Joel S. Bader

This study identifies blood-based biomarkers that predict early tuberculosis culture conversion by analyzing mRNA and small RNA changes during treatment.

This study identifies the phosphate transport gene pstA1 as a key contributor to rifampin tolerance in Mycobacterium tuberculosis, showing that its deletion reduces bacterial survival during antibiotic treatment.

cpiVAE improves cross-platform proteomics imputation between Olink and SomaScan, achieving higher correlation than KNN and WNN, and enabling better phenotype associations.

The paper uses random survival forests to identify 33 myocardial genes predictive of survival in HFpEF, outperforming clinical parameters in prognosis modeling.

This study shows that deleterious mitochondrial DNA mutations increase over time and are associated with higher mortality risk, suggesting positive selection rather than genetic drift.

This paper synthesizes the largest eukaryotic yeast chromosome, synIV, and investigates how its 3D structure affects gene regulation and transcription.

The paper constructs a synthetic yeast chromosome and identifies aging regulators through replicative lifespan studies and genome-scale analysis.

The paper constructs a synthetic disomic yeast using SCRaMbLE and a newly synthesized chromosome to study aneuploidy phenotypes, finding that both copy number and specific chromosomal regions affect fitness.

The paper uses CRISPR D-BUGS and chromosome swapping to identify and resolve genetic interactions in synthetic chromosomes, revealing unexpected links between transcription, inositol metabolism, and tRNA abundance.

The paper synthesizes a shorter yeast chromosome and studies its fusion with other chromosomes, revealing new 3D structural interactions and Red1 binding patterns.

The paper develops a statistical mechanics model called SPI to analyze recombination patterns in synthetic yeast chromosomes generated by SCRaMbLE, finding a random walk scaling exponent between 0.45 and 0.6.

The paper debugs a synthetic yeast chromosome and uses laboratory evolution to identify genomic rearrangements that suppress growth defects caused by synthetic modifications.

The paper constructs a synthetic yeast chromosome XI and demonstrates how non-coding DNA modifications affect cell fitness, enabling on-demand extrachromosomal circular DNA formation.

This paper compares the power of hypothesis testing in genome-wide studies using priors versus increasing cohort sizes, finding that larger cohorts provide greater power than strong priors.

The paper performs mediation analysis on schizophrenia-associated variants using brain gene expression datasets to determine how eQTL target genes mediate risk, finding that expression effects often have unexpected directions.

The paper investigates the transcriptomic response of induced excitatory neurons to Clozapine, finding significant upregulation of cholesterol metabolism genes.

This study identifies 47 novel genetic loci associated with PR interval through genome-wide association meta-analysis across multiple populations.

The paper introduces module-based methods to identify differentially regulated network sub-modules using temporal expression data and static network structures, showing improved performance over existing methods in simulations and applications to neural stem cell differentiation.

The paper develops a collection of 1406 validated monoclonal antibodies against human transcription factors and identifies factors contributing to their successful generation.