Marina Sirota

Comparative molecular analysis of histopathologic subtypes reveals shared epithelial remodeling yet distinct fibroblast programs in scleroderma lung disease

This study compares molecular features of SSc-NSIP and SSc-UIP with IPF, finding shared epithelial changes and distinct fibroblast programs.

GENOAR: Global Engine for Navigating the Omnicell space via Agent-based Research

GENOAR enables scalable, AI-compatible single-cell transcriptomic analysis of over 54 million cells from humans and mice, outperforming human experts in data retrieval and enabling new biological insights.

Advancing CD38 from a marker of disease activity to an active regulator of interferon responses in juvenile dermatomyositis

This study identifies CD38 as a regulator of interferon responses in juvenile dermatomyositis and suggests its inhibition as a potential therapeutic strategy.

Simvastatin and Primaquine Identified as Potential Endometriosis Therapeutics via a Novel Epithelial-Stromal Assembloid Drug Screening Assay

The paper identifies simvastatin and primaquine as potential endometriosis treatments using human assembloids, showing significant reversal of disease-related gene expression pathways.

Predicting Endometriosis Status and Menstrual Cycle Phase Using DNA Methylation

This study uses DNA methylation data to predict endometriosis status and menstrual cycle phase, finding strong performance for cycle phase and moderate performance for endometriosis.

A Transcriptomics-Based Computational Drug Repurposing Pipeline Identifies Simvastatin And Primaquine As Therapeutics For Endometriosis

This study identifies simvastatin and primaquine as potential therapeutics for endometriosis through computational drug repositioning, showing reduced pain and gene expression changes in animal models and lower disease risk in EMR data.

The SEA-AD DREAM Challenge: Community benchmarking human and AI agent solutions for Alzheimer's disease neuropathology prediction from single-nucleus transcriptomics

The paper presents a benchmarking challenge to predict Alzheimer's disease neuropathology from single-nucleus transcriptomics using human and AI models, finding that top methods achieve near-perfect categorical staging predictions.

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

CDRPipe integrates single-cell and bulk transcriptomic perturbation data to improve drug repurposing predictions by combining complementary resources.

Expanding vaginal microbiome pangenomes via a custom MIDAS database reveals Lactobacillus crispatus accessory genes associated with cervical dysplasia

Searching for influencers among placental immune cells in preeclampsia.

The paper identifies SPP1 and CD44 as influencers of inflammation in preeclampsia by analyzing single-cell transcriptional profiles of placental immune cells.

The Human Intolerome: a curated database to prioritize genomic variants in stillbirth, pregnancy loss, and neonatal death

The paper introduces the Intolerome Database, a curated resource of genes essential for human viability, to help prioritize genomic variants in cases of stillbirth, pregnancy loss, and neonatal death.

Computational discovery of precision therapeutics for hidradenitis suppurativa

A data-driven precision medicine approach identifies sirolimus, pioglitazone, and fulvestrant as novel therapies for hidradenitis suppurativa by targeting disease gene signatures in immune cells.

Benchmarking Large Language Models for Predictive Modeling in Biomedical Research With a Focus on Reproductive Health

This study evaluates large language models' ability to generate predictive modeling code for reproductive health using standardized datasets, finding R code generation more successful than Python and some models matching top DREAM challenge teams.

Tri-AD: Hippocampal cell-type-specific responses to age, sex and APOE genotype

The paper investigates how age, sex, and APOE genotype affect hippocampal cell-type-specific gene expression and communication in mice, revealing sex-divergent effects of APOE4.

Consensus Co-Expression Analysis Identifies A Common Set Of Co-Expressed Genes Associated With Diabetic Peripheral Neuropathy And Chemotherapy-Induced Peripheral Neuropathy

Discovering latent subtypes of preterm birth and genetic risk using tensor decomposition on electronic health records

This study uses tensor decomposition on EHR data to identify latent subtypes of preterm birth and links them to genetic risk factors for comorbid diseases.

Alternative Splicing And Global Transcriptome Changes Associated With LPS Stimulation In Human Peripheral Blood Mononuclear Cells

This study examines alternative splicing and transcriptome changes in human PBMCs after LPS stimulation, identifying novel pathways and splicing events involved in inflammation.

Transcriptomic comparison of early onset preeclampsia and placenta accreta identifies inverse trophoblast and decidua functions at the maternal-fetal interface

This study compares transcriptomes of early onset preeclampsia and placenta accreta, finding inverse gene expression in key cell types and pathways at the maternal-fetal interface.

Genetic Variants in Recurrent Euploid Pregnancy Loss

The paper identifies genetic variants in 30 families with unexplained euploid pregnancy loss, finding monogenic causes in 25% of cases and expanding understanding of early human lethality.

Single-cell-level digital twins for preterm birth prevention strategies

The paper introduces SIMCO, a single-cell digital twin framework for evaluating PTL prevention drugs, identifying tetrahydrofolate, maprotiline, and aspirin-lansoprazole as top candidates.

The Integrated Cellular and Molecular Landscape of Autoimmunity

The paper integrates transcriptomic data from 10 autoimmune diseases to identify core immune mechanisms and disease-specific signatures, revealing shared and distinct immunopathological patterns through 15 immune modules.

Anticlustering for Sample Allocation To Minimize Batch Effects

The paper introduces anticlustering to balance batches and minimize batch effects in high-throughput sequencing, showing improved balance compared to existing methods.

Single-Cell Profiling Reveals Altered Endometrial Cellular Features Across the Menstrual Cycle in Endometriosis Patients

The paper uses single-cell transcriptomics to analyze endometrial cells from endometriosis patients, revealing altered cellular features and immune communication networks across the menstrual cycle.

Integrative effects of Telomere Length, Epigenetic Age, and Mitochondrial DNA abundance in Alzheimer's Disease

This study examines how telomere length, epigenetic age, and mitochondrial DNA abundance interact in Alzheimer's Disease, finding that their combination affects grey-matter volume.

Transplant-Agents: A Multi-Agent Artificial Intelligence Framework for Reproducibility Assessment of Post-Transplant Risk Prediction and Rejection Biomarkers

Transplant-Agents uses a multi-agent AI framework to identify reproducible biomarkers and predict transplant rejection risk with high AUROC scores across multiple datasets.

Transcriptomic analysis reveals immune signatures associated with specific cutaneous manifestations of lupus in systemic lupus erythematosus

The paper identifies immune signatures in SLE cutaneous subtypes using transcriptomics, revealing subtype-specific pathways and potential therapeutic targets.

Data-driven discovery of cell-type-directed network-correcting combination therapy for Alzheimer's disease

The paper identifies a cell-type-directed combination therapy for Alzheimer's disease using single-cell transcriptomics and drug databases, showing improved memory and reduced pathologies in a mouse model.

Gene Expression Meta-Analysis Reveals Aging and Cellular Senescence Signatures in Scleroderma-associated Interstitial Lung Disease

This study identifies aging and senescence signatures in SSc-ILD through gene expression analysis and telomere length measurement, linking them to disease pathology.

Cell-Specific Transposable Element Gene Expression Analysis Identifies Associations with Systemic Lupus Erythematosus Phenotypes

The paper identifies cell-specific transposable element (TE) gene expression associations with SLE phenotypes, finding 731 differentially expressed TEs linked to antiviral pathways and IFN signaling.

Robust Harmonization of Microbiome Studies by Phylogenetic Scaffolding with MaLiAmPi

This paper harmonizes microbiome studies by placing amplicon sequence variants (ASV) on a common phylogenetic tree, improving community relationship accuracy compared to closed-OTU methods.