Andrea S. Foulkes, Sc.D. is an Associate Professor of Biostatistics at the University of Massachusetts School of Public Health and Health Sciences. Her research includes developing analytic methods for characterizing the relationships among high-dimensional molecular and cellular data and measures of disease progression. These methods draw from cluster analysis, recursive partitioning, mixed effects modeling and Markov modeling. She currently collaborates with investigators across multiple disciplines ranging from oncology to immunology to identify and develop appropriate techniques for analyzing single nucleotide polymorphisms (SNPs) and disease outcomes. In addition, Dr. Foulkes is working on establishing methods for understanding the complex relationships among HIV-1 genotypic markers of resistance to antiretroviral drugs, cellular immune modulation and clinical outcomes. Dr. Foulkes received a B.A. in Mathematics from Brown University in 1994 and an Sc.D. in Biostatistics from Harvard School of Public Health in 2000.
Reverse Transcriptase Polymerase Chain Reaction
Low-cost HIV-1 Diagnosis and Quantification in Dried Blood Spots by Real Time PCR (with Nishaki Mehta, Sonia Trzmielina, Bareng A. S. Nonyane, Melissa N. Eliot, Rongheng Lin, Kristina McNeal, Arthur Ammann, Vindu Eulalievyolo, John L. Sullivan, Katherine Luzuriaga, and Mohan Somasundaran), PloS one (2009)
BACKGROUND: Rapid and cost-effective methods for HIV-1 diagnosis and viral load monitoring would greatly enhance...
Humans
Low-cost HIV-1 Diagnosis and Quantification in Dried Blood Spots by Real Time PCR (with Nishaki Mehta, Sonia Trzmielina, Bareng A. S. Nonyane, Melissa N. Eliot, Rongheng Lin, Kristina McNeal, Arthur Ammann, Vindu Eulalievyolo, John L. Sullivan, Katherine Luzuriaga, and Mohan Somasundaran), PloS one (2009)
BACKGROUND: Rapid and cost-effective methods for HIV-1 diagnosis and viral load monitoring would greatly enhance...
Time Factors
Low-cost HIV-1 Diagnosis and Quantification in Dried Blood Spots by Real Time PCR (with Nishaki Mehta, Sonia Trzmielina, Bareng A. S. Nonyane, Melissa N. Eliot, Rongheng Lin, Kristina McNeal, Arthur Ammann, Vindu Eulalievyolo, John L. Sullivan, Katherine Luzuriaga, and Mohan Somasundaran), PloS one (2009)
BACKGROUND: Rapid and cost-effective methods for HIV-1 diagnosis and viral load monitoring would greatly enhance...
Disease Modeling
Validation and Discovery in Markov Models of Genetics Data (with Victor De Gruttola), Statistical Applications in Genetics and Molecular Biology (2012)
Markov models provide a natural framework for modeling cellular and molecular level changes over time....
Mothers
Low-cost HIV-1 Diagnosis and Quantification in Dried Blood Spots by Real Time PCR (with Nishaki Mehta, Sonia Trzmielina, Bareng A. S. Nonyane, Melissa N. Eliot, Rongheng Lin, Kristina McNeal, Arthur Ammann, Vindu Eulalievyolo, John L. Sullivan, Katherine Luzuriaga, and Mohan Somasundaran), PloS one (2009)
BACKGROUND: Rapid and cost-effective methods for HIV-1 diagnosis and viral load monitoring would greatly enhance...
Multivariate Analysis
Reader Reaction (with Victor De Gruttola), Statistical Applications in Genetics and Molecular Biology (2012)
This note is a response to the article "relating HIV-1 sequence variation to replication capacity...
Female
Low-cost HIV-1 Diagnosis and Quantification in Dried Blood Spots by Real Time PCR (with Nishaki Mehta, Sonia Trzmielina, Bareng A. S. Nonyane, Melissa N. Eliot, Rongheng Lin, Kristina McNeal, Arthur Ammann, Vindu Eulalievyolo, John L. Sullivan, Katherine Luzuriaga, and Mohan Somasundaran), PloS one (2009)
BACKGROUND: Rapid and cost-effective methods for HIV-1 diagnosis and viral load monitoring would greatly enhance...
