Ramirez HA, Ragle JM, Chan PP, Kiley PJ, Lowe TM, Auerbuch V. IscR is essential for yersinia pseudotuberculosis type III secretion and virulence. Plos Pathogens. 10: e1004194. PMID 24945271 DOI: 10.1371/Journal.Ppat.1004194  0.72
2013 Lui L, Lowe T. Small nucleolar RNAs and RNAguided post-transcriptional modification Essays in Biochemistry. 54: 53-77. PMID 23829527 DOI: 10.1042/Bse0540053  0.596
2013 Chan PP, Cozen AE, Lowe TM. Reclassification of Thermoproteus neutrophilus Stetter and Zillig 1989 as Pyrobaculum neutrophilum comb. nov. based on phylogenetic analysis. International Journal of Systematic and Evolutionary Microbiology. 63: 751-4. PMID 22561593 DOI: 10.1099/Ijs.0.043091-0  0.723
2012 Bernick DL, Karplus K, Lui LM, Coker JK, Murphy JN, Chan PP, Cozen AE, Lowe TM. Complete genome sequence of Pyrobaculum oguniense. Standards in Genomic Sciences. 6: 336-45. PMID 23407329 DOI: 10.4056/Sigs.2645906  0.79
2012 Chan PP, Brown JW, Lowe TM. Modeling the Thermoproteaceae RNase P RNA. Rna Biology. 9: 1155-60. PMID 23018780 DOI: 10.4161/rna.21502  0.499
2012 Bernick DL, Cox CL, Dennis PP, Lowe TM. Comparative genomic and transcriptional analyses of CRISPR systems across the genus Pyrobaculum. Frontiers in Microbiology. 3: 251. PMID 22811677 DOI: 10.3389/Fmicb.2012.00251  0.79
2012 Bernick DL, Dennis PP, Lui LM, Lowe TM. Diversity of Antisense and Other Non-Coding RNAs in Archaea Revealed by Comparative Small RNA Sequencing in Four Pyrobaculum Species. Frontiers in Microbiology. 3: 231. PMID 22783241 DOI: 10.3389/Fmicb.2012.00231  0.819
2012 Zargar K, Conrad A, Bernick DL, Lowe TM, Stolc V, Hoeft S, Oremland RS, Stolz J, Saltikov CW. ArxA, a new clade of arsenite oxidase within the DMSO reductase family of molybdenum oxidoreductases. Environmental Microbiology. 14: 1635-45. PMID 22404962 DOI: 10.1111/J.1462-2920.2012.02722.X  0.735
2012 Bernick DL, Dennis PP, Höchsmann M, Lowe TM. Discovery of Pyrobaculum small RNA families with atypical pseudouridine guide RNA features. Rna (New York, N.Y.). 18: 402-11. PMID 22282340 DOI: 10.1261/Rna.031385.111  0.82
2012 Chan PP, Holmes AD, Smith AM, Tran D, Lowe TM. The UCSC Archaeal Genome Browser: 2012 update. Nucleic Acids Research. 40: D646-52. PMID 22080555 DOI: 10.1093/nar/gkr990  0.396
2011 Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, ... ... Lowe TM, et al. RNAcentral: A vision for an international database of RNA sequences. Rna (New York, N.Y.). 17: 1941-6. PMID 21940779 DOI: 10.1261/Rna.2750811  0.475
2011 Esser D, Kouril T, Zaparty M, Sierocinski P, Chan PP, Lowe T, Van der Oost J, Albers SV, Schomburg D, Makarova KS, Siebers B. Functional curation of the Sulfolobus solfataricus P2 and S. acidocaldarius 98-3 complete genome sequences. Extremophiles : Life Under Extreme Conditions. 15: 711-2. PMID 21912952 DOI: 10.1007/S00792-011-0392-1  0.393
2011 Chan PP, Cozen AE, Lowe TM. Discovery of permuted and recently split transfer RNAs in Archaea. Genome Biology. 12: R38. PMID 21489296 DOI: 10.1186/Gb-2011-12-4-R38  0.806
2010 Lai LB, Chan PP, Cozen AE, Bernick DL, Brown JW, Gopalan V, Lowe TM. Discovery of a minimal form of RNase P in Pyrobaculum. Proceedings of the National Academy of Sciences of the United States of America. 107: 22493-8. PMID 21135215 DOI: 10.1073/Pnas.1013969107  0.788
2010 Underwood JG, Uzilov AV, Katzman S, Onodera CS, Mainzer JE, Mathews DH, Lowe TM, Salama SR, Haussler D. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nature Methods. 7: 995-1001. PMID 21057495 DOI: 10.1038/Nmeth.1529  0.769
