Summary of research interests
Dr. Chiaromonte’s interests cover Multivariate
Analysis and Regression
(dimension reduction, supervised and unsupervised classification,
non-parametric tools), computational techniques (re-sampling,
perturbation and permutation schemes), and Markov modelling.
Dr. Chiaromonte researches simplified representations
of high-dimensional problems, with a focus on dimension
reduction and visualization — areas that have
become increasingly important with the availability
of large-scale, high-dimensional data in many scientific
fields. She has made contributions to Sufficient Dimension
Reduction (SDR), a body of theory and methods for handling
high-dimensional regression and classification problems
prior to parametric modelling or non-parametric fits.
Through
various collaborations, she has worked on foundational
aspects, SDR in regressions with a mix of quantitative
and categorical predictors, novel SDR techniques, and
an ongoing attempt to extend SDR theoretical framework
and methodology to non-linear dimension reduction.
Dr. Chiaromonte is also involved in the analysis and
modelling of large-scale genomic data. She collaborates
with researchers at the Center for Comparative Genomics
and Bioinformatics (PSU) and other institutions, and
has been part of the Mouse, Rat and Chicken genome sequencing
consortia. Whole-genome comparisons across two or more
species permit the investigation of various aspects
of evolution and function; Dr. Chiaromonte has worked
on genome-wide variation and co-variation of divergence
processes, estimation of the share of the human genome
under purifying selection, genome-wide scores to aid
in the prediction of regulatory elements, etc. Ongoing
projects concern data reduction, modelling and computational
issues involved in using short alignment pattern information
for supervised and unsupervised classification of genomic
elements. Dr. Chiaromonte has also worked on the analysis
of global gene expression data (e.g. from microarrays),
and large-scale meteorological data for investigating
structure and evolution of cyclones.
Representative publications
Li B., Zha H. and Chiaromonte F. 2004. Contour regression:
a general approach to dimension reduction. Annals
of Statistics (to appear).
Arnott J., Evans J. and Chiaromonte F. 2004. Characterization
of extratropical transition using cluster analysis.
Monthly Weather Review 132(12): 2916-2937.
Yang S., Smit A.F., Schwartz S., Chiaromonte F., Roskin
K. M., Haussler D., Miller W. and Hardison R.C. 2004.
Patterns of insertions and their covariation with substitutions
in the rat, mouse and human genomes. Genome Research
14: 517-527.
Kolbe D., Taylor J., Elnitski L., Eswara P., Li J.,
Miller W., Hardison R.C. and Chiaromonte F. 2004. Regulatory
potential scores from genome-wide 3-way alignments of
human, mouse and rat. Genome Research 14: 700-707.
Chiaromonte F., Weber R. J., Roskin K.M., Diekhans
M., Kent W.J. and Haussler D. 2004. The share of human
genomic DNA under selection estimated from human-mouse
genomic alignments. Cold Spring Harbor Symposia
in Quantitative Biology: The Genome of Homo
Sapiens 68: 245-254.
Li B., Cook R.D., Chiaromonte F. 2003. Dimension reduction
for the conditional mean in regressions with categorical
predictors. Annals of Statistics 30: 1636-1668.
Chiaromonte F., Miller W. and Bouhassira E. 2003. Gene
length and proximity to neighbors affect genome-wide
expression levels. Genome Research 13: 2602-2608.
Elnitski L., Hardison R.C., Li J., Yang S., Kolbe D.,
Eswara P., O Connor M.J., Schwartz S., Miller W., Chiaromonte
F. 2003. Distinguishing regulatory DNA from neutral
sites. Genome Research 13: 64-72.
Chiaromonte F., Cook R.D., Li B. 2002. Sufficient dimension
reduction in regressions with categorical predictors.
Annals of Statistics 30(2): 475-497
Chiaromonte F., Martinelli J.A. 2002. Dimension reduction
strategies for analyzing global gene expression data
with a response. Mathematical Biosciences 176
(1): 123-144.
Chiaromonte F., Yang S., Elnitski L., Bing Yap V.,
Miller W., Hardison R.C. 2001. Association between divergence
and interspersed repeats in mammalian noncoding genomic
DNA. Proceedings Nat'l Acad. of Sciences USA
98(25): 14503-14508.
Last updated: 02 May
2005
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