Christopher E. Mason

Modulator Resolves Transcript-, Allele-, and Condition-associated RNA Modification Differences from Direct RNA Sequencing

Modulator processes nanopore direct-RNA sequencing data to differentiate transcript-, allele-, and condition-associated RNA modifications, improving the analysis of RNA modifications in single molecules.

Simulated microgravity induces aging phenotypes in human organoids

The paper shows that simulated microgravity causes aging-like transcriptional changes in human organoids, with effects varying by tissue type.

CellCage™ Technology Enables High-throughput Isolation of Defined Cell Combinations to Resolve the Determinants of CAR-T mediated Cytotoxicity

The paper introduces CellCage™ technology to isolate defined cell combinations for high-throughput analysis of CAR-T cell cytotoxicity, revealing functional heterogeneity and cooperative behavior in T cell-mediated killing.

On the ancestry and evolution of the extinct dire wolf

This study uses paleogenomes of dire wolves to resolve their evolutionary relationships and identify genes under diversifying selection.

Spatial remodeling of bone marrow architecture defines tissue-state signatures of disease activity and therapeutic response in myelodysplastic neoplasms

This study uses spatial imaging to identify architectural changes in bone marrow that predict disease activity and response to therapy in myelodysplastic neoplasms.

DERIVATION OF ELEPHANT INDUCED PLURIPOTENT STEM CELLS

This paper reports the first derivation of elephant induced pluripotent stem cells (emiPSCs) using a modified reprogramming protocol that inhibits TP53 expansion genes.

Transcript architecture sets the m6A landscape: CSTF2 and CSTF2T reshape m6A through cleavage-dependent and -independent mechanisms

The paper identifies CSTF2 and CSTF2T as factors that shape the m6A landscape through cleavage-dependent and -independent mechanisms by altering transcript architecture and polyadenylation sites.

BIOTIA-DX RESISTANCE Achieved the Best Antimicrobial Resistance Phenotype Prediction Accuracy at CAMDA 2026

The paper introduces BDXR, a method for antimicrobial resistance prediction, achieving high accuracy across six species-drug pairs in the CAMDA 2026 challenge.

A family portrait of the genomic factors shaping tandem repeat mutagenesis

This study identifies genomic factors influencing tandem repeat mutagenesis using long-read sequencing in a large family, finding that de novo mutations are more common at longer, uninterrupted, and heterozygous loci.

A near-complete human pancreatic cancer genome

This paper presents near-complete, haplotype-resolved assemblies of a pancreatic cancer genome and normal tissue, identifying extensive somatic variants and epigenetic changes in previously excluded regions.

Diverse high-fat diets drive multi-omic reprogramming that persists after dietary reversal

The paper investigates how different high-fat diets affect host and microbiome multi-omic states over time and shows that some changes persist even after returning to a control diet.

Simulated spaceflight disrupts the immune-gut-brain axis and drives sex-dependent neuroinflammation, axonal injury, and behavioral deficits.

This study shows that simulated spaceflight stressors disrupt the immune-gut-brain axis, causing sex-dependent neuroinflammation, axonal injury, and behavioral issues in mice.

CCAAT-enhancer binding protein delta functions as a tumor suppressor gene in acute myeloid leukemia

This study identifies CEBPD as a tumor suppressor gene in acute myeloid leukemia through functional experiments and genomic analyses.

Whole-genome benchmarking reveals context-specific error rates in the Ultima UG100 and Illumina NovaSeqX Platforms.

This study benchmarks two whole-genome sequencing platforms, showing context-specific error rates and highlighting the importance of whole-genome benchmarking for accuracy assessment.

Scalable and comprehensive mosaic variant calling using DRAGEN

The paper introduces DRAGEN, a scalable mosaic variant caller that detects low VAF variants with high accuracy and efficiency, and presents a benchmark for low-VAF variants.

Leveraging a hybrid cross-disciplinary training model to accelerate global bioinformatics capacity

This paper introduces a hybrid training model to enhance bioinformatics capacity globally, demonstrating its effectiveness through an Eastern European workshop series.

Spatial and Temporal Patterns of Public Transit Aerobiomes

This study examines spatial and temporal patterns in public transit aerobiomes across six global cities using shotgun metagenomics, revealing city-specific microbial signatures and the importance of bioinformatics pipelines for contaminant removal.

Use of Metagenomic Reference Materials to Compare Lysis and Extraction Methods Against a Known Input

The paper evaluates lysis and extraction methods using metagenomic reference materials to identify optimal techniques and highlights biases in compositional metrics due to poor lysis.

Signaling induced biophysical disruption of repressed chromatin domains drives immune cell fate

The paper identifies H3 serine 28 phosphorylation as a mechanism driving chromatin derepression and immune cell fate transitions by disrupting repressive chromatin domains.

Protamine lacunae preserve the paternal chromatin landscape in sperm

The paper uses Fiber-seq to study paternal chromatin repackaging in sperm, finding that protamine lacunae and nucleosome retention play distinct roles in epigenetic inheritance.

BIOTIA-DX RESISTANCE Achieved the Best Antimicrobial Resistance Phenotype Prediction Accuracy at CAMDA 2025

The paper introduces BDXR, a tool for predicting antimicrobial resistance from whole genome sequencing, achieving high accuracy in the CAMDA 2025 challenge.

African Pan Genome Contigs Expose Biologically Relevant Sequence Still Hidden from Human Reference Frameworks

The paper identifies African Pan Genome contigs that are missing from current human reference genomes, showing they contain functionally relevant sequences and are enriched in African ancestry.

Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair

The paper describes a comprehensive genomic dataset from a tumor-normal pair with broad consent, generated using multiple sequencing technologies for benchmarking somatic variant detection.

The Spatial Atlas of Human Anatomy (SAHA): A Multimodal Subcellular-Resolution Reference Across Human Organs

SAHA creates a multimodal, subcellular-resolution reference atlas of healthy human tissues, revealing spatial organization and disease-associated disruptions across multiple organ systems.

The impact of PCR duplication on RNA-seq data generated using NovaSeq 6000, NovaSeq X, AVITI and G4 sequencers.

This study evaluates how PCR duplication affects RNA-seq data quality across four sequencers, finding that input amount and PCR cycles significantly impact duplication rates, with UMIs effectively reducing duplicates without losing biological information.

A familial, telomere-to-telomere reference for human de novo mutation and recombination from a four-generation pedigree

The paper uses a four-generation family to systematically assess de novo mutations and recombination, finding high mutation rates and paternal bias, along with a detailed recombination map.

A benchmarking study of copy number variation inference methods using single-cell RNA-sequencing data

This study benchmarks five scCNV inference methods across multiple scRNA-seq platforms and mixed samples, finding variations in performance based on data characteristics and batch effects.

A robust benchmark for detecting low-frequency variants in the HG002 Genome In A Bottle NIST reference material.

The paper develops a benchmark for detecting low-frequency mosaic variants in the HG002 reference material using high-coverage sequencing data and validates its utility across multiple technologies.

Collection of Biospecimens from the Inspiration4 Mission Establishes the Standards for the Space Omics and Medical Atlas (SOMA)

This paper describes the collection and processing of biospecimens from the Inspiration4 space mission to establish standards for space omics and medical research.

Forecasting Dengue Fever in Brazil Using Multimodal Data, Including Climate Data

This paper introduces a dengue fever forecasting model for Brazil using multimodal data, achieving accurate monthly predictions up to 6 months ahead.