Alfredo Iacoangeli

Exploring transcriptomic and genomic latent variable correction approaches in differential expression analysis.

This paper evaluates combining expression-based surrogate variables and genotype-based principal components in differential expression analysis, finding the combined approach improves replicability and biological recall in ALS datasets.

Sex-dependent DNA methylation in amyotrophic lateral sclerosis

The paper identifies seven sex-dependent differentially methylated positions in ALS blood samples, suggesting sex-specific biological mechanisms in the disease.

Assessment of ATXN2 Repeat Expansion Length and Risk of ALS: A Meta-Analysis

This paper conducts a meta-analysis to determine the lower limit of ATXN2 repeat expansions associated with ALS risk, finding that ≥30 repeats define significant risk.

Microsecond molecular dynamics of SOD1 variants suggest a structural basis for divergent ALS clinical outcomes

The paper uses molecular dynamics simulations to analyze SOD1 variants and finds that structural stability and conformational rigidity correlate with clinical severity in ALS.

Enrichment of Repeat Expansions in FGF14 Associated with Amyotrophic Lateral Sclerosis

The paper identifies FGF14 GAA repeat expansions in ALS patients, showing enrichment compared to controls and suggesting a broader pathogenic role in motor neuron disease.

Plasma exosomal HERV-K transcripts are increased in amyotrophic lateral sclerosis

The paper quantifies exosomal HERV-K transcripts in ALS patients and controls, finding elevated pol expression that could serve as a biomarker for treatment monitoring.

An Integrated Knowledge Graph and Network Medicine Pipeline for Drug Repurposing: Benchmarking Across Human Diseases and Application to Amyotrophic Lateral Sclerosis

This paper presents a drug repurposing pipeline that integrates knowledge graphs and network medicine, benchmarked across diseases and applied to ALS, identifying 77 prioritized candidate drugs.

Machine learning evaluation of gene expression-based ALS subtypes across brain and blood tissues

The paper evaluates gene expression-based ALS subtypes across brain and blood tissues using machine learning, finding three subtypes with consistent classification in both tissues.

Trustworthy agentic genomics through versioned skill libraries

This paper shows that trustworthy agentic genome interpretation requires executing validated skills as code rather than relying on models to reason or retrieve information, ensuring deterministic and auditable results.

CRISPR/Cas9-mediated generation of a de novo C9ORF72 knock-in isogenic iPSC cell bank to model ALS and FTD

The paper generates isogenic iPSC lines with a C9ORF72 G4C2 repeat expansion to model ALS and FTD, showing both loss- and gain-of-function pathologies.

Systematic comparative benchmarking of computational methods for the detection of transposable elements in long-read sequencing data

This study benchmarks TE detection tools on long-read data, showing significant variation in performance and highlighting tool-specific strengths and limitations.

Investigating the performance of Oxford Nanopore long-read sequencing with respect to Illumina microarrays and short-read sequencing

This study compares Oxford Nanopore long-read sequencing with Illumina short-read sequencing and microarrays across 14 human genomes, finding LRS has competitive accuracy for SNVs and superior performance for structural variants.

Modelling population genetic screening in rare neurodegenerative diseases

The paper calculates the risk of developing rare neurodegenerative diseases following genetic screening, showing low risks for some variants and emphasizing the need for high sensitivity and specificity.

Towards a diagnostic test for sporadic ALS utilising deep learning and SNP microarrays

This paper develops a deep learning model using SNP microarray data to predict ALS risk with high accuracy across diverse populations and genotyping platforms.

Using polygenic and transcriptional risk scores to investigate psychiatric and cognitive symptoms in Parkinson's disease

This study uses polygenic and transcriptional risk scores to analyze psychiatric and cognitive symptoms in Parkinson's disease, finding distinct associations between genetic and transcriptional risks and symptom progression.

The oligogenic structure of amyotrophic lateral sclerosis has genetic testing, counselling, and therapeutic implications

The paper investigates oligogenic risk in ALS using genome sequencing data, finding that multiple rare variants in known ALS genes increase disease risk but not clinical outcomes.

Statistical examination of shared loci in neuropsychiatric diseases using genome-wide association study summary statistics

This study uses GWAS summary statistics to identify shared genetic loci across neuropsychiatric diseases and finds HLA region associations with potential shared causal variants.

Sex-specific DNA methylation differences in Amyotrophic lateral sclerosis

The paper identifies sex-associated DNA methylation differences in ALS using a large-scale epigenome-wide association study and links them to survival outcomes.

Identification of novel myelodysplastic syndromes prognostic subgroups by integration of inflammation, cell-type composition, and immune signatures in the bone marrow

The paper integrates inflammation, cell-type composition, and immune signatures in MDS to identify prognostic subgroups using MOFA, finding that high inflammation correlates with better prognosis while SRSF2 mutations are linked to poor outcomes.

Harnessing Transcriptomic Signals for Amyotrophic Lateral Sclerosis to Identify Novel Drugs and Enhance Risk Prediction

This study uses GWAS and functional genomics to identify ALS risk genes, repurpose drugs, and improve risk prediction using polytranscriptomic scores.

predicTTE: An accessible and optimal tool for time-to-event prediction in neurological diseases

The paper introduces predicTTE, a tool for time-to-event prediction in neurological diseases, demonstrating its utility in genetic discovery and personalized medicine.

Sex-specific risk loci and modified MEF2C expression in ALS

The paper identifies sex-specific risk loci for ALS, including MEF2C, which is upregulated in female ALS motor neurons, and an X-chromosome locus at IL1RAPL2.

Computing Linkage Disequilibrium Aware Genome Embeddings using Autoencoders

The paper introduces a method to compress genetic data using autoencoders that leverage linkage disequilibrium structure, achieving high reconstruction accuracy while reducing data size.

Genetic and phenotype analyses of primary lateral sclerosis datasets from international cohorts

This study analyzes genetic and clinical data from PLS patients to assess the role of genetic testing and identify potential disease-associated variants.

Investigating the genetic relationship between depression symptoms and Alzheimer's disease in clinically diagnosed and proxy cases

This study investigates the genetic relationship between depression symptoms and Alzheimer's disease using GWAS and finds significant genetic correlations but no causal link, suggesting proxy cases may drive the overlap.

Mutafy: A webserver to identify high quality mutant protein structures in the Protein Data Bank

Mutafy identifies high-quality mutant protein structures from the PDB for given human genes, annotates them with biomedical data, and provides interactive visualization.

Large-scale Analyses of CAV1 and CAV2 Suggest Their Expression is Higher in Post-mortem ALS Brain Tissue and Affects Survival

The paper analyzes CAV1 and CAV2 expression in ALS brain tissue and finds higher expression in ALS patients, associated with increased survival and slower disease progression.

An assessment of bioinformatics tools for the detection of human endogenous retroviral insertions in short-read genome sequencing data

The paper evaluates bioinformatics tools for detecting human endogenous retroviral insertions in short-read genome sequencing data, finding performance variability across datasets and recommending a consensus approach.

Molecular dynamics analysis of Superoxide Dismutase 1 mutations suggests decoupling between mechanisms underlying ALS onset and progression

This study uses molecular dynamics and clinical data to show structural and dynamic differences between WTL and MBR SOD1 variants, linking these to distinct ALS clinical outcomes.

Calculating variant penetrance using family history of disease and population data

This paper introduces a method to estimate penetrance for autosomal dominant traits using population data and family history, validated through simulations and case studies.