Karolina Palucka

The paper introduces SparTile, a computational method for analyzing multiplex proteomics images to identify clinically relevant spatial microenvironments in TNBC, finding specific markers and distances associated with poor survival.

The paper validates an LLM-guided gene prioritization framework for sepsis and tests its generalizability to obesity and infection using clinical and proteomic data.

This study shows that bacterial species and individual donors differentially modulate airway gene expression and alternative splicing in human epithelial cells.

This paper develops a framework using large language models for gene prioritization, validated against literature, identifying 30 high-confidence therapeutic candidates for sepsis.

The paper identifies intron retention in STAT2 as a regulator of immune signaling and a predictor of immunotherapy response in lung cancer.

The paper examines how different microbes affect host immune and barrier responses in respiratory epithelial cultures, finding that interferon variability is not linked to microbial diversity or other innate pathways.

This paper introduces a method using Large Language Models to perform deep functional profiling of gene sets, demonstrating its ability to uncover detailed immune functions and improve upon traditional annotation tools.

This paper develops an API-driven workflow using GPT-4 to automate candidate gene prioritization, demonstrating high consistency and scalability in identifying sepsis-related genes.

This paper develops a novel humanized mouse model to improve long-term engraftment of adult hematopoietic progenitor cells and tissue colonization of human myeloid cells.

This study creates a single-cell aging atlas of mouse mammary tissues, identifying shared epigenomic and transcriptomic changes between aging and cancer.

This study develops a 3D printed lung model to investigate how ventilation affects viral infection and lung responses in vitro.

This paper presents a protocol for creating human lung organoid-derived air-liquid interface cultures to study SARS-CoV-2 infection and includes quality control and monitoring methods.

The paper uses long-read RNA sequencing to identify novel isoforms in breast cancer, finding splicing events associated with patient survival.

The paper develops a targeted transcriptome fingerprinting assay using modular transcriptional repertoires to assess immune functions in clinical settings.