| 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,
follow the "[offcampus]" links below or
look at the
library "proxy server" instructions.
You will be prompted for your UW net ID and password once per
session.
03/31: ---- Organizational Meeting ----
04/07: Thermodynamic Error Regulation in Biochemical Reactions -- Field Cady
| | Abstract: It is known that DNA replication has fidelity far
above what would be predicted by equilibrium thermodynamics.
Attempts to explain the phenomena in terms of reaction rate
constants have neglected thermodynamic treatment of the subject.
I present a new, stochastic model of replication which shows the
critical role of sustained nonequilibrium for reaction fidelity,
and shows how the error rate can be modulated in real time. The
model constructed is very general, and the mechanism I identify
may be widespread in biochemistry.
|
04/14: Learning a predictive model of the transcriptional regulatory dynamics of a free, living cell: Version 2 -- David Reiss, ISB
| | Abstract: Our group recently published the first draft of a predictive
model of the genome-wide transcriptional regulatory dynamics of
Halobacterium salinarum, an extremophile that thrives in
extremely high salinity. This "regulatory influence" network was
derived through an iterative process of directed experimentation
followed by statistical modeling and data integration. I will
briefly review this first draft model, the methods behind its
development, and its current limitations. Then, I will present
our recent ongoing efforts to decipher the mechanics which
underly the predictions, through modeling of high-resolution
tiling array (ChIP-chip and mRNA hybridization) data.
- R Bonneau, MT Facciotti, DJ Reiss, AK Schmid, M Pan, A Kaur, V Thorsson, P Shannon, MH Johnson, JC Bare, W Longabaugh, M Vuthoori, K Whitehead, A Madar, L Suzuki, T Mori, DE Chang, J Diruggiero, CH Johnson, L Hood, NS Baliga, "A predictive model for transcriptional control of physiology in a free living cell." Cell, 131, #7 (2007) 1354-65.
[offcampus]
(and references therein, including Inferelator and cMonkey algorithms)
|
04/21: Inferring Biological Pathways through Constrained Searching of Molecular Interaction Graphs -- Imran Rashid
| | Abstract: Recent advances in biology have provided a great deal
of information on single genes and on the interactions between
pairs of genes. Yet true biological pathways involve a large
number of genes working in concert. Even when biologists know
that two genes are indirectly related, in general they cannot
discern the underlying pathway, without a great deal of
additional experimentation.
Here, we propose a method to discover novel biological pathways
by integrating previously existing knowledge of gene
interactions. We model interacting genes as a graph, and use
direct graph search methods to discover pathways. Finally, we
propose novel biologically sensible (yet computationally simple)
pathway constraints to improve accuracy.
|
04/28: Systematic discovery of vertebrate regulatory elements -- Adrienne Wang
| | Abstract: A few groups have constructed whole-genome catalogs of
vertebrate regulatory elements using comparative genomic
approaches. However, determining truly orthologous promoter
sequences, which is a prerequisite for identifying conserved
regulatory elements, remains a very challenging problem. Prakash
and Tompa observed that the regions upstream of annotated
transcription start sites are often not orthologous. Starting from
such non-orthologous sequences could very possibly affect the
downstream analyses. Studies in the past have applied various
filters to ensure orthology, resulting in a very limited set of
genes and species to start with. Our goal is to build a catalog of
regulatory elements for most human genes. For each human gene, we
align its promoter region and syntenic vertebrate regions from
both Ensembl and the UCSC Genome Browser. To avoid the adverse
effect described above, we apply StatSigMA, an assessment tool for
multiple sequence alignments, as a filter to retain only the genes
where there is compelling evidence that the promoter regions are
truly orthologous. Well conserved motifs extracted from the
alignments are strong candidates for regulatory elements.
|
05/05: Finding non-coding RNAs through genome-scale clustering -- Elizabeth Tseng
| | Abstract: Non-coding RNAs (ncRNAs) are transcripts that do not
code for proteins. Recent findings have shown that RNA-mediated
regulatory mechanisms influence a substantial portion of typical
microbial genomes. We present an efficient method for finding
potential ncRNAs in bacteria by clustering genomic sequences based
on homology inferred from both primary sequence and secondary
structure. We evaluate our approach using a set of Firmicutes
sequences, and the results show promise for discovering new
ncRNAs.
|
05/12: TBA -- Harlan Robins, FHCRC
05/19: String Matching and Next Generation Sequencing -- Robert Gentleman, FHCRC
| | Abstract: The advent of several technologies (454, BASE, Solexa)
has made many new biological experiments possible and changed the
way that some experiments will be carried out. These technologies
produce tens of thousands to tens of millions of short reads (250
nt or less). The computational problems that arise are largely
related to matching of these many query sequences to somewhat
longer target sequences. There is great interest in tools for
quality assessment and for performing imperfect matching. I will
discuss some of the basic problems, and some solutions that are
available through the Bioconductor project.
Familiarity with some string processing methods like the
Aho-Corasick algorithm
( http://en.wikipedia.org/wiki/Aho-Corasick_algorithm ) or suffix
trees ( http://en.wikipedia.org/wiki/Suffix_tree ) might be helpful,
but not essential, background.
|
05/26: Holiday
06/02: Join us all afternoon in room CSE 403,
especially for the keynote at 4:00:
Dr.
Joseph Felsenstein, 2008 Darwin-Wallace Medal Winner,
``Developing and distributing a phylogeny package: tales of the
PHYLIP''
-- Special Event:
CMB Symposium
| | Abstract: I will describe how the PHYLIP phylogeny inference
package developed and has been distributed. In its 27 years of
continuous development, it has grown and improved greatly and
its developer is wiser, and perhaps sadder. I will explain some
of the decisions made, assess whether they were correct ones,
and try to give some sense of the reactions it has gotten, the
triumphs, the tragedies, and the dilemmas that it faces in the
future.
|
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