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Research Output 1993 2019

  • 9557 Citations
  • 35 h-Index
  • 67 Article
  • 2 Comment/debate
  • 1 Paper
  • 1 Review article
2019

Covariate Information Matrix for Sufficient Dimension Reduction

Yao, W., Nandy, D., Lindsay, B. G. & Chiaromonte, F., Oct 2 2019, In : Journal of the American Statistical Association. 114, 528, p. 1752-1764 13 p.

Research output: Contribution to journalArticle

Sufficient Dimension Reduction
Information Matrix
Covariates
Central Subspace
Reduction Method

Evidence for sharp increase in the economic damages of extreme natural disasters

Coronese, M., Lamperti, F., Keller, K., Chiaromonte, F. & Roventini, A., Oct 22 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 43, p. 21450-21455 6 p.

Research output: Contribution to journalArticle

Open Access
Disasters
Economics
Economic Models
Climate Change
Climate
1 Citation (Scopus)

Functional data analysis for computational biology

Cremona, M., Xu, H., Makova, K. D., Reimherr, M. L., Chiaromonte, F. & Madrigal, P., Sep 1 2019, In : Bioinformatics. 35, 17, p. 3211-3213 3 p.

Research output: Contribution to journalArticle

Functional Data Analysis
Computational Biology
Bioinformatics
2018
5 Citations (Scopus)

Child Weight Gain Trajectories Linked To Oral Microbiota Composition

Craig, S., Blankenberg, D., Parodi, A. C. L., Paul, I., Birch, L. L., Williams, J. S., Marini, M. E., Stokes, J. L., Nekrutenko, A., Reimherr, M. L., Chiaromonte, F. & Makova, K. D., Dec 1 2018, In : Scientific reports. 8, 1, 14030.

Research output: Contribution to journalArticle

Microbiota
Weight Gain
Growth
Bacteroidetes
Diet
70 Citations (Scopus)

Computational pan-genomics: Status, promises and challenges

The Computational Pan-Genomics Consortium, Jan 1 2018, In : Briefings in bioinformatics. 19, 1, p. 118-135 18 p., bbw089.

Research output: Contribution to journalArticle

Genomics
Genes
Computational Biology
Genome
Bioinformatics
2 Citations (Scopus)

IWTomics: Testing high-resolution sequence-based 'Omics' data at multiple locations and scales

Cremona, M., Pini, A., Cumbo, F., Makova, K. D., Chiaromonte, F. & Vantini, S., Jul 1 2018, In : Bioinformatics. 34, 13, p. 2289-2291 3 p.

Research output: Contribution to journalArticle

Galaxies
Workflow
Epigenomics
Genomics
High Resolution
4 Citations (Scopus)

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

Guiblet, W. M., Cremona, M., Cechova, M., Harris, R. S., Kejnovská, I., Kejnovsky, E., Eckert, K., Chiaromonte, F. & Makova, K. D., Dec 1 2018, In : Genome research. 28, 12, p. 1767-1778 12 p.

Research output: Contribution to journalArticle

Polymerization
Genome
Technology
DNA
G-Quadruplexes
2017

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

Bartolucci, F., Chiaromonte, F., Don, P. K. & Lindsay, B. G., Apr 3 2017, In : Journal of Computational and Graphical Statistics. 26, 2, p. 388-402 15 p.

Research output: Contribution to journalArticle

Composite Likelihood
Latent Variable Models
Likelihood Inference
Discrete Variables
Discrete Model
Sufficient Dimension Reduction
Ordinary Least Squares
Least-Squares Analysis
least squares
Predictors
2016
12 Citations (Scopus)

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

Campos-Sánchez, R., Cremona, M. A., Pini, A., Chiaromonte, F. & Makova, K. D., Jun 2016, In : PLoS computational biology. 12, 6, e1004956.

Research output: Contribution to journalArticle

Retroviridae
Endogenous Retroviruses
Functional Data Analysis
Fixation
fixation
5 Citations (Scopus)

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

Don, P. K., Evans, J., Chiaromonte, F. & Kowaleski, A. M., Jan 1 2016, In : Monthly Weather Review. 144, 9, p. 3301-3320 20 p.

Research output: Contribution to journalArticle

tropical cyclone
aid
trajectory
forecast
2015
7 Citations (Scopus)

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

Goldstein, J., Haran, M., Simeonov, I., Fricks, J. & Chiaromonte, F., Jun 1 2015, In : Biometrics. 71, 2, p. 376-385 10 p.

