Publications & Papers
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Peer-Reviewed Publications
2026
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A Time-Varying Branching Process Approach to Model Self-Renewing Cells.Methodology and Computing in Applied Probability, 28(38).
2025
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Uncovering position-specific patterns in codon and codon-pair usage in candidate genes associated with blood coagulation diseases.NAR Genomics and Bioinformatics, 7(4), lqaf169.
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High Dimensional Space Oddity.The American Statistician, 1–12.
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Uncovering codon usage patterns during murine embryogenesis and tissue-specific developmental diseases.Frontiers in Genetics, Volume 16 - 2025.
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Navigating the road ahead: using concept mapping to assess Clinical and Translational Science Award (CTSA) program goals.Front. Public Health, 13(1562191).
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A Conversation with Dr. David S. Salsburg.Journal of Data Science, 23(1), 70–89.
2024
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Portfolio selection revisited.Annals of Operations Research.
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Mouse embryo CoCoPUTs: novel murine transcriptomic-weighted usage website featuring multiple strains, tissues, and stages.BMC Bioinformatics, 25(294).
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The Geometry of Dynamic Time-Dependent Best–Worst Choice Pairs.Axioms, 13(641).
2023
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On graphical models and convex geometry.Computational Statistics & Data Analysis, 187, 107800.
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Legendary Career and Colorful Life: A Conversation with Dr. Bob Riffenburgh.Journal of Data Science, 21(4), 818–837.
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Deep Adaptation of Adult-Child Facial Expressions by Fusing Landmark Features.IEEE Transactions on Affective Computing, 1-12.
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Analysis of 3.5 million SARS-CoV-2 sequences reveals unique mutational trends with consistent nucleotide and codon frequencies..Virology Journal, 20(31).
2022
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A phenotypic screen for compounds that reverse cAMP-mediated suppression of T cell functions..SLAS Discovery.
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Structural, functional, and immunogenicity implications of F9 gene recoding.Blood Advances.
2021
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Zinc Status Index (ZSI) for Quantification of Zinc Physiological Status.Nutrients, 13(3399).
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Mixed effect modelling and variable selection for quantile regression.Statistical Modelling, 1471082X211033490.
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Distinct signatures of codon and codon pair usage in 32 primary tumor types in the novel database CancerCoCoPUTs for cancer-specific codon usage.Genome Medicine, 13(122).
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New approaches to predict the effect of co-occurring variants on protein characteristics.The American Journal of Human Genetics, 108, 1502-1511.
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Reproducible Science with LATEX.Journal of Data Science, 19(1), 111-125.
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A mixture model to detect edges in sparse co-expression graphs with an application for comparing breast cancer subtypes.PLoS ONE, 16(2), e0246945.
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A spatial capture-recapture model with attractions between individuals.Environmetrics, 32(1), e2653.
2020
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A Scalable Empirical Bayes Approach to Variable Selection in Generalized Linear Models.Journal of Computational and Graphical Statistics, 1-12.
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Z' Does Not Need to Be > 0.5.SLAS DISCOVERY: Advancing the Science of Drug Discovery, 25(9), 1000-1008.
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In silico features of ADAMTS13 contributing to plasmatic ADAMTS13 levels in neonates with congenital heart disease.Thrombosis Research, 193, 66-76.
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TissueCoCoPUTs: Novel Human Tissue-Specific Codon and Codon-Pair Usage Tables Based on Differential Tissue Gene Expression.Journal of Molecular Biology, 432(11), 3369-3378.
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Ribosome profiling of HEK293T cells overexpressing codon optimized coagulation factor IX.F1000 Research.
2019
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A Single Synonymous Variant (c.354G$>$A [p.P118P]) in ADAMTS13 Confers Enhanced Specific Activity.International Journal of Molecular Sciences, 20(5734).
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Effects of codon optimization on coagulation factor IX translation and structure: Implications for protein and gene therapies.Scientific Reports, 9, 15449.
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Differential variation and expression analysis.Stat, 8(1), e237.
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Murine Genetic Background Has a Stronger Impact on the Composition of the Gut Microbiota than Maternal Inoculation or Exposure to Unlike Exogenous Microbiota.Applied and Environmental Microbiology, 85(18).
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Splicing dysregulation contributes to the pathogenicity of several F9 exonic point variants.Molecular Genetics & Genomic Medicine, 7(8), e840.
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Codon and Codon-Pair Usage Tables (CoCoPUTs): Facilitating Genetic Variation Analyses and Recombinant Gene Design.Journal of Molecular Biology, 431(13), 2434-2441.