Adolescent
Low-cost HIV-1 Diagnosis and Quantification in Dried Blood Spots by Real Time PCR (with Nishaki Mehta, Sonia Trzmielina, Bareng A. S. Nonyane, Melissa N. Eliot, Rongheng Lin, Kristina McNeal, Arthur Ammann, Vindu Eulalievyolo, John L. Sullivan, Katherine Luzuriaga, and Mohan Somasundaran), PloS one (2009)
BACKGROUND: Rapid and cost-effective methods for HIV-1 diagnosis and viral load monitoring would greatly enhance...
General Biostatistics
Ridge Regression for Longitudinal Biomarker Data (with Melissa Eliot, Jane Ferguson, and Muredach P. Reilly), The International Journal of Biostatistics (2012)
Technological advances facilitating the acquisition of large arrays of biomarker data have led to new...
A Resampling-Based Approach to Multiple Testing with Uncertainty in Phase (with Victor G. DeGruttola), The International Journal of Biostatistics (2012)
Characterizing the genetic correlates to complex diseases requires consideration of a large number of potentially...
An Expectation Maximization Approach to Estimate Malaria Haplotype Frequencies in Multiply Infected Children (with Xiaohong Li, Recai M. Yucel, and Stephen M. Rich), Statistical Applications in Genetics and Molecular Biology (2012)
Characterizing genetic variability in the human pathogenic Plasmodium species, the group of parasites that cause...
Genotype
Low-cost HIV-1 Diagnosis and Quantification in Dried Blood Spots by Real Time PCR (with Nishaki Mehta, Sonia Trzmielina, Bareng A. S. Nonyane, Melissa N. Eliot, Rongheng Lin, Kristina McNeal, Arthur Ammann, Vindu Eulalievyolo, John L. Sullivan, Katherine Luzuriaga, and Mohan Somasundaran), PloS one (2009)
BACKGROUND: Rapid and cost-effective methods for HIV-1 diagnosis and viral load monitoring would greatly enhance...
Male
Low-cost HIV-1 Diagnosis and Quantification in Dried Blood Spots by Real Time PCR (with Nishaki Mehta, Sonia Trzmielina, Bareng A. S. Nonyane, Melissa N. Eliot, Rongheng Lin, Kristina McNeal, Arthur Ammann, Vindu Eulalievyolo, John L. Sullivan, Katherine Luzuriaga, and Mohan Somasundaran), PloS one (2009)
BACKGROUND: Rapid and cost-effective methods for HIV-1 diagnosis and viral load monitoring would greatly enhance...
Computational Biology/Bioinformatics
Validation and Discovery in Markov Models of Genetics Data (with Victor De Gruttola), Statistical Applications in Genetics and Molecular Biology (2012)
Markov models provide a natural framework for modeling cellular and molecular level changes over time....
A Resampling-Based Approach to Multiple Testing with Uncertainty in Phase (with Victor G. DeGruttola), The International Journal of Biostatistics (2012)
Characterizing the genetic correlates to complex diseases requires consideration of a large number of potentially...
Multiple Imputation and Random Forests (MIRF) for Unobservable, High-Dimensional Data (with Bareng A. S. Nonyane), The International Journal of Biostatistics (2012)
Understanding the genetic underpinnings to complex diseases requires consideration of sophisticated analytical methods designed to...
Adult
Low-cost HIV-1 Diagnosis and Quantification in Dried Blood Spots by Real Time PCR (with Nishaki Mehta, Sonia Trzmielina, Bareng A. S. Nonyane, Melissa N. Eliot, Rongheng Lin, Kristina McNeal, Arthur Ammann, Vindu Eulalievyolo, John L. Sullivan, Katherine Luzuriaga, and Mohan Somasundaran), PloS one (2009)
BACKGROUND: Rapid and cost-effective methods for HIV-1 diagnosis and viral load monitoring would greatly enhance...