Research output: Contribution to journalArticle

Respiratory Syncytial Virus Infections
Point Process
Viruses
Process Model
Virus
2 Citations (Scopus)

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

Liu, Y., Chiaromonte, F., Ross, H., Malhotra, R., Elleder, D. & Poss, M., Dec 12 2015, In : BMC bioinformatics. 16, 1, 202.

Research output: Contribution to journalArticle

Feline Immunodeficiency Virus
Error correction
Error Correction
Viruses
Sequencing
2014
13 Citations (Scopus)

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

Campos-Sánchez, R., Kapusta, A., Feschotte, C., Chiaromonte, F. & Makova, K. D., Jul 2014, In : Molecular biology and evolution. 31, 7, p. 1816-1822 7 p.

Research output: Contribution to journalArticle

DNA Transposable Elements
bat
transposons
Chiroptera
genomics

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

Rebolledo-Jaramillo, B., Su, M. S. W., Stoler, N., McElhoe, J. A., Dickins, B., Blankenberg, D., Korneliussen, T. S., Chiaromonte, F., Nielsen, R., Holland, M. M., Paul, I. M., Nekrutenko, A. & Makova, K. D., Oct 28 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 43, p. 15474-15479 6 p.

Research output: Contribution to journalArticle

Maternal Age
Mitochondrial DNA
Germ Cells
Mothers
Mitochondrial Diseases
83 Citations (Scopus)

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

Rebolledo-Jaramillo, B., Su, M. S. W., Stoler, N., McElhoe, J. A., Dickins, B., Blankenberg, D., Korneliussen, T. S., Chiaromonte, F., Nielsen, R., Holland, M. M., Paul, I. M., Nekrutenko, A. & Makova, K. D., Oct 28 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 43, p. 15474-15479 6 p.

Research output: Contribution to journalArticle

Maternal Age
Mitochondrial DNA
Germ Cells
Mothers
Mitochondrial Diseases
2013
24 Citations (Scopus)

A general theory for nonlinear sufficient dimension reduction: Formulation and estimation

Lee, K. Y., Li, B. & Chiaromonte, F., Feb 1 2013, In : Annals of Statistics. 41, 1, p. 221-249 29 p.

Research output: Contribution to journalArticle

Sufficient Dimension Reduction
Formulation
Dimension Reduction
Estimator
Sliced Inverse Regression
29 Citations (Scopus)

Distinct mutational behaviors differentiate short tandem repeats from micro satellites in the human genome

Ananda, G., Walsh, E., Jacob, K. D., Krasilnikova, M., Eckert, K. A., Chiaromonte, F. & Makova, K. D., Apr 29 2013, In : Genome biology and evolution. 5, 3, p. 606-620 15 p.

Research output: Contribution to journalArticle

Tandem Repeat Sequences
tandem repeat sequences
Human Genome
Microsatellite Repeats
polymorphism
6 Citations (Scopus)

Segmenting the human genome based on states of neutral genetic divergence

Don, P. K., Ananda, G., Chiaromonte, F. & Makova, K. D., Sep 3 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, 36, p. 14699-14704 6 p.

Research output: Contribution to journalArticle

Human Genome
Genome
Microsatellite Repeats
Biochemical Phenomena
Pongo
2012
75 Citations (Scopus)

A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?

Fungtammasan, A., Walsh, E., Chiaromonte, F., Eckert, K. A. & Makova, K. D., Jun 1 2012, In : Genome research. 22, 6, p. 993-1005 13 p.

Research output: Contribution to journalArticle

Aphidicolin
Chromosomal Instability
Human Genome
Genome
Logistic Models
23 Citations (Scopus)

Rescuing Alu: Recovery of New Inserts Shows LINE-1 Preserves Alu Activity through A-Tail Expansion

Wagstaff, B. J., Hedges, D. J., Derbes, R. S., Campos Sanchez, R., Chiaromonte, F., Makova, K. D. & Roy-Engel, A. M., Aug 1 2012, In : PLoS genetics. 8, 8, e1002842.

Research output: Contribution to journalArticle

preserves
Tail
tail
Short Interspersed Nucleotide Elements
Retroelements
2011
19 Citations (Scopus)

A genome-wide view of mutation rate co-variation using multivariate analyses

Ananda, G., Chiaromonte, F. & Makova, K. D., Mar 22 2011, In : Genome biology. 12, 3, R27.

