Francesca Chiaromonte

Director of the Genome Sciences Institute; Professor of Statistics

Francesca Chiaromonte

Research Summary

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

Huck Institutes Affiliations

Links

Most Recent Papers

IWTomics

Marzia A. Cremona, Alessia Pini, Fabio Cumbo, Kateryna D. 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, 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

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 A. Cremona, Alessia Pini, Francesca Chiaromonte, Kateryna D. Makova, 2016, PLoS Computational Biology

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

Prabhani Kuruppumullage Don, Jenni L. 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

An attraction-repulsion point process model for respiratory syncytial virus infections

Joshua Goldstein, Murali Haran, Ivan Simeonov, John Fricks, Francesca Chiaromonte, 2015, Biometrics on p. 376-385

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 M. Holland, Ian M. Paul, Anton Nekrutenko, Kateryna D. Makova, 2014, Proceedings of the National Academy of Sciences of the United States of America on p. 15474-15479

Genomic landscape of human, bat, and ex vivo DNA transposon integrations

Rebeca Campos-Sánchez, Aurélie Kapusta, Cédric Feschotte, Francesca Chiaromonte, Kateryna D. Makova, 2014, Molecular Biology and Evolution on p. 1816-1822

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 S. 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, B. Franklin Pugh, Kateryna D. Makova, Anton Nekrutenko, Elaine R. Mardis, Nick Patterson, Tom H. Pringle, Francesca Chiaromonte, James C. Mullikin, Evan E. Eichler, Ross C. Hardison, Richard A. Gibbs, Timothy T. Harkins, Vanessa M. Hayes, 2010, Nature on p. 943-947

The genome-wide determinants of human and chimpanzee microsatellite evolution

Yogeshwar D. Kelkar, Svitlana Tyekucheva, Francesca Chiaromonte, Kateryna D. Makova, 2008, Genome Research on p. 30-38

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 C. 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, 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 C. Hardison, 2011, Genome research on p. 1659-1671

What is a microsatellite

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

A genome-wide analysis of common fragile sites

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

Envelope models for parsimonious and efficient multivariate linear regression

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

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 M. Holland, Ian M. Paul, Anton Nekrutenko, Kateryna D. Makova, 2014, Proceedings of the National Academy of Sciences of the United States of America on p. 15474-15479

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

A matter of life or death

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