Francesca Chiaromonte

Director of the Genome Sciences Institute; Huck Chair in Statistics for the Life Sciences; Professor of Statistics

0325 Thomas
University Park, PA
fxc11@psu.edu
814-865-7075

Research Summary

Developing methods for the analysis of large, high-dimensional and complex data.

Huck Affiliations

Bioinformatics and Genomics

Genome Sciences Institute

Most Recent Publications

Evolutionary dynamics of predicted G-quadruplexes in human and other great apes

Saswat K. Mohanty, Francesca Chiaromonte, Kateryna D. Makova, 2025, Genome Biology

Non-canonical DNA in human and other ape telomere-to-telomere genomes

Linnéa Smeds, Kaivan Kamali, Iva Kejnovská, Eduard Kejnovský, Francesca Chiaromonte, Kateryna D. Makova, 2025, Nucleic Acids Research

Raided by the storm: How three decades of thunderstorms shaped U.S. incomes and wages

Matteo Coronese, Federico Crippa, Francesco Lamperti, Francesca Chiaromonte, Andrea Roventini, 2025, Journal of Environmental Economics and Management

funBIalign: a hierachical algorithm for functional motif discovery based on mean squared residue scores

Jacopo Di Iorio, Marzia Cremona, Francesca Chiaromonte, 2025, Statistics and Computing

The public use of early-stage scientific advances in carbon dioxide removal: a science-technology-policy-media perspective

Giorgio Tripodi, Fabrizio Lillo, Roberto Mavilia, Andrea Mina, Francesca Chiaromonte, Francesco Lamperti, 2024, Environmental Research Letters

White-box validation of quantitative product lines by statistical model checking and process mining

Roberto Casaluce, Andrea Burattin, Francesca Chiaromonte, Alberto Lluch Lafuente, Andrea Vandin, 2024, Journal of Systems and Software

Investigating Functional Data Analysis for Wearable Physiological Sensor Data in Stress Evaluation

Luca Carmisciano, Tobia Boschi, Francesca Chiaromonte, Franca Delmastro, Andrea Vandin, 2024,

Methylation profiles at birth linked to early childhood obesity

Delphine Larivier, Delphine Lariviere, Sarah J.C. Craig, Ian M. Paul, Emily E. Hohman, Jennifer S. Savage, Robert O. Wright, Francesca Chiaromonte, Kateryna D. Makova, Matthew L. Reimherr, 2024, Journal of Developmental Origins of Health and Disease on p. e7

FAStEN: An Efficient Adaptive Method for Feature Selection and Estimation in High-Dimensional Functional Regressions

Tobia Boschi, Lorenzo Testa, Francesca Chiaromonte, Matthew Logan Reimherr, 2024, Journal of Computational and Graphical Statistics

Enhancing Threat Model Validation: A White-Box Approach based on Statistical Model Checking and Process Mining

Roberto Casaluce, Andrea Burratin, Francesca Chiaromonte, Alberto Lluch Lafuente, Andrea Vandin, 2024, CEUR Workshop Proceedings on p. 9-20

Most-Cited Papers

Computational pan-genomics: Status, promises and challenges

Tobias Marschall, Manja Marz, Thomas Abeel, Louis Dijkstra, Bas E. Dutilh, Ali Ghaffaari, Paul Kersey, Wigard P. Kloosterman, Veli Mäkinen, Adam M. Novak, Benedict Paten, David Porubsky, Eric Rivals, Can Alkan, Jasmijn A. Baaijens, Paul I.W. De Bakker, Valentina Boeva, Raoul J.P. Bonnal, Francesca Chiaromonte, Rayan Chikhi, Francesca D. Ciccarelli, Robin Cijvat, Erwin Datema, Cornelia M. Van Duijn, Evan E. Eichler, Corinna Ernst, Eleazar Eskin, Erik Garrison, Mohammed El-Kebir, Gunnar W. Klau, Jan O. Korbel, Eric Wubbo Lameijer, Benjamin Langmead, Marcel Martin, Paul Medvedev, John C. Mu, Pieter Neerincx, Klaasjan Ouwens, Pierre Peterlongo, Nadia Pisanti, Sven Rahmann, Ben Raphael, Knut Reinert, Dick de Ridder, Jeroen de Ridder, Matthias Schlesner, Ole Schulz-Trieglaff, Ashley D. Sanders, Siavash Sheikhizadeh, Carl Shneider, 2018, Briefings in Bioinformatics on p. 118-135

Evidence for sharp increase in the economic damages of extreme natural disasters

Matteo Coronese, Francesco Lamperti, Klaus Keller, Francesca Chiaromonte, Andrea Roventini, 2019, Proceedings of the National Academy of Sciences of the United States of America on p. 21450-21455

Non-B DNA: A major contributor to small-and large-scale variation in nucleotide substitution frequencies across the genome

Wilfried Guiblet, Marzia Cremona, Robert Harris, Di Chen, Kristin A. Eckert, Francesca Chiaromonte, Yi Fei Huang, Kateryna D. Makova, 2021, Nucleic Acids Research on p. 1497--1516

Age-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues

Barbara Arbeithuber, James Hester, Marzia A. Cremona, Nicholas Stoler, Arslan Zaidi, Bonnie Higgins, Kate Anthony, Francesca Chiaromonte, Francisco J. Diaz, Kateryna D. Makova, 2020, PLoS Biology

Honey bee colony loss linked to parasites, pesticides and extreme weather across the United States

