Adams Analytics Group

Teaching: Past, Present, and Future

Applied Regression

Graduate-level course on regression procedures, models, and applications. Generalized linear models, regularization, model building, feature selection, dimensionality reduction, shrinkage, non-linear methods and basis expansions, Bayesian regression, logistic regression and other classifier algorithms, other facets of supervised machine learning for regression problems.

Design and Analysis of Experiments

Graduate-level course on design and analyses of experimental data. Experimental design, linear models, ANOVA, ANCOVA, hypothesis testing, model adequacy and diagnostics, balanced designs, inbalanced designs, factorial designs, confounded designs, blocks, variance components, generalized linear models, linear mixed models, and more.

Introduction to Data Science for Biologists

Learn an array of skills for handling “Big Data” in biology and beyond! Data wrangling, visualization, hypothesis testing, inference, predictive modeling, supervised and unsupervised learning introductions

Principles of Experimention

Graduate-level course on design of experiments. Variable and data-types, hypothesis testing, grad-level introductory probability and statistics, distributions, categorical data analyses, introduction to regression, experimental designs, F-tests, and other hypotheses tests

Fantastic Genes And Where To Find Them

Hands-on genomics with beetles!

Principles of Biology

Fundamentals of biology for majors (2022)

Insights from a stinky genome

Machine learning for trait evolution

Model selection and ILS

Graduate students present at Evolution 2026!

Rokeya and Miya gave fantastic poster presentations at Evolution 2026 in Cleveland, OH

Choosing trees and robust regression

Collaborative paper on rediscovery of the Chestnut weevil!

Collaborative paper on snake hybrid zones

A tale of too many trees

Towards more robust regression

Supervised and unsupervised learning of protein diversity

We are statisticians.

We are biologists.

We are people.

Adams Analytics Group: learning the rules of life one python script at a time.

Rich Adams (PI)

Assistant Professor of Agricultural Statistics
Center for Agricultural Data Analytics
Department of Entomology and Plant Pathology
University of Arkansas | Division of Agriculture radamsrha@gmail.com

Rokeya Akter

Graduate Student (MS): Statistics and Analytics (2025-present)

Mahamad Miya

Graduate Student (PhD): Entomology and Plant Pathology (2026-present)

Clarissa Stracener

Graduate Student (MS): Statistics and Analytics (2026-present)

Kallahan Minor

Hourly researcher (post-baucc; 2026-present)

Adrian Munoz

Undergraduate Researcher (2024-present)

Alumni: Jennifer Roa Lozano

Graduate student (MS): Statistics and Analytics (graduated: 2025)

Alumni: Mataya Duncan

Graduate student (MS): Cell and Molecular Biology (graduated: 2025)

Alumni: Surbhit Jangra

Hourly researcher (post-baucc; 2025-2026)

Alumni: Byron Gagnon

Undergraduate Reseacher; Adair and Bollenbacher Scholar (2024)

Alumni: Emilee Walden

Undergraduate Reseacher (2024-2025)

Alumni: Emma Turner

Undergraduate Reseacher (2024-2025)

Alumni: Jack Green

Undergraduate Reseacher (2024-2025)

Alumni: Julio Morales

Undergraduate Reseacher (2023)

Alumni: A'aden Redhead

GCSU Undergraduate Reseacher (2022)

Alumni: Margo Mason

GCSU Undergraduate Reseacher (2021-2022)

Alumni: Wesley Demontigny

GCSU Undergraduate Reseacher (2021-2022)

Alumni: Zoe Cain

GCSU Undergraduate Reseacher (2021-2022)

