Recent Publications

Chan P.P., Brown J.W. and Lowe T.M. (2012) Modeling the Thermoproteaceae RNase P RNA. RNA Biol. (In Press)

Bernick D.L., Karplus K., Lui L.M., Coker J.K.C., Murphy J.N., Chan P.P., Cozen A.E. and Lowe T.M. (2012) Complete genome sequence of Pyrobaculum oguniense. Stand. Genomic Sci. 6:3.

Bernick D.L., Cox C.L., Dennis P.P. and Lowe T.M. (2012) Comparative genomic and transcriptional analyses of CRISPR systems across the genus Pyrobaculum. Front Microbiol. 3:251.

Bernick D.L., Dennis P.P., Lui L.M. and Lowe T.M. (2012) Diversity of antisense and other non-coding RNAs in Archaea revealed by comparative small RNA sequencing in four Pyrobaculum species. Front Microbiol. 3:231.

Chan P.P., Cozen A.E. and Lowe T.M. (2012) Reclassification of Thermoproteus neutrophilus Stetter and Zillig 1989 as Pyrobaculum neutrophilum comb. nov. based on phylogenetic analysis. Int J Syst Evol Microbiol. Epub. May 4, 2012.

Bernick D.L., Dennis P.P., Höchsmann M. and Lowe T.M. (2012) Discovery of Pyrobaculum small RNA families with atypical pseudouridine guide RNA features. RNA 18(3):402-11.

Ochs S.M., Thumann S., Richau R., Weirauch M.T., Lowe T.M., Thomm M. and Hausner W. (2012) Activation of archaeal transcription mediated by recruitment of transcription factor B. J Biol Chem. 287(22):18863-71.

Chan P.P., Holmes A.D., Smith A.M., Tran D. and Lowe T.M. (2012) The UCSC Archaeal Genome Browser: 2012 update. Nucleic Acids Res. 40(1):D646-52.

Bateman A., Agrawal S., Birney E., Bruford E.A., Bujnicki J.M., Cochrane G., Cole J.R., Dinger M.E., Enright A.J., Gardner P.P., Gautheret D., Griffiths-Jones S., Harrow J., Herrero J., Holmes I.H., Huang H.D., Kelly K.A., Kersey P., Kozomara A., Lowe T.M., Marz M., Moxon S., Pruitt K.D., Samuelsson T., Stadler P.F., Vilella A.J., Vogel J.H., Williams K.P., Wright M.W. and Zwieb C. (2011) RNAcentral: A vision for an international database of RNA sequences. RNA 17(11):1941-6.

Esser D., Kouril T., Zaparty M., Sierocinski P., Chan P.P., Lowe T.M., Van der Oost J., Albers S., Schomburg D., Makarova K.S. and Siebers B. (2011) Functional curation of the Sulfolobus solfataricus P2 and S. acidocaldarius 98-3 complete genome sequences. Extremophiles 15(6):711-2.

Chan P.P., Cozen A.E. and Lowe T.M. (2011) Discovery of permuted and recently split transfer RNAs in Archaea. Genome Biol. 12(4):R38.

Lai L.B., Chan P.P., Cozen A.E., Bernick D.L., Brown J.W., Gopalan V. and Lowe T.M. (2010) Discovery of a minimal form of RNase P in Pyrobaculum. Proc Natl Acad Sci U S A. 107(52):22493-8.

Underwood J.G., Uzilov A.V., Katzman S., Onodera C.S., Mainzer J.E., Mathews D.H., Lowe T.M., Salama S.R. and Haussler D. (2010) FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat Methods. 7(12):995-1001.

Walker C.B., de la Torre J.R., Klotz M.G., Urakawa H., Pinel N., Arp D.J., Brochier-Armanet C., Chain P.S., Chan P.P., Gollabgir A., Hemp J., Hügler M., Karr E.A., Könneke M., Shin M., Lawton T.J., Lowe T.M., Martens-Habbena W., Sayavedra-Soto L.A., Lang D., Sievert S.M., Rosenzweig A.C., Manning G. and Stahl D.A. (2010) Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proc Natl Acad Sci U S A. 107(19):8818-23.

Hartman A.L., Norais C., Badger J.H., Delmas S., Haldenby S., Madupu R., Robinson J., Khouri H., Ren Q., Lowe T.M., Maupin-Furlow J., Pohlschroder M., Daniels C., Pfeiffer F., Allers T. and Eisen J.A. (2010) The complete genome sequence of Haloferax volcanii DS2, a model archaeon. PLoS One 5(3):e9605.

Cozen A.E., Weirauch M.T., Pollard K.S., Bernick D.L., Stuart J.M. and Lowe T.M. (2009) Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. J Bacteriol. 191(3):782-94.

Chan P.P. and Lowe T.M. (2009) GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 37(Database issue):D93-7.

Baltrus D.A., Amieva M.R., Covacci A., Lowe T.M., Merrell D.S., Ottemann K.M., Stein M., Salama N.R. and Guillemin K. (2009) The complete genome sequence of Helicobacter pylori strain G27. J Bacteriol. 191(1):447-8.

ENCODE Project Consortium (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature447(7146):799-816.

Williams, E., Lowe, T.M., Savas, J. and Diruggiero, J. (2006) Microarray analysis of the hyperthermophilic archaeon Pyrococcus furiosus exposed to gamma irradiation. Extremophiles 11(1):19-29.

Schneider, K.L., Pollard, K.S., Baertsch, R., Pohl, A. and Lowe, T.M. (2006) The UCSC Archaeal Genome Browser. Nucleic Acids Res. 34(Database issue):D407-410.

Schattner, P., Barberan-Soler, S. and Lowe, T.M. (2006) A computational screen for mammalian pseudouridylation guide H/ACA RNAs. RNA 12(1):15-25.

Schattner, P., Brooks, A.N. and Lowe, T.M. (2005) The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 33(Web Server issue):W686-9.

Schattner P., Decatur W.A., Davis C.A., Ares M. Jr, Fournier M.J. and Lowe T.M. (2004) Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome. Nucleic Acids Res. 32(14):4281-96.

Brown J.W., Echeverria M., Qu L.H., Lowe T.M., Bachellerie J.P., Hüttenhofer A., Kastenmayer J.P., Green P.J., Shaw P. and Marshall D.F. (2003) Plant snoRNA database. Nucleic Acids Res. 31(1):432-5.