Francesca Chiaromonte 

My coordinates
 

Department of Statistics (my official page there)

email chiaro@stat.psu.edu 

422A Thomas Bldg. ph  814 863-8677, fax 814 863 7114

Pennsylvania State University, University Park, PA 16802              

Center for Comparative Genomics and Bioinformatics

email chiaro@bx.psu.edu

505A Wartik Lab. ph  814 865 7075, fax 814 863 1357

Pennsylvania State University, University Park, PA 16802

Starting Sept 2004, I will be visiting the Courant Institute and the Department of Biology at NYU.

email chiaro@cims.nyu.edu

1127 WW Hall. ph 212 998 3307, fax 212 995 4121

New York University, New York, NY 10012

Research Description

My interests as a statistician cover Multivariate analysis and Regression (including dimension reduction, supervised and unsupervised classification, non-parametric tools), computational techniques (including re-sampling, perturbation and permutation schemes for the empirical assessment of significance), and Markov modeling. In collaboration with R. Dennis Cook (Statistics, UMN), Bing Li and Hongyuan Zha (Statistics, PSU) I do research on Sufficient Dimension Reduction (SDR). SDR is a body of theory and methods for handling high-dimensional regression and classification problems prior to the use of parametric models or non-parametric fits, and it is closely related to graphics and data visualization. Its popularity and application scope have increased steadily in the last decade, along with the availability of large-scale, high-dimensional data in many scientific fields. Our recent work concerns foundational aspects, SDR in regressions with a mix of quantitative and categorical predictors, novel SDR techniques, and an ongoing attempt to extend SDR's theoretical framework and methodology to non-linear dimension reduction.

In the last years, I have become heavily involved in the analysis and modeling of large-scale genomic data; most of my research has been at the crossroads between statistics and genomics, computational biology and bioinformatics. This work comprises collaborations with Webb Miller, Ross Hardison, Kateryna Makova and other researchers at the Center for Comparative Genomics and Bioinformatics (PSU), as well as David Haussler and other researchers at the Center for Biomolecular Science and Engeneering (UCSC), and has seen us participate to the Mouse, Rat and Chicken Genome Consortia. Pair-wise and/or multiple whole-genome alignments between human and such species, allowed us to exploit comparative information to investigate various aspects of evolution and function.  Among others, I have been involved in projects concerning alignment scoring methodology, 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 (RP scores), etc. Ongoing work with graduate students at PSU (James Taylor, Svitlana Tyekucheva) concerns data reduction, modeling and computational issues involved in using short alignment patterns information for supervised and unsupervised classification of genomic elements. I also worked on the analysis of global gene expression data (e.g. from microarrays),  which offer an excellent application ground for the type of statistical methods I am interested in.

In a recent collaboration with Jenni Evans (Meteorology, PSU), we are also applying these methods to large-scale meteorological data, for investigating structure and evolution of  cyclones.

(the above research is currently funded by NIH and NSF grants)

Recent Articles

• 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. 

• Chiaromonte F., Bing Yap V., Miller W. (2002) Scoring pairwise genomic sequence alignments. Proceedings Pacific Symposium on Biocomputing 2002. 

• Chiaromonte F., Martinelli J.A. (2002) Dimension reduction strategies for analyzing global gene expression data with a response. Math'l Biosciences 176 (1): 123-144. 

• 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., Cook R.D. (2002) Sufficient dimension reduction and graphics in regression. Annals of the Institute of Statistical Mathematics 54(4): 768-795.

• Waterston, R. et al., Mouse genome sequencing consortium (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.

• 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.

• Hardison R.C., Roskin K.M., Yang S., Diekhans M., Kent J.W., Weber R., Elnitski L., Li J., O Connor M., Kolbe D., Schwartz S., Furey T.S., Whelan S., Goldman N., Smit A., Miller W., Chiaromonte F., Haussler D. (2003) Co-variation in frequencies of substitution, deletion, transposition and recombination during eutherian evolution. Genome Research 13: 13-26.

• Chiaromonte F., Miller W. and Bouhassira E. (2003) Gene length and proximity to neighbors affect genome-wide expression levels. Genome Research 13: 2602-2608.

• 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.

• Hardison R.C., Chiaromonte F., Kolbe D., Wang H., Petrykowska H., Elnitski L., Yang S., Giardine B., Zhang Y., Riemer C., Schwartz S., Haussler D., Roskin K., Weber R., Diekhans M., Kent W.J., Weiss M.J., Welch J. and Miller W. (2004) Global prediction and tests for erythroid regulatory regions. Cold Spring Harbor Symposia in Quantitative Biology: The Genome of Homo Sapiens 68: 335-345.

• 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.

• Gibbs, R. et al., Rat Genome Sequencing Project Consortium (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428: 493-521.