Publications

Underlined authors: members of the Adams Analytics Group

• Concatenation, conflict, and complexity: genealogical heterogeneity mimics substitutional heterogeneity for nucleotide model selection. Lozano JR, Miya M, Turner E, McKenna D, Adams R. Journal of Molecular Evolution 2026. LINK
• Discriminating models of trait evolution. Lozano JR, Jangra S, Degiorgio M, Assis R, Adams R. Evolution 2026. LINK
• Chromosome-scale genome assembly of the rice stink bug illuminates genome structure and gene family evolution in Pentatomidae. Akter R, Miya M, Szalanski A, McKenna D, Adams R. Journal of Heredity 2026. LINK
• Robust regression rescues poor phylogenetic decisions. Duncan M, DeGiorgio M, Assis R, Adams R. BMC Ecology and Evolution 2025. LINK
• Learning the structural diversity of olfactory receptors: a genomic case study in two longhorn beetles. Duncan M, Sylvester T, Walden E, Lozano JR, Turner E, Duncan S, Mitchell R, McKenna D, Adams R. Insects 2026. LINK
• A tale of too many trees: a conundrum for phylogenetic regression. Adams R, Roa Lozano J, Duncan M, Green J, Assis R, DeGiorgio M. Molecular Biology and Evolution 2025. LINK
• AdmixLD: fast genome-scale inference of ancestry disequilibrium in hybrid zones. Francioli Y, Adams R, Ballard K, Gompert Z, Castoe T Bioinformatics 2026. LINK
• TraitTrainR: accelerating large-scale simulation under models of continuous trait evolution. Roa Lozano J, Duncan M, McKenna D, Castoe T, DeGiorgio M, Adams R. Bioinformatics Advances 2025. LINK
• Robust Phylogenetic Regression. Adams R, Cain Z, Assis R, DeGiorgio D. 2024 Systematic Biology 2024. LINK
• Estimation of genome-wide coupling in rattlesnake hybrids provides insight into the process of speciation and its progress. Francioli Y, Bernstein J, Adams R, Guss H, Schield D, Smith S, Gopalan S, Maag D, Meik J, Jezkova T, Demuth J, Clark R, Mackessy S, Gompert Z, Castoe T. Nature Communications 2025. LINK
• Rediscovery of the greater chestnut weevil highlights the power of digital platforms in biodiversity research and conservation. Charles M, Adams R, Anderson R, Bird K, Johnson L, Kelso N, Kerwien L, Santos K, Sarver M, Seltzer C, Shin N, Wild A, McKenna D. Current Biology 2025. LINK
• Functional and evolutionary insights into chemosensation and specialized herbivory from the genome of the red milkweed beetle. Adams R, Terrence S, Mitchell R, Price M, Shen R, McKenna D Journal of Heredity 2025. LINK
• 250 Million Years of Convergent Evolution and Functional Divergence of Glycoside Hydrolase Family 28 Genes in Xylophagous Beetles (Cerambycidae and Buprestidae): Insights Into Horizontal Gene Transfer, Gene Dynamics, Synteny and Adaptive Divergence. Shin N, Duncan M, Adams R, McKenna D Molecular Ecology 2025. LINK
• Genomic Architecture of the Pole Borer, Neandra brunnea (Cerambycidae: Parandrinae), Sheds Light on the Evolution of Wood-Feeding in Longhorn Beetles. Sylvester T, Adams R, Mitchell R, Rongron S, McKenna D. Journal of Heredity 2026. LINK
• Insights into longhorn beetle evolution from comparative analyses of the red-headed ash borer genome. Sylvester T, Adams R, Mitchell R, Ray A, Shen R, Shin N, Daundasekara K, McKenna D. Journal of Heredity 2025. LINK
• Host-dependent virus accumulation dynamics of blackberry chlorotic ringspot virus in two Rubus species. Sierra-Mejia A, Adams R, Tzanetakis I. Virology Journal 2025. LINK
• Genetic variation of rice stink bugs, Oebalus spp. from Southeastern United States and Cuba. Szalanski A, Hix R, Cleary D, Bateman N, Adams R, Cherry R Florida Entomologist 2025. LINK