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Human Salivary Amylase Gene Copy Number Impacts Oral and Gut Microbiomes.Cell Host & Microbe, 25(4), 553-564.e7.
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Empirical Bayes methods in variable selection.WIREs Computational Statistics, 11(2), e1455.
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Translational and transcriptional responses in human primary hepatocytes under hypoxia.Am J Physiol Gastrointest Liver Physiol., 316(6), G720-G734.
2018
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Facilitating high-dimensional transparent classification via empirical Bayes variable selection.Applied Stochastic Models in Business and Industry, 34(6), 949-961.
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Capturing changes in HIV-infected, breastfeeding mothers' cognitive processes from before delivery to five months postpartum: An application of the pile sorting technique in Haiti.Current Developments in Nutrition, nzy017.
2017
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A tailored multivariate mixture model for detecting proteins of concordant change in the pathogenesis of Necrotic Enteritis.Journal of the American Statistical Association.
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Missing data - mechanisms and possible solutions / Datos ausentes: mecanismos y posibles soluciones.Culture and Education, 29(3), 492-525.
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R-CMap - An open-source software for concept mapping.Evaluation and Program Planning, 60(C), 284-292.
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Acrolein increases macrophage atherogenicity in association with gut microbiota remodeling in atherosclerotic mice: protective role for the polyphenol-rich pomegranate juice.Arch Toxicol., 4(91), 1709-1725.
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The importance of mRNA structure in determining the pathogenicity of synonymous and non-synonymous mutations in haemophilia.Haemophilia : the official journal of the World Federation of Hemophilia, 23(1), e8-e17.
2016
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The Combined Application of the Caco-2 Cell Bioassay Coupled with In Vivo (Gallus gallus) Feeding Trial Represents an Effective Approach to Predicting Fe Bioavailability in Humans.Nutrients, 8(732).
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Transcriptome analysis of human cumulus cells reveals hypoxia as the main determinant of follicular senescence.MHR: Basic science of reproductive medicine, 22(8), 866-876.
2015
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Methods for Analyzing Secondary Outcomes in Public Health Case-Control Studies.In Chen DG. and Wilson J. (Ed.), Innovative Statistical Methods for Public Health Data. ICSA Book Series in Statistics., pp. 3-15. Springer.
2014
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A Bivariate Model for Simultaneous Testing in Bioinformatics Data.Journal of the American Statistical Association, 109(506), 537-547.
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Vitamin D Status Affects Serum Metabolomic Profiles in Pregnant Adolescents.Reproductive Sciences, 22(6), 685–695.
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Intermediate-Type Vancomycin Resistance (VISA) in Genetically-Distinct Staphylococcus aureus Isolates Is Linked to Specific , Reversible Metabolic Alterations.PloS one, 9(5), e97137.
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Extensive Translational Regulation of Gene Expression in an Allopolyploid (Glycine dolichocarpa).The Plant Cell, 26(1), 136–150.
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Heat treatment and turbo extractor rotational speed effects on rheological and physico-chemical properties of varietal applesauce.Journal of Food Engineering, 136, 19-27.
2013
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Epigenetic Deregulation In Relapsed Acute Myeloid Leukemia.Blood, 122(21), 2499-2499.
2012
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Accounting for heaping in retrospectively reported event data - a mixture-model approach.Statistics in Medicine, 31(27), 3347-3365.
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A mixture-model approach for parallel testing for unequal variances..Statistical applications in genetics and molecular biology, 11(1), Article 8.
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Pregnancy Induces Transcriptional Activation of the Peripheral Innate Immune System and Increases Oxidative DNA Damage among Healthy Third Trimester Pregnant Women..PloS one, 7(11), e46736.
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Pregnancy status and choline intake alter DNA integrity, epigenetic marks and gene expression.The FASEB Journal, 26(1), 116.1.
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Transcriptional analysis of Shewanella oneidensis MR-1 with an electrode compared to Fe(III)citrate or oxygen as terminal electron acceptor..PloS one, 7(2), e30827.
2011
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Empirical and fully Bayesian approaches for random effects models in microarray data analysis..Statistical Modelling, 11(1), 71–78.
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A higher maternal choline intake favorably alters placental gene expression of biological pathways related to disease risk.The FASEB Journal, 25(1), 599.5.
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Classical conditioning through auditory stimuli in Drosophila: methods and models.Journal of Experimental Biology, 214(17), 2864-2870.
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Shewanella oneidensis in a lactate-fed pure-culture and a glucose-fed co-culture with Lactococcus lactis with an electrode as electron acceptor..Bioresource technology, 102(3), 2623–8.
