Francesca Chiaromonte

Professor of Statistics, Dorothy Foehr Huck and J. Lloyd Huck Chair in Statistics for the Life Sciences
Francesca Chiaromonte
Francesca
Chiaromonte
Professor of Statistics, Dorothy Foehr Huck and J. Lloyd Huck Chair in Statistics for the Life Sciences
Interests
High-dimensional & Undersampled data
Dimension Reduction & Feature Selection Methods
Regression & Multivariate Methods
Bioinformatics
"Omics" & Biomedical applications
Meteorology, Climate, Economics applications
Address
Phone
(814) 865-7075
Website
Penn State Personal Site

Biography

Francesca Chiaromonte is a Professor of Statistics and, since 2019, the Dorothy Foehr Huck and J. Lloyd Huck Chair in Statistics for the Life Sciences at Penn State.

She received a Laurea (cum laude) in Statistic and Economic Sciences from the University of Rome La Sapienza (Rome, IT), and a Ph.D. in Statistics from the University of Minnesota.

Her research interests as a statistician include methods to analyze high-dimensional, complex and potentially under-sampled regression and classification problems (in particular dimension reduction and feature selection methods); computational techniques for the empirical assessment of significance and stability (e.g., re-sampling, perturbation and permutation schemes); latent structure and Markov modeling approaches; and functional data analysis methods. She applies these methods in contemporary “Omics” sciences and other scientific fields – including Meteorology and Economics.

At Penn State, Francesca holds a courtesy affiliation with the Department of Public Health Sciences. She is a member of the Center for Computational Biology and Bioinformatics and of the Center for Medical Genomics, and the director of the Institute for Genome Sciences (one of the Huck Institutes of the Life Sciences). In addition to the graduate program in Statistics, she belongs to the faculty of the interdisciplinary Bioinformatics & Genomics graduate program.

She also works in the Institute of Economics of the Sant’Anna School of Advanced Studies (Pisa, IT), where she is the scientific coordinator for EMbeDS (Economics and Management in the era of Data Science), and she contributes to the PhD in Data Science (established as a consortium with the Scuola Normale Superiore, the University of Pisa, and other partners in the area) and to the PhD in AI for Society (one of the five graduate programs constituting the National Doctorate in Artificial Intelligence).

Francesca is a Fellow of the American Statistical Association since 2016, “for outstanding collaborative work in high throughput biology, contributions to methodology in statistics and bioinformatics, commitment to interdisciplinary research, and leadership in developing training programs at the interface of statistics, computation and the life sciences.” She is also a Fellow of the Institute for Mathematical Statistics since 2022, "for outstanding contributions to methodology for the analysis of large, complex and structured data, in particular to the fields of sufficient dimension reduction and envelope models, for outstanding interdisciplinary work in the 'Omics' and biomedical sciences, and for leadership in interdisciplinary training and mentoring efforts."

 

Selected recent Penn State news

Chiaromonte and Hunter Named 2022 IMS Fellows (2022)

New approach can help identify young children most at risk for obesity (2022)

Staying home, primary care, and limiting contagion hubs may curb COVID-19 deaths (2021)

A new class of functional elements in the human genome? (2021)

Unusual DNA folding increases the rates of mutations (2021)

Scientists take a step toward understanding 'jumping genes' effect on the genome (2020)

Connecting the dots: using curves to analyze multifaceted data may hold the key to understanding childhood obesity (2020)

Costs of natural disasters are increasing at the high end (2019)

Chiaromonte named first Huck Chair in Statistics for the Life Sciences (2019)

 

