Francesca Chiaromonte

Director of the Genome Sciences Institute; Professor of Statistics; Dorothy Foehr Huck and J. Lloyd Huck Chair in Statistics for the Life Sciences

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

Most Recent Papers

Covariate Information Matrix for Sufficient Dimension Reduction

Weixin Yao, Debmalya Nandy, Bruce G. Lindsay, Francesca Chiaromonte, 2019, Journal of the American Statistical Association

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

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

Child Weight Gain Trajectories Linked To Oral Microbiota Composition

Sarah Craig, Daniel Blankenberg, Alice Carla Luisa Parodi, Ian Paul, Leann L. Birch, Jennifer Savage Williams, Michele E. Marini, Jennifer L. Stokes, Anton Nekrutenko, Matthew Logan Reimherr, Francesca Chiaromonte, Kateryna Dmytrivna Makova, 2018, Scientific reports

IWTomics

Marzia Cremona, Alessia Pini, Fabio Cumbo, Kateryna Dmytrivna Makova, Francesca Chiaromonte, Simone Vantini, 2018, Bioinformatics on p. 2289-2291

Computational pan-genomics

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, Francesca Chiaromonte, 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, Paul Medvedev, Paul Medvedev, Jeroen de Ridder, Matthias Schlesner, Ole Schulz-Trieglaff, Ashley D. Sanders, Siavash Sheikhizadeh, Carl Shneider, 2018, Briefings in bioinformatics on p. 118-135

Structured Ordinary Least Squares

Yang Liu, Francesca Chiaromonte, Bing Li, 2017, Biometrics on p. 529-539

Composite Likelihood Inference in a Discrete Latent Variable Model for Two-Way “Clustering-by-Segmentation” Problems

Francesco Bartolucci, Francesca Chiaromonte, Prabhani Kuruppumullage Don, Bruce G. Lindsay, 2017, Journal of Computational and Graphical Statistics on p. 388-402

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

Rebeca Campos-Sánchez, Marzia Cremona, Alessia Pini, Francesca Chiaromonte, Kateryna Dmytrivna Makova, 2016, PLoS computational biology

Mixture-based path clustering for synthesis of ECMWF ensemble forecasts of tropical cyclone evolution

Prabhani Kuruppumullage Don, Jenni Evans, Francesca Chiaromonte, Alex M. Kowaleski, 2016, Monthly Weather Review on p. 3301-3320

Error correction and statistical analyses for intra-host comparisons of feline immunodeficiency virus diversity from high-throughput sequencing data

Yang Liu, Francesca Chiaromonte, Howard Ross, Raunaq Malhotra, Daniel Elleder, Mary Poss, 2015, BMC bioinformatics

High-Impact Papers

Complete Khoisan and Bantu genomes from southern Africa

Stephan C. Schuster, Webb Miller, Aakrosh Ratan, Lynn P. Tomsho, Belinda Giardine, Lindsay R. Kasson, Robert Scott Harris, Desiree C. Petersen, Fangqing Zhao, Ji Qi, Can Alkan, Jeffrey M. Kidd, Yazhou Sun, Daniela I. Drautz, Pascal Bouffard, Donna M. Muzny, Jeffrey G. Reid, Lynne V. Nazareth, Qingyu Wang, Richard Burhans, Cathy Riemer, Nicola E. Wittekindt, Priya Moorjani, Elizabeth A. Tindall, Charles G. Danko, Wee Siang Teo, Anne M. Buboltz, Zhenhai Zhang, Qianyi Ma, Arno Oosthuysen, Abraham W. Steenkamp, Hermann Oostuisen, Philippus Venter, John Gajewski, Yu Zhang, Benjamin Franklin Pugh, Kateryna Dmytrivna Makova, Anton Nekrutenko, Elaine R. Mardis, Nick Patterson, Tom H. Pringle, Francesca Chiaromonte, James C. Mullikin, Evan E. Eichler, Ross Cameron Hardison, Richard A. Gibbs, Timothy T. Harkins, Vanessa M. Hayes, 2010, Nature on p. 943-947

Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression

Yong Cheng, Weisheng Wu, Swathi Ashok Kumar, Duonan Yu, Wulan Deng, Tamara Tripic, David C. King, Kuan Bei Chen, Ying Zhang, Daniela Drautz, Belinda Giardine, Stephan C. Schuster, Webb Miller, Francesca Chiaromonte, Yu Zhang, Gerd A. Blobel, Mitchell J. Weiss, Ross Cameron Hardison, 2009, Genome Research on p. 2172-2184

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

Weisheng Wu, Yong Cheng, Cheryl A. Keller Capone, Jason Ernst, Swathi Ashok Kumar, Tejaswini Mishra, Christapher Morrissey, Christine M. Dorman, Kuan Bei Chen, Daniela Drautz, Belinda Giardine, Yoichiro Shibata, Lingyun Song, Max Pimkin, Gregory E. Crawford, Terrence S. Furey, Manolis Kellis, Webb Miller, James Taylor, Stephan C. Schuster, Yu Zhang, Francesca Chiaromonte, Gerd A. Blobel, Mitchell J. Weiss, Ross Cameron Hardison, 2011, Genome research on p. 1659-1671

A genome-wide analysis of common fragile sites

Arkarachai Fungtammasan, Erin Walsh, Francesca Chiaromonte, Kristin Eckert, Kateryna Dmytrivna Makova, 2012, Genome Research on p. 993-1005

Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA

Boris Rebolledo-Jaramillo, Marcia Shu Wei Su, Nicholas Stoler, Jennifer A. McElhoe, Benjamin Dickins, Daniel Blankenberg, Thorfinn S. Korneliussen, Francesca Chiaromonte, Rasmus Nielsen, Mitchell Mark Holland, Ian Paul, Anton Nekrutenko, Kateryna Dmytrivna Makova, 2014, Proceedings of the National Academy of Sciences of the United States of America on p. 15474-15479

What is a microsatellite

Yogeshwar D. Kelkar, Noelle Strubczewski, Suzanne E. Hile, Francesca Chiaromonte, Kristin Eckert, Kateryna Dmytrivna Makova, 2010, Genome Biology and Evolution on p. 620-635

Envelope models for parsimonious and efficient multivariate linear regression

R. Dennis Cook, Bing Li, Francesca Chiaromonte, 2010, Statistica Sinica on p. 927-960

Windshield splatter analysis with the Galaxy metagenomic pipeline

Sergei Kosakovsky Pond, Samir Wadhawan, Francesca Chiaromonte, Guruprasad Ananda, Wen Yu Chung, James Taylor, Anton Nekrutenko, 2009, Genome research on p. 2144-2153

Computational pan-genomics

A matter of life or death

Yogeshwar D. Kelkar, Kristin Eckert, Francesca Chiaromonte, Kateryna Dmytrivna Makova, 2011, Genome research on p. 2038-2048

News Articles Featuring Francesca Chiaromonte

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