My research is focused on computational analysis of complex human phenotypes in context of changes and perturbations of underlying molecular networks. The input data for these studies is supplied by large-scale mining of free text, computation over clinical records, and high-throughput systems biology experiments.
My main interest is in gaining an (asymptotic) understanding how phenotypes, such as human healthy diversity and maladies, are implemented at the level of genes and networks of interacting molecules.
To harvest as much information about known molecular interactions as possible, my group runs a large-scale text-mining effort aiming at analysis of a vast corpus of biomedical publications. Currently we can extract from text automatically about 500 distinct flavors of relations among biomedical entities (such as bind, activate, merystilate, and transport).
To sharpen our text-mining axes, we are actively designing related models and computational applications. Furthermore, in cooperation with our experimentally talented colleagues, we are striving to use text-mined networks to understand, interpret and refine high- or low-throughput experimental data. We are also computationally generating biological hypotheses that our generous collaborators are attempting to test experimentally.
My older passion is in developing and applying computational methods related to phylogenetics and evolutionary biology.
Longitudinal Analysis of Electronic Health Records Reveals Medical Conditions Associated with Subsequent Alzheimer's Disease Development.
Longitudinal Analysis of Electronic Health Records Reveals Medical Conditions Associated with Subsequent Alzheimer's Disease Development. medRxiv. 2025 Mar 24.
PMID: 40196258
Digital twins as global learning health and disease models for preventive and personalized medicine.
Digital twins as global learning health and disease models for preventive and personalized medicine. Genome Med. 2025 Feb 07; 17(1):11.
PMID: 39920778
Prevalence and incidence measures for schizophrenia among commercial health insurance and medicaid enrollees.
Prevalence and incidence measures for schizophrenia among commercial health insurance and medicaid enrollees. Schizophrenia (Heidelb). 2024 Aug 22; 10(1):68.
PMID: 39174558
Air quality and mental health: evidence, challenges and future directions.
Air quality and mental health: evidence, challenges and future directions. BJPsych Open. 2023 Jul 05; 9(4):e120.
PMID: 37403494
Author Correction: The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci.
Author Correction: The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci. Nat Comput Sci. 2023 Jul; 3(7):658.
PMID: 38214655
The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci.
The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci. Nat Comput Sci. 2023 May; 3(5):403-417.
PMID: 38177845
Peri- and Post-natal Risk Factors Associated with Health of Newborns: A pregnant mother's infections and immune diseases, and her baby's delivery method predict immune health of the newborn.
Peri- and Post-natal Risk Factors Associated with Health of Newborns: A pregnant mother's infections and immune diseases, and her baby's delivery method predict immune health of the newborn. medRxiv. 2023 Jan 17.
PMID: 36711636
OrganoID: A versatile deep learning platform for tracking and analysis of single-organoid dynamics.
OrganoID: A versatile deep learning platform for tracking and analysis of single-organoid dynamics. PLoS Comput Biol. 2022 11; 18(11):e1010584.
PMID: 36350878
Discerning asthma endotypes through comorbidity mapping.
Discerning asthma endotypes through comorbidity mapping. Nat Commun. 2022 11 07; 13(1):6712.
PMID: 36344522
Gene-environment interactions explain a substantial portion of variability of common neuropsychiatric disorders.
Gene-environment interactions explain a substantial portion of variability of common neuropsychiatric disorders. Cell Rep Med. 2022 09 20; 3(9):100736.
PMID: 36070757