Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases. - Alexander V. Alekseyenko; Christopher J. Lee (Bioinform., 2007)

The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species. - Namshin Kim; Alexander V. Alekseyenko; Meenakshi Roy; Christopher J. Lee (Nucleic Acids Res., 2007)

Accurate Stochastic Simulation via the Step Anticipation τ-Leaping (SAL) Algorithm. - Mary E. Sehl; Alexander V. Alekseyenko; Kenneth Lange (J. Comput. Biol., 2009)

Visualization and Statistical Comparisons of Microbial Communities Using R Packages on Phylochip Data. - Susan P. Holmes; Alexander V. Alekseyenko; Alden Timme; Tyrrell Nelson; Pankaj Jay Pasricha; Alfred Spormann (Pacific Symposium on Biocomputing, 2011)

Heteroscedastic Omics Data Analysis: Distance-Based Multivariate Approach. - Alexander V. Alekseyenko (AMIA, 2016)

The Human Microbiome: Informatics Challenges and Opportunities. - Alexander V. Alekseyenko; Michael J. Becich; Todd Z. DeSantis; Jack A. Gilbert; Georg K. Gerber (AMIA, 2016)

Comprehensive Evaluation of Univariate and Multivariate Distributions for Machine Learning With Microbiome Data. - Ali Shojaee Bakhtiari; Alexander V. Alekseyenko (AMIA, 2016)

Multivariate Welch t-test on distances. - Alexander V. Alekseyenko (Bioinform., 2016)

PERMANOVA-S: association test for microbial community composition that accommodates confounders and multiple distances. - Zheng-Zheng Tang; Guanhua Chen 002; Alexander V. Alekseyenko (Bioinform., 2016)

The Impact of Human Microbiome on Precision Medicine. - Alexander V. Alekseyenko; Lita M. Proctor; Paul Carlson; Scott A. Jackson; Connie Chen (AMIA, 2017)

Local Causal Networks Discover Predictive Cytokine Biomarkers of Scleroderma. - Ali Shojaee Bakhtiari; Galina S. Bogatkevich; Alexander V. Alekseyenko (AMIA, 2017)

A general framework for association analysis of microbial communities on a taxonomic tree. - Zheng-Zheng Tang; Guanhua Chen 002; Alexander V. Alekseyenko; Hongzhe Li (Bioinform., 2017)

The Hidden Microbiome Pipeline: Providing Access to Clinical Microbiome Specimens, Sequences, and Informatics Resources. - Bashir Hamidi; Leslie A. Lenert; Jihad S. Obeid; Alexander V. Alekseyenko (AMIA, 2018)

BioSimulator.jl: Stochastic simulation in Julia. - Alfonso Landeros; Timothy Stutz; Kevin L. Keys; Alexander V. Alekseyenko; Janet S. Sinsheimer; Kenneth Lange; Mary E. Sehl (Comput. Methods Programs Biomed., 2018)

Multivariate Pathway Enrichment Analysis for Interpreting Expression Profiles. - Ali Shojaee Bakhtiari; Kristin Wallace; Alexander V. Alekseyenko (AMIA, 2019)

Simulation Study of Just-in-Time Specimen Recruitment from University-Wide e-Phenotypes of Interest. - Bashir Hamidi; Leslie A. Lenert; Alexander V. Alekseyenko (AMIA, 2019)

Actionable opportunities for improving knowledge at intersectionof dental and medical data. - Neel A. Shimpi; Karmen S. Williams; Alexander V. Alekseyenko (AMIA, 2019)

OHMI: the ontology of host-microbiome interactions. - Yongqun He; Haihe Wang; Jie Zheng 001; Daniel P. Beiting; Anna Maria Masci; Hong Yu 014; Kaiyong Liu; Jianmin Wu; Jeffrey L. Curtis; Barry Smith 001; Alexander V. Alekseyenko; Jihad S. Obeid (J. Biomed. Semant., 2019)

Informatics Architecture for Phenotyped Microbiome Data Generation from Just-in-Time Clinical Microbiology Specimens from CTSA Network Producers. - Alexander V. Alekseyenko (AMIA, 2020)

Informatics Challenges of COVID-19 Crisis: A Comprehensive Response from An Academic Health System. - Alexander V. Alekseyenko; Leslie A. Lenert (AMIA, 2020)

Actionable Opportunities for Improving Opioid Prescribing through Use of Informatics. - Neel A. Shimpi; Karmen S. Williams; Alexander V. Alekseyenko (AMIA, 2020)

Colonizing Microbiome as a Determinant of COVID-19 Outcome: A Pilot Study. - Alexander V. Alekseyenko; Bashir Hamidi; Stéphane M. Meystre (AMIA, 2021)

Natural Language Processing and COVID-19 Predictive Analytics to Enable and Optimize SARS-CoV-2 Pooled Testing. - Stéphane M. Meystre; Paul M. Heider; Jihad S. Obeid; Alexander V. Alekseyenko; James E. Madory (AMIA, 2021)

A phylogenetic approach for weighting genetic sequences. - Nicola De Maio; Alexander V. Alekseyenko; William J. Coleman-Smith; Fabio Pardi; Marc A. Suchard; Asif U. Tamuri; Jakub Truszkowski; Nick Goldman (BMC Bioinform., 2021)

A deep learning segmentation strategy that minimizes the amount of manually annotated images. - Thierry Pécot; Alexander V. Alekseyenko; Kristin Wallace (F1000Research, 2021)

Each patient is a research biorepository: informatics-enabled research on surplus clinical specimens via the living BioBank. - Alexander V. Alekseyenko; Bashir Hamidi; Trevor D. Faith; Keith A. Crandall; Jennifer G. Powers; Christopher Metts; James E. Madory; Steven L. Carroll; Jihad S. Obeid; Leslie A. Lenert (J. Am. Medical Informatics Assoc., 2021)

Natural language processing enabling COVID-19 predictive analytics to support data-driven patient advising and pooled testing. - Stéphane M. Meystre; Paul M. Heider; Youngjun Kim; Matthew Davis; Jihad S. Obeid; James E. Madory; Alexander V. Alekseyenko (J. Am. Medical Informatics Assoc., 2021)

Building Determinants of Health Ontology of Mappable Elements (DHOME). - Lauren Cuppy; Tami Crawford; Nikunja Swain; Alexander V. Alekseyenko (AMIA, 2022)

Online algorithm for assignment of specimens to pooled or individual testing using risk models provides a practical way to increase testing capacity. - Alexander V. Alekseyenko (F1000Research, 2023)

Not all phenotypes are created equal: covariates of success in e-phenotype specification. - Bashir Hamidi; Patrick A. Flume; Kit N. Simpson; Alexander V. Alekseyenko (J. Am. Medical Informatics Assoc., 2023)

Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup. - Nephi A. Walton; Radhakrishnan Nagarajan; Chen Wang 001; Murat Sincan; Robert R. Freimuth; David B. Everman; Derek C. Walton; Scott P. McGrath; Dominick J. Lemas; Panayiotis V. Benos; Alexander V. Alekseyenko; Qianqian Song; et al. (J. Am. Medical Informatics Assoc., 2024)

Machine learning in healthcare citizen science: A scoping review. - Ranga Baminiwatte; Blessing Torsu; Dmitry Scherbakov; Abolfazl Mollalo; Jihad S. Obeid; Alexander V. Alekseyenko; Leslie A. Lenert (Int. J. Medical Informatics, 2025)