Interests
- Development of statistical methods to analyze large, high-dimensional, and complex data and its application in various scientific fields
- Computational techniques for the empirical assessment of significance
- Latent structure and Markov modeling approaches
- Functional data analysis methods
Education
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Laurea (cum laude) in Statistic and Economic Sciences,
University of Rome La Sapienza, Italy
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Ph.D. in Statistics,
University of Minnesota
Biography
Francesca is a statistician developing methods for the analysis of large, high-dimensional and complex data, and applying such methods in contemporary “Omics” sciences and other scientific fields – including Meteorology and Economics.
Publications
SK Mohanty, F Chiaromonte, KD Makova.
Evolutionary Dynamics of G-Quadruplexes in Human and Other Great Ape Telomere-to-Telomere Genomes.
BIORXIV,
2024.
D Lariviere, SJC Craig, IM Paul, E Hohman, JS Savage, RO Wright, F Chiaromonte, KD Makova, ML Reimherr.
Methylation profiles at birth linked to early childhood obesity.
J DEV ORIG HEALTH DIS,
2024.
M Weissensteiner, MA Cremona, WM Guiblet, N Stoler, RS Harris, M Cechova, KA Eckert, F Chiaromonte, YF Huang, KD Makova.
Accurate sequencing of DNA motifs able to form alternative (non-B) structures.
GENOME RES,
2023.
SJC Craig, AM Kenney, J Lin, IM Paul, LL Birch, JS Savage, ME Marini, F Chiaromonte, ML Reimherr, KD Makova.
Constructing a polygenic risk score for childhood obesity using functional data analysis.
ECONOM STAT,
2023.
B Arbeithuber, MA Cremona, J Hester, A Barrett, B Higgins, K Anthony, F Chiaromonte, FJ Diaz, KD Makova.
Advanced age increases frequencies of de novo mitochondrial mutations in macaque oocytes and somatic tissues.
P NATL ACAD SCI USA,
2022.
D Nandy, SJ Craig, J Cai, Y Tian, IM Paul, JS Savage, ME Marini, EE Hohman, ML Reimherr, AD Patterson, KD Makova, F Chiaromonte.
Metabolomic profiling of stool of two-year old children from the INSIGHT study reveals links between butyrate and child weight outcomes.
PED OBESITY,
2022.
WM Guiblet, M DeGiorgio, X Cheng, F Chiaromonte, KA Eckert, YF Huang, KD Makova.
Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome.
GENOME RES,
2021.
WM Guiblet, MA Cremona, RS Harris, D Chen, KA Eckert, F Chiaromonte, Y Huang, KD Makova.
Non-B DNA: A major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome.
NUCLEIC ACIDS RES,
2021.
D Chen, MA Cremona, Z Qi, RD Mitra, F Chiaromonte, KD Makova.
Human L1 Transposition Dynamics Unraveled with Functional Data Analysis.
MOL BIOL EVOL,
2020.
B Arbeithuber, J Hester, MA Cremona, N Stoler, A Zaidi, B Higgins, K Anthony, F Chiaromonte, FJ Diaz, KD Makova.
Age-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues.
PLOS BIOL,
2020.
M Cechova, RS Harris, M Tomaszkiewicz, B Arbeithuber, F Chiaromonte, KD Makova.
High Satellite Repeat Turnover in Great Apes Studied with Short- and Long-read Technologies.
MOL BIOL EVOL,
2019.
SJC Craig, AM Kenney, J Lin, IM Paul, LL Birch, JS Savage, ME Marini, F Chiaromonte, M Reimherr, KD Makova.
Polygenic risk score based on weight gain trajectories is a strong predictor of childhood obesity.
BIORXIV,
2019.
MA Cremona, H Xu, KD Makova, M Reimherr, F Chiaromonte, P Madrigal.
Functional data analysis for computational biology.
BIOINFORMATICS,
2019.
WM Guiblet, MA Cremona, M Cechova, RS Harris, I Kejnovská, E Kejnovsky, KA Eckert, F Chiaromonte, KD Makova.
Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate.
GENOME RES,
2018.