Selected recent publications

STATISTICS AND BIOINFORMATICS METHODS

  • Boschi T., Reimherr M.L., Chiaromonte F. (2021) A highly efficient Group Elastic Net algorithm with applications to Function-on-Scalar regression. NeurIPS 2021.
  • Insolia L., Kenney A., Calovi M., Chiaromonte F. (2021) Robust Variable Selection with Optimality Guarantees for High-dimensional Logistic Regression. Stats (special issue on Robust Statistics in Action) 4(3), 665-681. doi.org/10.3390/stats4030040.
  • Insolia L., Kenney A., Chiaromonte F., Felici G. (2021) Simultaneous Feature Selection and Outlier Detection with Optimality Guarantees. Biometrics. doi.org/10.1111/biom.13553.
  • Boschi T., Chiaromonte F., Li B., Secchi P. (2021) Covariance based low-dimensional registration for function-on-function regression. STAT. 10(1) e404. doi.org/10.1002/sta4.404.
  • Insolia L., Chiaromonte F., Riani M. (2021) A Robust Estimation Approach for Mean-Shift and Variance-Inflation Outliers. Festschrift in Honor of R. Dennis Cook. E. Bura and B. Li (eds), Springer, Cham. doi.org/10.1007/978-3-030-69009-0_2.
  • Nandy D. Chiaromonte F., Li R. (2021). Covariate Information Number for Feature Screening in Ultrahigh-Dimensional Supervised Problems. Journal of the American Statistical Association. doi.org/10.1080 /01621459.2020.1864380.
  • Kenney A., Chiaromonte F. and Felici G. (2020) MIP-BOOST: Efficient and Effective L0 Feature Selection for Linear Regression. Journal of Computational and Graphical Statistics. doi.org/10.1080/10618600.2020. 1845184.
  • Di Iorio J., Chiaromonte F., Cremona M.A. (2020) On the bias of H-scores for comparing biclusters, and how to correct it. Bioinformatics 36(9) 2955–2957. doi.org/10.1093/bioinformatics/btaa060.
  • Cremona M.A., Xu H., Makova K.M., Reimherr M., Chiaromonte F., Madrigal P. (2019) Functional data analysis for computational biology. Bioinformatics. doi.org/10.1093/bioinformatics/btz045.
  • Yao W., Nandy D., Lindsay B.G., Chiaromonte F. (2018). Covariate Information Matrix for Sufficient Dimension Reduction. Journal of the American Statistical Association. doi.org/10.1080/01621459.2018.1515080.
  • Cremona M.A., Pini A., Cumbo F., Makova K.D., Chiaromonte F. and Vantini S. (2018) IWTomics: testing high-resolution sequence-based “Omics” data at multiple locations and scales. Bioinformatics. doi.org/10.1093/bioinformatics/bty090.
  • Liu Y., Chiaromonte F. and Li B. (2017) Structured Ordinary Least Squares: a sufficient dimension reduction approach for regressions with partitioned predictors and heterogeneous units. Biometrics. doi:10.1111/biom.12579.
  • Bartolucci F., Chiaromonte F., Kuruppumullage Don P. and Lindsay B.G. (2016) Composite likelihood inference in a discrete latent variable model for two-way “clustering-by-segmentation” problems. Journal of Computational and Graphical Statistics doi:10.1080/10618600.2016.1172018

