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Date
(
Winter 2007
) |
Category |
Seminar Info |
| 2007/04/30 |
Bioinformatics |
Place: Duff Medical Building, 3775 University Street, Main Amphitheatre 1
Time: 12:00 - 13:00
Speaker:
Mark
Gerstein
Affiliation: Molecular Biophysics & Biochemistry, Computer Science, Yale University
Area:
Analysis and understanding of the human genome
Title: Human Genome Annotation
Abstract: A central problem for 21st century science will be the analysis and
understanding of the human genome. My talk will be concerned with topics
within this area, in particular annotating pseudogenes (protein
fossils) in the genome. I will discuss a comprehensive pseudogene
identification pipeline and storage database we have built. This has enabled
use to identify >10K pseudogenes in the human and mouse genomes and analyze
their distribution with respect to age, protein family, and chromosomal
location. One interesting finding is the large number of ribosomal
pseudogenes in the human genome, with 80 functional ribosomal proteins
giving rise to ~2,000 ribosomal protein pseudogenes.
I will try to inter-relate our studies on pseudogenes with those on tiling
arrays, which enable one to comprehensively probe the activity of intergenic
regions. At the end I will bring these together, trying to assess the
transcriptional activity of pseudogenes.
Throughout I will try to introduce some of the computational algorithms and
approaches that are required for genome annotation and tiling arrays -- i.e.
the construction of annotation pipelines, developing algorithms for optimal
tiling, and refining approaches for scoring microarrays.
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| 2007/04/30 |
Faculty Candidate Talk |
Place: MC437
Time: 9:30 - 10:30
Speaker:
Christine
Vogel
Affiliation: nstitute for Cellular and Molecular Biology, The University of Texas at Austin
Area:
aspects of domain duplication and combination
Title: The Evolution of Complex Protein Repertoires - and beyond
Abstract: Much of an organism's physiology is determined by the proteins encoded in
its genes. Proteins in turn are composed of smaller structural, functional
and evolutionary units called domains. Duplication, combination and
divergence of these domains have shaped the protein repertoire by forming
protein families and multi-domain proteins.
My talk discusses different aspects of domain duplication and combination
from a genomic, structural and functional perspective; it describes the
relationship between the two processes, and their likely contributions to
the evolution of complex organisms.
I will also briefly describe more recent work which addresses 'faster'
processes that shape the protein repertoire, e.g., a mass-spectrometry-based
method to determine absolute protein abundance and its applications
Biography of Speaker:
-
Since 2005, Christine Vogel is a Post-doctoral Fellow at the
Institute for Cellular and Molecular Biology at the University of Texas at
Austin. In 2004, she received a Ph.D. in Computational and Structural
Biology from the University of Cambridge, MRC Laboratory of Molecular
Biology, U.K. Her research interests lie in the understanding of eukaryotic
complexity, with a focus on development and application of an integrative
and quantitative definition of eukaryotic cell types, combining
morphological and large-scale molecular data for various eukaryotic model
organisms.
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| 2007/04/17 |
General |
Place: MC437
Time: 9:30 - 10:30
Speaker:
Jernej
Barbič
Affiliation: Carnegie Mellon University
Area:
Graphics
Title: Real-time Deformable Objects: Graphics, Haptics, Sound
Abstract: Real-time deformable objects are an exciting research area in computer
graphics, with applications to computer games, movie industry, CAD/CAM, and
virtual medicine.
Deformable objects are well-understood in solid mechanics, however the
standard simulation algorithms are too slow for interactive simulation with
detailed geometry. How can we support real-time simulation on commodity
workstations, while compromising physical correctness as little as possible?
First, I will present reduced-coordinate nonlinear deformable objects, a
novel class of deformable objects obtained by applying statistical model
reduction to finite element models. The idea is to replace the general
degrees of freedom of a deformable object for a much smaller set of reduced
degrees of freedom, thereby trading accuracy for speed. The reduced degrees
of freedom incorporate geometric and material
information, and are chosen automatically from the first principles of
continuum mechanics.
In addition, I will present a time-critical algorithm for collision
detection, deformable object simulation and contact force computation
between reduced-coordinate deformable (or rigid) objects with detailed
geometry. The algorithm runs at haptic rates (1000 Hz), enabling
applications in interactive path planning, virtual assembly and game
haptics.
Finally, I will present an algorithm for real-time sound synthesis where
both the mechanical vibrations (deformations) that cause sound, and the
sound propagation (wave equation) into the surrounding air for detailed
geometries, are (approximately) simulated at audio rates (44,100 Hz). This
captures effects such as object self-shadowing and diffraction of sound
around corners, and further improves realism of real-time virtual
environments.