Regional variation Non-B DNA & Microsatellite Paper Link Press Release
SJC Craig, D Blankenberg, ACL Parodi, IM Paul, LL Birch, JS Savage, ME Marini, JL Stokes, A Nekrutenko, M Reimherr, F Chiaromonte, KD Makova.
Child Weight Gain Trajectories Linked To Oral Microbiota Composition.
SCI REP-UK,
2018.
MA Cremona, A Pini, F Cumbo, KD Makova, F Chiaromonte, S Vantini.
IWTomics: testing high-resolution sequence-based `Omics' data at multiple locations and scales.
BIOINFORMATICS,
2018.
R Campos-Sánchez, MA Cremona, A Pini, F Chiaromonte, KD Makova.
Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis.
PLOS COMPUT BIOL,
2016.
F Chiaromonte, KD Makova.
Using Statistics to Shed Light on the Dynamics of the Human Genome: A Review.
CONTRIB STAT,
2015.
B Rebolledo-Jaramillo, MS-W Su, N Stoler, JA McElhoe, B Dickins, D Blankenberg, TS Korneliussen, F Chiaromonte, R Nielsen, MM Holland, IM Paul, A Nekrutenko, KD Makova.
Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA.
P NATL ACAD SCI USA,
2014.
R Campos-Sánchez, A Kapusta, C Feschotte, F Chiaromonte, KD Makova.
Genomic Landscape of Human, Bat, and Ex Vivo DNA Transposon Integrations.
MOL BIOL EVOL,
2014.
P Kuruppumullage Don, G Ananda, F Chiaromonte, KD Makova.
Segmenting the human genome based on states of neutral genetic divergence.
P NATL ACAD SCI USA,
2013.
G Ananda, E Walsh, KD Jacob, MM Krasilnikova, KA Eckert, F Chiaromonte, KD Makova.
Distinct Mutational Behaviors Differentiate Short Tandem Repeats from Microsatellites in the Human Genome.
GENOME BIOL EVOL,
2013.
BJ Wagstaff, DJ Hedges, RS Derbes, R Campos-Sánchez, F Chiaromonte, KD Makova, AM Roy-Engel.
Rescuing Alu: Recovery of New Inserts Shows LINE-1 Preserves Alu Activity through A-Tail Expansion.
PLOS GENET,
2012.
A Fungtammasan, E Walsh, F Chiaromonte, KA Eckert, KD Makova.
A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?.
GENOME RES,
2012.
G Ananda, F Chiaromonte, KD Makova.
A genome-wide view of mutation rate co-variation using multivariate analyses.
GENOME BIOL,
2011.
YD Kelkar, KA Eckert, F Chiaromonte, KD Makova.
A matter of life or death: How microsatellites emerge in and vanish from the human genome.
GENOME RES,
2011.
SC Schuster, W Miller, A Ratan, LP Tomsho, B Giardine, LR Kasson, RS Harris, DC Petersen, F Zhao, J Qi, C Alkan, JM Kidd, Y Sun, DI Drautz, P Bouffard, DM Muzny, JG Reid, LV Nazareth, Q Wang, RC Burhans, C Riemer, NE Wittekindt, P Moorjani, EA Tindall, CG Danko, WS Teo, AM Buboltz, Z Zhang, Q Ma, A Oosthuysen, AW Steenkamp, H Oostuisen, P Venter, J Gajewski, Y Zhang, BF Pugh, KD Makova, A Nekrutenko, ER Mardis, N Patterson, TH Pringle, F Chiaromonte, JC Mullikin, EE Eichler, RC Hardison, RA Gibbs, TT Harkins, VM Hayes.
Complete Khoisan and Bantu genomes from southern Africa.
NATURE,
2010.
YD Kelkar, N Strubczewski, SE Hile, F Chiaromonte, KA Eckert, KD Makova.
What Is a Microsatellite: A Computational and Experimental Definition Based upon Repeat Mutational Behavior at A/T and GT/AC Repeats.
GENOME BIOL EVOL,
2010.
EM Kvikstad, F Chiaromonte, KD Makova.
Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions.
GENOME RES,
2009.
S Tyekucheva, KD Makova, JE Karro, RC Hardison, W Miller, F Chiaromonte.
Human-macaque comparisons illuminate variation in neutral substitution rates.
