Research

My research has focused chiefly on estimation problems. Most publications concern statistical experimental design, machine learning/predictive modeling, creating high-quality data analysis software, and/or drug discovery.

Confidence Regions for Constrained Optima in Response Surface Experiments with Noise Factors

article

experimental design

Kuhn M (1999). “Confidence Regions for Constrained Optima in Response Surface Experiments with Noise Factors.” Proceedings of the ASA Sections on Physical & Engineering…

Empirical Power for Distribution-Free Tests of Incomplete Longitudinal Data with Applications to AIDS Clinical Trials

article

Kuhn M, DeMasi RA (1999). “Empirical Power for Distribution-Free Tests of Incomplete Longitudinal Data with Applications to AIDS Clinical Trials.” Journal of…

Incorporating Noise Factors into Experiments with Censored Data

article

experimental design

Kuhn M, Carter WH, Myers RH (2000). “Incorporating noise factors into experiments with censored data.” Technometrics, 376-383.

Optimizing Response Surface Experiments with Noise Factors Using Confidence Regions

article

experimental design

Kuhn M (2003). “Optimizing Response Surface Experiments with Noise Factors Using Confidence Regions.” Quality Engineering, 15(3), 419-426.

Homogeneous Real-Time Detection of Single-Nucleotide Polymorphisms by Strand Displacement Amplification on the BD ProbeTec ET System

article

moledular diagnostics

Wang S, Thornton K, Kuhn M, Nadeau JG, Hellyer TJ (2003). “Homogeneous real-time detection of single-nucleotide polymorphisms by strand displacement amplification on the BD…

Ridge Analysis With Noise Variables

article

experimental design

Peterson J, Kuhn M (2005). “Ridge Analysis With Noise Variables.” Technometrics, 47, 274-283.

Sweave and the Open Document Format - the odfWeave Package

article

software

Kuhn M (2006). “Sweave and the open document format-the odfWeave package.” R News, 6(4), 2-8.

Building Predictive Models in R using the caret Package

article

software

machine learning

Kuhn M (2008). “Building predictive models in R using the caret package.” Journal of Statistical Software, 28(5), 1-26.

Postnatal PPARδ Activation and Myostatin Inhibition Exert Distinct yet Complimentary Effects on the Metabolic Profile of Obese Insulin-Resistant Mice

article

drug discovery

Bernardo BL, Wachtmann TS, Cosgrove PG, Kuhn M, Opsahl AC, Judkins KM, Freeman TB, Hadcock JR, LeBrasseur NK (2010). “Postnatal PPARδ activation and myostatin inhibition…

Novel CSF Biomarkers for Alzheimer’s Disease and Mild Cognitive Impairment

article

drug discovery

Hu WT, Chen-Plotkin A, Arnold SE, Grossman M, Clark CM, Shaw LM, Pickering E, Kuhn M, Chen Y, McCluskey L, others (2010). “Novel CSF biomarkers for Alzheimer’s disease and…

P3-380: Dendritic Spine Density Deficits in the Hippocampal CA1 Region of Young Tg2576 Mice are Ameliorated with the PDE9A Inhibitor PF-04447943

article

drug discovery

Kleiman RJ, Lanz TA, Finley JE, Bove SE, Majchrzak MJ, Becker SL, Carvajal-Gonzales S, Kuhn M, Wood KM, Mariga A, others (2010). “P3-380: Dendritic spine density deficits in…

P2-093: Multiplex Plasma Panels as Screening Tools in Alzheimer’s Disease.

article

drug discovery

Soares H, Hu W, Grossman M, Clark C, Pickering E, Chen Y, Kuhn M, Chen-Plotkin A, Arnold S, Shaw L, others (2010). “P2-093: Multiplex plasma panels as screening tools in…

New Analyses of MIC 90 Data to Aid Antibacterial Drug Discovery

article

drug discovery

Brown MF, Gupta RR, Kuhn M, Flanagan ME, Mitton-Fry M (2011). “New analyses of MIC 90 data to aid antibacterial drug discovery.” MedChemComm, 2(8), 735-742.

