Boris Oskotsky

Mapping chemical-gene interactions for developmental lethality and pregnancy loss

Syed Hassan Bukhari, Amrita Nagasuri, Boris Oskotsky, Leen Arnaout et autres

Purpose: Pregnancy loss affects 10-15% of clinically recognized pregnancies and is driven by genetic and environmental factors. Interactions between genes and chemicals critically shape developmental outcomes, yet existing resources do not organize chemical-gene evidence by gestational timing, maternal-fetal compartment, or lethality context. …

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Integrating single-cell and bulk transcriptomic perturbation resources reveals complementary therapeutic spaces for drug repurposing

Enock Niyonkuru, Umair Khan, Xinyu Tang, Laura Almonte et autres

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Dementia Prior to MCI? Exploring Frequency and Factors Associated with Diagnostic Discrepancies in a Large EMR System

Silvia Miramontes, Hunter Mills, Boris Oskotsky, Evan Phelps et autres

BACKGROUND: Mild cognitive impairment (MCI) is an early stage of cognitive decline, typically preceding dementia. However, the temporal order of these diagnostic categories in real-world clinical practice may be reversed, having significant clinical implications for patient care and family burden. This study …

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Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research

Jonathan L. Golob, Tomiko Oskotsky, Alice Tang, Alennie Roldan et autres

Anticlustering for sample allocation to minimize batch effects

Martin Papenberg, Cheng Wang, Maïgane Diop, Syed A. Bukhari et autres

High-throughput sequencing enables efficient processing of DNA and RNA samples in batches, but batch effects can obscure true biological signal. We propose using anticlustering as an automated method to assign samples to balanced batches, minimizing covariate imbalance and supporting user-defined constraints such …

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Diagnostic Reversion in Dementia Care: A Real-World Analysis of Mild Cognitive Impairment Diagnoses Following Dementia in a Large Electronic Medical Record System

Silvia Miramontes, Umair Khan, Scott C. Zimmerman, Erin L. Ferguson et autres

INTRODUCTION: If mild cognitive impairment (MCI) is diagnosed after dementia, it suggests either the dementia diagnosis was premature, or the MCI diagnosis is incorrect. We investigated the prevalence and predictors of such "diagnostic reversion"-MCI diagnosis following dementia diagnosis-in a large academic health …

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Author Correction: AI-guided precision parenteral nutrition for neonatal intensive care units

Thanaphong Phongpreecha, Marc Ghanem, Jonathan D. Reiss, Tomiko Oskotsky et autres

In the version of this article initially published, Tomiko T. Oskotsky was listed without a middle initial as is now amended in the HTML and PDF versions of the article.

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AI-guided precision parenteral nutrition for neonatal intensive care units

Thanaphong Phongpreecha, Marc Ghanem, Jonathan D. Reiss, Tomiko Oskotsky et autres

One in ten neonates are admitted to neonatal intensive care units, highlighting the need for precise interventions. However, the application of artificial intelligence (AI) in guiding neonatal care remains underexplored. Total parenteral nutrition (TPN) is a life-saving treatment for preterm neonates; however, …

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Anticlustering for Sample Allocation To Minimize Batch Effects

Martin Papenberg, Cheng Wang, Maïgane Diop, Syed A. Bukhari et autres

Abstract High throughput sequencing is a powerful tool for processing large amounts of DNA and RNA samples in batches. Proper experimental design and statistical methods are required to mitigate systematic technical factors due to differences in batches (“batch effects”), as data variation …

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VMAP: Vaginal Microbiome Atlas during Pregnancy

Antonio Párraga-Leo, Tomiko Oskotsky, Boris Oskotsky, Camilla Wibrand et autres

Objectives: To enable interactive visualization of the vaginal microbiome across the pregnancy and facilitate discovery of novel insights and generation of new hypotheses. Material and Methods: Vaginal Microbiome Atlas during Pregnancy (VMAP) was created with R shiny to generate visualizations of structured …

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Generation of guideline-based clinical decision trees in oncology using large language models

Brenda Y. Miao, Eduardo Rodriguez Almaraz, Amir Ashraf‐Ganjouei, Arvind Suresh et autres

Background: Molecular biomarkers play a pivotal role in the diagnosis and treatment of oncologic diseases but staying updated with the latest guidelines and research can be challenging for healthcare professionals and patients. Large Language Models (LLMs), such as MedPalm-2 and GPT-4, have …

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Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research

Jonathan L. Golob, Tomiko Oskotsky, Alice Tang, Alennie Roldan et autres

Every year, 11% of infants are born preterm with significant health consequences, with the vaginal microbiome a risk factor for preterm birth. We crowdsource models to predict (1) preterm birth (PTB; <37 weeks) or (2) early preterm birth (ePTB; <32 weeks) from …

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