PSU Profiles
Last Name

Francesca Chiaromonte

TitleProfessor of Statistics and Health Evaluation Sciences
InstitutionEberly College of Science
Address505A Wartik Lab
University Park, PA 16802
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    Other Positions
    TitleDirector of the Genomics Institute
    InstitutionHuck Institutes of the Life Sciences

    Collapse Overview 
    Collapse overview

    Professor of Statistics and Health Evaluation Sciences
    Director, Genomics Institute


    Bioinformatics and Genomics


    Ph.D. in Statistics, University of Minnesota


    Dr. Chiaromonte's research focuses on multivariate analysis and regression, computational techniques (re-sampling, perturbation and permutation schemes), Markov modelling, and analysis and modelling of large-scale genomic data.

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    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Fungtammasan A, Walsh E, Chiaromonte F, Eckert KA, Makova KD. Corrigendum: A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome? Genome Res. 2016 10; 26(10):1451. PMID: 27698254.
      View in: PubMed
    2. Liu Y, Chiaromonte F, Li B. Structured Ordinary Least Squares: A Sufficient Dimension Reduction approach for regressions with partitioned predictors and heterogeneous units. Biometrics. 2017 Jun; 73(2):529-539. PMID: 27649087.
      View in: PubMed
    3. Campos-Sánchez R, Cremona MA, Pini A, Chiaromonte F, Makova KD. Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis. PLoS Comput Biol. 2016 06; 12(6):e1004956. PMID: 27309962; PMCID: PMC4911145.
    4. Liu Y, Chiaromonte F, Ross H, Malhotra R, Elleder D, Poss M. Error correction and statistical analyses for intra-host comparisons of feline immunodeficiency virus diversity from high-throughput sequencing data. BMC Bioinformatics. 2015 Jun 30; 16:202. PMID: 26123018; PMCID: PMC4486422.
    5. Goldstein J, Haran M, Simeonov I, Fricks J, Chiaromonte F. An attraction-repulsion point process model for respiratory syncytial virus infections. Biometrics. 2015 Jun; 71(2):376-85. PMID: 25660222.
      View in: PubMed
    6. Rebolledo-Jaramillo B, Su MS, Stoler N, McElhoe JA, Dickins B, Blankenberg D, Korneliussen TS, Chiaromonte F, Nielsen R, Holland MM, Paul IM, Nekrutenko A, Makova KD. Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA. Proc Natl Acad Sci U S A. 2014 Oct 28; 111(43):15474-9. PMID: 25313049; PMCID: PMC4217420.
    7. Campos-Sánchez R, Kapusta A, Feschotte C, Chiaromonte F, Makova KD. Genomic landscape of human, bat, and ex vivo DNA transposon integrations. Mol Biol Evol. 2014 Jul; 31(7):1816-32. PMID: 24809961; PMCID: PMC4069622.
    8. Kuruppumullage Don P, Ananda G, Chiaromonte F, Makova KD. Segmenting the human genome based on states of neutral genetic divergence. Proc Natl Acad Sci U S A. 2013 Sep 03; 110(36):14699-704. PMID: 23959903; PMCID: PMC3767554.
    9. Ananda G, Walsh E, Jacob KD, Krasilnikova M, Eckert KA, Chiaromonte F, Makova KD. Distinct mutational behaviors differentiate short tandem repeats from microsatellites in the human genome. Genome Biol Evol. 2013; 5(3):606-20. PMID: 23241442; PMCID: PMC3622297.
    10. Wagstaff BJ, Hedges DJ, Derbes RS, Campos Sanchez R, Chiaromonte F, Makova KD, Roy-Engel AM. Rescuing Alu: recovery of new inserts shows LINE-1 preserves Alu activity through A-tail expansion. PLoS Genet. 2012; 8(8):e1002842. PMID: 22912586; PMCID: PMC3415434.
    11. Fungtammasan A, Walsh E, Chiaromonte F, Eckert KA, Makova KD. A genome-wide analysis of common fragile sites: what features determine chromosomal instability in the human genome? Genome Res. 2012 Jun; 22(6):993-1005. PMID: 22456607; PMCID: PMC3371707.
    12. Kelkar YD, Eckert KA, Chiaromonte F, Makova KD. A matter of life or death: how microsatellites emerge in and vanish from the human genome. Genome Res. 2011 Dec; 21(12):2038-48. PMID: 21994250; PMCID: PMC3227094.
    13. Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen KB, Drautz D, Giardine B, Shibata Y, Song L, Pimkin M, Crawford GE, Furey TS, Kellis M, Miller W, Taylor J, Schuster SC, Zhang Y, Chiaromonte F, Blobel GA, Weiss MJ, Hardison RC. Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Res. 2011 Oct; 21(10):1659-71. PMID: 21795386; PMCID: PMC3202283.
