István Csabai

Sexing carnivores from faecal metagenomes: calibrating Rx for stone marten and red fox

The paper evaluates the use of the X-to-autosome ratio (Rx) for sexing carnivores from faecal metagenomes, finding it effective above a certain read depth.

One-carbon metabolism controls colorectal cancer cell state and chemosensitivity through chromatin remodeling

This study shows that folate metabolism remodels epithelial states in colorectal cancer cells, affecting their response to fluoropyrimidine chemotherapy.

Metagenomic peek into a corn mummy

The paper uses metagenomic analysis to identify ancient organisms in a corn mummy from ancient Egypt, finding potential historical contaminants alongside modern ones.

Zero-shot biological reasoning with open-weights large language models reproduces CRISPR screen based prediction of synthetic lethal interactions.

This paper uses open-weight large language models to predict synthetic lethal interactions, outperforming random chance and non-LLM methods in reproducing CRISPR screen results.

Clinical considerations on antimicrobial resistance potential of complex microbiological samples

The paper explores the clinical interpretation of genomic analysis results to assess antimicrobial resistance potential in complex microbiological samples.

Histopathology and proteomics are synergistic for High-Grade Serous Ovarian Cancer platinum response prediction

This study combines histopathology and proteomics with a multimodal deep learning framework to improve platinum response prediction in HGSOC, outperforming HRD scores.

Time-series sewage metagenomics can separate the seasonal, human-derived and environmental microbial communities, holding promise for source-attributed surveillance

This study uses sewage metagenomics to distinguish seasonal, human-derived, and environmental microbial communities, offering potential for improved AMR surveillance.

Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses

The paper describes open data sharing, analysis tools, and lessons learned from the European COVID-19 Data Platform's SARS-CoV-2 data collection and analysis efforts.

Bacterial colony size growth estimation by deep learning

The paper uses CNNs to estimate bacterial colony growth rates from images, finding that colony density affects growth rates differently in control and rifampicin-treated cultures.

Impact evaluation of score classes and annotation regions in deep learning-based dairy cow body condition prediction

This study evaluates how deep learning models predict dairy cow body condition scores using image annotations, finding stronger agreement with fewer classes and larger error ranges.

Porcine cytomegalovirus detection by nanopore-based metagenomic sequencing in a Hungarian pig farm

The paper uses nanopore sequencing to detect porcine cytomegalovirus in nasal swabs from a Hungarian pig farm.

Mobile antimicrobial resistance genes in probiotics

The paper analyzes probiotic samples to identify antimicrobial resistance genes and their potential for horizontal gene transfer.

Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth

The paper develops predictive models for preterm birth using maternal blood multi-omics data, finding transcriptomic and proteomic markers can predict gestational age and spontaneous preterm birth with high accuracy.

A glimpse of antimicrobial resistance gene diversity in kefir and yoghurt

The paper analyzes antimicrobial resistance gene diversity in kefir and yoghurt using metagenomic approaches, identifying various ARGs and their potential mobility.

Raw milk for human consumption may carry antimicrobial resistance genes

This study identifies antimicrobial resistance genes in raw milk samples, showing their potential to transfer resistance to human gut bacteria.

Strand Orientation Bias Detector (SOBDetector) to remove FFPE sequencing artifacts

SOBDetector removes FFPE sequencing artifacts by using a Bayesian logistic regression model trained on TCGA whole exomes, achieving high accuracy and AUC.

The COMPARE Data Hubs

The paper describes an informatics platform for structured data storage and pre-publication sharing of pathogen sequencing data with stakeholders.