LungChat is a conversational multi-agent AI system that integrates multi-omics analysis and biomedical discovery, identifying potential therapeutics for pulmonary diseases.

bioRxiv · Aug 18, 2026 · PreprintBioinformatics

Accelerating Drug Discovery and Repurposingby Combining Transcriptional Signature Connectivity with Docking

Alexander William Thorman, James K. Reigle, Somchai Chutipongtanate, Juechen Yang, Behrouz Shamsaei, Marcin Pilarczyk, Mehdi Fazel‐Najafabadi, Rafał Adamczak, Michal Kouril, Surbhi Bhatnagar, Sarah A. Hummel, Wen Niu, Ardythe Luxion Morrow, Maria Czyzyk-Krzeska, Robert Erne McCullumsmith, , Jarek Meller

This paper introduces ceSAR, a method combining docking and transcriptional signature connectivity to improve drug discovery and repurposing by reducing false positives and computational costs.

Science Advances · Aug 30, 2024Peer-reviewedBioinformatics

Guided construction of single cell reference for human and mouse lung

Minzhe Guo, Michael P. Morley, Cheng Jiang, Yixin Wu, Guangyuan Li, Yina Du, Shuyang Zhao, Andrew F. Wagner, Adnan Cihan Cakar, Michal Kouril, Kang Jin, Nathan Gaddis, Joseph A. Kitzmiller, Kathleen M. Stewart, Maria Ciocca Basil, , Yan Juan Xu

The paper constructs a single-cell reference atlas for human and mouse lung tissues to improve cell type annotation and data integration.

Nature Communications · Jul 29, 2023Peer-reviewedBioinformatics

LungMAP Portal Ecosystem: Systems-Level Exploration of the Lung

Nathan Gaddis, Joshua D. Fortriede, Minzhe Guo, Eric E. Bardes, Michal Kouril, Scott Tabar, Kevin A. Burns, Mary-Anne Ardini, Stephanie Loos, Daniel Schnell, Kang Jin, Balaji Iyer, Yina Du, Bing‐Xing Huo, Anukana Bhattacharjee, , Nathan Salomonis

The paper describes the LungMAP Portal Ecosystem, a centralized resource integrating multi-omics and imaging data across species to enable standardized analysis of lung biology and disease.

American Journal of Respiratory Cell and Molecular Biology · Nov 22, 2022Peer-reviewedSystems Biology

Connecting omics signatures of diseases, drugs, and mechanisms of actions with iLINCS

Marcin Pilarczyk, Mehdi Fazel‐Najafabadi, Michal Kouril, Behrouz Shamsaei, Juozas Vasiliauskas, Wen Niu, Naim Al Mahi, Lixia Zhang, Nicholas A. Clark, Yan Ren, Shana White, Rashid Saadman Karim, Huan Xu, Jacek Biesiada, Mark F. Bennett, , Mario Medvedovic

iLINCS provides a web-based platform for analyzing omics signatures of diseases and cellular perturbations through integrative analytics and visualization tools.

Nature Communications · Aug 9, 2022Peer-reviewedBioinformatics

piNET: a versatile web platform for downstream analysis and visualization of proteomics data

Behrouz Shamsaei, Szymon Chojnacki, Marcin Pilarczyk, Mehdi Fazel Najafabadi, Wen Niu, Chuming Chen, Karen E. ROSS, Andrea D. Matlock, Jeremy L. Muhlich, Somchai Chutipongtanate, Jie Zheng, John Turner, Dušica Vidović, Jacob D. Jaffe, Michael J. MacCoss, , Jarek Meller

piNET is a web platform for analyzing and visualizing proteomics data, including PTMs, by connecting them to biological knowledge and LINCS signatures.

Nucleic Acids Research · May 27, 2020Peer-reviewedBioinformatics

GREIN: An interactive web platform for re-analyzing GEO RNA-seq data

Naim Al Mahi, Mehdi Fazel Najafabadi, Marcin Pilarczyk, Michal Kouril, Mario Medvedovic

GREIN provides a web platform for re-analyzing GEO RNA-seq data with tools for data manipulation, visualization, and functional analysis.

Scientific Reports · May 20, 2019Peer-reviewedBioinformatics