    14. Ananda G, Chiaromonte F, Makova KD. A genome-wide view of mutation rate co-variation using multivariate analyses. Genome Biol. 2011; 12(3):R27. PMID: 21426544; PMCID: PMC3129677.
    15. Simeonov I, Gong X, Kim O, Poss M, Chiaromonte F, Fricks J. Exploratory Spatial Analysis of in vitro Respiratory Syncytial Virus Co-infections. Viruses. 2010 12; 2(12):2782-802. PMID: 21994640; PMCID: PMC3185596.
    16. Kelkar YD, Strubczewski N, Hile SE, Chiaromonte F, Eckert KA, Makova KD. 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; 2:620-35. PMID: 20668018; PMCID: PMC2940325.
    17. Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, Muzny DM, Reid JG, Nazareth LV, Wang Q, Burhans R, Riemer C, Wittekindt NE, Moorjani P, Tindall EA, Danko CG, Teo WS, Buboltz AM, Zhang Z, Ma Q, Oosthuysen A, Steenkamp AW, Oostuisen H, Venter P, Gajewski J, Zhang Y, Pugh BF, Makova KD, Nekrutenko A, Mardis ER, Patterson N, Pringle TH, Chiaromonte F, Mullikin JC, Eichler EE, Hardison RC, Gibbs RA, Harkins TT, Hayes VM. Complete Khoisan and Bantu genomes from southern Africa. Nature. 2010 Feb 18; 463(7283):943-7. PMID: 20164927; PMCID: PMC3890430.
    18. Cheng Y, Wu W, Kumar SA, Yu D, Deng W, Tripic T, King DC, Chen KB, Zhang Y, Drautz D, Giardine B, Schuster SC, Miller W, Chiaromonte F, Zhang Y, Blobel GA, Weiss MJ, Hardison RC. Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. Genome Res. 2009 Dec; 19(12):2172-84. PMID: 19887574; PMCID: PMC2792182.
    19. Zhang Y, Wu W, Cheng Y, King DC, Harris RS, Taylor J, Chiaromonte F, Hardison RC. Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1. Nucleic Acids Res. 2009 Nov; 37(21):7024-38. PMID: 19767611; PMCID: PMC2790884.
    20. Kosakovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung WY, Taylor J, Nekrutenko A. Windshield splatter analysis with the Galaxy metagenomic pipeline. Genome Res. 2009 Nov; 19(11):2144-53. PMID: 19819906; PMCID: PMC2775585.
    21. Roy S, Lavine J, Chiaromonte F, Terwee J, VandeWoude S, Bjornstad O, Poss M. Multivariate statistical analyses demonstrate unique host immune responses to single and dual lentiviral infection. PLoS One. 2009 Oct 06; 4(10):e7359. PMID: 19806226; PMCID: PMC2752991.
    22. Kvikstad EM, Chiaromonte F, Makova KD. Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions. Genome Res. 2009 Jul; 19(7):1153-64. PMID: 19502380; PMCID: PMC2704434.
    23. Cheng Y, King DC, Dore LC, Zhang X, Zhou Y, Zhang Y, Dorman C, Abebe D, Kumar SA, Chiaromonte F, Miller W, Green RD, Weiss MJ, Hardison RC. Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif. Genome Res. 2008 Dec; 18(12):1896-905. PMID: 18818370; PMCID: PMC2593580.
    24. Tyekucheva S, Makova KD, Karro JE, Hardison RC, Miller W, Chiaromonte F. Human-macaque comparisons illuminate variation in neutral substitution rates. Genome Biol. 2008 Apr 30; 9(4):R76. PMID: 18447906.
      View in: PubMed
    25. Kelkar YD, Tyekucheva S, Chiaromonte F, Makova KD. The genome-wide determinants of human and chimpanzee microsatellite evolution. Genome Res. 2008 Jan; 18(1):30-8. PMID: 18032720; PMCID: PMC2134767.
    26. Cesari P, Chiaromonte F, Newell KM. Support vector machines categorize the scaling of human grip configurations. Behav Res Methods. 2007 Nov; 39(4):1001-7. PMID: 18183918.
      View in: PubMed
    27. Kvikstad EM, Tyekucheva S, Chiaromonte F, Makova KD. A macaque's-eye view of human insertions and deletions: differences in mechanisms. PLoS Comput Biol. 2007 Sep; 3(9):1772-82. PMID: 17941704; PMCID: PMC1976337.
    28. King DC, Taylor J, Zhang Y, Cheng Y, Lawson HA, Martin J. Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data. Genome Res. 2007 Jun; 17(6):775-86. PMID: 17567996; PMCID: PMC1891337.
    29. Gutiérrez RA, Lejay LV, Dean A, Chiaromonte F, Shasha DE, Coruzzi GM. Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis. Genome Biol. 2007; 8(1):R7. PMID: 17217541; PMCID: PMC1839130.