Luca Insolia, Roberto Molinari, Stephanie R. Rogers, Geoffrey R. Williams, Francesca Chiaromonte, Martina Calovi, 2022, Scientific Reports

Child Weight Gain Trajectories Linked To Oral Microbiota Composition

Sarah J.C. Craig, Daniel Blankenberg, Alice Carla Luisa Parodi, Ian M. Paul, Leann L. Birch, Jennifer S. Savage, Michele E. Marini, Jennifer L. Stokes, Anton Nekrutenko, Matthew Reimherr, Francesca Chiaromonte, Kateryna D. Makova, 2018, Scientific Reports

Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate

Wilfried M. Guiblet, Marzia A. Cremona, Monika Cechova, Robert S. Harris, Iva Kejnovská, Eduard Kejnovsky, Kristin Eckert, Francesca Chiaromonte, Kateryna D. Makova, 2018, Genome Research on p. 1767-1778

Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis

Rebeca Campos-Sánchez, Marzia A. Cremona, Alessia Pini, Francesca Chiaromonte, Kateryna D. Makova, 2016, PLoS Computational Biology

Functional data analysis characterizes the shapes of the first COVID-19 epidemic wave in Italy

Tobia Boschi, Jacopo Di Iorio, Lorenzo Testa, Marzia A. Cremona, Francesca Chiaromonte, 2021, Scientific Reports

High Satellite Repeat Turnover in Great Apes Studied with Short- And Long-Read Technologies

Monika Cechova, Robert S. Harris, Marta Tomaszkiewicz, Barbara Arbeithuber, Francesca Chiaromonte, Kateryna D. Makova, 2019, Molecular Biology and Evolution on p. 2415-2431

News Articles Featuring Francesca Chiaromonte

May 16, 2025

Beyond the Double Helix: Strange New DNA Structures Discovered in Ape Genomes

Researchers utilized recently published telomere-to-telomere genomes of humans, chimpanzees, bonobos, gorillas, and two orangutans to predict where DNA sequences might form alternative structures beyond the traditional double helix.

Full Article

Apr 24, 2025

Beyond the double helix: Alternative DNA conformations in ape genomes

Researchers used recently published telomere-to-telomere genomes of humans, chimpanzee, bonobo, gorilla and two orangutans to predict locations of DNA sequences that can form other structures besides the double helix.

Full Article

Feb 17, 2023

For a best friend to Florida bees, each rescue is personal

Melissa Sorokin sees herself as "a bee advocate," deeply passionate about helping to rescue the at-risk creatures that play such a critical role in biodiversity.

Full Article

Feb 01, 2023

Penn State study shows many causes of Honey bee colony loss

For years, honey bee colonies have been dying off at alarming rates. According to one study, between April 2019 and April 2020, there was a 43% colony loss across the United States. When you consider that one-third of the food we eat comes from crops pollinated by honey bees, “alarming” really is the right word for the situation.

Full Article

Jan 30, 2023

Parasites, pesticides, climate change linked to loss of honey bee colonies

About 43% of honey bee colonies were lost in the span of one year, according to a new study that considered multiple factors that put a crucial part of the ecosystem at risk.

Full Article

Jan 30, 2023

Honey bee colony loss in the U.S. linked to mites, extreme weather, pesticides

About one-third of the food eaten by Americans comes from crops pollinated by honey bees, yet the insect is dying off at alarming rates.

Full Article

Aug 30, 2021

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

Staying home and limiting local travel, supporting access to primary care, and limiting contacts in contagion hubs — including hospitals, schools, and workplaces — are strategies that might help reduce COVID-19-related deaths, according to new research.

Full Article

Feb 04, 2021

Unusual DNA folding increases the rates of mutations

DNA sequences that can fold into shapes other than the classic double helix tend to have higher mutation rates than other regions in the human genome. New research by a team of Penn State scientists shows that the elevated mutation rate in these sequences plays a major role in determining regional variation in mutation rates across the genome.

Full Article

Sep 29, 2020

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

Using state-of-the-art statistical methods, a team of researchers said they may have taken a leap closer to understanding a class of jumping genes, sequences that move to different locations in the human genome, which is the body’s complete set of DNA.

Full Article

Dec 12, 2019

Hurricanes Wreak Greater Havoc as Temperatures Soar

Devastation caused by the most powerful hurricanes has increased by up to twentyfold, according to a newly-identified pattern in natural disasters.

Full Article

Oct 08, 2019

Cost of natural disasters like hurricanes Katrina, Maria are increasing at high end

According to an international team of researchers, The costs of major disasters like hurricanes Katrina, Maria and Dorian or the massive tornado swarms in the Midwest have increased to a disproportionately larger extent than those of lesser events, and these major disasters have become far more expensive.

Full Article

Oct 07, 2019

Data scientists put a staggering price tag on climate change's effects

Hurricanes, floods, and other natural disasters can destroy and displace communities. Beyond the human cost, this damage is unimaginably expensive for many who are affected. New research out Monday puts a price tag on how bad things might get.

Full Article

Oct 07, 2019

Costs of natural disasters are increasing at the high end

While the economic cost of natural disasters has not increased much on average, averages can be deceptive. The costs of major disasters like hurricanes Katrina, Maria and Dorian or the massive tornado swarms in the Midwest have increased to a disproportionately larger extent than those of lesser events, and these major disasters have become far more expensive, according to an international team of researchers.

Full Article

Sep 17, 2019