PDF version
Biography of Speaker:
-
|
| 2007/04/16 |
General |
Place: MC437
Time: 9:30 - 10:30
Speaker:
Vivek
Kwatra
Affiliation: University of North Carolina
Area:
Vision
Title: Spatio-temporal Textural Modeling for Data-driven Synthesis and Visualization
Abstract: With the increased accessibility of capture devices and techniques, rich
amounts of real-world data is available to us in various forms including
images, video, 3D models, motion capture, weather patterns, etc. On the
other hand, one of the primary goals in computer graphics has been to
synthesize this data from first principles either through simulation or user
interaction. My research goal has been to develop synthesis-friendly models
from spatio-temporal data that not only exploit the richness of real data,
but also afford the controllability of simulation and interaction.
In this talk, I will focus on synthesis methods that treat visual as well as
dynamic data as texture. Such textural modeling is especially conducive for
controllable synthesis because of its locality in space and time. I will
first demonstrate a technique that allows for spatio-temporal extension of
image and video data, and combined with intelligent user interfaces, can be
used for computational photography applications such as smart image
compositing and storyboarding. I will then describe a more flexible texture
model that can be used to augment fluid simulation with appearance and shape
textures to generate complex fluid effects such as ripples and foam in
turbulent flow and patterns in the crust of flowing lava. I will also show
how we can incorporate physical and geometric characteristics of the flow
into the synthesis process in a temporally coherent manner. This technique,
besides adding to the visual realism of the simulated fluid, also provides a
handy visualization tool that lays bare significant features on the surface
of the flowing fluid, which may not be apparent otherwise.
Biography of Speaker:
-
|
| 2007/04/16 |
Bioinformatics |
Place: Duff Medical Building, 3775 University Street, Main Amphitheatre 1
Time: 13:30 - 14:30
Speaker:
Dr. Daniel
Figeys
Affiliation: The Ottawa Institute of Systems Biology, BMI, University of Ottawa
Area:
Analyzing specific portions of the proteome (sub-proteome)
Title: Probing sub-proteomes using affinity purification
Abstract: The concentration range of protein present in biological samples remains a serious challenge for proteomic technologies. The proteome is defined as the ensemble of the proteins in a sample; however, the reality is that a good portion of the proteome remains invisible because of detection and processing limitations in proteomic technologies. We have developed technologies to analyze specific portions of the proteome (sub-proteome) that combine affinity purification, mass spectrometry, and bioinformatics. In this presentation, we will provide some examples of sub-proteome studies. First, we will report our results on mapping protein-protein interaction for over 330 human genes using immunopurification coupled to mass spectrometry and bioinformatics. Using this approach, 2235 human proteins were observed to participate in 6463 interactions with the bait proteins. A suite of bioinformatic approaches were used to assess the validity of the results. Second, we will discuss the mapping of protein polyubiquitination sites using affinity purification coupled to the proteome reactor and mass spectrometry and will discuss the potential applications of this approach.
Biography of Speaker:
-
|
| 2007/04/12 |
Faculty Candidate Talk |
Place: MC437
Time: 9:30 - 10:30
Speaker:
Martin
Isenburg
Affiliation: University California, Berkeley
Area:
HCI
Title: Streaming Geometry Processing
Abstract: Modern technology enables the creation of digital 3D models that represent
objects or processes for scientific or engineering applications with
incredible detail. Operating on these large data sets is difficult because
they cannot be completely loaded into the main memory of common desktop PCs.
We have developed new streaming representations for geometric data sets that
we use as input to new streaming algorithms that can process data sets
without first loading them into memory. The key insight is to keep the data
in streams and document, for example, when all triangles around a vertex or
all points in a particular spatial region have arrived with "finalization
tags". These tags allow us to complete operations, output
results, and de-allocate data structures.
We have designed streaming simplification, compression, triangulation, and
extraction algorithms that can operate on data sets much larger than the
available memory. An added benefit of streaming is the ability to pipe
several stream modules together and avoid storing temporary results to disk.
I present two example processing pipelines: One extracts, simplifies, and
compresses iso-surfaces from a volume grid. The other generates elevation
contours from densely sampled terrain points via a temporarily constructed
and then simplified triangulation.
Biography of Speaker:
-
Martin Isenburg is currently a postdoc at UC Berkeley. He received a Ph.D.
in Computer Science from UNC Chapel Hill in 2004 and a M.Sc. in Computer
Science from UBC Vancouver in 1999. He has published over 25 papers
including three SIGGRAPH, five Visualization, and five journal publications.
His dissertation is on compressing and streaming of polygon meshes, both
in-core and out-of-core. Recently has worked on streaming other processing
tasks for large geometric data sets. His SIGGRAPH'06 paper on Streaming
Computation of Delaunay Triangulations is his showcase example for an
extremely scalable streaming algorithm.
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