Potential to Enhance Large Scale Molecular Assessments of Skin Photoaging through Virtual Inference of Spatial Transcriptomics from Routine Staining
Pac Symp Biocomput. 2024;29:477-491.ABSTRACTThe advent of spatial transcriptomics technologies has heralded a renaissance in research to advance our understanding of the spatial cellular and transcriptional heterogeneity within tissues. Spatial transcriptomics allows investigation of the interplay between cells, molecular pathways, and the surrounding tissue architecture and can help elucidate developmental trajectories, disease pathogenesis, and various niches in the tumor microenvironment. Photoaging is the histological and molecular skin damage resulting from chronic/acute sun exposure and is a major risk factor for ski...
Source: Pacific Symposium on Biocomputing - December 31, 2023 Category: Bioinformatics Authors: Gokul Srinivasan Matthew J Davis Matthew R LeBoeuf Michael Fatemi Zarif L Azher Yunrui Lu Alos B Diallo Marietta K Saldias Montivero Fred W Kolling Laurent Perrard Lucas A Salas Brock C Christensen Thomas J Palys Margaret R Karagas Scott M Palisoul Gregor Source Type: research
PEPSI: Polarity measurements from spatial proteomics imaging suggest immune cell engagement
Pac Symp Biocomput. 2024;29:492-505.ABSTRACTSubcellular protein localization is important for understanding functional states of cells, but measuring and quantifying this information can be difficult and typically requires high-resolution microscopy. In this work, we develop a metric to define surface protein polarity from immunofluorescence (IF) imaging data and use it to identify distinct immune cell states within tumor microenvironments. We apply this metric to characterize over two million cells across 600 patient samples and find that cells identified as having polar expression exhibit characteristics relating to tumo...
Source: Pacific Symposium on Biocomputing - December 31, 2023 Category: Bioinformatics Authors: Eric Wu Zhenqin Wu Aaron T Mayer Alexandro E Trevino James Zou Source Type: research
KombOver: Efficient k-core and K-truss based characterization of perturbations within the human gut microbiome
Pac Symp Biocomput. 2024;29:506-520.ABSTRACTThe microbes present in the human gastrointestinal tract are regularly linked to human health and disease outcomes. Thanks to technological and methodological advances in recent years, metagenomic sequencing data, and computational methods designed to analyze metagenomic data, have contributed to improved understanding of the link between the human gut microbiome and disease. However, while numerous methods have been recently developed to extract quantitative and qualitative results from host-associated microbiome data, improved computational tools are still needed to track micro...
Source: Pacific Symposium on Biocomputing - December 31, 2023 Category: Bioinformatics Authors: Nicolae Sapoval Marko Tanevski Todd J Treangen Source Type: research
nSEA: n-Node Subnetwork Enumeration Algorithm Identifies Lower Grade Glioma Subtypes with Altered Subnetworks and Distinct Prognostics
This study offers a comprehensive molecular classification of LGG, providing insights beyond traditional genetic markers. By integrating network analysis with patient clustering, we unveil a previously overlooked patient subgroup with potential implications for prognosis and treatment strategies. Our approach sheds light on the synergistic nature of driver genes and highlights the biological relevance of the identified subnetworks. With broad implications for glioma research, our findings pave the way for further investigations into the mechanistic underpinnings of LGG subtypes and their clinical relevance.Availability: So...
Source: Pacific Symposium on Biocomputing - December 31, 2023 Category: Bioinformatics Authors: Zhihan Zhang Christiana Wang Ziyin Zhao Ziyue Yi Arda Durmaz Jennifer S Yu Gurkan Bebek Source Type: research
Application of quantile discretization and bayesian network analysis to publicly available cystic fibrosis data sets
Pac Symp Biocomput. 2024;29:534-548.ABSTRACTThe availability of multiple publicly-available datasets studying the same phenomenon has the promise of accelerating scientific discovery. Meta-analysis can address issues of reproducibility and often increase power. The promise of meta-analysis is especially germane to rarer diseases like cystic fibrosis (CF), which affects roughly 100,000 people worldwide. A recent search of the National Institute of Health's Gene Expression Omnibus revealed 1.3 million data sets related to cancer compared to about 2,000 related to CF. These studies are highly diverse, involving different tiss...
Source: Pacific Symposium on Biocomputing - December 31, 2023 Category: Bioinformatics Authors: Kiyoshi Ferreira Fukutani Thomas H Hampton Carly A Bobak Todd A MacKenzie Bruce A Stanton Source Type: research
