| Papers, etc. |
Note on Electronic Access to Journals
Links to full papers below are often to journals that require a
paid subscription. The UW Library is generally a paid
subscriber, and you can freely access these articles if you do
so from an on-campus computer. For off-campus access,
look at the
library "proxy server" instructions.
During Autumn 2004, the Library deployed a new proxy
server; if you are accessing this page from an offcampus
computer, the "[offcampus]" links below may be more convenient.
You will be prompted for your UW net ID and password once per
session.
01/10: Alternative Splicing -- Brig, Nan (Michal)
Abstract: A combination of experimental and bioinformatics
approaches leads Burge and colleagues (Wang et al., 2004 [this
issue of Cell]) to a global view of how an RNA segment may be
selected or avoided in mature mRNAs due to biased distributions
of exonic enhancers and silencers, a process vital for genome
evolution, developmental control, and disease onset.
Abstract: Exonic splicing silencers (ESSs) are cis-regulatory
elements that inhibit the use of adjacent splice sites, often
contributing to alternative splicing (AS). To systematically
identify ESSs, an in vivo splicing reporter system was developed
to screen a library of random decanucleotides. The screen
yielded 141 ESS decamers, 133 of which were unique. The silencer
activity of over a dozen of these sequences was also confirmed
in a heterologous exon/intron context and in a second cell type.
Of the unique ESS decamers, most could be clustered into groups
to yield seven putative ESS motifs, some resembling known motifs
bound by hnRNPs H and A1. Potential roles of ESSs in
constitutive splicing were explored using an algorithm,
ExonScan, which simulates splicing based on known or putative
splicing-related motifs. ExonScan and related bioinformatic
analyses suggest that these ESS motifs play important roles in
suppression of pseudoexons, in splice site definition, and in
AS.
01/17: --- Holiday --- --
01/24: RNA Folding -- Zizhen (Larry)
01/31: Shotgun Mass Spec -- Ross, Jonathon (Bill)
02/07: Multiple Sequence Alignment: Basics -- Mathias, Mukund (Emily)
- Thompson J.D., Higgins D.G., Gibson T.J.(1994),
CLUSTAL W: improving the sensitivity of progressive multiple sequence
alignment through sequence weighting,position-specific gap penalties
and weight matrix choice,
Nucleic Acids Res. 22:4673-4680 [offcampus]
02/14: Multiple Sequence Alignment: With phylogeny -- Zasha (Joe)
02/21: --- Holiday --- --
02/28: Multiple Sequence Alignment: Genome-scale -- Becky (Emily)
- Mathieu Blanchette, W. James Kent, Cathy Riemer, Laura Elnitski, Arian
F.A. Smit, Krishna M. Roskin, Robert Baertsch, Kate Rosenbloom, Hiram
Clawson, Eric D. Green, David Haussler, and Webb Miller,
Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner,
Genome Res., Apr 2004; 14: 708 - 715 [offcampus]
03/07: Conserved Non-coding Sequences -- Amol, Mike (Martin)
- Elliott H. Margulies, Mathieu Blanchette, NISC Comparative
Sequencing Program, David Haussler and Eric D. Green,
Identification and Characterization of Multi-Species Conserved
Sequences,
Genome Research 13:2507-2518, 2003 [offcampus]
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