Multiplexed Immunoassay Panel Identifies Novel CSF Biomarkers for Alzheimer’s Disease Diagnosis and Prognosis

article

drug discovery

Craig-Schapiro R, Kuhn M, Xiong C, Pickering EH, Liu J, Misko TP, Perrin RJ, Bales KR, Soares H, Fagan AM, others (2011). “Multiplexed immunoassay panel identifies novel CSF…

Modeling the Mechanism of Action of a DGAT1 Inhibitor using a Causal Reasoning Platform

article

drug discovery

Enayetallah AE, Ziemek D, Leininger MT, Randhawa R, Yang J, Manion TB, Mather DE, Zavadoski WJ, Kuhn M, Treadway JL, others (2011). “Modeling the mechanism of action of a…

P1-089: Plasma Multianalyte Profiling of Mild Cognitive Impairment and Alzheimer’s Disease in Two Academic Centers and the Alzheimer’s Disease Neuroimaging Initiative

article

drug discovery

Hu WT, Holtzman D, Clark C, Grossman M, Karlawish J, Fagan A, Lee V, Swenson F, Craig-Schapiro R, Perrin RJ, others (2011). “P1-089: Plasma multianalyte profiling of mild…

Chronic Suppression of Phosphodiesterase 10a Alters Striatal Expression of Genes Responsible for Neurotransmitter Synthesis, Neurotransmission, and Signaling Pathways Implicated in Huntington’s Disease

article

drug discovery

Kleiman RJ, Kimmel LH, Bove SE, Lanz TA, Harms JF, Romegialli A, Miller KS, Willis A, des Etages S, Kuhn M, others (2011). “Chronic suppression of phosphodiesterase 10A…

Changes in Plasma Based Biomarkers in Alzheimer’s Disease, Mild Cognitively Impaired and Aged Matched Normal Controls from the ADNI Cohort

article

drug discovery

Soares H, Potter W, Immermann F, Pickering E, Kuhn M, Shera D, Zagouras P, Swenson F, Wan H, Ferm M, others (2011). “Changes in plasma based biomarkers in Alzheimer’s…

Polyomic Profiling Reveals Significant Hepatic Metabolic Alterations in Glucagon-Receptor (GCGR) Knockout Mice: Implications on Anti-Glucagon Therapies for Diabetes

article

drug discovery

Yang J, MacDougall ML, McDowell MT, Xi L, Wei R, Zavadoski WJ, Molloy MP, Baker JD, Kuhn M, Cabrera O, others (2011). “Polyomic profiling reveals significant hepatic…

Plasma Multianalyte Profiling in Mild Cognitive Impairment and Alzheimer Disease

article

drug discovery

Hu WT, Holtzman DM, Fagan AM, Shaw LM, Perrin R, Arnold SE, Grossman M, Xiong C, Craig-Schapiro R, Clark CM, others (2012). “Plasma multianalyte profiling in mild cognitive…

The Use of the R Language for Medicinal Chemistry Applications

article

software

drug discovery

machine learning

Mente S, Kuhn M (2012). “The use of the R language for medicinal chemistry applications.” Current Topics in Medicinal Chemistry, 12(18), 1957-1964.

P1-320: Cerebrospinal Fluid (CSF) vs. Plasma-Based Biomarkers in Alzheimer’s Disease (AD), Mild Cognitive Impaired (MCI) and Age-Matched Healthy Controls (HC) from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) Cohort

article

drug discovery

Potter W, Pickering EH, Immermann F, Kuhn M, Siuciak J, Shaw L, (ADNI) ADNI, for NIH Biomarkers Consortium CSF Proteomics Project Team F (2012). “P1-320: Cerebrospinal fluid…

Silencing of Enzymes Involved in Ceramide Biosynthesis Causes Distinct Global Alterations of Lipid Homeostasis and Gene Expression

article

drug discovery

Ruangsiriluk W, Grosskurth SE, Ziemek D, Kuhn M, des Etages SG, Francone OL (2012). “Silencing of enzymes involved in ceramide biosynthesis causes distinct global…

