Ali Bashir

A Vast Navigable Protein Sequence Subspace

The paper maps the genome packaging landscape of AAV2 capsid protein using high-throughput synthesis and machine learning, revealing navigable subspaces of functionally viable sequences.

A foundational atlas of autism protein interactions reveals molecular convergence

The paper constructs a PPI network of 100 high-confidence ASD genes, identifies novel interactions, and uses AlphaFold-Multimer to prioritize variants for functional validation in organoids.

Longitudinal fundus imaging and its genome-wide association analysis provide evidence for a human retinal aging clock

This paper develops a retinal aging clock from fundus images to predict chronological age and identifies genetic variants associated with accelerated aging.

Characterization of the immunoglobulin lambda chain locus from diverse populations reveals extensive genetic variation

The paper characterizes the immunoglobulin lambda chain locus in diverse populations, identifying novel alleles and highlighting limitations of short-read sequencing.

A novel framework for characterizing genomic haplotype diversity in the human immunoglobulin heavy chain locus

The paper introduces a framework combining long-read sequencing and a new tool to fully characterize haplotype diversity in the human immunoglobulin heavy chain locus, demonstrating high accuracy and scalability.

Epigenomic and functional characterization of a core DNA methyltransferase in the human pathogen Clostridium difficile

This study characterizes the epigenome of C. difficile and identifies a conserved DNA methyltransferase that impacts sporulation and other biological processes.

A robust benchmark for germline structural variant detection

Genome in a Bottle benchmark of 12745 sequence-resolved insertions and deletions of 50 bp or more, integrating 19 calling methods, scores false negatives and false positives alike.

Multi-platform discovery of haplotype-resolved structural variation in human genomes

This study identifies a large number of structural variants in human genomes using multiple sequencing technologies and presents them as a gold standard for future studies.

Extensive sequencing of seven human genomes to characterize benchmark reference materials

The paper presents extensive sequencing data from seven human genomes to serve as benchmark reference materials for improving sequencing technologies and variant calling.