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GENE YEO
Curriculum Vitae (in
pdf) (in html) Salk Institute-CNL 10010 North Torrey Pines Road
La Jolla, CA
92037 Work Phone: |
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You shall no
longer take things at second or third hand, nor look through the eyes of the
dead, nor feed on the spectres in books, You shall not
look through my eyes either, nor take things from me, You shall
listen to all sides and filter them from your self...Walt Whitman |
What's in the works
October 1st 2008. I've recently started my new job as an assistant professor at UCSD's department of cellular and molecular medicine, and am faculty in the UCSD Stem Cell Program, Biomedical Sciences and Bioinformatics Graduate Programs . 2nd May 2008. A collaboration on analyses of piRNAs in planarian regeneration with Brenton Graveley has been published at RNA . 9th November 2007. A collaboration on analyses of small RNAs from Dicer knockout mouse ES cells with Mauro Calabrese and Amy Seila at Phillip Sharp's lab at MIT has recently been published at PNAS . 19th October 2007. I gave a talk at the 2nd Annual Stem Cell on the Mesa conference, which was a really fun one day conference held at the Salk. The program is listed here . October 2007. I'm very honored to play a small part in a paper with Brent Graveley, Marco Blanchette, Joanne Yeakley, Yiannis Savva and Don Rio identifying a Regulator of Dscam Mutually Exclusive Splicing Fidelity . September 2007. We recently published a method we call REAP (Regression-based Exon Array Protocol) for Affymetrix Exon Array analysis and applied it to identifying alternative splicing changes during neural progenitor specification during human embryonic stem cell differentiation. We are currently performing RNAi knockdowns of particular splicing factors in ES cells. I've deposited the CEL files here August 2007. Together with Melissa Moore at Brandeis (now at U Mass Medical), we published a recent study showing that a splicing associated factor can modulate synaptic strength and neuronal expression, and we've identified ~100 other candidates genes with conserved introns in the 3'UTR. June 2007. We published a set of intronic splicing regulatory elements identified in the mammalian genomes. We are currently performing experiments to identify their RNA binding partners. I've deposited the Intronic Splicing Regulatory Elements here I'm a Junior Fellow at the Crick-Jacobs Center
for Computational and Theoretical Biology at the Salk Institute and my fellowship mentors are Rusty Gage and Sean Eddy.
Among other goals, one of my objectives here is to uncover the impact of alternative splicing on adult neuronal stem cell differentiation. I'm also involved with exciting collaborations with other groups in the United States and in Singapore. In particular, I am interested in pursuing more cross-continental joint projects to train the next generation of young researchers in Singapore. See article about alternative splicing in the Sept 05 HHMI bulletin.
Download pdf from the HHMI website . |
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RESEARCH INTERESTS My primary research interest is to understand the molecular network-level changes during the specification of neural/neuronal stem cell fate from human/mouse ES and neural stem cells. Specifically, I am interested in (1) identifying alternative splicing (AS) events that are crucial for fate specification, and the RNA binding proteins (splicing factors) that regulate these AS events; and (2) analyzing the small RNA repertoire that change during fate specification. My secondary research interest is in molecular sequence evolution using multiple genomes, which I use as a basis for the systematic computational discovery of RNA regulatory elements important in post-transcriptional processing, such as elements important for alternative splicing and RNA stability. I pursue my objectives with multidisciplinary techniques ranging from developing my own computational tools (machine learning, statistical sequence analysis, graphical modeling), using molecular and cell biological approaches, and coupled with high-throughput approaches (high-density Exon Arrays, 454 or Solexa deep sequencing). PHD DISSERTATION Download pdfMy thesis work focused on developing a
hybrid of computational and experimental methods to identify and model cis-regulatory
sequence elements that regulate both constitutive and alternative splicing in
eukaryotic genomes, integrating these models to predict constitutive and
alternative exons conserved in mammalian genomes in silico, followed by in
vivo experimental validation. |
QUICK LINKS
Summer triathlons Linear Methods in
Matlab Pointers and Arrays in
C Web of Science
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COMPUTATIONAL BIOLOGY/
BIOINFORMATICS Perldoc for BioPerl; Bioperl
Open Source DNA/RNA sequence
analysis Tools SNP
Consortium (CSHL) Virtual
Library of Biochemistry and Cell Biology |
Bold represents first authorship. Underline represents papers where I am co/corresponding author.