P1-319: Cerebrospinal Fluid (CSF) Biomarkers in Alzheimer’s Disease (AD), Mild Cognitively Impaired (MCI) and Age-Matched Healthy Controls (HC) from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) Cohort

article

drug discovery

Siuciak J, Pickering EH, Immermann F, Kuhn M, Shaw L, Potter W, (ADNI) ADNI, for NIH Biomarkers Consortium CSF Proteomics Project Team F (2012). “P1-319: Cerebrospinal fluid…

Plasma Biomarkers Associated with the Apolipoprotein E Genotype and Alzheimer Disease

article

drug discovery

Soares HD, Potter WZ, Pickering E, Kuhn M, Immermann FW, Shera DM, Ferm M, Dean RA, Simon AJ, Swenson F, others (2012). “Plasma biomarkers associated with the apolipoprotein…

Perinatal Suppression of Tau P301L Has a Long Lasting Preventive Effect Against Neurodegeneration

article

drug discovery

Caouette D, Xie Z, Milici A, Kuhn M, Bocan T, Yang D (2013). “Perinatal suppression of Tau P301L has a long lasting preventive effect against neurodegeneration.” Internationa…

Applied Predictive Modeling

book

software

machine learning

Kuhn M, Johnson K (2013). Applied predictive modeling. Springer New York.

Improving the Odds of Success in Drug Discovery: Choosing the Best Compounds for in Vivo Toxicology Studies

article

drug discovery

Wager TT, Kormos BL, Brady JT, Will Y, Aleo MD, Stedman DB, Kuhn M, Chandrasekaran RY (2013). “Improving the odds of success in drug discovery: choosing the best compounds…

Active Glucagon-Like Peptide 1 Quantitation in Human Plasma: a Comparison of Multiple Ligand Binding Assay Platforms

article

drug discovery

Fraser S, Dysinger M, Soderstrom C, Kuhn M, Durham R (2014). “Active glucagon-like peptide 1 quantitation in human plasma: a comparison of multiple ligand binding assay…

Futility Analysis in the Cross-Validation of Machine Learning Models

article

machine learning

Kuhn M (2014). “Futility analysis in the cross-validation of machine learning models.” arXiv preprint arXiv:1405.6974.

Who’s Afraid of the Big Black Box?: Statisticians’ Vital Role in Big Data and Predictive Modelling

article

machine learning

Kuhn M, Johnson K (2014). “Who’s afraid of the big black box?: Statisticians’ vital role in big data and predictive modelling.” Significance, 11(3), 35-37.

More than Just Hormones: H295R Cells as Predictors of Reproductive Toxicity

article

drug discovery

machine learning

Maglich JM, Kuhn M, Chapin RE, Pletcher MT (2014). “More than just hormones: H295R cells as predictors of reproductive toxicity.” Reproductive toxicology, 45, 77-86.

Downstream Effects of Striatal-Enriched Protein Tyrosine Phosphatase Reduction on RNA Expression in Vivo and in Vitro

article

drug discovery

Reinhart V, Nguyen T, Gerwien Jr R, Kuhn M, Yates P, Lanz T (2014). “Downstream effects of striatal-enriched protein tyrosine phosphatase reduction on RNA expression in vivo…

Quantitative-Structure Activity Relationship Modeling and Cheminformatics

book chapter

drug discovery

machine learning

Kuhn M (2016). “Quantitative-Structure Activity Relationship Modeling and Cheminformatics.” In Nonclinical Statistics for Pharmaceutical and Biotechnology Industries, volume…

Statistical Methods for Drug Discovery

book chapter

drug discovery

Kuhn M, Yates P, Hyde C (2016). “Statistical Methods for Drug Discovery.” In Nonclinical Statistics for Pharmaceutical and Biotechnology Industries, volume 1, 53-82. Springer.

Quantitative Assessment of the Impact of Fluorine Substitution on P-Glycoprotein (P-Gp) Mediated Efflux, Permeability, Lipophilicity, and Metabolic Stability

article

drug discovery

Pettersson M, Hou X, Kuhn M, Wager TT, Kauffman GW, Verhoest PR (2016). “Quantitative assessment of the impact of fluorine substitution on P-glycoprotein (P-gp) mediated…

Nonclinical Statistics for Pharmaceutical and Biotechnology Industries

book

drug discovery

Zhang L, Kuhn M, Peers I, Altan S (Eds.). (2016). Nonclinical statistics for pharmaceutical and biotechnology industries. Springer.

