Alexander V. Alekseyenko

Publication Activity (10 Years)

Years Active: 2007-2024
Publications (10 Years): 28

Top Topics

Natural Language Processing

Predictive Analytics

Stochastic Simulation

Annotated Images

Top Venues

J. Am. Medical Informatics Assoc.

Publications

Nephi A. Walton, Radhakrishnan Nagarajan, Chen Wang, 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, Ece Gamsiz Uzun, Casey Overby Taylor, Alper Uzun, Thomas N. Person, Nadav Rappoport, Zhongming Zhao, Marc S. Williams
Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup. J. Am. Medical Informatics Assoc. 31 (2) (2024)
Alexander V. Alekseyenko
Online algorithm for assignment of specimens to pooled or individual testing using risk models provides a practical way to increase testing capacity. F1000Research 12 (2023)
Bashir Hamidi, Patrick A. Flume, Kit N. Simpson, Alexander V. Alekseyenko
Not all phenotypes are created equal: covariates of success in e-phenotype specification. J. Am. Medical Informatics Assoc. 30 (2) (2023)
Lauren Cuppy, Tami Crawford, Nikunja Swain, Alexander V. Alekseyenko
Building Determinants of Health Ontology of Mappable Elements (DHOME). AMIA (2022)
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
Each patient is a research biorepository: informatics-enabled research on surplus clinical specimens via the living BioBank. J. Am. Medical Informatics Assoc. 28 (1) (2021)
Thierry Pécot, Alexander V. Alekseyenko, Kristin Wallace
A deep learning segmentation strategy that minimizes the amount of manually annotated images. F1000Research 10 (2021)
Stéphane M. Meystre, Paul M. Heider, Youngjun Kim, Matthew Davis, Jihad S. Obeid, James E. Madory, Alexander V. Alekseyenko
Natural language processing enabling COVID-19 predictive analytics to support data-driven patient advising and pooled testing. J. Am. Medical Informatics Assoc. 29 (1) (2021)
Stéphane M. Meystre, Paul M. Heider, Jihad S. Obeid, Alexander V. Alekseyenko, James E. Madory
Natural Language Processing and COVID-19 Predictive Analytics to Enable and Optimize SARS-CoV-2 Pooled Testing. AMIA (2021)
Nicola De Maio, Alexander V. Alekseyenko, William J. Coleman-Smith, Fabio Pardi, Marc A. Suchard, Asif U. Tamuri, Jakub Truszkowski, Nick Goldman
A phylogenetic approach for weighting genetic sequences. BMC Bioinform. 22 (1) (2021)
Alexander V. Alekseyenko, Bashir Hamidi, Stéphane M. Meystre
Colonizing Microbiome as a Determinant of COVID-19 Outcome: A Pilot Study. AMIA (2021)
Alexander V. Alekseyenko
Informatics Architecture for Phenotyped Microbiome Data Generation from Just-in-Time Clinical Microbiology Specimens from CTSA Network Producers. AMIA (2020)
Alexander V. Alekseyenko, Leslie A. Lenert
Informatics Challenges of COVID-19 Crisis: A Comprehensive Response from An Academic Health System. AMIA (2020)
Neel A. Shimpi, Karmen S. Williams, Alexander V. Alekseyenko
Actionable Opportunities for Improving Opioid Prescribing through Use of Informatics. AMIA (2020)
Yongqun He, Haihe Wang, Jie Zheng, Daniel P. Beiting, Anna Maria Masci, Hong Yu, Kaiyong Liu, Jianmin Wu, Jeffrey L. Curtis, Barry Smith, Alexander V. Alekseyenko, Jihad S. Obeid
OHMI: the ontology of host-microbiome interactions. J. Biomed. Semant. 10 (1) (2019)
Neel A. Shimpi, Karmen S. Williams, Alexander V. Alekseyenko
Actionable opportunities for improving knowledge at intersectionof dental and medical data. AMIA (2019)
Bashir Hamidi, Leslie A. Lenert, Alexander V. Alekseyenko
Simulation Study of Just-in-Time Specimen Recruitment from University-Wide e-Phenotypes of Interest. AMIA (2019)
Ali Shojaee Bakhtiari, Kristin wallace, Alexander V. Alekseyenko
Multivariate Pathway Enrichment Analysis for Interpreting Expression Profiles. AMIA (2019)
Alfonso Landeros, Timothy Stutz, Kevin L. Keys, Alexander V. Alekseyenko, Janet S. Sinsheimer, Kenneth Lange, Mary E. Sehl
BioSimulator.jl: Stochastic simulation in Julia. CoRR (2018)
Alfonso Landeros, Timothy Stutz, Kevin L. Keys, Alexander V. Alekseyenko, Janet S. Sinsheimer, Kenneth Lange, Mary E. Sehl
BioSimulator.jl: Stochastic simulation in Julia. Comput. Methods Programs Biomed. 167 (2018)
Bashir Hamidi, Leslie A. Lenert, Jihad S. Obeid, Alexander V. Alekseyenko
The Hidden Microbiome Pipeline: Providing Access to Clinical Microbiome Specimens, Sequences, and Informatics Resources. AMIA (2018)
Zheng-Zheng Tang, Guanhua Chen, Alexander V. Alekseyenko, Hongzhe Li
A general framework for association analysis of microbial communities on a taxonomic tree. Bioinform. 33 (9) (2017)
Alexander V. Alekseyenko, Lita M. Proctor, Paul Carlson, Scott A. Jackson, Connie Chen
The Impact of Human Microbiome on Precision Medicine. AMIA (2017)
Ali Shojaee Bakhtiari, Galina S. Bogatkevich, Alexander V. Alekseyenko
Local Causal Networks Discover Predictive Cytokine Biomarkers of Scleroderma. AMIA (2017)
Zheng-Zheng Tang, Guanhua Chen, Alexander V. Alekseyenko
PERMANOVA-S: association test for microbial community composition that accommodates confounders and multiple distances. Bioinform. 32 (17) (2016)
Alexander V. Alekseyenko
-test on distances. Bioinform. 32 (23) (2016)
Ali Shojaee Bakhtiari, Alexander V. Alekseyenko
Comprehensive Evaluation of Univariate and Multivariate Distributions for Machine Learning With Microbiome Data. AMIA (2016)
Alexander V. Alekseyenko
Heteroscedastic Omics Data Analysis: Distance-Based Multivariate Approach. AMIA (2016)
Alexander V. Alekseyenko, Michael J. Becich, Todd Z. DeSantis, Jack A. Gilbert, Georg K. Gerber
The Human Microbiome: Informatics Challenges and Opportunities. AMIA (2016)
Susan P. Holmes, Alexander V. Alekseyenko, Alden Timme, Tyrrell Nelson, Pankaj Jay Pasricha, Alfred Spormann
Visualization and Statistical Comparisons of Microbial Communities Using R Packages on Phylochip Data. Pacific Symposium on Biocomputing (2011)
Mary E. Sehl, Alexander V. Alekseyenko, Kenneth Lange
-Leaping (SAL) Algorithm. J. Comput. Biol. 16 (9) (2009)
Namshin Kim, Alexander V. Alekseyenko, Meenakshi Roy, Christopher J. Lee
The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species. Nucleic Acids Res. 35 (Database-Issue) (2007)
Alexander V. Alekseyenko, Christopher J. Lee
Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases. Bioinform. 23 (11) (2007)