Prospective Studies
Low-cost HIV-1 Diagnosis and Quantification in Dried Blood Spots by Real Time PCR (with Nishaki Mehta, Sonia Trzmielina, Bareng A. S. Nonyane, Melissa N. Eliot, Rongheng Lin, Kristina McNeal, Arthur Ammann, Vindu Eulalievyolo, John L. Sullivan, Katherine Luzuriaga, and Mohan Somasundaran), PloS one (2009)
BACKGROUND: Rapid and cost-effective methods for HIV-1 diagnosis and viral load monitoring would greatly enhance...
AIDS Serodiagnosis
Low-cost HIV-1 Diagnosis and Quantification in Dried Blood Spots by Real Time PCR (with Nishaki Mehta, Sonia Trzmielina, Bareng A. S. Nonyane, Melissa N. Eliot, Rongheng Lin, Kristina McNeal, Arthur Ammann, Vindu Eulalievyolo, John L. Sullivan, Katherine Luzuriaga, and Mohan Somasundaran), PloS one (2009)
BACKGROUND: Rapid and cost-effective methods for HIV-1 diagnosis and viral load monitoring would greatly enhance...
Child
Low-cost HIV-1 Diagnosis and Quantification in Dried Blood Spots by Real Time PCR (with Nishaki Mehta, Sonia Trzmielina, Bareng A. S. Nonyane, Melissa N. Eliot, Rongheng Lin, Kristina McNeal, Arthur Ammann, Vindu Eulalievyolo, John L. Sullivan, Katherine Luzuriaga, and Mohan Somasundaran), PloS one (2009)
BACKGROUND: Rapid and cost-effective methods for HIV-1 diagnosis and viral load monitoring would greatly enhance...
Anti-Retroviral Agents
Low-cost HIV-1 Diagnosis and Quantification in Dried Blood Spots by Real Time PCR (with Nishaki Mehta, Sonia Trzmielina, Bareng A. S. Nonyane, Melissa N. Eliot, Rongheng Lin, Kristina McNeal, Arthur Ammann, Vindu Eulalievyolo, John L. Sullivan, Katherine Luzuriaga, and Mohan Somasundaran), PloS one (2009)
BACKGROUND: Rapid and cost-effective methods for HIV-1 diagnosis and viral load monitoring would greatly enhance...
Longitudinal Data Analysis and Time Series
Ridge Regression for Longitudinal Biomarker Data (with Melissa Eliot, Jane Ferguson, and Muredach P. Reilly), The International Journal of Biostatistics (2012)
Technological advances facilitating the acquisition of large arrays of biomarker data have led to new...
Validation and Discovery in Markov Models of Genetics Data (with Victor De Gruttola), Statistical Applications in Genetics and Molecular Biology (2012)
Markov models provide a natural framework for modeling cellular and molecular level changes over time....
Computation
An Expectation Maximization Approach to Estimate Malaria Haplotype Frequencies in Multiply Infected Children (with Xiaohong Li, Recai M. Yucel, and Stephen M. Rich), Statistical Applications in Genetics and Molecular Biology (2012)
Characterizing genetic variability in the human pathogenic Plasmodium species, the group of parasites that cause...
HIV-1
Low-cost HIV-1 Diagnosis and Quantification in Dried Blood Spots by Real Time PCR (with Nishaki Mehta, Sonia Trzmielina, Bareng A. S. Nonyane, Melissa N. Eliot, Rongheng Lin, Kristina McNeal, Arthur Ammann, Vindu Eulalievyolo, John L. Sullivan, Katherine Luzuriaga, and Mohan Somasundaran), PloS one (2009)
BACKGROUND: Rapid and cost-effective methods for HIV-1 diagnosis and viral load monitoring would greatly enhance...
Genetics
Validation and Discovery in Markov Models of Genetics Data (with Victor De Gruttola), Statistical Applications in Genetics and Molecular Biology (2012)
Markov models provide a natural framework for modeling cellular and molecular level changes over time....
A Resampling-Based Approach to Multiple Testing with Uncertainty in Phase (with Victor G. DeGruttola), The International Journal of Biostatistics (2012)
Characterizing the genetic correlates to complex diseases requires consideration of a large number of potentially...