GENOME BIOL,
2008.
YD Kelkar, S Tyekucheva, F Chiaromonte, KD Makova.
The genome-wide determinants of human and chimpanzee microsatellite evolution.
GENOME RES,
2008.
EM Kvikstad, S Tyekucheva, F Chiaromonte, KD Makova.
A Macaque's-Eye View of Human Insertions and Deletions: Differences in Mechanisms.
PLOS COMPUT BIOL,
2007.
L Carrel, C Park, S Tyekucheva, J Dunn, F Chiaromonte, KD Makova.
Genomic Environment Predicts Expression Patterns on the Human Inactive X Chromosome.
PLOS GENET,
2006.
J Taylor, S Tyekucheva, M Zody, F Chiaromonte, KD Makova.
Strong and Weak Male Mutation Bias at Different Sites in the Primate Genomes: Insights from the Human-Chimpanzee Comparison.
MOL BIOL EVOL,
2006.
International Chicken Genome Sequencing Consortium, LW Hillier, W Miller, E Birney, W Warren, RC Hardison, CP Ponting, P Bork, DW Burt, MAM Groenen, ME Delany, JB Dodgson, AT Chinwalla, PF Cliften, SW Clifton, KD Delehaunty, C Fronick, RS Fulton, TA Graves, C Kremitzki, D Layman, V Magrini, JD McPherson, TL Miner, P Minx, WE Nash, MN Nhan, JO Nelson, LG Oddy, CS Pohl, J Randall-Maher, SM Smith, JW Wallis, S-P Yang, MN Romanov, CM Rondelli, B Paton, J Smith, D Morrice, L Daniels, HG Tempest, L Robertson, JS Masabanda, DK Griffin, A Vignal, V Fillon, L Jacobbson, S Kerje, L Andersson, RPM Crooijmans, J Aerts, JJ van der Poel, H Ellegren, RB Caldwell, SJ Hubbard, DV Grafham, AM Kierzek, SR McLaren, IM Overton, H Arakawa, KJ Beattie, Y Bezzubov, PE Boardman, JK Bonfield, MDR Croning, RM Davies, MD Francis, SJ Humphray, CE Scott, RG Taylor, C Tickle, WRA Brown, J Rogers, J-M Buerstedde, SA Wilson, L Stubbs, I Ovcharenko, L Gordon, S Lucas, MM Miller, H Inoko, T Shiina, J Kaufman, J Salomonsen, K Skjoedt, GK-S Wong, J Wang, B Liu, J Wang, J Yu, H Yang, M Nefedov, M Koriabine, PJ deJong, L Goodstadt, C Webber, NJ Dickens, I Letunic, M Suyama, D Torrents, C von Mering, EM Zdobnov, KD Makova, A Nekrutenko, L Elnitski, P Eswara, DC King, S Yang, S Tyekucheva, A Radakrishnan, RS Harris, F Chiaromonte, J Taylor, J He, M Rijnkels, S Griffiths-Jones, A Ureta-Vidal, MM Hoffman, J Severin, SMJ Searle, AS Law, D Speed, D Waddington, Z Cheng, E Tuzun, EE Eichler, Z Bao, P Flicek, DD Shteynberg, MR Brent, JM Bye, EJ Huckle, S Chatterji, C Dewey, L Pachter, A Kouranov, Z Mourelatos, AG Hatzigeorgiou, AH Paterson, R Ivarie, M Brandstrom, E Axelsson, N Backstrom, S Berlin, MT Webster, O Pourquie, A Reymond, C Ucla, SE Antonarakis, M Long, JJ Emerson, E Betrán, I Dupanloup, H Kaessmann, AS Hinrichs, G Bejerano, TS Furey, RA Harte, B Raney, A Siepel, WJ Kent, D Haussler, E Eyras, R Castelo, JF Abril, S Castellano, F Camara, G Parra, R Guigo, G Bourque, G Tesler, PA Pevzner, AFA Smit, LA Fulton, ER Mardis, RK Wilson.
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
NATURE,
2004.
