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Genomics
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 Intron Removal, Alternative Splicing, and Genomics
Manuel Ares, Jr., MCD Biology
Work in the Ares laboratory centers on the mechanisms and regulation of splicing. Splicing is required to remove intron sequences from pre-mRNA and create coding sequences for translation. The lab studies yeast, mouse and human tissues and cells, which share many fundamental features but also have distinct and important differences from each other. They are generally interested in the structure and function of RNAs that play important regulatory and catalytic roles. [More]
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 Genome Sequence Assembly and Comparative Genome Analysis
Ed Green, Dept. of Biomolecular Engineering
The Green lab is interested in understanding molecular and evolutionary biology through comparative genomics. They are particularly focused on the many applications of high-throughput sequencing including genome assembly, gene expression analysis, and population genetics. Green maintains a wide range of collaborative projects that currently include: investigating sex-specific gene expression and splicing, denovo assembly of bacterial genomes that produce potentially useful natural products, and application of Neandertal and other ancient hominin genomes to detect and interpret positive selection in humans. [More]
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 Genome
Bioinformatics: Comparative Sequence Analysis of Mammalian Genomes
David Haussler, Dept. of Biomolecular Engineering
Dr. Haussler's research lies at the interface of mathematics,
computer science, and molecular biology. He has focused on computational analysis
and classification of DNA, RNA, and protein sequences. As a collaborator on
the public Human Genome Project, his team posted the first publicly available
computational assembly of the human genome sequence on the Internet, and it
now maintains UCSC's Genome Browser, which is used extensively in biomedical
research. [More]
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 Large
Scale Approaches to Study Whole-Genome Biology
Todd Lowe, Dept. of Biomolecular Engineering
Todd Lowe's research group uses a mixture of computational
and experimental genomics to identify and characterize non-coding RNA (ncRNA)
genes and to study the unique biology of Archaeal “extremophiles” – microbes
that live at the edge of the limits of life. His team has created several
classes of non-coding RNAs gene-finders, and has created full-genome DNA microarrays
for two different hyperthermophile species to study ancient forms of respiration
and strategies for thermo-tolerance. The group has also created a genome
browser and functional genomics resource for all archaeal and extremophile species
(archaea.ucsc.edu), now funded by the NSF. [More]
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 Tools
for Studying Genes and Proteins
Nader Pourmand, Dept. of Biomolucular Engineering
The Pourmand lab develops new tools and technologies
that integrate biology, electronics, and nanofabrication for the detection and
study of genes and proteins. These tools are specifically designed to increase
the speed and lower the cost of sample analysis. The lab directs particular
attention to the development of medically relevant technology, such as instruments
for pathogen detection. Pourmand is also spearheading UCSC's effort to establish
a new high-throughput, high-quality sequencing facility. [More]
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 Origin
and Regulation of Mammalian Stem Cells
Amy Ralston, Dept. MCD Biology
Understanding the origins of stem cells in the embryo is
essential for understanding how to guide formation of stem cell-derived tissues.
Several stem cell-producing tissues exist in the early mouse embryo, which provides
an ideal system for exploring mechanisms that guide stem cell development. In
addition, stem cells can be artificially created by genetic reprogramming mature
cells. We are interested in understanding how natural and reprogrammed stem
cells compare. We use a variety of techniques, including mouse transgenics,
bioinformatics, molecular biology, and confocal microscopy to examine the establishment
and use of stem cells during normal development. From these studies, we hope
to understand the molecular basis of cell fate and plasticity, as they relate
to normal development and regenerative medicine. [ More] |
 Post
Transcriptional Control of Gene Expression
Jeremy Sanford , Dept. of
MCD Biology
Our work attempts to dissect the myriad
roles of RNA binding proteins in mammalian gene expression. RNA processing reactions
such as pre-mRNA splicing, mRNA export, translation and mRNA decay are influenced
by the interplay of trans-acting proteins with their cognate cis-acting RNA
elements. We believe that by elucidating the cis-acting RNA elements recognized
by specific RNA binding proteins it will be possible to gain a better understanding
of both the physiological relevance and mechanisms of action for these critical
regulators of gene expression. [More]
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 Regulation
of Chromatin Structure and Gene Expression
John Tamkun, Dept. of MCD Biology
The Tamkun lab investigates regulation of chromatin's
high order structure and its role in gene expression. Composed of DNA and proteins,
chromatin's ability to fold enables the eukaryotic genome to be packaged into
an extremely small space inside the nucleus of the cell. Proper transcription
and replication of the genome also depend upon precise regulation of these dynamic
structures, with defects in these processes believed to underly many human diseases.
[More]
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 Regulation
of Pre-mRNA Splicing and Post-Transcriptional Regulation by Micro RNAs
Alan Zahler, MCD Biology
The human genome carries the blueprint for the creation
of proteins, the molecular machines that carry out most of the work in the body.
However, the diversity of the pool of available proteins is greatly enhanced
by alterative splicing of our genes. The Zahler laboratory examines the nematode
Caenorhabditis elegans in order to understand the regulatory mechanisms of this
alternative splicing.. [More]
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 Ex-vivo
Survival Mechanisms Used by Vibrio cholerae between Epidemics
Fitnat Yildiz, Dept. of Microbiology and Environmental
Toxicology
Ex-vivo Survival Mechanisms used by Vibrio
cholerae between Epidemics: Fitnat Yildiz's laboratory investigates signaling
and regulatory networks of Vibrio cholerae, the causative agent of the
Asiatic cholera. She and her colleagues are particularly interested in those
mechanisms that allow the pathogen to adapt to changes in its habitat. The bacteria's
ability to survive in different growth modes in aquatic environments is closely
linked to seasonal epidemics of cholera. Yildiz's laboratory is attempting to
identify and characterize genes and processes associated with phase variations
of the pathogen. Their results will be useful for prediction and control of
epidemics of this devastating disease. [More]
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