Francesca
Chiaromonte
MY COORDINATES: I can be found at the Center for Comparative Genomics and Bioinformatics of the
ABOUT
ME:
I was born in
PASSING ON SOME WISDOM: I taught many graduate and undergraduate
courses, often concerning regression methods, bioinformatics, and the
statistical analysis of data produced by high-throughput genomic technologies.
Here are links to a few representative course websites: Applied Regression Analysis,
Bioinformatics II, Current Research in
Statistical Genomics. My colleagues (including statisticians, computer
scientists and biologists) and I maintain a close-knit co-advising network to
train and mentor students working at the interfaces between our disciplines.
Examples of recent graduates mentored through this network are Erika Kvikstad
(PhD in Genetics, 2009, now a post-doc at the University Claude Bernard Lyon 1
in France), Svitlana Tyekucheva (PhD in Statistics, 2008, then a post-doc at
Johns Hopkins and now at Harvard), James Taylor (PhD in Computer
Science, 2006, now a Biology and Math&CS faculty at Emory University), and
Shan Yang (PhD in Biochemistry and Molecular Biology, 2004, now a senior
bioinformatics scientist at Applied Biosystems).
MY WORK IN STATISTICS: My interests
as a statistician cover multivariate analysis and regression (including
dimension reduction, supervised and unsupervised classification, non-parametric
tools and parametric regression modeling), computational techniques (including
re-sampling, perturbation and permutation schemes for the empirical assessment
of significance), approaches to the analysis of high-dimensional and
under-sampled data (which are very common in genomics applications), and Markov
models (as applied to genomic sequences and alignments). With funding from the
NSF, R. Dennis Cook (Statistics,
U of MN), Bing Li
(Statistics, Penn State) and I have pursued research on Sufficient Dimension Reduction, a body of theory and methods for
handling high-dimensional regression and classification problems, which is also
closely related to graphics and data visualization. Representative publications.
MY WORK IN BIOINFORMATICS AND GENOMICS: Most of
my research occurs at the interfaces between statistics, bioinformatics and
genomics. Over the years, this work has comprised NIH and NSF funded
collaborations with Ross Hardison, Kateryna Makova, Webb Miller, Anton Nekrutenko,
Mary Poss and other
researchers at the Center for Comparative Genomics and Bioinformatics,
the Center
for Medical Genomics, and the Center for Infectious Disease Dynamics of
Penn State, as well as other institutions (e.g. the Center
for Biomolecular Science and Engineering of UC Santa Cruz). Starting
with our participation in several genome Consortia (e.g. Mouse, Rat, Chicken),
we used sequence and alignment data to investigate various aspects of evolution
and function. Among others, I have been involved in projects concerning
alignment scoring methodology, estimation of the share of the human genome
under purifying selection, genome-wide computational prediction of regulatory
elements (see ESPERR and RP scores), local variation and co-variation of
divergence processes and the determinants of mutagenesis, X chromosome
inactivation, etc. Recently, we have begun utilizing data from next generation
sequencing technologies both in our studies of mutagenesis and genome dynamics,
and in studies associating epigenomic signatures to sequence, alignment and
transcriptional information. We are also initiating projects in which genomic
information is linked to aspects of the spatio-temporal dynamics of infectious
diseases, investigated in in vitro
and in vivo systems. Representative publications.
MY WORK IN METEOROLOGY: Through
an NSF funded collaboration with Jenni
Evans (Meteorology, PSU), I also work on the application of dimension
reduction, clustering, regression and re-sampling methods to large-scale
meteorological data. In particular, we investigate the structure and lifecycle
evolution of cyclones with a focus on the process of extra-tropical
transition. Representative publications.
(last updated Sept 2010)