• Makova K.D., Yang S. and Chiaromonte F. (2004) Insertions and deletions are male-biased too: a whole-genome analysis in rodents. Genome Research 14: 567-573.

• 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.

• 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.

• Arnott J., Evans J. and Chiaromonte F. (2004) Characterization of extratropical transition using cluster analysis. Monthly Weather Review (to appear).

• Li B., Zha H. and Chiaromonte F. (2004) Contour regression: a general approach to dimension reduction. Annals of Statistics, accepted pending minor revisions.

• Hillier, L., et al., International Chicken Sequencing Consortium (2004) Sequencing and comparative analysis of the chicken genome. In revision for Nature.

Recent invited presentations

at Conferences:

• Third World Congress of Non-Linear Analysis. Catania IT. 07/2000.

• Complex Systems ad Computational Statistics SCO, Bressanone IT. 09/2001.

• Pacific Symposium on Biocomputing PSB. Kauai, Hawaii 01/2002.

• IMS/ENAR Meetings. Washington, DC. 03/2002.

• Int'l Conference on Current Advances and Trends in Nonparametric Statistics. Crete, Greece. 07/2002.

• ASA Joint Statistical Meetings. New York, NY. 08/2002.

• Int'l Agency for Research on Cancer (WHO). Int'l course on genetic epidemiology – focus on emerging biostatistical and bioinformatical issues. Veyrier du Lac, FR. 06/2003.

• Symposium on Patterns and Networks in Genomes, NYU. New York, NY. 04/2004.

• Int'l Conference on the Analysis of Genomic Data, Harvard Medical School. Boston, MA. 05/2004.

• 6th World Congress of the Bernoulli Society and 67th Annual Meeting of the IMS. Barcelona, Spain 07/2004.

• Int'l Conference on the future of Statistical Theory, Practice and Education. Hyderabad, India 12/2004.

and Universities:

• Department of Statistics, Univ. of Perugia, Perugia, IT. 01/2001.

• Dept. of Statistics, Univ. of Insubria, Varese, IT. 01/2001. 

• Inst. of Quantitative Methods, Bocconi Univ., Milano, IT. 01/2001.

• Dept. of Statistics. George Washington Univ., Washington, DC 05/2001.

• Dept. of Biostatistics. Columbia Univ., New York, NY 02/2002.

• Dept. of Biomathematics. Mount Sinai School of Medicine, New York, NY 02/2002.

• Dept. of Biology. New York Univ., New York, NY 11/2002.

• Courant Institute of the Mathematical Sciences, New York Univ., New York, NY 12/2002.

• Dept. of Statistics, Univ. of Minnesota, Minneapolis, MN 01/2003.

• Dept. of Health Evaluation Sciences, Penn State College of Medicine, Hershey PA. 10/2003.

Education
 

06/1996, Ph.D. in Statistics, University of Minnesota, Minneapolis MN. Advisor: R.D. Cook. Thesis title: A Reduction Paradigm for Multivariate Laws.
05/1990, Laurea (cum laude) in Statistic and Economic Sciences, University La Sapienza, Rome ITALY. Advisor: G. Dosi. Thesis title: Processes of Microeconomic Innovation and Macroeconomic Dynamics.

Professional Appointments and Positions
 

09/2004 – present, Visiting Associate Professor of Mathematics and Biology, New York University, New York NY.

07/2004 – present, Associate Professor of Statistics, Pennsylvania State University, University Park PA.
07/2004 – present, Associate Professor of Health Evaluation Sciences, Pennsylvania State University College of Medicine, Hershey PA (courtesy).
07/2003 – present, Member Comparative Genomics and Bioinformatics Center, Pennsylvania State University, University Park PA.

10/1998 – 07/2004, Assistant Professor of Statistics, Pennsylvania State University, University Park PA.
07/2002 – 07/2004, Assistant Professor of Health Evaluation Sciences, Pennsylvania State University College of Medicine, Hershey PA (courtesy).
07/1996 – 09/1998, Research Scholar, International Institute for Applied Systems Analysis, Laxenburg AUSTRIA.
06/1994 – 12/1994, Resident Researcher, International Institute for Applied Systems Analysis, Laxenburg AUSTRIA.

11/1990 – 07/1991, Resident Researcher, Santa Fe Institute, Santa Fe NM.

Recent Courses at Penn State

STAT/MATH200: Elementary Statistics. Undergraduate.
STAT/MATH414: Introduction to Probability Theory. Undergraduate.
STAT/MATH415: Introduction to Mathematical Statistics. Undergraduate.
STAT/MAT418: Probability Theory. Undergraduate.
STAT501: Regression Methods. Graduate, majors other than Statistics.
STAT511: Regression Methods. Graduate, majors in Statistics.
STAT/CSE/BIO598: Bioinformatics II. Graduate, majors in Statistics, Life Sciences, Computer Science.

(last updated Sept 2004)