UCSB CS Colloquium

UCSB CS Colloquium: "Eric Xing
University of California Berkeley

Date: Monday April 12
Time: 3:00-4:00
Place: Engineering 1, 2114



Abstract:
I discuss two probabilistic modeling problems arising in metazoan genomic analysis: identifying motifs and cis-regulatory modules (CRMs) from transcriptional regulatory DNA sequences, and inferring haplotypes from genotypes of single nucleotide polymorphisms. Motif and CRM identification is important for understanding the gene regulatory network underlying metazoan development and functioning. I discuss a modular Bayesian model that captures rich structural characteristics of the transcriptional regulatory sequences and supports a variety of tasks such as learning motif representations, model-based motif and CRM prediction, and de novo motif detection. Haplotype inference is essential for the understanding of genetic variation within and among populations, with important applications to the genetic analysis of disease propensities and other complex traits. I discuss a Bayesian model based on a prior constructed from a Chinese restaurant process -- a nonparametric prior which provides control over the size of the unknown pool of population haplotypes, and on a likelihood that allows statistical errors in the haplotype/genotype relationship. Our models use the 'probabilistic graphical model' formalism, a formalism that exploits the conjoined talents of graph theory and probability theory to build complex models out of simpler pieces. I discuss the mathematical underpinnings for the models, how they formally incorporate biological prior knowledge about the data, and the related computational issues.
Biography:
Eric Xing received his B.S. with honors in Physics and Biology from Tsinghua University, his Ph.D. in Molecular Biology and Biochemistry "

USC College : College Magazine : Fall 2003 : Virtually Aging

USC College : College Magazine : Fall 2003 : Virtually Aging: "Faced with an aging population and a maturing research community, investigations of aging and aging-related diseases have exploded at USC over the past 30 years. Today, by one estimate, more than 100 USC scholars, representing natural science and social science disciplines and professional schools, are studying biological, social, health, economic, policy or other aspects of aging. For a glimpse of just how extensive the USC aging research enterprise has become, and for information on aging-related research and resources, visit University Wide Aging Nexus at USC, a new web site designed by Caleb Finch, the ARCO/William F. Kieschnick Chair in the Neurobiology of Aging in the School of Gerontology and a College professor of biology, and his team. "

Innovative Funding

Article - Fishing for Answers: "When businessman and longtime philanthropist Ralph C. Wilson Jr.
decided to begin supporting biomedical research, he convened experts from six of the country's top medical institutions to suggest the most effective way he could help. Together, the institutions - including the University of Michigan - identified a problem in research funding: because so many scientists are competing for limited grant dollars, most grants go to 'safe' research projects, where success is almost certain. Researchers who come with creative ideas and new ways of thinking often have trouble finding support.

So Wilson established his Ralph C. Wilson Sr. and Ralph C. Wilson Jr. Medical Foundation with a mission of funding innovative research by the nation's top biomedical scientists.

Though they have only been in existence since 2001, Wilson Foundation grants carry enormous weight and prestige. Only six institutions are even eligible to apply, with the U-M among this select group. What's more, only the top researchers and most creative projects at those institutions pass the rigorous peer review process. At each institution, only one to three projects receive funding annually.



One of the U-M's four researchers receiving funding is Dr. Daniel Goldman, a professor of biological chemistry and senior research professor, who is 'almost bursting' with excitement over his Wilson-funded research. Dr. Daniel Goldman works with zebrafish in his lab.Dr. Goldman explores new ways of repairing damage to the central nervous system, such as from strokes or spinal cord injuries. Fish, unlike humans, can recover from similar injuries and regenerate their nervous systems. Studying a lab full of zebrafish, Dr. Goldman hopes he is on the trail of information that could revolutionize treatments for stroke, pa"

Metabolic Engineering Working Group

Metabolic Engineering Working Group: "Metabolic Engineering is a new approach to understanding and using metabolic processes. As the name implies, ME is the targeted and purposeful alteration of metabolic pathways found in an organism in order to better understand and use cellular pathways for chemical transformation, energy transduction, and supramolecular assembly. Knowledge acquired from this research will benefit society in a number of ways, including the ability to modify biological pathways to produce biological substitutes for less desirable chemical processes; allowing greater agricultural production, permitting more efficient and safer energy production, and; providing better understanding of the metabolic basis for some medical conditions that could assist in the development of new cures."

Intelligent design - Wikipedia

Intelligent design - Wikipedia: "Intelligent design (ID) is the phrase coined for the argument that life and living things show signs of having been designed by an intelligent agent, and that therefore abiogenesis must be a false hypothesis. Specifically, the conjecture focuses on the 'what' of the origin of life on Earth, i.e. saying that it is not possible for 'non-living' matter to become 'living' matter (with the level of organization that is observed today) without intervention, and that life itself shows signs of design. The 'Who, why, when, where and how' are theoretically excluded from the debate, although the idea is more often than not identified with religious arguments, with inevitable extension into those other domains. Religious proponents of ID use the argument from design to argue for the existence of a god, usually � in the context of Christianity � God.
Opponents of ID, who include the overwhelming majority of the scientific community, claim that this argument is deceptive and has no standing as a scientific hypothesis, i.e. it is considered pseudoscience. They say that ID does not present falsifiable hypotheses, and violates the principle of naturalism within scientific philosophy. They also point to examples of seemingly poor design within biology."

Society of Mind - Wikipedia

Society of Mind - Wikipedia, the free encyclopedia: "What magical trick makes us intelligent? The trick is that there is no trick. The power of intelligence stems from our vast diversity, not from any single, perfect principle."

Symbiosis - Wikipedia

"The biologist Lynn Margulis, contends that symbiosis is a major driving force behind evolution. She considers Darwin's notion of evolution, driven by competition, as incomplete, and claims evolution is strongly based on co-operation, interaction, and mutual dependence among organisms. According to Margulis and Sagan (1986), 'Life did not take over the globe by combat, but by networking'. As in humans, organisms that cooperate with others of their own or different species can sometimes outcompete those that don't."
Symbiosis - Wikipedia: