Eleazar Eskin

This study examines epigenomic and spatial changes during human reprogramming, finding distinct molecular and spatial patterns in productive versus unsuccessful trajectories.

The paper introduces taxutils, a tool for managing NCBI taxonomy and accession mappings, and demonstrates its use in assessing assembly quality through taxonomic mapping analysis.

TDKC improves metagenomic pathogen detection by reducing memory and computational costs while maintaining accuracy.

This study identifies genetic and transcriptomic factors associated with severe coccidioidomycosis, finding a founder variant in NLRX1 linked to African ancestry and increased disease risk.

The paper evaluates 24 metagenomic sequencing workflows for SARS-CoV-2 detection in saliva, finding that RNA-Seq library preparation has a greater impact on viral read recovery than extraction methods.

This study creates a 3D multi-omic atlas of developing human basal ganglia and inhibitory neurons, revealing lineage-specific 3D genomic dynamics and regulatory programs associated with neuropsychiatric disease risk.

The paper presents a single-cell DNA methylation and transcriptomics analysis of ASD, identifying cell type-specific methylation changes and age-related effects in the brain.

The paper identifies genetic loci associated with saline self-administration in mice, finding distinct genetic bases compared to cocaine self-administration.

VISTA improves structural variant detection by integrating multiple callers with a novel filtering algorithm, achieving high accuracy across various SV types and genomic contexts.

This study benchmarks large language models in bioinformatics tasks, finding GPT-4 leads in most areas while Gemini excels in math and LLaMA struggles with code generation.

This study investigates the genetic basis of dietary iron overload and associated pathologies in mice using the Hybrid Mouse Diversity Panel, identifying genetic loci and pathways involved.

This paper introduces MR-Twin, a Mendelian Randomization method robust to population stratification, and shows it reduces false positives compared to standard methods in UK Biobank data.

The paper identifies genetic loci and pathways associated with cocaine self-administration in mice using GWAS and TWAS, highlighting Trpv2 as a key gene.

The paper develops a statistical framework to model replication rates in GWAS by accounting for winner's curse and study-specific heterogeneity, showing significant variation in confounding factors across studies.

The paper investigates epigenomic and 3D chromatin conformation changes in human frontal cortex and hippocampus development using sn-m3C-seq, finding distinct chromatin conformations in neurons and glial cells and linking risk variants to regulatory regions.

The paper evaluates metagenomic software tools using realistic datasets, highlighting improvements in assembly and taxon profiling while identifying remaining challenges in virus/archaea detection and reproducibility.

This paper introduces sensitivity analysis tools for Mendelian randomization to assess robustness against population stratification, batch effects, and horizontal pleiotropy.

This paper introduces MsCAVIAR, a method for fine mapping causal variants across multiple GWAS studies, showing it reduces causal set sizes by over 20% in Type 2 Diabetes analysis.

The paper benchmarks two methods for detecting cell-type-specific differential DNA methylation, finding TCA superior to CellDMC and discussing best practices for cell-type resolution analysis.

PLEIO maps and interprets pleiotropic loci by jointly analyzing summary statistics of multiple traits, identifying 20 novel loci related to cardiovascular disease.

The paper presents a large ASE resource from GTEx v8 with 431 million SNP-level and 153 million haplotype-level measurements, and extends phASER to estimate cis regulatory variant effect sizes.

The paper uses bulk RNA-seq data to estimate cell type abundances and identifies cell type interaction QTLs that provide finer resolution of tissue specificity than bulk cis-eQTLs.

Metalign improves metagenomic profiling by using containment min hash for efficient alignment-based analysis, achieving better results than existing methods on benchmark datasets.

The paper examines telomere length variation across 6,391 tissue samples from 952 individuals, showing tissue-specific differences, positive correlations between tissues, and associations with age and ancestry.

Integrating expression, allelic expression and splicing across tissues identifies rare variants with relevance to traits.

The paper quantifies protein levels across 32 human tissues and compares them to transcriptome data, revealing insights into post-transcriptional regulation and disease mechanisms.

The paper introduces V-seq, a cost-effective method for viral genome sequencing that uses multiplexed RT primers to improve coverage and reduce costs.

This paper introduces PAT, a method for joint analysis of multiple traits in GWAS, showing increased power and novel associations in UK Biobank data.

This study benchmarks WGS-based structural variant callers using a PCR-confirmed gold standard, finding wide performance variation and identifying tools best suited for low and ultra-low pass data.

The paper evaluates existing microbial databases and proposes guidelines for creating a unified reference database to enhance the quality and comprehensiveness of metagenomics research.