Maximillian G. Marin

HipHap: Haplotype Assignment and Confidence Scoring for Diploid Reference Genomes

HipHap improves haplotype assignment and confidence scoring for diploid genomes by aligning reads to each haplotype separately and introducing a quality score.

Gene conversion is a key driver of diversity hotspots in M. tuberculosis antigens and virulence-associated loci

Complete genomes from 151 clinical M. tuberculosis isolates show gene conversion between paralogs creating diversity hotspots in PE/PPE/ESX genes and T cell antigens, including PPE18.

Population-level genome sequencing reveals distinct Mycobacterium tuberculosis intrahost mutational trajectories in simian immunodeficiency virus co-infected and antiretroviral treated non-human primates

This study uses whole genome sequencing of Mycobacterium tuberculosis in non-human primates to identify distinct mutational trajectories in SIV-co-infected and ART-treated animals, revealing differential immune pressures and mutation patterns.

HPRC2: A human pangenome reference with near-complete coverage of common genetic variation

460 haplotypes from 230 genomes, selected to maximize common-variant coverage, capture 99.43% of All of Us common small variants and halve structurally unreliable regions and base errors versus HPRC1.

Variation and selection at predicted G-quadruplexes across the human pangenome

The paper analyzes G-quadruplexes across the human pangenome, finding that they show distinct selection patterns and influence gene expression.

Benchmarking within-sample minority variant detection with short-read sequencing in M. tuberculosis

This study benchmarks seven variant callers for detecting low-frequency variants in M. tuberculosis using simulated short-read data, finding FreeBayes performs best and introducing an error model to filter false positives.

High-resolution metagenome assembly for modern long reads with myloasm

Myloasm improves metagenome assembly using long reads, recovering more complete contigs and resolving antibiotic resistance genes.

Analysis of the limited M. tuberculosis accessory genome reveals potential pitfalls of pan-genome analysis approaches

The paper evaluates pan-genome analysis methods using M. tuberculosis isolates, finding that annotation discrepancies and assembly quality affect results, and introduces panqc to address these issues.

Evaluating generalizability of artificial intelligence models for molecular datasets

This paper evaluates how well deep learning models generalize to new molecular sequences using a new framework called SPECTRA across 18 datasets and 19 models.

The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference

The paper quantifies the MTBC pangenome, revealing a small, closed genome with lineage-specific regions of difference and implications for virulence and drug resistance.

The discovery of genome-wide mutational dependence in naturally evolving populations

The paper identifies genome-wide mutational dependencies in Mycobacterium tuberculosis evolution, showing how mutations interact to confer antibiotic resistance and detect environmental pressures.

GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning

GenTB predicts tuberculosis drug resistance from genomic data using machine learning, achieving higher sensitivity than existing tools with slightly lower specificity.

Genomic sequence characteristics and the empiric accuracy of short-read sequencing

The paper evaluates short-read variant calling accuracy in Mycobacterium tuberculosis using Illumina and PacBio data, finding high precision with optimized mapping thresholds and identifying 68% of excluded repetitive regions as accurately called.

In-host population dynamics of M. tuberculosis during treatment failure

The paper analyzes M. tuberculosis population dynamics during treatment failure using whole-genome sequencing data from clinical isolates to identify resistance mutations and in-host evolutionary patterns.

Whole genome and RNA sequencing of 1,220 cancers reveals hundreds of genes deregulated by rearrangement of cis-regulatory elements

The paper identifies hundreds of genes deregulated by SVs in cancer, showing increased expression linked to SV breakpoints and enhancer elements.

Nanopore sequencing reveals U2AF1 S34F-associated full-length isoforms

The paper uses long-read sequencing to identify U2AF1 S34F mutation-induced isoform changes in lung cancer, revealing novel transcripts and functional consequences.

Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types

The paper analyzes RNA alterations across 27 cancer types using whole-genome sequencing data, identifying gene expression associations with DNA variants and structural fusions.