Research output: Contribution to journalArticle

Mutation Rate
mutation
genomics
Multivariate Analysis
genome
41 Citations (Scopus)

A matter of life or death: How microsatellites emerge in and vanish from the human genome

Kelkar, Y. D., Eckert, K. A., Chiaromonte, F. & Makova, K. D., Dec 1 2011, In : Genome research. 21, 12, p. 2038-2048 11 p.

Research output: Contribution to journalArticle

Human Genome
Microsatellite Repeats
Parturition
DNA Transposable Elements
Life Cycle Stages
78 Citations (Scopus)

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

Wu, W., Cheng, Y., Keller, C. A., Ernst, J., Kumar, S. A., Mishra, T., Morrissey, C., Dorman, C. M., Chen, K. B., Drautz, D., Giardine, B., Shibata, Y., Song, L., Pimkin, M., Crawford, G. E., Furey, T. S., Kellis, M., Miller, W., Taylor, J., Schuster, S. C. & 5 others, Zhang, Y., Chiaromonte, F., Blobel, G. A., Weiss, M. J. & Hardison, R. C., Oct 1 2011, In : Genome research. 21, 10, p. 1659-1671 13 p.

Research output: Contribution to journalArticle

Epigenomics
Chromatin
Histone Code
GATA1 Transcription Factor
Transcription Factors
2010
255 Citations (Scopus)

Complete Khoisan and Bantu genomes from southern Africa

Schuster, S. C., Miller, W., Ratan, A., Tomsho, L. P., Giardine, B., Kasson, L. R., Harris, R. S., Petersen, D. C., Zhao, F., Qi, J., Alkan, C., Kidd, J. M., Sun, Y., Drautz, D. I., Bouffard, P., Muzny, D. M., Reid, J. G., Nazareth, L. V., Wang, Q., Burhans, R. & 28 others, Riemer, C., Wittekindt, N. E., Moorjani, P., Tindall, E. A., Danko, C. G., Teo, W. S., Buboltz, A. M., Zhang, Z., Ma, Q., Oosthuysen, A., Steenkamp, A. W., Oostuisen, H., Venter, P., Gajewski, J., Zhang, Y., Pugh, B. F., Makova, K. D., Nekrutenko, A., Mardis, E. R., Patterson, N., Pringle, T. H., Chiaromonte, F., Mullikin, J. C., Eichler, E. E., Hardison, R. C., Gibbs, R. A., Harkins, T. T. & Hayes, V. M., Feb 18 2010, In : Nature. 463, 7283, p. 943-947 5 p.

Research output: Contribution to journalArticle

Southern Africa
Genome
Botswana
Medical History Taking
Exome
72 Citations (Scopus)

Envelope models for parsimonious and efficient multivariate linear regression

Cook, R. D., Li, B. & Chiaromonte, F., Jul 1 2010, In : Statistica Sinica. 20, 3, p. 927-960 34 p.

Research output: Contribution to journalArticle

Linear regression
Maximum Likelihood Estimator
Envelope
Covariance matrix
Reducing Subspace
4 Citations (Scopus)

Exploratory spatial analysis of in vitro respiratory syncytial virus co-infections

Simeonov, I., Gong, X., Kim, O., Poss, M., Chiaromonte, F. & Fricks, J., Dec 1 2010, In : Viruses. 2, 12, p. 2782-2802 21 p.

Research output: Contribution to journalArticle

Respiratory Syncytial Virus Infections
Spatial Analysis
Coinfection
Viruses
Infection

Rejoinder

Cook, R. D., Li, B., Chiaromonte, F. & Su, Z., Jul 2010, In : Statistica Sinica. 20, 3, p. 999-1010 12 p.

Research output: Contribution to journalComment/debate

69 Citations (Scopus)

What is a microsatellite: A computational and experimental definition based upon repeat mutational behavior at A/T and GT/AC repeats

Kelkar, Y. D., Strubczewski, N., Hile, S. E., Chiaromonte, F., Eckert, K. A. & Makova, K. D., Oct 29 2010, In : Genome biology and evolution. 2, 1, p. 620-635 16 p.

