lowelab.ucsc.edu

The Lowe Lab

Todd M. Lowe. Microbiology and Environmental Toxicology. Molecular, Cell and Developmental Biology. The Center for Molecular Biology of RNA. Study of Non-coding RNAs and Extremophile Biology. The research in our lab uses a mixture of computational and experimental genomics to Identify and characterize of non-coding RNA (ncRNA) genes, and study the unique biology of archaeal "extremophiles" - microbes that live at the edge of the limits of life (high/low temperature, pH, salt, pressure). The lab is curren...

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The Lowe Lab | lowelab.ucsc.edu Reviews

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Todd M. Lowe. Microbiology and Environmental Toxicology. Molecular, Cell and Developmental Biology. The Center for Molecular Biology of RNA. Study of Non-coding RNAs and Extremophile Biology. The research in our lab uses a mixture of computational and experimental genomics to Identify and characterize of non-coding RNA (ncRNA) genes, and study the unique biology of archaeal extremophiles - microbes that live at the edge of the limits of life (high/low temperature, pH, salt, pressure). The lab is curren...

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1 research

2 people

3 publications

4 tools and databases

5 teaching

6 professor

7 biomolecular engineering

8 affiliated with

9 pyrococcus furiosus

10 pyrobaculum aerophilum

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The Lowe Lab | lowelab.ucsc.edu Reviews

https://lowelab.ucsc.edu

Todd M. Lowe. Microbiology and Environmental Toxicology. Molecular, Cell and Developmental Biology. The Center for Molecular Biology of RNA. Study of Non-coding RNAs and Extremophile Biology. The research in our lab uses a mixture of computational and experimental genomics to Identify and characterize of non-coding RNA (ncRNA) genes, and study the unique biology of archaeal "extremophiles" - microbes that live at the edge of the limits of life (high/low temperature, pH, salt, pressure). The lab is curren...

INTERNAL PAGES

lowelab.ucsc.edu

1

The Lowe Lab - Teaching

http://lowelab.ucsc.edu/teaching.html

BME 237: Applied RNA Bioinformatics ( Website. BME 110: Computational Biology Tools ( Spring 2011. BME 110: Computational Biology Tools ( Spring 2010. BME 110: Computational Biology Tools ( Spring 2009. BME 200: Research and Teaching in Bioinformatics ( Fall 2008. BME 210: Application and Analysis of Microarrays ( Fall 2008. BME 110: Computational Biology Tools ( Spring 2008. BME 280B: Seminar on Bioinformatics ( Winter 2008. BME 210: Application and Analysis of Microarrays ( Spring 2007.

2

The Lowe Lab - Publications

http://lowelab.ucsc.edu/publications.html

Chan P.P., Brown J.W. and Lowe T.M. (2012) Modeling the Thermoproteaceae RNase P RNA. 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. 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. Chan P.P., Cozen A.E. and Lowe T.M. (2012) Reclassification of. Stetter and Zillig 1989 as. Comb nov. based on phylogenetic analysis. Lai LB.,...

3

The Lowe Lab - People

http://lowelab.ucsc.edu/people.html

Lab Manager, Associate Research Specialist). Thomas Atanasov (Research Assistant). Sergio Barberan (currently - Scientist, SomaGenics). Currently - Assistant Adjunct Professor, UCSC). Lauren Lui (currently - Postdoc, Arkin Lab, University of California Berkeley). Andy Pohl (currently - Postdoc, Morgridge Institute for Research). Currently - Senior Investigator and Professor, Gladstone Institutes). Kevin Schneider (currently - Graduate Student, University of Hawaii).

4

The Lowe Lab - Tools and Databases

http://lowelab.ucsc.edu/databases.html

UCSC Archaeal Genome Browser. TRNA alignments in GtRNAdb. TRNAscan-SE for tRNA predictions ( http:/ lowelab.ucsc.edu/tRNAscan-SE/. Snoscan for C/D box snoRNA predictions ( http:/ lowelab.ucsc.edu/snoscan/. SnoGPS for H/ACA snoRNA predictions ( http:/ lowelab.ucsc.edu/snoGPS/. UCSC Archaeal Genome Browser ( http:/ archaea.ucsc.edu. UCSC Microbial Genome Browser ( http:/ microbes.ucsc.edu. Genomic tRNA Database ( http:/ gtrnadb.ucsc.edu.