• Greenhouse Gas Emissions from Flood-Irrigated Rice as Affected by Phosphorus Fertilizer Source. Arel C, Brye K, Della Lunga D, Roberts T, Adams R Agriculture 2025. LINK
• Struvite Effects on Greenhouse Gas Emissions from Furrow-irrigated Rice in the Greenhouse Arel C, Brye K, Della Lunga D, Roberts T, Adams R Journal of Rice Research and Developments 2025. LINK
• Were bed bugs the first urban pest insect? Genome-wide patterns of bed bug demography mirror global human expansion. Lindsay M, Verrelli B, Adams R, Francioli Y, Card D, Balvin O, Castoe T, Booth W. Biology Letters 2025. LINK
• Unique physiological and regulatory activity drives divergent toxin and non-toxin gene expression in rattlesnake accessory venom glands. Kim C, Smith S, Gopalan S, Kerwin S, Ballard K, Perry B, Smith C, Saviola A, Adams R, Mackessy S, Castoe T Toxicon. 2025. LINK
• Disentangling a genome-wide mosaic of conflicting phylogenetic signals in Western Rattlesnakes. Bernstein J, Francioli Y, Schield R, Adams R, Perry B, Farleigh K, Smith C, Meik J, Mackessy S, Castoe T. Molecular Phylogenetics and Evolution 2025. LINK
• A chromosome-level reference genome for the common bed bug, Cimex lectularius, with identification of sex chromosomes. Miles L, Adams R, Francioli Y, Card D, Castoe T, Booth W. Journal of Heredity 2024. LINK
• Mitochondrial DNA Genetic Variation of Feral and Managed Honey Bee, Apis mellifera, Colonies from Oklahoma. Szalanski A, Cleary D, Adams R. Southwestern Entomologist 2024. LINK
• Investigating a Role for Model-Based Inquiry in an Undergraduate Introductory Biology Lab. Karen K, Snyder B, Adams R. The American Biology Teacher 2024. LINK
• The genome of the invasive and broadly polyphagous Diaprepes root weevil, Diaprepes abbreviatus (Coleoptera), reveals an arsenal of putative polysaccharide-degrading enzymes. Sylvester T, Adams R, Hunter W, Li X, Rivera-Marchand B, Shen R, Shin NR, McKenna D. Journal of Heredity 2024. LINK
• Comparative analyses of the banded alder borer (Rosalia funebris) and Asian longhorned beetle (Anoplophora glabripennis) genomes reveal significant differences in genome architecture and gene content among these and other Cerambycidae. Sylvester T, Adams R, Mitchell R, Ray A, Shen R, Shin N R, McKenna D. Journal of Heredity 2024. LINK
• Diverse gene regulatory mechanisms alter rattlesnake venom gene expression at fine evolutionary scales. Gopalan S, Perry B, Francioli Y, Schield D, Guss H, Bernstein J, Ballard K, Smith C, Saviola A, Adams R, Mackessy S, Castoe T. Genome Biology and Evolution 2024. LINK
• Likelihood-based tests of species tree hypotheses. Adams R, DeGiorgio M. Molecular Biology and Evolution 2023. LINK
• Mitochondrial DNA variation in honey bee colonies from Arkansas. Cleary D, Adams R, Szalanski A. 2024 Journal of Apicultural Research 2023. LINK
• Single-cell heterogeneity in snake venom expression is hardwired by co-option of regulators from progressively activated pathways. Westfall A, Gopalan S, Perry B, Adams R, Saviola A, Mackessy S, Castoe T. Genome Biology and Evolution 2022. LINK
• The roles of balancing selection and recombination in the evolution of rattlesnake venom. Schield D, Perry B, Adams R, Holding M, Nikolakis Z, Gopalan S, Smith C, Parker S, DeGiorgio M, Mackessy S, and Castoe T. Nature Ecology and Evolution 2022. LINK
• Fifty million years of beetle evolution along the Antarctic Polar Front. Baird H, Shin S, Oberprieler R, Hullé M, Vernon P, Moon K, Adams R, McKenna D, Chown S. Proceedings of the National Academy of Sciences 2021. LINK
