Todd Lowe - Publications

Affiliations: 
University of California, Santa Cruz, Santa Cruz, CA, United States 
Area:
Microbiology Biology, Molecular Biology, Biogeochemistry

50 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
2020 Fernandes JD, Hinrichs AS, Clawson H, Gonzalez JN, Lee BT, Nassar LR, Raney BJ, Rosenbloom KR, Nerli S, Rao AA, Schmelter D, Fyfe A, Maulding N, Zweig AS, Lowe TM, et al. The UCSC SARS-CoV-2 Genome Browser. Nature Genetics. PMID 32908258 DOI: 10.1038/s41588-020-0700-8  0.32
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  0.32
2019 Lin BY, Chan PP, Lowe TM. tRNAviz: explore and visualize tRNA sequence features. Nucleic Acids Research. PMID 31127306 DOI: 10.1093/nar/gkz438  0.48
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  0.48
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  0.52
2017 Qin W, Amin SA, Lundeen RA, Heal KR, Martens-Habbena W, Turkarslan S, Urakawa H, Costa KC, Hendrickson EL, Wang T, Beck DA, Tiquia-Arashiro SM, Taub F, Holmes AD, Vajrala N, ... ... Lowe TM, et al. Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations. The Isme Journal. PMID 29053148 DOI: 10.1038/ismej.2017.186  0.32
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.52
2015 Udy DB, Voorhies M, Chan PP, Lowe TM, Dumont S. Draft De Novo Transcriptome of the Rat Kangaroo Potorous tridactylus as a Tool for Cell Biology. Plos One. 10: e0134738. PMID 26252667 DOI: 10.1371/journal.pone.0134738  0.52
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  0.52
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  0.48
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. DOI: 10.1186/s12864-015-1839-z  0.52
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, Chan PP, ... Lowe TM, et al. RNAcentral: An international database of ncRNA sequences Nucleic Acids Research. 43: D123-D129. DOI: 10.1093/nar/gku991  0.48
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  0.52
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  0.52
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  0.52
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  0.52
2012 Robb FT, Lowe TM, Kelman Z. The modern "3G" age of archaeal molecular biology. Frontiers in Microbiology. 3: 430. PMID 23267357 DOI: 10.3389/fmicb.2012.00430  0.52
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  0.52
2012 Susanti D, Johnson EF, Rodriguez JR, Anderson I, Perevalova AA, Kyrpides N, Lucas S, Han J, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Mavrommatis K, Peters L, Land ML, ... ... Lowe TM, et al. Complete genome sequence of Desulfurococcus fermentans, a hyperthermophilic cellulolytic crenarchaeon isolated from a freshwater hot spring in Kamchatka, Russia. Journal of Bacteriology. 194: 5703-4. PMID 23012283 DOI: 10.1128/JB.01314-12  0.52
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  0.52
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  0.52
2012 Ochs SM, Thumann S, Richau R, Weirauch MT, Lowe TM, Thomm M, Hausner W. Activation of archaeal transcription mediated by recruitment of transcription factor B. The Journal of Biological Chemistry. 287: 18863-71. PMID 22496454 DOI: 10.1074/jbc.M112.365742  0.52
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  0.52
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  0.52
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  0.48
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  0.52
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  0.48
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  0.52
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  0.52
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  0.52
2010 Hartman AL, Norais C, Badger JH, Delmas S, Haldenby S, Madupu R, Robinson J, Khouri H, Ren Q, Lowe TM, Maupin-Furlow J, Pohlschroder M, Daniels C, Pfeiffer F, Allers T, et al. The complete genome sequence of Haloferax volcanii DS2, a model archaeon. Plos One. 5: e9605. PMID 20333302 DOI: 10.1371/journal.pone.0009605  0.52
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  0.52
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  0.48
2009 Baltrus DA, Amieva MR, Covacci A, Lowe TM, Merrell DS, Ottemann KM, Stein M, Salama NR, Guillemin K. The complete genome sequence of Helicobacter pylori strain G27. Journal of Bacteriology. 191: 447-8. PMID 18952803 DOI: 10.1128/JB.01416-08  0.52
2007 Williams E, Lowe TM, Savas J, DiRuggiero J. Microarray analysis of the hyperthermophilic archaeon Pyrococcus furiosus exposed to gamma irradiation. Extremophiles : Life Under Extreme Conditions. 11: 19-29. PMID 16896524 DOI: 10.1007/s00792-006-0046-x  0.52
2006 Schneider KL, Pollard KS, Baertsch R, Pohl A, Lowe TM. The UCSC Archaeal Genome Browser. Nucleic Acids Research.. 34: D407-410. PMID 16381898  0.52
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  0.52
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  0.52
2003 Brown JW, Echeverria M, Qu LH, Lowe TM, Bachellerie JP, Hüttenhofer A, Kastenmayer JP, Green PJ, Shaw P, Marshall DF. Plant snoRNA database. Nucleic Acids Research. 31: 432-5. PMID 12520043 DOI: 10.1093/nar/gkg009  0.4
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  0.52
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  0.52
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  0.52
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  0.52
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  0.52
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  0.52
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