5

Genomic tRNA Database

http://lowelab.ucsc.edu/GtRNAdb

This genomic tRNA database contains tRNA gene predictions made by the program tRNAscan-SE ( Lowe and Eddy, Nucl Acids Res. On complete or nearly complete genomes. Unless otherwise noted, all annotation is automated, and has not been inspected for agreement with published literature. Inevitably with automated sequence analysis, we find exceptions to general identification rules, isoacceptor type predictions ( esp. Pristionchus pacificus (WUGSC 5.0 Feb 2007). Brachypodium distachyon (JGI v1.0 8X). Caenorha...

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archaea.ucsc.edu

About

http://archaea.ucsc.edu/about-browser

The UCSC Archaeal Genome Browsers were developed by members of the Lowe Lab. With significant support from the UCSC Genome Browser group. The Archaeal Browsers are run by a slightly modified version of the UCSC Genome Browser. Current support for this project is generously provided by the National Science Foundation (Award #0641061). The Lowe Lab, Biomolecular Engineering, University of California Santa Cruz.

gtrnadb2009.ucsc.edu

Genomic tRNA Database: BLAST Server

http://gtrnadb2009.ucsc.edu/blast.html

BLAST Similarity Search of Genomic tRNA Database. Blastn: nucleotide query vs. nucleotide db. Formatted (FASTA, GenBank, EMBL, GCG, IG). OR Load query from file:. The Genomic tRNA Database is curated by Todd Lowe. And Patricia Chan. Please email lowe@soe.ucsc.edu. With any questions and comments. To submit corrections, please use our Bug and Request Tracking System.

gtrnadb2009.ucsc.edu

Genomic tRNA Database: Brachypodium distachyon (JGI v1.0 8X)

http://gtrnadb2009.ucsc.edu/Bdist

TRNAscan-SE Analysis of Brachypodium distachyon (JGI v1.0 8X). TRNAs Decoding Standard 20 AA. Possible suppressor tRNAs (CTA,TTA). Four Box tRNA Sets. TRNA Count by Anticodon. Six Box tRNA Sets. TRNA Count by Anticodon. Two Box tRNA Sets. TRNA Count by Anticodon. Two Box and Other tRNA Sets. TRNA Count by Anticodon. The Genomic tRNA Database is curated by Todd Lowe. And Patricia Chan. Please email lowe@soe.ucsc.edu.

gtrnadb2009.ucsc.edu

Genomic tRNA Database: Legend & Search Methods

http://gtrnadb2009.ucsc.edu/legend.html

TRNAscan-SE Output Legend and Search Methods. Each new tRNA in a sequence is consecutively numbered in the "tRNA #" column. "tRNA Bounds" specify the starting (5') and ending (3') nucleotide bounds for the tRNA. tRNAs found on the reverse (lower) strand are indicated by having the Begin (5') bound greater than the End (3') bound (see tRNAs #4 and #5 in output above). TRNA with Anticodon CAT. The current version of tRNAscan-SE does not include the analysis of identifying between initiator tRNA-Met, elonga...

blog.neuinfo.org

NIF Blog » Curation

http://blog.neuinfo.org/index.php/category/essays/curation

Archive for the ‘Curation’ Category. Laquo; Previous Entries. Eating my own Dog Food! Posted on July 4th, 2015 in Anita Bandrowski. While not all of you have been fortunate enough to attend the first Beyond the PDF meeting, I will say this; it was eye opening for this scientist. To me, the most memorable statement from the meeting was when Geoffrey Bilder argued from the back of the room that we should all Eat Our Own Dog Food. Easier said than done, Geoffrey! Why did I feel so strongly that I should not...

gtrnadb2009.ucsc.edu

Genomic tRNA Database: Physcomitrella patens (Version 1.1)

http://gtrnadb2009.ucsc.edu/Ppate

TRNAscan-SE Analysis of Physcomitrella patens (Version 1.1). TRNAs Decoding Standard 20 AA. Possible suppressor tRNAs (CTA,TTA). Four Box tRNA Sets. TRNA Count by Anticodon. Six Box tRNA Sets. TRNA Count by Anticodon. Two Box tRNA Sets. TRNA Count by Anticodon. Two Box and Other tRNA Sets. TRNA Count by Anticodon. The Genomic tRNA Database is curated by Todd Lowe. And Patricia Chan. Please email lowe@soe.ucsc.edu.

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Todd M. Lowe. Microbiology and Environmental Toxicology. Molecular, Cell and Developmental Biology. The Center for Molecular Biology of RNA. Study of Non-coding RNAs and Extremophile Biology. The research in our lab uses a mixture of computational and experimental genomics to Identify and characterize of non-coding RNA (ncRNA) genes, and study the unique biology of archaeal "extremophiles" - microbes that live at the edge of the limits of life (high/low temperature, pH, salt, pressure). The lab is curren...

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