The PIWI proteins SMEDWI-2 and SMEDWI-3 are required for stem cell function and piRNA expression in planarians. Palakodeti D., Smielewska M., Lu Y, Yeo, G.W. , Graveley B.R. RNA 2008 RNA sequence analysis defines Dicer's role in mouse embryonic stem cells. Calabrese J.M., Seila, A.C., Yeo, G.W., Sharp, P.A. PNAS
2007 Alternative Splicing Events Identified in Human Embryonic Stem Cells and Neural Progenitors Yeo, G., Xu, X, Liang, T.Y., Muotri, A.R., Carson, C.T., Coufal, N.G., Gage, F.H. PLoS Computational Biology
2007 The EJC factor eIFAIII modulates synaptic strength and neuronal protein expression Giorgi. C, Yeo, G., Stone, M.E., Katz, D.B., Burge. C., Turrigiano, C., Moore, M.J. Cell
2007 Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements in mammalian genomes. Yeo, G, Van Nostrand, E, Liang, Y.T. PLoS Genetics 2007 Inference of splicing regulatory activities by sequence neighborhood analysis. Stadler M.B., Shomron N, Yeo G.W., Schneider, A, Xiao, X, Burge C.B. PLoS Genetics
2006 Noncoding RNAs in the Mammalian Central Nervous System Xinwei Cao, Gene Yeo, Alysson Muotri, Tomoko Kuwabara, Fred H. Gage Annual Review of Neuroscience
2006 Minireview: Splicing regulators: targets and drugs Yeo, G Genome Biology
2005 A Combinatorial Code for Splicing Silencing: UAGG and GGGG Motifs. Han, K.H., Yeo, G, An, P., Burge, C.B. and Grabowski, P. PLOS Biology
2005 Identification and analysis of alternative splicing events conserved in human and mouse. Yeo, G, Van Nostrand, E, Holste, D, Poggio, T
and Burge, C.B. PNAS
2005. Systematic identification and analysis of exonic splicing
silencers. Wang, Z, Rolish, M, Yeo, G, Burge C.B. Cell, 2004. Variation in alternative splicing across human tissues. Yeo, G, Holste D, Kreiman, G, and Burge,
C.B. Genome
Biology, 2004. Variation in the splicing regulatory elements and their
organization in vertebrate genomes. Yeo, G, Hoon S, Venkatesh, B, and Burge, C.B. PNAS, 2004.
Maximum entropy modeling of short sequence motifs with
applications to RNA splicing signals Yeo, G, and Burge, C., RECOMB03 and Journal
of Computational Biology, 2004. Regularized Least-squares Classification. Rifkin, R, Yeo, G and Poggio, T. Advances in
Learning Theory: Methods, Model and Applications, NATO Science Series
III: Computer and System Sciences, Vol. 190, ISO Press, Amsterdam
2003. Edited by Suykens, Horvath, Basu, Micchelli and Vandewalle.
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THE COMPLEXITY OF RNA The RNA World Website
Structural Classification of RNA CONSTITUTIVE & ALTERNATIVE SPLICINGGENE's ALGORITHMS: |
JOURNALS
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COLLABORATORS
Phillip Sharp |
NEWS
ASTAR |
INFORMATION THEORY/ MACHINE LEARNINGIntroduction to Information
Theory/ Entropy Adam Berger's Links
(Maximum Entropy) |
PEOPLE LINKSThomas Gingeras |
CONSULTING Neuron
Systems |
BOSTON BIOTECH COMPANIES/ VENTURE
5AM ventures |