"OMICS" AND BIOMEDICAL APPLICATIONS

  • Arbeithuber B., Cremona M., Hester J., Barrett A., Higgins B., Anthony K., Chiaromonte F., Diaz F.J., Makova K.D. (2022). Advanced age increases frequencies of de novo mitochondrial mutations in macaque oocytes and somatic tissues. Proceedings of the National Academy of Sciences USA, 119 (15) e2118740119. doi.org/10.1073/pnas.2118740119.
  • Nandy D., Craig S.J.C., Cai J., Tian Y., Paul I.M., Savage J.S., Marini M.E., Hohman E.E., Reimherr M.L., Patterson A.D., Makova K.D., Chiaromonte F. (2021) Metabolomic profiling of stool of two-year old children from the INSIGHT study reveals links between butyrate and child weight outcomes. Pediatric Obesity, 17(1) e12833. doi.org/10.1111/ijpo.12833.
  • Craig S., Kenney A.M., Lin J., Paul I.M., Birch L.L., Savage J.S., Marini M.E., Chiaromonte F., Reimherr M.L. and Makova K.D. (2021) Constructing a polygenic risk score for childhood obesity using functional data analysis. Econometrics and Statistics. doi.org/10.1016/ j.ecosta.2021.10.014.
  • Boschi T., Di Iorio J., Testa L., Cremona M., Chiaromonte F. (2021) Functional Data Analysis characterizes the shapes of the first COVID-19 epidemic wave in Italy. Scientific Reports 11, 17054. doi.org/10.1038/s41598-021-95866-y.
  • Guiblet W., Cremona M.A., Harris R.S., Chen D., Eckert K.A., Chiaromonte F., Huang Y., Makova K.D. (2021) Non-B DNA: A major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome. Nucleic Acids Research gkaa1269. doi.org/10.1093/nar/gkaa1269.
  • Chen D., Cremona M.A., Qi Z., Mitra R., Chiaromonte F., Makova K.D. (2020) Human L1 Transposition Dynamics Unraveled with Functional Data Analysis. Molecular Biology and Evolution 37(12), 3576–3600. doi.org/10.1093/molbev/msaa194.
  • Mughal M., Koch H., Huang J., Chiaromonte F., De Giorgio M. (2020) Learning the properties of adaptive regions with functional data analysis. PLoS Genetics 16(8): e1008896. doi.org/10.1371/journal.pgen.1008896.
  • Arbeithuber B., Hester J., Cremona M.A., Stoler N., Zaidi A., Higgins B., Anthony K., Chiaromonte F., Diaz F.J., Makova K.D. (2020) Age-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues. PLoS Biology. 18(7): e3000745. doi.org/10.1371/journal.pbio.3000745.
  • Cechova M., Harris R.S., Tomaszkiewicz M., Arbeithuber B., Chiaromonte F., Makova K.D. (2019) High satellite repeat turnover in great apes studied with short- and long-read technologies. Molecular Biology and Evolution. 36(11), 2415–2431. doi.org/10.1093/molbev/msz156.
  • Guiblet W.M., Cremona M.A., Cechova M., Harris R.S., Kejnovská I., Kejnovsky E., Eckert K., Chiaromonte F., Makova K.D.(2018). Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate. Genome Research 28(12), 1767-1778. doi.org/10.1101/gr.241257.118.
  • Craig S., Blankenberg D., Parodi A., Paul I.M., Birch L.L., Savage J.S., Marini M.E., Stokes J.L., Nekrutenko A., Reimherr M., Chiaromonte F., Makova K.D. (2018). Child weight gain trajectories linked to oral microbiota composition. Scientific Reports 8(1), 14030. doi.org/10.1038/s41598-018-31866-9.
  • Pangenomics Consortium (2018). Computational pan-genomics: status, promises and challenges. Briefings in Bioinformatics 19(1), 118-135. doi.org/10.1093/bib/bbw089.
  • Campos-Sanchez R., Cremona M., Pini A., Chiaromonte F. and Makova K.D. (2016) Integration and fixation preferences of human and mouse endogenous retroviruses uncovered with Functional Data Analysis. PLoS Computational Biology 12(6): e1004956. doi.org/10.1371/ journal.pcbi.1004956.
  • Rebolledo-Jaramilloa B., Shu-Wei M., Stoler N., McElhoec J.A., Dickins B., Blankenberg D., Korneliussen T.S., Chiaromonte F., Nielsen R., Holland M.M., Paul I., Nekrutenko A. and Makova K.D. (2014). Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA. Proceedings of the National Academy of Sciences USA 111(43), 15474–15479. doi.org/10.1073/pnas.1409328111.

METEOROLOGY, CLIMATE, ECONOMICS AND SOCIAL SCIENCES APPLICATIONS

  • Esposito C., Gortan M., Testa L., Chiaromonte F., Fagiolo G., Mina A., Rossetti G. (2022). Venture capital investments through the lens of network and functional data analysis. Applied Network Science. 7, 42 (2022). doi.org/10.1007/s41109-022-00482-y.
  • Vandin A., Giachini D., Lamperti F., Chiaromonte F. (2022) Automated and distributed statistical analysis of economic agent-based models. Journal of Economic Dynamics and Control. doi.org/10.1016/j.jedc.2022.104458.
  • Nanni, M., Andrienko, G., Barabási, A. et al. (2021). Give more data, awareness and control to individual citizens, and they will help COVID-19 containment. Ethics and Information Technology. doi.org/10.1007/s10676-020-09572-w
  • Tripodi G., Chiaromonte F. and Lillo F. (2020) Knowledge and social relatedness shape research portfolio diversification. Scientific Reports. 10, 14232. doi.org/10.1038/s41598-020-71009-7.
  • Coronese M., Lamperti F., Keller K., Chiaromonte F. and Roventini A. (2020) Reply to Geiger and Stomper: On capital intensity and observed increases in the economic damages of extreme natural disasters. Proceedings of the National Academy of Sciences USA. 117 (12) 6314-6315. doi.org/10.1073/pnas.1922722117.
  • Coronese M., Lamperti F., Keller K., Chiaromonte F. and  Roventini A. (2019) Evidence of sharp increase in the economic damages of natural disasters (2019). Proceedings of the National Academy of Sciences USA (43) doi.org/10.1073/pnas.1907826116.
  • Kuruppumullage Don P., Evans J.L., Chiaromonte F. and Kowaleski A.M. (2016) Mixture-Based Path Clustering for Synthesis of ECMWF Ensemble Forecasts of Tropical Cyclone Evolution. Monthly Weather Review. doi:10.1175/MWR-D-15-0214.1