Rat Genome Sequencing Project Consortium, RA Gibbs, GM Weinstock, ML Metzker, DM Muzny, EJ Sodergren, S Scherer, G Scott, D Steffen, KC Worley, PE Burch, GO Okwuonu, S Hines, LR Lewis, C DeRamo, O Delgado, S Dugan-Rocha, G Miner, M Morgan, AC Hawes, R Gill, CRA Holt, MD Adams, PG Amanatides, H Baden-Tillson, M Barnstead, S Chin, CA Evans, S Ferriera, C Fosler, A Glodek, Z Gu, D Jennings, CL Kraft, T Nguyen, CM Pfannkoch, C Sitter, GG Sutton, JC Venter, T Woodage, D Smith, H-M Lee, E Gustafson, P Cahill, A Kana, L Doucette-Stamm, K Weinstock, K Fechtel, RB Weiss, DM Dunn, ED Green, RW Blakesley, GG Bouffard, PJ de Jong, K Osoegawa, B Zhu, MA Marra, JE Schein, I Bosdet, C Fjell, SM Jones, M Krzywinski, C Mathewson, A Siddiqui, N Wye, JD McPherson, S Zhao, CM Fraser, J Shetty, S Shatsman, K Geer, Y Chen, S Abramzon, WC Nierman, RA Gibbs, GM Weinstock, PH Havlak, R Chen, K James Durbin, A Egan, Y Ren, HX-Z Song, B Li, Y Liu, X Qin, S Cawley, GM Weinstock, KC Worley, AJ Cooney, RA Gibbs, LM D’Souza, K Martin, J Qian Wu, ML Gonzalez-Garay, AR Jackson, KJ Kalafus, MP McLeod, A Milosavljevic, D Virk, A Volkov, DA Wheeler, Z Zhang, JA Bailey, EE Eichler, E Tuzun, E Birney, E Mongin, A Ureta-Vidal, C Woodwark, EM Zdobnov, P Bork, M Suyama, D Torrents, M Alexandersson, BJ Trask, JM Young, D Smith, H Huang, K Fechtel, H Wang, H Xing, K Weinstock, S Daniels, D Gietzen, J Schmidt, K Stevens, U Vitt, J Wingrove, F Camara, M Mar Albà, JF Abril, R Guigo, AFA Smit, I Dubchak, EM Rubin, O Couronne, A Poliakov, N Hübner, D Ganten, C Goesele, O Hummel, T Kreitler, Y-A Lee, J Monti, H Schulz, H Zimdahl, H Himmelbauer, H Lehrach, HJ Jacob, S Bromberg, J Gullings-Handley, MI Jensen-Seaman, AE Kwitek, J Lazar, D Pasko, PJ Tonellato, S Twigger, CP Ponting, JM Duarte, S Rice, L Goodstadt, SA Beatson, RD Emes, EE Winter, C Webber, P Brandt, G Nyakatura, M Adetobi, F Chiaromonte, L Elnitski, P Eswara, RC Hardison, M Hou, D Kolbe, KD Makova, W Miller, A Nekrutenko, C Riemer, S Schwartz, J Taylor, S Yang, Y Zhang, K Lindpaintner, TD Andrews, M Caccamo, M Clamp, L Clarke, V Curwen, R Durbin, E Eyras, SMJ Searle, GM Cooper, S Batzoglou, M Brudno, A Sidow, EA Stone, J Craig Venter, BA Payseur, G Bourque, C López-Otín, XS Puente, K Chakrabarti, S Chatterji, C Dewey, L Pachter, N Bray, VB Yap, A Caspi, G Tesler, PA Pevzner, D Haussler, KM Roskin, R Baertsch, H Clawson, TS Furey, AS Hinrichs, D Karolchik, WJ Kent, KR Rosenbloom, H Trumbower, M Weirauch, DN Cooper, PD Stenson, B Ma, MR Brent, M Arumugam, DD Shteynberg, RR Copley, MS Taylor, H Riethman, U Mudunuri, J Peterson, M Guyer, A Felsenfeld, S Old, S Mockrin, F Collins.
Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
NATURE,
2004.
KD Makova, S Yang, F Chiaromonte.
Insertions and Deletions Are Male Biased Too: A Whole-Genome Analysis in Rodents.
GENOME RES,
2004.