Francesca Chiaromonte - Publications

Pennsylvania State University, State College, PA, United States 
Statistics, Biostatistics Biology

68 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Nandy D, Craig SJC, Cai J, Tian Y, Paul IM, Savage JS, Marini ME, Hohman EE, Reimherr ML, Patterson AD, Makova KD, Chiaromonte F. Metabolomic profiling of stool of two-year old children from the INSIGHT study reveals links between butyrate and child weight outcomes. Pediatric Obesity. e12833. PMID 34327846 DOI: 10.1111/ijpo.12833  1
2021 Guiblet WM, DeGiorgio M, Cheng X, Chiaromonte F, Eckert KA, Huang YF, Makova KD. Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome. Genome Research. PMID 34187812 DOI: 10.1101/gr.269589.120  1
2021 Nanni M, Andrienko G, Barabási AL, Boldrini C, Bonchi F, Cattuto C, Chiaromonte F, Comandé G, Conti M, Coté M, Dignum F, Dignum V, Domingo-Ferrer J, Ferragina P, Giannotti F, et al. Give more data, awareness and control to individual citizens, and they will help COVID-19 containment. Ethics and Information Technology. 1-6. PMID 33551673 DOI: 10.1007/s10676-020-09572-w  0.01
2021 M Guiblet W, Cremona MA, Harris RS, Chen D, Eckert KA, Chiaromonte F, Huang YF, Makova KD. Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome. Nucleic Acids Research. PMID 33450015 DOI: 10.1093/nar/gkaa1269  1
2020 Tripodi G, Chiaromonte F, Lillo F. Knowledge and social relatedness shape research portfolio diversification. Scientific Reports. 10: 14232. PMID 32859944 DOI: 10.1038/S41598-020-71009-7  0.01
2020 Mughal MR, Koch H, Huang J, Chiaromonte F, DeGiorgio M. Learning the properties of adaptive regions with functional data analysis. Plos Genetics. 16: e1008896. PMID 32853200 DOI: 10.1371/Journal.Pgen.1008896  1
2020 Chen D, Cremona MA, Qi Z, Mitra RD, Chiaromonte F, Makova KD. Human L1 Transposition Dynamics Unraveled with Functional Data Analysis. Molecular Biology and Evolution. PMID 32722770 DOI: 10.1093/Molbev/Msaa194  1
2020 Arbeithuber B, Hester J, Cremona MA, Stoler N, Zaidi A, Higgins B, Anthony K, Chiaromonte F, Diaz FJ, Makova KD. Age-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues. Plos Biology. 18: e3000745. PMID 32667908 DOI: 10.1371/Journal.Pbio.3000745  1
2020 Coronese M, Lamperti F, Keller K, Chiaromonte F, Roventini A. Reply to Geiger and Stomper: On capital intensity and observed increases in the economic damages of extreme natural disasters. Proceedings of the National Academy of Sciences of the United States of America. PMID 32156737 DOI: 10.1073/Pnas.1922722117  0.01
2020 Di Iorio J, Chiaromonte F, Cremona MA. On the bias of H-scores for comparing biclusters, and how to correct it. Bioinformatics (Oxford, England). PMID 31985794 DOI: 10.1093/Bioinformatics/Btaa060  1
2019 Coronese M, Lamperti F, Keller K, Chiaromonte F, Roventini A. Evidence for sharp increase in the economic damages of extreme natural disasters. Proceedings of the National Academy of Sciences of the United States of America. PMID 31591192 DOI: 10.1073/Pnas.1907826116  0.01
2019 Cechova M, Harris RS, Tomaszkiewicz M, Arbeithuber B, Chiaromonte F, Makova KD. High satellite repeat turnover in great apes studied with short- and long-read technologies. Molecular Biology and Evolution. PMID 31273383 DOI: 10.1093/Molbev/Msz156  1
2019 Cremona M, Xu H, Makova K, Reimherr M, Chiaromonte F, Madrigal P. Functional data analysis for computational biology. Bioinformatics (Oxford, England). PMID 30668667 DOI: 10.1093/Bioinformatics/Btz045  1
2019 Larivière D, Don PK, Wickham L, Chiaromonte F, Keiler K, Nekrutenko A. Transposon insertion sequencing analysis in Galaxy F1000research. 8. DOI: 10.7490/F1000Research.1117141.1  1
2019 Yao W, Nandy D, Lindsay BG, Chiaromonte F. Covariate Information Matrix for Sufficient Dimension Reduction Journal of the American Statistical Association. 114: 1752-1764. DOI: 10.1080/01621459.2018.1515080  0.01
2018 Guiblet W, Cremona M, Cechova M, Harris R, Kejnovska I, Kejnovsky E, Eckert KA, Chiaromonte F, Makova KD. Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate. Genome Research. PMID 30401733 DOI: 10.1101/Gr.241257.118  1
2018 Craig SJC, Blankenberg D, Parodi ACL, Paul IM, Birch LL, Savage JS, Marini ME, Stokes JL, Nekrutenko A, Reimherr M, Chiaromonte F, Makova KD. Child Weight Gain Trajectories Linked To Oral Microbiota Composition. Scientific Reports. 8: 14030. PMID 30232389 DOI: 10.1038/S41598-018-31866-9  1
2018 Cremona MA, Pini A, Cumbo F, Makova KD, Chiaromonte F, Vantini S. IWTomics: testing high-resolution sequence-based "Omics" data at multiple locations and scales. Bioinformatics (Oxford, England). PMID 29474526 DOI: 10.1093/Bioinformatics/Bty090  1
