Adil Mardinoğlu

Integrative Analysis of Left Ventricle and Epicardial Adipose Tissue Identifies SDHA and OGDH as Candidate Targets for Ischemic Heart Disease

Metacontam: A Negative Control-Free Decontamination Method for Metagenomic Analysis

Metacontam is a decontamination method for metagenomic data that improves detection of low-abundance contaminants without needing negative controls.

G-VEP: GPU-Accelerated Variant Effect Prediction for Clinical Whole-Genome Sequencing Analysis

G-VEP accelerates variant effect prediction in clinical whole-genome sequencing by using GPU acceleration, reducing runtime from 72 minutes to 4 minutes with no loss of accuracy.

Systematic Analysis of Human Tissue- and Cell-Specific Metabolic Models Identifies High-Sugar, High Fat Diet Induced Liver Dysregulation

The paper constructs tissue- and cell-type-specific metabolic models to study the effects of a high-sugar, high-fat diet on liver metabolism, revealing metabolic reprogramming and dysfunction.

Microbial oral-gut translocation in advanced chronic liver disease is linked to exacerbation of intestinal barrier dysfunction and hepatic fibrosis

The paper identifies oral-gut microbial translocation in ACLD patients linked to intestinal barrier dysfunction and hepatic fibrosis, with prtC encoding bacteria as a biomarker.

Microbiome signatures of virulence in the oral-gut-brain axis influence Parkinson's disease and cognitive decline pathophysiology

This study investigates microbiome signatures in the oral-gut-brain axis and their role in Parkinson's disease and cognitive decline.

Extensively acquired antimicrobial resistant bacteria restructure the individual microbial community in post-antibiotic conditions

The paper identifies two types of antimicrobial resistant bacteria in the gut microbiome after antibiotic treatment and shows how one type persists and reshapes the microbial community.

Multi-tissue network analysis reveals the effect of JNK inhibition on dietary sucrose-induced metabolic dysfunction in rats

This study investigates the effects of JNK inhibition on metabolic dysfunction caused by sucrose overconsumption in rats using multi-tissue network analysis.

Standard-GEM supports reproducible development of genome-scale metabolic models

Standard-GEM provides a template for reproducible genome-scale metabolic model development following FAIR principles and software best practices.

Network-based multi-omics integration reveals metabolic at-risk profile within treated HIV-infection

The paper identifies three metabolic at-risk profiles in HIV-treated patients using multi-omics integration, highlighting dysregulated metabolism and microbiome interactions.

Drug repositioning for immunotherapy in breast cancer using single-cell and spatial transcriptomics analysis

This study identifies immunomodulatory peptides deregulated in breast cancer using single-cell and spatial transcriptomics, and proposes drugs to modulate their expression.

Discovery of therapeutic agents targeting PKLR for NAFLD using drug repositioning

This study identifies PKLR as a therapeutic target for NAFLD and validates two drug candidates through in vitro and in vivo experiments.

Genome-wide single cell annotation of the human protein-coding genes

The paper annotates all human protein-coding genes with their function and spatial distribution across cell types using single-cell transcriptomics data and introduces a new classification tool.

GutMicroNet: an interactive platform for gut microbiome interaction exploration

GutMicroNet provides an interactive platform to explore gut microbiome interaction networks using data from the Human Gut Microbiome Atlas.

A network-based approach reveals the dysregulated transcriptional regulation in non-alcohol fatty liver disease

This study identifies dysregulated transcriptional regulators in NAFLD using network analysis and integrates transcriptomic data with metabolic models.

Systems analysis reveals ageing-related perturbations in retinoids and sex hormones in Alzheimer's and Parkinson's diseases

This study identifies retinoids and sex hormone dysregulation as ageing-related features in Alzheimer's and Parkinson's disease subclasses using transcriptomic and metabolic analyses.

Integrative transcriptomic analysis of tissue-specific metabolic crosstalk after myocardial infarction

The paper analyzes transcriptomic changes in heart and other metabolically active tissues after myocardial infarction in mice, identifying common and tissue-specific biological responses.

iNetModels 2.0: an interactive visualization and database of multi-omics data

iNetModels 2.0 provides an interactive platform for visualizing and exploring multi-omics associations in human health and disease.

Combined Metabolic Activators decrease liver steatosis by activating mitochondrial metabolism in a Golden Syrian hamster study

Discovery of functional alternatively spliced PKM transcripts in human cancers

The paper investigates the prognostic significance of PKM transcripts in 25 cancers and identifies a prognostic signature in KIRC, revealing functional roles of alternatively spliced PKM transcripts.

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

Memote, open-source Python software, runs a community-maintained, partly scored test suite (consistency, biomass, annotations, optional experimental data) on SBML-encoded genome-scale metabolic models, once or through continuous integration.

Classification of clear cell renal cell carcinoma based on PKM alternative splicing

The paper identifies two ccRCC subtypes based on PKM alternative splicing and proposes drug repurposing for each subtype.

RMetD2: a tool for integration of relative transcriptomics data into Genome-scale metabolic models

RMetD2 integrates differentially expressed genes into genome-scale metabolic models to reveal metabolic differences between conditions, outperforming existing methods in capturing experimentally observed features.

The human secretome - the proteins secreted from human cells

The paper maps and characterizes the human secretome by annotating 2,623 predicted secreted proteins and their spatial distribution, using a high-throughput cell factory for recombinant protein production and analysis.