• Evidence that genomic incompatibilities and other multilocus processes impact fitness in a rattlesnake hybrid zone. Nikolakis Z, Schield D, Westfall A, Perry B, Ivey K, Orton R, Hales N, Adams R, Meik J, Parker J, Smith C, Gompert Z, Mackessy S, and Castoe T. Evolution 2022. LINK
• Prospects for genomic surveillance for selection in schistosomiasis. Nikolakis Z, Adams R, Wade K, Lund A, Carlton E, Castoe T, Pollock D Frontiers in Epidemiology 2022. LINK
• Of traits and trees: probabilistic distances for dissecting the interplay among phylogeny, model, and data. Adams R, Blackmon H, and DeGiorgio M. Systematic Biology 2021. LINK
• Probabilistic species tree distances: implementing the multispecies coalescent to compare species trees within the same model-based framework used to estimate them. Adams R, and Castoe T. Systematic Biology 2020. LINK
• PhyloWGA: chromosome-aware phylogenetic interrogation of whole genome alignments. Adams R, Castoe T., and DeGiorgio M. Bioinformatics 2020. LINK
• Microchromosomes exhibit distinct features of vertebrate chromosome structure and function with underappreciated ramifications for genome evolution. Perry B, Schield D, Adams R, and Castoe T. Molecular Biology and Evolution 2020. LINK
• Genome-wide SNPs clarify lineage diversity confused by coloration in coralsnakes of the Micrurus diastema (Serpentes: Elapidae) species complex. *Reyes-Velasco J, *Adams R, S. Boissinot, C.L. Parkinson, J.A. Campbell, Castoe T, and E.N. Smith. Molecular Phylogenetics and Evolution 2020. LINK *Joint primary authors
• Snake Recombination Landscapes Are Concentrated in Functional Regions despite PRDM9. Schield D, Pasquesi G, Perry B, Adams R Nikolakis Z, Orton R, Meik J, Mackessy S, and Castoe T Molecular Biology and Evolution 2020. LINK
• Recent advances in the inference of gene flow from population genomic data. Adams R, Schield D, and Castoe T. Current Molecular Biology Reports 2019. LINK
• Statistical binning suffers profound model violation due to gene tree error incurred by trying to avoid gene tree error. Adams R and Castoe T Molecular Phylogenetics and Evolution 2019. LINK
• Supergene validation: a model-based protocol for assessing the accuracy of non-model-based supergene methods. Adams R and Castoe T MethodsX 2019. LINK
• Genomic basis of convergent island phenotypes in boa constrictors. Card D, Adams RGenome Biology and Evolution 2019. LINK
• Allopatric divergence and secondary contact with gene flow – a recurring theme in rattlesnake speciation. Schield D, Perry B, Adams R, Card D, Jezkova T, Pasquesi G, Nikolakis Z, Row K, Meik J, Smith C, Mackessy S, and Castoe T. Biological Journal of the Linnean Society 2019. LINK
• The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes. Schield D, Card D, Hales N, Perry B, Pasquesi G, Blackmon H, Adams R, Corbin A, Smith C, B. Ramesh, Demuth J, Betran E, Tollis M, Meik J, Mackessy S and Castoe T. Genome Research 2019. LINK
• A database of amphibian karyotypes. Perkins R, Gamboa J, Jonika M, Lo J, Shum A, Adams R, and Blackmon H Chromosome Research 2019. LINK
• Assessing the impacts of positive selection on coalescent-based species tree estimation and species delimitation. Adams R, Card D, Schield D, and Castoe T. Systematic Biology 2018. LINK
• ThetaMater: Bayesian estimation of population size parameter θ from genomic data. Adams R, Card D, Schield D, Corbin A, and Castoe T Bioinformatics 2018. LINK
• Novel ecological and climatic conditions drive rapid adaptation in invasive Florida Burmese pythons. Card D, B. Perry, Adams R, Schield D, Young A, Andrew A, Jezkova T, Walsh M, Rockford M, Mazzotti F, Hart K, Hunter M, and Castoe T. Molecular Ecology 2018. LINK