Research output: Contribution to journalArticle

Microsatellite Repeats
microsatellite repeats
polymorphism
genetic polymorphism
genome
2009
153 Citations (Scopus)

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

Cheng, Y., Wu, W., Kumar, S. A., Yu, D., Deng, W., Tripic, T., King, D. C., Chen, K. B., Zhang, Y., Drautz, D., Giardine, B., Schuster, S. C., Miller, W., Chiaromonte, F., Zhang, Y., Blobel, G. A., Weiss, M. J. & Hardison, R. C., Dec 1 2009, In : Genome research. 19, 12, p. 2172-2184 13 p.

Research output: Contribution to journalArticle

Histone Code
Transcription Factors
Genome
Messenger RNA
Genes
9 Citations (Scopus)

Multivariate statistical analyses demonstrate unique host immune responses to single and dual lentiviral infection

Roy, S., Lavine, J., Chiaromonte, F., Terwee, J., VandeWoude, S., Bjornstad, O. & Poss, M., Oct 6 2009, In : PloS one. 4, 10, e7359.

Research output: Contribution to journalArticle

Viruses
Feline Immunodeficiency Virus
Feline immunodeficiency virus
Cats
Multivariate Analysis
8 Citations (Scopus)

Novel metrics for evaluation of ensemble forecasts of tropical cyclone structure

Veren, D., Evans, J. L., Jones, S. & Chiaromonte, F., Nov 11 2009, In : Monthly Weather Review. 137, 9, p. 2830-2850 21 p.

Research output: Contribution to journalArticle

tropical cyclone
prediction
cyclone
evaluation
forecast
23 Citations (Scopus)

Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1

Zhang, Y., Wu, W., Cheng, Y., King, D. C., Harris, R. S., Taylor, J., Chiaromonte, F. & Hardison, R. C., Sep 18 2009, In : Nucleic acids research. 37, 21, p. 7024-7038 15 p., gkp747.

Research output: Contribution to journalArticle

Epigenomics
DNA
Lysine
Binding Sites
Erythroid Cells
22 Citations (Scopus)

Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions

Kvikstad, E. M., Chiaromonte, F. & Makova, K. D., Jul 1 2009, In : Genome research. 19, 7, p. 1153-1164 12 p.

Research output: Contribution to journalArticle

Mutagenesis
Recombinational DNA Repair
Wavelet Analysis
Untranslated RNA
Pan troglodytes
49 Citations (Scopus)

Windshield splatter analysis with the Galaxy metagenomic pipeline

Pond, S. K., Wadhawan, S., Chiaromonte, F., Ananda, G., Chung, W. Y., Taylor, J. & Nekrutenko, A., Nov 1 2009, In : Genome research. 19, 11, p. 2144-2153 10 p.

Research output: Contribution to journalArticle

Galaxies
Metagenomics
Statistical Data Interpretation
Workflow
Quality Control
2008
6 Citations (Scopus)

Augmenting the bootstrap to analyze high dimensional genomic data

Tyekucheva, S. & Chiaromonte, F., May 1 2008, In : Test. 17, 1, p. 1-18 18 p.

Research output: Contribution to journalArticle

Bootstrap
Genomics
High-dimensional
Covariance matrix
DNA Microarray
35 Citations (Scopus)

Human-macaque comparisons illuminate variation in neutral substitution rates

Tyekucheva, S., Makova, K. D., Karro, J. E., Hardison, R. C., Miller, W. & Chiaromonte, F., Apr 30 2008, In : Genome biology. 9, 4, R76.

Research output: Contribution to journalArticle

Macaca
Genetic Recombination
substitution
telomeres
Telomere

Rejoinder on: Augmenting the bootstrap to analyze high dimensional genomic data

Tyekucheva, S. & Chiaromonte, F., May 1 2008, In : Test. 17, 1, p. 47-55 9 p.

Research output: Contribution to journalComment/debate

Bootstrap
164 Citations (Scopus)

The genome-wide determinants of human and chimpanzee microsatellite evolution

Kelkar, Y. D., Tyekucheva, S., Chiaromonte, F. & Makova, K. D., Jan 1 2008, In : Genome research. 18, 1, p. 30-38 9 p.

Research output: Contribution to journalArticle

Pan troglodytes
Microsatellite Repeats
Genome
Isochores
Forensic Genetics
29 Citations (Scopus)

Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif

Cheng, Y., King, D. C., Dore, L. C., Zhang, X., Zhou, Y., Zhang, Y., Dorman, C., Abebe, D., Kumar, S. A., Chiaromonte, F., Miller, W., Green, R. D., Weiss, M. J. & Hardison, R. C., Dec 1 2008, In : Genome research. 18, 12, p. 1896-1905 10 p.

