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Research Interests
Study of Non-coding RNAs and Extremophile Biology
The research in our lab uses a mixture of computational and
experimental genomics to study two main areas:
- Identification and characterization of non-coding RNA
(ncRNA) genes
On the computational side of the lab, we develop and
refine
methods to
detect RNA genes in genomic sequence using probabilistic models and
comparative genomics. We have created RNA genefinders for known
classes of RNAs (transfer RNAs, C/D box & H/ACA guide snoRNAs), and
seek to identify and model new classes of RNAs that, among other
traits, are highly structured or contain stretches of complementarity
to other DNA/RNA targets (like microRNAs).
On the experimental side, we do ncRNA discovery via
next-generation RNA sequencing (454/SOLiD), and analysis of
transcriptional
profiles using
hybridization to in-house generated DNA microarrays, augmented by
traditional molecular biology characterization. We believe tight
integration of theoretical and experimental approaches is the
quickest, most efficient path to discovery.
- Understanding the unique biology of Archaeal
"extremophiles"
--
microbes that live at the edge of the limits of life (high/low
temperature, pH, salt, pressure)
We have created full genome DNA microarrays for two of
the
most
extreme hyperthermophilic Archaea sequenced to date, Pyrococcus
furiosus and Pyrobaculum aerophilum, which natively grow at
boiling temperatures. The organisms are particularly
mysterious because no genetic systems exist to study individual gene
function -- all analyses to date have been biochemical or by
computational methods. Graduate student Aaron Cozen's thesis work
studying four different forms of respiration Pyrobaculum
aerophilum was recently published in the Journal of Bacteriology.
On the computational side, we analyze our extremophile
array
data
to predict functional roles for genes of unknown function, identify
the major players in various cellular stresses, and develop robust
functional clusters. By comparing expression profiles from multiple
different species that live in similar extreme environments, we hope
to identify key genes important for survival under particular extreme
conditions. We also use array data with sequence analysis to look for
new RNA genes, predict more accurate operon structure, and define
Archaeal-specific transcriptional control elements.
The lab is currently taking both MCD biology and School of
Engineering graduate students who have a keen interest in one or more
of these areas. Postdocs with strong backgrounds in RNA biochemistry
(esp. small RNAs) or microbiology/prokaryotic physiology (esp. in
Archaea) are encouraged to apply to the lab (please send an email and
CV to the address below). If you are not currently a graduate student
at UCSC, please see information here for
CS/Bioinformatics students or here if you are a
potential biology graduate student. I only take enrolled grad
students after a rotation in the lab (please do not email requests for
direct admittance to either program through my lab).
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