2010
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Laplace Approximated EM Microarray Analysis: An Empirical Bayes Approach for Comparative Microarray Experiments.Statistical Science, 25(3), 388-407.
2003
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Competition and cooperation in neuronal processing.IEEE Transactions on Neural Networks, 14(4), 860-868.
Invited Talks
- On graphical models and convex geometry. Consortium for Data Analytics in Risk, Berkeley, CA, November 2023; SIAM Conference on Financial Mathematics and Engineering, Philadelphia, PA, June 2023; Mathematics and Statistics Department, Old Dominion University, March 2023; Statistics Department, The Hebrew University, Jerusalem, Israel, June 2022.
- Large-P Variable Selection in Two-Stage Models. CMStatistics, London, UK, December 2020; University of Connecticut, March 2020; University of Haifa, Israel, May 2020.
- Quantile Regression Modelling via Location and Scale Mixtures of Normal Distributions. Cornell University, October 2019.
- A Mixture Model to Detect Edges in Sparse Co-expression Graphs. The 3rd Eastern Asia Meeting on Bayesian Statistics, Seoul, South Korea, July 2018; Yonsei University, Seoul, South Korea, July 2018; Korea University, Seoul, South Korea, July 2018; Bayesian Modeling, Computation, and Applications, Storrs, CT, May 2018.
- A Scalable Empirical Bayes Approach to Variable Selection in Generalized Linear Models. The 34th Quality and Productivity Research Conference, Storrs, CT, June 2017; The 10th ICSA International Conference, Shanghai, China, December 2016; Temple University, Research Colloquium, April 2017; Baruch College, CUNY, November 2016.
- A Scalable Empirical Bayes Approach to Variable Selection. 2016 Joint Statistical Meetings, Chicago, IL, July 2016; Joint UConn/UMass Statistics Colloquium, University of Massachusetts Amherst, October 2015; Statistics Seminar, University of Maryland, October 2015; Mathematical Biosciences Institute, Ohio State University, September 2015.
- An Empirical Bayes Approach to Variable Selection and QTL Analysis. Purdue University, Research Colloquium, October 2014; Modern Modeling Methods (M³) Conference, Storrs, CT, May 2014.
- Model-based approaches for big-data problems, with applications in genomics. Institute for Systems Genomics Annual Networking Workshop, Storrs, CT, May 2014.
- A Bivariate Model for Simultaneous Testing in Bioinformatics Data. 3rd International Conference on Biometrics & Biostatistics, Baltimore, MD, October 2014; University of Iowa, February 2013; NIH/NCI, March 2013; University of Connecticut, February 2013; University of Rochester, February 2013; Cornell University, October 2012.
- Accounting for Heaping in Retrospectively Reported Event Data – A Mixture Model Approach. ICSA Applied Statistics Symposium, New York City, NY, June 2011.
- A Heap of Trouble? Accounting for Mismatch Bias in Retrospectively Collected Data on Smoking. 3rd Biennial Conference of the American Society of Health Economists, Ithaca, NY, June 2010.
Patents
2023
- U.S. Patent 20230041627 (published February 9, 2023). Assay Compound Screening.
2016
- U.S. Patent 9,384,677 (granted July 5, 2016).
2015
- U.S. Patent 9,076,342 (granted July 7, 2015).
- U.S. Patent 20150213730 (published July 30, 2015).
- U.S. Patent 8,984,396 (granted March 17, 2015). Identifying and representing changes between XML files. Inventors: Tingstrom, D.J.; Joyce, R.A.; Stillerman, M.A.; Brueckner, S.K.; Bar, H.Y.
- U.S. Patent 20150143355 (published May 21, 2015). Service Oriented Architecture Version and Dependency Control. Inventors: Tingstrom, D.J.; Joyce, R.A.; Stillerman, M.A.; Brueckner, S.K.; Bar, H.Y.
2014
- U.S. Patent 8,898,285 (granted November 25, 2014). Service Oriented Architecture Version and Dependency Control. Inventors: Tingstrom, D.J.; Joyce, R.A.; Stillerman, M.A.; Brueckner, S.K.; Bar, H.Y.
2012
- U.S. Patent 8,286,249 (granted October 9, 2012).
2010
- U.S. Patent 7,748,040 (granted June 29, 2010). Attack correlation using marked information. Inventors: Adelstein, F.N.; Bar, H.; Alla, P.; Proskourine, N.
2009
- U.S. Patent 20090208910 (published August 20, 2009). Automated execution and evaluation of network-based training exercises. Inventors: Brueckner, S.; Adelstein, F.N.; Bar, H.; Donovan, M.