Predictive Modeling of Response to Pregabalin for the Treatment of Neuropathic Pain using 6-Week Observational Data: a Spectrum of Modern Analytics Applications

article

machine learning

Emir B, Johnson K, Kuhn M, Parsons B (2017). “Predictive modeling of response to pregabalin for the treatment of neuropathic pain using 6-week observational data: a spectrum…

Accurate and Fast Feature Selection Workflow for High-Dimensional Omics Data

article

drug discovery

Perez-Riverol Y, Kuhn M, Vizcaíno JA, Hitz M, Audain E (2017). “Accurate and fast feature selection workflow for high-dimensional omics data.” PloS one, 12(12), e0189875.

Ultra-Sensitive Measurement of IL-17a and IL-17f in Psoriasis Patient Serum and Skin

article

drug discovery

Soderstrom C, Berstein G, Zhang W, Valdez H, Fitz L, Kuhn M, Fraser S (2017). “Ultra-sensitive measurement of IL-17A and IL-17F in psoriasis patient serum and skin.” The…

Leveraging of Rifampicin-Dosed Cynomolgus Monkeys to Identify Bile Acid 3-O-Sulfate Conjugates as Potential Novel Biomarkers for Organic Anion-Transporting Polypeptides

article

drug discovery

Thakare R, Gao H, Kosa RE, Bi Y, Varma MV, Cerny MA, Sharma R, Kuhn M, Huang B, Liu Y, others (2017). “Leveraging of rifampicin-dosed cynomolgus monkeys to identify bile…

Feature Engineering and Selection: A Practical Approach for Predictive Models

book

machine learning

Kuhn M, Johnson K (2019). Feature engineering and selection: A practical approach for predictive models. Chapman and Hall/CRC.

Welcome to the Tidyverse

article

software

Hadley Wickham, Mara Averick, Jennifer Bryan, Winston Chang, Lucy D’Agostino McGowan, Romain François, Garrett Grolemund, Alex Hayes, Lionel Henry, Jim Hester, Max Kuhn…

The Advantages of Describing Covalent Inhibitor in Vitro Potencies by IC50 at a Fixed Time Point. IC50 Determination of Covalent Inhibitors Provides Meaningful Data to Medicinal Chemistry for SAR Optimization

article

drug discovery

Thorarensen A, Balbo P, Banker ME, Czerwinski RM, Kuhn M, Maurer TS, Telliez J, Vincent F, Wittwer AJ (2021). “The advantages of describing covalent inhibitor in vitro…

SIMON: Open-Source Knowledge Discovery Platform

article

software

Tomic A, Tomic I, Waldron L, Geistlinger L, Kuhn M, Spreng RL, Dahora LC, Seaton KE, Tomaras G, Hill J, others (2021). “SIMON: open-source knowledge discovery platform.” Patt…

Stacks: Stacked Ensemble Modeling with Tidy Data Principles

article

software

machine learning

Couch SP, Kuhn M (2022). “stacks: Stacked ensemble modeling with tidy data principles.” Journal of Open Source Software, 7(75), 4471.

Tidy Modeling with R: A Framework for Modeling in the Tidyverse

book

software

machine learning

Kuhn M, Silge J (2022). “Tidy modeling with R: A framework for modeling in the tidyverse.”

Assessing the Performance of Spatial Cross-Validation Approaches for Models of Spatially Structured Data

article

software

machine learning

Mahoney MJ, Johnson LK, Silge J, Frick H, Kuhn M, Beier CM (2023). “Assessing the performance of spatial cross-validation approaches for models of spatially structured data.” …

Applied Machine Learning for Tabular Data

book

machine learning

Kuhn M, Johnson K (2024). Applied Machine Learning for Tabular Data. Unpublished, in-progress

What They Forgot to Tell you About Machine Learning with an Application to Pharmaceutical Manufacturing

article

drug discovery

machine learning

Johnson K, Kuhn M (2025). “What they forgot to tell you about machine learning with an application to pharmaceutical manufacturing.” Pharmaceutical Statistics, 24(1), e2366.

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