Biology subjects

Bongiovanni, D.

Publications and source records attributed to Bongiovanni, D..

3 recordsLinked to original sources

bioRxiv2021

A Systematic Comparison of Differential Analysis Methods for CyTOF Data

Cytometry techniques are widely used to discover cellular characteristics at single-cell resolution. Many data analysis methods for cytometry data focus solely on identifying subpopulations via clustering and testing for differential cell abundance. For differential expression analysis of markers between conditions, only few tools exist. These tools either reduce the data distribution to medians, discarding valuable information, or have underlying assumptions that may not hold for all expression patterns. Here, we systematically evaluated existing and novel approaches for differential expression analysis on real and simulated CyTOF data. We found that methods using median marker expressions compute fast and reliable results when the data is not strongly zero-inflated. Methods using all data detect changes in strongly zero-inflated markers, but partially suffer from overprediction or cannot handle big datasets. We present a new method, CyEMD, based on calculating the Earth Movers Distance between expression distributions that can handle strong zero-inflation without being too sensitive. Additionally, we developed CYANUS, a user-friendly R Shiny App allowing the user to analyze cytometry data with state-of-the-art tools, including well-performing methods from our comparison. A public web interface is available at https://exbio.wzw.tum.de/cyanus/.

bioinformatics↗

bioRxiv2021

Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases

Alternative splicing (AS) is an important aspect of gene regulation. Nevertheless, its role in molecular processes and pathobiology is far from understood. A roadblock is that tools for the functional analysis of AS-set events are lacking. To mitigate this, we developed NEASE, a tool integrating pathways with protein-protein and domain-domain interactions to functionally characterize AS events. We show in four application cases how NEASE can identify pathways contributing to tissue identity and cell type development, and how it highlights splicing-related biomarkers. With a unique view on AS, NEASE generates unique and meaningful biological insights complementary to classical pathways analysis.

bioinformatics↗

bioRxiv2019

Predicting factors for long-term survival in patients with out-of-hospital cardiac arrest - a propensity score-matched analysis

BackgroundOut-of-hospital cardiac arrest (OHCA) is one of the leading causes of death worldwide, with acute coronary syndromes accounting for most of the cases.\n\nWhile the benefit of early revascularization has been clearly demonstrated in patients with ST-segment-elevation myocardial infarction (STEMI), diagnostic pathways remain unclear in the absence of STEMI. We aimed to characterize OHCA patients presenting to 2 tertiary cardiology centers and identify predicting factors associated with survival.\n\nMethodsWe retrospectively analyzed 519 patients after OHCA from February 2003 to December 2017 at 2 centers in Munich, Germany. Patients undergoing immediate coronary angiography (CAG) were compared to those without. Propensity score (PS) matching analysis and multivariate regression analysis were performed to identify predictors for improved outcome.\n\nResultsImmediate CAG was performed in 385 (74.1%) patients after OHCA with presumed cardiac cause of arrest.\n\nAs a result of multivariate analysis after propensity score matching, we found that ROSC at admission and immediate CAG were associated with better 30-days-survival [(OR, 6.54; 95% CI, 2.03-21.02), (OR, 2.41; 95% CI, 1.04-5.55)], and 1-year-survival [(OR, 4.49; 95% CI, 1.55-12.98), (OR, 2.54; 95% CI, 1.06-6.09)].\n\nConclusionsIn our study, ROSC at admission and immediate CAG were independent predictors of survival in cardiac arrest survivors. Improvement in prehospital management including bystander CPR and best practice post-resuscitation care with optimized triage of patients to an early invasive strategy may help ameliorate overall outcome of this critically-ill patient population.

epidemiology↗