An Expectation Maximization Approach to Estimate Malaria Haplotype Frequencies in Multiply Infected Children (with Xiaohong Li, Recai M. Yucel, and Stephen M. Rich), Statistical Applications in Genetics and Molecular Biology (2012)
Characterizing genetic variability in the human pathogenic Plasmodium species, the group of parasites that cause...
Multiple Imputation and Random Forests (MIRF) for Unobservable, High-Dimensional Data (with Bareng A. S. Nonyane), The International Journal of Biostatistics (2012)
Understanding the genetic underpinnings to complex diseases requires consideration of sophisticated analytical methods designed to...
HIV Infections
Low-cost HIV-1 Diagnosis and Quantification in Dried Blood Spots by Real Time PCR (with Nishaki Mehta, Sonia Trzmielina, Bareng A. S. Nonyane, Melissa N. Eliot, Rongheng Lin, Kristina McNeal, Arthur Ammann, Vindu Eulalievyolo, John L. Sullivan, Katherine Luzuriaga, and Mohan Somasundaran), PloS one (2009)
BACKGROUND: Rapid and cost-effective methods for HIV-1 diagnosis and viral load monitoring would greatly enhance...
Statistical Theory and Methods
A Resampling-Based Approach to Multiple Testing with Uncertainty in Phase (with Victor G. DeGruttola), The International Journal of Biostatistics (2012)
Characterizing the genetic correlates to complex diseases requires consideration of a large number of potentially...
Multiple Imputation and Random Forests (MIRF) for Unobservable, High-Dimensional Data (with Bareng A. S. Nonyane), The International Journal of Biostatistics (2012)
Understanding the genetic underpinnings to complex diseases requires consideration of sophisticated analytical methods designed to...
Metabolic and Anthropometric Parameters Contribute to ART-Mediated CD4+ T Cell Recovery in HIV-1-Infected Individuals: an Observational Study (with Livio Azzoni, Cynthia Firnhaber, Xiangfan Yin, Nigel J. Crowther, Deborah Glencross, Denise Lawrie, Wendy Stevens, Emmanouil Papasavvas, Ian Sanne, and Luis J. Montaner), Journal of the International AIDS Society (2011)
Background The degree of immune reconstitution achieved in response to suppressive ART is associated with...
Reproducibility of Results
Low-cost HIV-1 Diagnosis and Quantification in Dried Blood Spots by Real Time PCR (with Nishaki Mehta, Sonia Trzmielina, Bareng A. S. Nonyane, Melissa N. Eliot, Rongheng Lin, Kristina McNeal, Arthur Ammann, Vindu Eulalievyolo, John L. Sullivan, Katherine Luzuriaga, and Mohan Somasundaran), PloS one (2009)
BACKGROUND: Rapid and cost-effective methods for HIV-1 diagnosis and viral load monitoring would greatly enhance...
No subject area
Ridge regression for longitudinal data with application to biomarkers (with Melissa N. Eliot, Muredach P. Reilly, and Jane Ferguson), Clinical and Translational Science Research Retreat (2011)
Introduction: Technological advances facilitating the acquisition of large arrays of biomarker data have led to...
Latent Variable Modeling Paradigms for Genotype-Traits Associated Studies, Biometrical Journal (2011)
Mixture Modeling as an Exploratory Framework for Genotype-Trait Associations, Journal of the Royal Statistical Society: Series C (2011)
Association between HIV replication and serum leptin levels: an observational study of a cohort of HIV-1-infected South African women (with Livio Azzoni, Nigel J. Crowther, and Cynthia Firnhaber), Journal of the International AIDS Society (2010)
Background - Advanced HIV infection can result in lipoatrophy and wasting, even in the absence...
Prediction-Based Classification for Longitudinal Biomarkers (with Livio Azzoni, Xiaohong Li, Margaret A. Johnson, Colette Smith, Karam Mounzer, and Luis J. Montaner), Annals of Applied Statistics (2010)
Assessment of circulating CD4 count change over time in HIV-infected subjects on antiretroviral therapy (ART)...