2018 Marschall T, Marz M, Abeel T, Dijkstra L, Dutilh BE, Ghaffaari A, Kersey P, Kloosterman WP, Makinen V, Novak AM, Paten B, Porubsky D, Rivals E, Alkan C, Baaijens JA, ... ... Chiaromonte F, et al. Computational pan-genomics: status, promises and challenges. Briefings in Bioinformatics. 19: 118-135. PMID 27769991 DOI: 10.1093/Bib/Bbw089  1
2016 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 Research. 26: 1451. PMID 27698254 DOI: 10.1101/gr.214460.116  1
2016 Liu Y, Chiaromonte F, Li B. Structured Ordinary Least Squares: A Sufficient Dimension Reduction approach for regressions with partitioned predictors and heterogeneous units. Biometrics. PMID 27649087 DOI: 10.1111/Biom.12579  0.01
2016 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 Computational Biology. 12: e1004956. PMID 27309962 DOI: 10.1371/Journal.Pcbi.1004956  1
2015 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. 16: 202. PMID 26123018 DOI: 10.1186/S12859-015-0607-Z  1
2015 Goldstein J, Haran M, Simeonov I, Fricks J, Chiaromonte F. An attraction-repulsion point process model for respiratory syncytial virus infections. Biometrics. 71: 376-85. PMID 25660222 DOI: 10.1111/Biom.12267  1
2014 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. Proceedings of the National Academy of Sciences of the United States of America. 111: 15474-9. PMID 25313049 DOI: 10.1073/Pnas.1409328111  1
2014 Campos-Sánchez R, Kapusta A, Feschotte C, Chiaromonte F, Makova KD. Genomic landscape of human, bat, and ex vivo DNA transposon integrations. Molecular Biology and Evolution. 31: 1816-32. PMID 24809961 DOI: 10.1093/Molbev/Msu138  1
2013 Kuruppumullage Don P, Ananda G, Chiaromonte F, Makova KD. Segmenting the human genome based on states of neutral genetic divergence. Proceedings of the National Academy of Sciences of the United States of America. 110: 14699-704. PMID 23959903 DOI: 10.1073/Pnas.1221792110  1
2013 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 Biology and Evolution. 5: 606-20. PMID 23241442 DOI: 10.1093/Gbe/Evs116  1
2012 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 Genetics. 8: e1002842. PMID 22912586 DOI: 10.1371/Journal.Pgen.1002842  1
2012 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 Research. 22: 993-1005. PMID 22456607 DOI: 10.1101/Gr.134395.111  1
2011 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 Research. 21: 2038-48. PMID 21994250 DOI: 10.1101/Gr.122937.111  1
2011 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, ... ... Chiaromonte F, et al. Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Research. 21: 1659-71. PMID 21795386 DOI: 10.1101/Gr.125088.111  1
2011 Ananda G, Chiaromonte F, Makova KD. A genome-wide view of mutation rate co-variation using multivariate analyses. Genome Biology. 12: R27. PMID 21426544 DOI: 10.1186/Gb-2011-12-3-R27  1
2010 Simeonov I, Gong X, Kim O, Poss M, Chiaromonte F, Fricks J. Exploratory Spatial Analysis of in vitro Respiratory Syncytial Virus Co-infections. Viruses. 2: 2782-802. PMID 21994640 DOI: 10.3390/V2122782  1
2010 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 Biology and Evolution. 2: 620-35. PMID 20668018 DOI: 10.1093/Gbe/Evq046  1
2010 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, ... ... Chiaromonte F, et al. Complete Khoisan and Bantu genomes from southern Africa. Nature. 463: 943-7. PMID 20164927 DOI: 10.1038/Nature08795  1
2009 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, et al. Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. Genome Research. 19: 2172-84. PMID 19887574 DOI: 10.1101/Gr.098921.109  1
2009 Kosakovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung WY, Taylor J, Nekrutenko A. Windshield splatter analysis with the Galaxy metagenomic pipeline. Genome Research. 19: 2144-53. PMID 19819906 DOI: 10.1101/Gr.094508.109  1
2009 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. 4: e7359. PMID 19806226 DOI: 10.1371/Journal.Pone.0007359  1
2009 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 Research. 37: 7024-38. PMID 19767611 DOI: 10.1093/Nar/Gkp747  1
2009 Kvikstad EM, Chiaromonte F, Makova KD. Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions. Genome Research. 19: 1153-64. PMID 19502380 DOI: 10.1101/Gr.088922.108  1
2009 Veren D, Evans JL, Jones S, Chiaromonte F. Novel metrics for evaluation of ensemble forecasts of tropical cyclone structure Monthly Weather Review. 137: 2830-2850. DOI: 10.1175/2009Mwr2655.1  1
2008 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 Research. 18: 1896-905. PMID 18818370 DOI: 10.1101/Gr.083089.108  1