    30. Taylor J, Tyekucheva S, King DC, Hardison RC, Miller W, Chiaromonte F. ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements. Genome Res. 2006 Dec; 16(12):1596-604. PMID: 17053093; PMCID: PMC1665643.
    31. Wang H, Zhang Y, Cheng Y, Zhou Y, King DC, Taylor J, Chiaromonte F, Kasturi J, Petrykowska H, Gibb B, Dorman C, Miller W, Dore LC, Welch J, Weiss MJ, Hardison RC. Experimental validation of predicted mammalian erythroid cis-regulatory modules. Genome Res. 2006 Dec; 16(12):1480-92. PMID: 17038566; PMCID: PMC1665632.
    32. Carrel L, Park C, Tyekucheva S, Dunn J, Chiaromonte F, Makova KD. Genomic environment predicts expression patterns on the human inactive X chromosome. PLoS Genet. 2006 Sep 29; 2(9):e151. PMID: 17009873; PMCID: PMC1584270.
    33. Taylor J, Tyekucheva S, Zody M, Chiaromonte F, Makova KD. Strong and weak male mutation bias at different sites in the primate genomes: insights from the human-chimpanzee comparison. Mol Biol Evol. 2006 Mar; 23(3):565-73. PMID: 16280537.
      View in: PubMed
    34. King DC, Taylor J, Elnitski L, Chiaromonte F, Miller W, Hardison RC. Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. Genome Res. 2005 Aug; 15(8):1051-60. PMID: 16024817; PMCID: PMC1182217.
    35. Yang S, Smit AF, Schwartz S, Chiaromonte F, Roskin KM, Haussler D, Miller W, Hardison RC. Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes. Genome Res. 2004 Apr; 14(4):517-27. PMID: 15059992; PMCID: PMC383295.
    36. Makova KD, Yang S, Chiaromonte F. Insertions and deletions are male biased too: a whole-genome analysis in rodents. Genome Res. 2004 Apr; 14(4):567-73. PMID: 15059997; PMCID: PMC383300.
    37. Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 Apr 01; 428(6982):493-521. PMID: 15057822.
      View in: PubMed
    38. Kolbe D, Taylor J, Elnitski L, Eswara P, Li J, Miller W, Hardison R, Chiaromonte F. Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat. Genome Res. 2004 Apr; 14(4):700-7. PMID: 15060013; PMCID: PMC383316.
    39. Chiaromonte F, Miller W, Bouhassira EE. Gene length and proximity to neighbors affect genome-wide expression levels. Genome Res. 2003 Dec; 13(12):2602-8. PMID: 14613975; PMCID: PMC403802.
    40. Hardison RC, Roskin KM, Yang S, Diekhans M, Kent WJ, Weber R, Elnitski L, Li J, O'Connor M, Kolbe D, Schwartz S, Furey TS, Whelan S, Goldman N, Smit A, Miller W, Chiaromonte F, Haussler D. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res. 2003 Jan; 13(1):13-26. PMID: 12529302; PMCID: PMC430971.
    41. Hardison RC, Chiaromonte F, Kolbe D, Wang H, Petrykowska H, Elnitski L, Yang S, Giardine B, Zhang Y, Riemer C, Schwartz S, Haussler D, Roskin KM, Weber RJ, Diekhans M, Kent WJ, Weiss MJ, Welch J, Miller W. Global predictions and tests of erythroid regulatory regions. Cold Spring Harb Symp Quant Biol. 2003; 68:335-44. PMID: 15338635.
      View in: PubMed
    42. Chiaromonte F, Weber RJ, Roskin KM, Diekhans M, Kent WJ, Haussler D. The share of human genomic DNA under selection estimated from human-mouse genomic alignments. Cold Spring Harb Symp Quant Biol. 2003; 68:245-54. PMID: 15338624.
      View in: PubMed
    43. Elnitski L, Hardison RC, Li J, Yang S, Kolbe D, Eswara P, O'Connor MJ, Schwartz S, Miller W, Chiaromonte F. Distinguishing regulatory DNA from neutral sites. Genome Res. 2003 Jan; 13(1):64-72. PMID: 12529307; PMCID: PMC430974.
    44. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002 Dec 05; 420(6915):520-62. PMID: 12466850.
      View in: PubMed
    45. Chiaromonte F, Martinelli J. Dimension reduction strategies for analyzing global gene expression data with a response. Math Biosci. 2002 Mar; 176(1):123-44. PMID: 11867087.
      View in: PubMed
    46. Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002; 115-26. PMID: 11928468.
      View in: PubMed
    47. Chiaromonte F, Yang S, Elnitski L, Yap VB, Miller W, Hardison RC. Association between divergence and interspersed repeats in mammalian noncoding genomic DNA. Proc Natl Acad Sci U S A. 2001 Dec 04; 98(25):14503-8. PMID: 11717405; PMCID: PMC64711.
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