Adam Godzik

Evolutionary history of ligand binding by the LRR domain of innate immunity receptors: the story of the TLR2 cavity

This study investigates the evolutionary history of the TLR2 cavity in vertebrates and invertebrates using AI protein structure predictions, showing its ancestral origin and convergent evolution in different species.

Spatial Transcriptomics Using Archived Formalin-Fixed Paraffin-Embedded Core Needle Biopsy Tissues Revealed Unique Transcriptomic Signatures in Kidney Transplant Rejections

This study uses spatial transcriptomics on FFPE kidney biopsy tissues to identify distinct transcriptomic signatures for different types of kidney transplant rejections.

Global atlas of predicted functional domains in Legionella pneumophila Dot/Icm translocated effectors

The paper provides a global atlas of predicted functional domains in Legionella pneumophila effectors using 3D structure prediction, identifying novel domains and demonstrating their functional impact.

Divergence of the Individual repeats in the leucine-rich repeat domains of human Toll-like receptors explain their diversity and functional adaptations.

This study shows how small variations in LRR repeats of human TLRs lead to structural and functional diversity, enabling recognition of different ligands and immune responses.

Deciphering Abnormal Platelet Subpopulations in Inflammatory Diseases through Machine Learning and Single-Cell Transcriptomics

The paper uses single-cell transcriptomics and machine learning to analyze platelet subpopulations in sepsis, COVID-19, and SLE, identifying disease-associated transcriptional signatures and potential therapeutic targets.

Monitoring for SARS-CoV-2 drug resistance mutations in broad viral populations

The paper introduces a drug resistance tracker to monitor and predict the emergence of mutations in SARS-CoV-2 that confer resistance to antiviral drugs targeting Mpro and PLpro.

Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2

The paper reports the high-resolution crystal structure of SARS-CoV-2 Nsp15/NendoU and compares it with structures from SARS and MERS coronaviruses.

Difference contact maps: from what to why in the analysis of the conformational flexibility of proteins

The paper introduces difference contact maps (DCMs) to analyze conformational flexibility in proteins by identifying critical interactions and functional residues across alternative conformations.

Unraveling Oxidative Stress Resistance: Molecular Properties Govern Proteome Vulnerability

The paper identifies molecular properties that determine oxidative stress resistance in bacteria by analyzing protein susceptibility to oxidation in Escherichia coli and Deinococcus radiodurans.

Stratification of amyotrophic lateral sclerosis patients: a crowdsourcing approach

This study uses a crowdsourcing approach to stratify ALS patients, identifying four distinct clusters with unique predictors and improving outcome prediction.

Cancer3D 2.0: interactive analysis of 3D patterns of cancer mutations in cancer subsets

Cancer3D 2.0 provides an interactive platform to analyze 3D mutation patterns in cancer subsets, enabling identification of novel driver regions in specific patient subgroups.

A Pan-cancer catalogue of driver protein interaction interfaces

The paper identifies 128 PPI interfaces enriched with somatic mutations across 5,989 tumors, showing how mutations in cancer driver genes affect protein interactions and tumor behavior.