2010 Walker CB, de la Torre JR, Klotz MG, Urakawa H, Pinel N, Arp DJ, Brochier-Armanet C, Chain PS, Chan PP, Gollabgir A, Hemp J, Hügler M, Karr EA, Könneke M, Shin M, ... ... Lowe T, et al. Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proceedings of the National Academy of Sciences of the United States of America. 107: 8818-23. PMID 20421470 DOI: 10.1073/Pnas.0913533107  0.373
2009 Cozen AE, Weirauch MT, Pollard KS, Bernick DL, Stuart JM, Lowe TM. Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum Journal of Bacteriology. 191: 782-794. PMID 19047344 DOI: 10.1128/Jb.00965-08  0.737
2009 Chan PP, Lowe TM. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Research. 37: D93-7. PMID 18984615 DOI: 10.1093/nar/gkn787  0.492
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Lowe TM, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  0.315
2006 Schattner P, Barberan-Soler S, Lowe TM. A computational screen for mammalian pseudouridylation guide H/ACA RNAs. Rna (New York, N.Y.). 12: 15-25. PMID 16373490 DOI: 10.1261/Rna.2210406  0.475
2005 Schattner P, Brooks AN, Lowe TM. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Research. 33: W686-9. PMID 15980563 DOI: 10.1093/Nar/Gki366  0.469
2004 Schattner P, Decatur WA, Davis CA, Ares M, Fournier MJ, Lowe TM. Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome. Nucleic Acids Research. 32: 4281-96. PMID 15306656 DOI: 10.1093/Nar/Gkh768  0.522
2003 Wood V, Gwilliam R, Rajandream M, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, Baker S, Basham D, Bowman S, Brooks K, Brown D, Brown S, ... ... Lowe T, et al. Erratum: corrigendum: The genome sequence of Schizosaccharomyces pombe Nature. 421: 94-94. DOI: 10.1038/Nature01203  0.383
2002 Wood V, Gwilliam R, Rajandream MA, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, Baker S, Basham D, Bowman S, Brooks K, Brown D, Brown S, ... ... Lowe T, et al. The genome sequence of Schizosaccharomyces pombe. Nature. 415: 871-80. PMID 11859360 DOI: 10.1038/Nature724  0.481
2002 Speckmann WA, Li ZH, Lowe TM, Eddy SR, Terns RM, Terns MP. Archaeal guide RNAs function in rRNA modification in the eukaryotic nucleus. Current Biology : Cb. 12: 199-203. PMID 11839271 DOI: 10.1016/S0960-9822(02)00655-3  0.492
2001 Dennis PP, Omer A, Lowe T. A guided tour: small RNA function in Archaea. Molecular Microbiology. 40: 509-19. PMID 11359559 DOI: 10.1046/J.1365-2958.2001.02381.X  0.566
2000 Ng WV, Kennedy SP, Mahairas GG, Berquist B, Pan M, Shukla HD, Lasky SR, Baliga NS, Thorsson V, Sbrogna J, Swartzell S, Weir D, Hall J, Dahl TA, Welti R, ... ... Lowe TM, et al. Genome sequence of Halobacterium species NRC-1. Proceedings of the National Academy of Sciences of the United States of America. 97: 12176-81. PMID 11016950 DOI: 10.1073/Pnas.190337797  0.339
2000 Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP. Homologs of small nucleolar RNAs in Archaea. Science (New York, N.Y.). 288: 517-22. PMID 10775111 DOI: 10.1126/Science.288.5465.517  0.582
2000 Dunbar DA, Wormsley S, Lowe TM, Baserga SJ. Fibrillarin-associated box C/D small nucleolar RNAs in Trypanosoma brucei. Sequence conservation and implications for 2'-O-ribose methylation of rRNA. The Journal of Biological Chemistry. 275: 14767-76. PMID 10747997 DOI: 10.1074/jbc.M001180200  0.341
1999 Lowe TM, Eddy SR. A computational screen for methylation guide snoRNAs in yeast Science. 283: 1168-1171. PMID 10024243 DOI: 10.1126/science.283.5405.1168  0.466
1996 Lowe TM, Eddy SR. TRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence Nucleic Acids Research. 25: 955-964. DOI: 10.1093/nar/25.5.0955  0.459
1990 Lowe T, Sharefkin J, Yang SQ, Dieffenbach CW. A computer program for selection of oligonucleotide primers for polymerase chain reactions Nucleic Acids Research. 18: 1757-1761. PMID 1692404 DOI: 10.1093/Nar/18.7.1757  0.358
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