Research output: Contribution to journalArticle

Binding Sites
GATA1 Transcription Factor
DNA
Erythroid Cells
Chromosomes, Human, Pair 7
2007
42 Citations (Scopus)

A macaque's-eye view of human insertions and deletions: Differences in mechanisms

Kvikstad, E. M., Tyekucheva, S., Chiaromonte, F. & Makova, K. D., Sep 1 2007, In : PLoS computational biology. 3, 9, p. 1772-1782 11 p.

Research output: Contribution to journalArticle

Macaca
Genetic Recombination
Deletion
recombination
Insertion
49 Citations (Scopus)

Dimension reduction in regression without matrix inversion

Cook, R. D., Li, B. & Chiaromonte, F., Sep 14 2007, In : Biometrika. 94, 3, p. 569-584 16 p.

Research output: Contribution to journalArticle

Matrix Inversion
Dimension Reduction
Regression
Sufficient Dimension Reduction
Predictors
57 Citations (Scopus)

Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data

King, D. C., Taylor, J., Zhang, Y., Cheng, Y., Lawson, H. A., Martin, J., Chiaromonte, F., Miller, W. & Hardison, R. C., Jun 1 2007, In : Genome research. 17, 6, p. 775-786 12 p.

Research output: Contribution to journalArticle

Nucleic Acid Regulatory Sequences
Genomics
Primates
Genes
197 Citations (Scopus)

Qualitative network models and genome-wide expression data define carbon/ nitrogen-responsive molecular machines in Arabidopsis

Gutiérrez, R. A., Lejay, L. V., Dean, A., Chiaromonte, F., Shasha, D. E. & Coruzzi, G. M., Jan 11 2007, In : Genome biology. 8, 1, R7.

Research output: Contribution to journalArticle

Arabidopsis
Nitrogen
Carbon
genome
Genome
3 Citations (Scopus)

Support vector machines categorize the scaling of human grip configurations

Cesari, P., Chiaromonte, F. & Newell, K. M., Jan 1 2007, In : Behavior research methods. 39, 4, p. 1001-1007 7 p.

Research output: Contribution to journalArticle

Hand Strength
Hand
Support Vector Machine
Scaling
Length
2006
94 Citations (Scopus)

ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements

Taylor, J., Tyekucheva, S., King, D. C., Hardison, R. C., Miller, W. & Chiaromonte, F., Dec 1 2006, In : Genome research. 16, 12, p. 1596-1604 9 p.

Research output: Contribution to journalArticle

Sequence Alignment
Base Composition
Learning
Nucleic Acid Regulatory Sequences
Protein Sorting Signals
22 Citations (Scopus)

Evaluation of operational model cyclone structure forecasts during extratropical transition

Evans, J., Arnott, J. M. & Chiaromonte, F., Nov 2006, In : Monthly Weather Review. 134, 11, p. 3054-3072 19 p.

Research output: Contribution to journalArticle

cyclone
weather
evaluation
forecast
structural change
49 Citations (Scopus)

Experimental validation of predicted mammalian erythroid cis-regulatory modules

Wang, H., Zhang, Y., Cheng, Y., Zhou, Y., King, D. C., Taylor, J., Chiaromonte, F., Kasturi, J., Petrykowska, H., Gibb, B., Dorman, C., Miller, W., Dore, L. C., Welch, J., Weiss, M. J. & Hardison, R. C., Dec 1 2006, In : Genome research. 16, 12, p. 1480-1492 13 p.

Research output: Contribution to journalArticle

Binding Sites
Genome
GATA1 Transcription Factor
Transcription Factors
Leukemia, Erythroblastic, Acute
64 Citations (Scopus)

Genomic environment predicts expression patterns on the human inactive X chromosome

Carrel, L., Park, C., Tyekucheva, S., Dunn, J., Chiaromonte, F. & Makova, K. D., Oct 10 2006, In : PLoS genetics. 2, 9, p. 1477-1486 10 p.

Research output: Contribution to journalArticle

Chromosomes, Human, X
X chromosome
chromosome
genomics
inactivation

Phase space-based evaluation of numerical forecasts of cyclone structure evolution

Evans, J. L., Arnott, J. M. & Chiaromonte, F., Dec 1 2006.

Research output: Contribution to conferencePaper

cyclone
evaluation
forecast