From microarrays to networks: integrated analysis and visualization of
functional genomics data

Olga Troyanskaya
Princeton University

Now that genomic sequencing is a routine technology, the next key
challenge in systems biology is understanding protein function,
interactions, and regulation.  Experimental approaches to this problem
generated vast amounts of diverse functional genomics data, but an
equivalent explosion in biological understanding has not yet followed
the near-exponential growth in experimental results.  I will discuss
how computer science approaches for integrated analysis of these data
combined with targeted, computation-driven experiments can address
this gap and substantially contribute to our understanding of biology.

Specifically, I will discuss my group’s work on development of novel
methods for study of gene function and regulation in biological
systems through integration, analysis, and visualization of
heterogeneous biological data.  I will focus on our machine learning
and search-based methods for function prediction, context-specific
biological network modeling, and integrated analysis and visualization
of microarray data.  I will describe biological insights that
motivated our algorithms, their evaluation, and implementation in
publicly available systems; and present how using these systems, we
have modeled multiple known processes in the yeast S. cerevisiae,
characterized unknown components in these processes through
computational predictions and experimental validation, and identified
novel cross-talk relationships between biological processes.
Throughout the talk, I will also outline related challenges for
computer science and insights we gained in developing algorithms for
these problems.

Brief Biography:
Olga Troyanskaya is an Assistant Professor in the Department of
Computer Science and the Lewis-Sigler Institute for Integrative
Genomics at Princeton University, where she runs the Laboratory of
Bioinformatics and Functional Genomics. Her work bridges computer
science and molecular biology in an effort to develop better methods
for analysis of diverse genomic data with the goal of understanding
and modeling protein function and interactions in biological
pathways. Dr. Troyanskaya is an associate editor for Bioinformatics,
PLOS Computational Biology, and editorial board member of Journal of
Biomedical Informatics, Briefings in Bioinformatics, and Biology
Direct.  She is also a member of the Board of Directors of the
International Society for Computational Biology. She received her
Ph.D. from Stanford University and is a recipient of the Sloan
Research Fellowship, the NSF CAREER award, and the Howard Wentz
faculty award. She has also been honored as one of the top young
technology innovators by the MIT Technology Review.