• Molecular adaptations for sensing and securing prey, and insight into amniote genome diversity, from the garter snake genome. Perry B, Card D, Pasquesi G, Adams R, Schield D, Hales N, Corbin A, Demuth J, Hoffmann F, Vandewege M, Schott R, Bhattacharyya N, Chang B, Casewell N, Whiteley G, Reyes-Velasco J, Mackessy S, Storey K, Gamble T, Biggar K, Passow C, Kuo C, McGaugh D, Bronikowski A, de Koning J, Edwards S, Pfrender M, Minx P, Brodie III E, Brodie Jr E, Warren W, and Castoe T Genome Biology and Evolution 2018. LINK
• Cryptic genetic diversity, population structure, and gene flow in Mohave rattlesnakes Crotalus scutulatus. Schield D, Card D, Adams R, Corbin A, Jezkova T, Hales N, Meik J, Spencer C, Smith L, Campillo Garcia G, Bouzid N, Strickland J, Bryson Jr. R, Parkinson C, Flores-Viella O, Mackessy S and Castoe T. Molecular Phylogenetics and Evolution 2018. LINK
• Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals. Pasquesi G, Adams R, Card D, Schield D, Perry B, Corbin A, Reyes-Velasco J, Ruggiero R, Vandewege M, Shortt J, and Castoe T. Nature Communications 2018. LINK
• Insight into the roles of selection in speciation from genomic patterns of divergence and introgression in secondary contact in venomous rattlesnakes. Schield D, Adams R, Card D, Perry B, Pasquesi G, T. Jezkova, D.M. Portik, Andrew A, C.L. Spencer, E.E. Sanchez, M.K. Fujita, Mackessy S, and Castoe T. Ecology and Evolution 2017. LINK
• GppFst: Genomic posterior predictive simulations of FST and dXY for identifying outlier loci from population genomic data. Adams R, Schield D, Card D, Blackmon H, and Castoe T. Bioinformatics 2017. LINK
• Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution. Adams R, Blackman H, Reyes-Velasco J, Schield D, Card D, Andrew A, Waynewood N, and Castoe T. Genome 2016. LINK
• A suite of potentially amplifiable microsatellite loci for reptiles of conservation concern from Africa and Asia. Shaney K, Adams R, Kurniawan N, Hamidy A, Smith E, and Castoe T. Conservation Genetics Resources 2016. LINK
• Phylogeographic and population genetic analyses reveal multiple species of Boa and independent origins of insular dwarfism. Card D, D.R Schield, Adams R, Corbin A, Perry B, Andrew A, Pasquesi G, E.N. Smith, T. Jezkova, S.M. Boback, W. Booth, and Castoe T. Molecular Phylogenetics and Evolution 2016. LINK
• EpiRadSeq: genome-wide analysis of shifts in DNA methylation using next-generation sequencing. Schield D, M.F. Walsh, Card D, Andrew A, Adams R, and Castoe T. Methods in Ecology and Evolution 2016. LINK
• Rapid changes in gene expression direct rapid shifts in intestinal form and function in the Burmese python after feeding. Andrew, A.L., Card D, R.P. Ruggiero, Schield D, Adams R, D.D. Pollock, S.M. Secor, and Castoe T. Physiological Genomics 2015. LINK
• Incipient speciation with biased gene flow between two lineages of the Western Diamondback Rattlesnake Crotalus atrox. Schield D, Card D, Adams R, T. Jezkova, J. Reyes-Velasco, F.N. Proctor, C.L. Spencer, H-W. Herrmann, Mackessy S, and Castoe T. Molecular Phylogenetics and Evolution 2015. LINK
• Expression of venom gene homologs in diverse python tissues suggests a new model for the evolution of snake venom. Reyes-Velasco J., Card D, Andrew A, K.J. Shaney, Adams R, Schield D, N.R. Casewell, Mackessy S, and Castoe T. Molecular Biology and Evolution 2015. LINK

Contact

Elements

i = 0;

while (!deck.isInOrder()) {
    print 'Iteration ' + i;
    deck.shuffle();
    i++;
}

print 'It took ' + i + ' iterations to sort the deck.';