2008 Tyekucheva S, Makova KD, Karro JE, Hardison RC, Miller W, Chiaromonte F. Human-macaque comparisons illuminate variation in neutral substitution rates. Genome Biology. 9: R76. PMID 18447906 DOI: 10.1186/Gb-2008-9-4-R76  1
2008 Kelkar YD, Tyekucheva S, Chiaromonte F, Makova KD. The genome-wide determinants of human and chimpanzee microsatellite evolution. Genome Research. 18: 30-8. PMID 18032720 DOI: 10.1101/Gr.7113408  1
2008 Tyekucheva S, Chiaromonte F. Rejoinder on: Augmenting the bootstrap to analyze high dimensional genomic data Test. 17: 47-55. DOI: 10.1007/S11749-008-0107-9  1
2008 Tyekucheva S, Chiaromonte F. Augmenting the bootstrap to analyze high dimensional genomic data Test. 17: 1-18. DOI: 10.1007/S11749-008-0098-6  1
2007 Cesari P, Chiaromonte F, Newell KM. Support vector machines categorize the scaling of human grip configurations. Behavior Research Methods. 39: 1001-7. PMID 18183918 DOI: 10.3758/Bf03192996  0.01
2007 Kvikstad EM, Tyekucheva S, Chiaromonte F, Makova KD. A macaque's-eye view of human insertions and deletions: differences in mechanisms. Plos Computational Biology. 3: 1772-82. PMID 17941704 DOI: 10.1371/Journal.Pcbi.0030176  1
2007 King DC, Taylor J, Zhang Y, Cheng Y, Lawson HA, Martin J, Chiaromonte F, Miller W, Hardison RC. Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data. Genome Research. 17: 775-86. PMID 17567996 DOI: 10.1101/Gr.5592107  1
2007 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 Biology. 8: R7. PMID 17217541 DOI: 10.1186/Gb-2007-8-1-R7  1
2006 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 Research. 16: 1596-604. PMID 17053093 DOI: 10.1101/Gr.4537706  1
2006 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, et al. Experimental validation of predicted mammalian erythroid cis-regulatory modules. Genome Research. 16: 1480-92. PMID 17038566 DOI: 10.1101/Gr.5353806  1
2006 Carrel L, Park C, Tyekucheva S, Dunn J, Chiaromonte F, Makova KD. Genomic environment predicts expression patterns on the human inactive X chromosome. Plos Genetics. 2: e151. PMID 17009873 DOI: 10.1371/Journal.Pgen.0020151  1
2006 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. Molecular Biology and Evolution. 23: 565-73. PMID 16280537 DOI: 10.1093/Molbev/Msj060  1
2006 Evans JL, Arnott JM, Chiaromonte F. Evaluation of operational model cyclone structure forecasts during extratropical transition Monthly Weather Review. 134: 3054-3072. DOI: 10.1175/Mwr3236.1  1
2005 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 Research. 15: 1051-60. PMID 16024817 DOI: 10.1101/Gr.3642605  1
2004 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 Research. 14: 700-7. PMID 15060013 DOI: 10.1101/Gr.1976004  1
2004 Makova KD, Yang S, Chiaromonte F. Insertions and deletions are male biased too: a whole-genome analysis in rodents. Genome Research. 14: 567-73. PMID 15059997 DOI: 10.1101/Gr.1971104  1
2004 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 Research. 14: 517-27. PMID 15059992 DOI: 10.1101/Gr.1984404  1
2003 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, et al. Global predictions and tests of erythroid regulatory regions. Cold Spring Harbor Symposia On Quantitative Biology. 68: 335-44. PMID 15338635 DOI: 10.1101/Sqb.2003.68.335  1
2003 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 Harbor Symposia On Quantitative Biology. 68: 245-54. PMID 15338624  1
2003 Chiaromonte F, Miller W, Bouhassira EE. Gene length and proximity to neighbors affect genome-wide expression levels. Genome Research. 13: 2602-8. PMID 14613975 DOI: 10.1101/Gr.1169203  1
2003 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 Research. 13: 64-72. PMID 12529307 DOI: 10.1101/Gr.817703  1
2003 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, ... ... Chiaromonte F, et al. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Research. 13: 13-26. PMID 12529302 DOI: 10.1101/Gr.844103  1
2002 Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, ... ... Chiaromonte F, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420: 520-62. PMID 12466850 DOI: 10.1038/Nature01262  1
2002 Chiaromonte F, Martinelli J. Dimension reduction strategies for analyzing global gene expression data with a response. Mathematical Biosciences. 176: 123-44. PMID 11867087 DOI: 10.1016/S0025-5564(01)00106-7  0.01
2001 Chiaromonte F, Yang S, Elnitski L, Yap VB, Miller W, Hardison RC. Association between divergence and interspersed repeats in mammalian noncoding genomic DNA Proceedings of the National Academy of Sciences of the United States of America. 98: 14503-14508. PMID 11717405 DOI: 10.1073/Pnas.251423898  1
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