Jef D. Boeke

This study examines how humanized nucleosomes in yeast affect chromatin structure, replication, and rDNA stability, revealing species-specific impacts on nuclear organization and function.

The paper uses synthetic regulatory genomics to study Sox2 expression in mESCs, finding that some enhancer regions are context-dependent and can enhance core regulatory elements.

The paper shows that missense mutations in kinetochore proteins reduce chromosome instability in histone-humanized yeast by weakening microtubule attachments, promoting euploidy.

The paper develops a method to measure LINE-1 retrotransposon expression in single cells and identifies its presence in epithelial and neuronal cells, with age-related increases.

This paper designs and synthesizes a functional neochromosome in yeast that replaces a native chromosome arm, demonstrating genome plasticity and synthetic chromosome viability.

This paper demonstrates the successful restoration of valine biosynthesis in mammalian cells by integrating synthetic pathways from E. coli, showing that ancient metabolic pathways can be reactivated in metazoans.

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.

This study shows that synthetic mouse L1 retrotransposition efficiency is due to sequence changes and a 3UTR deletion, not just ORF GC content, and highlights the need to reconsider synthetic L1 constructs.

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.

MenDEL is a web tool that automatically designs PCR primers for DNA assemblies by optimizing primer pairs for each junction based on user constraints.

MenDEL automates the selection of BAC sets to cover long DNA regions by allowing users to define criteria and find optimal combinations from existing libraries.

This study demonstrates that a circular human artificial chromosome can be transmitted through three generations of mice without health or reproductive issues.

The paper introduces a reversed synthetic locus into yeast and mouse genomes to study default chromatin states, finding widespread transcription in yeast but not in mouse.

This paper introduces CREEPY, a method for efficiently editing large episomal DNA constructs in yeast, demonstrating its application to a mouse Sox2-harboring episome.

The paper investigates the functional interdependence of super-enhancer elements in erythroid -globin gene regulation, revealing the necessity of facilitator elements for optimal activity.

This study shows that twin rDNA loci in brewer's yeast form a single nucleolus and reveals position-dependent size changes in rDNA loci.

The paper uses scRNAseq data from mouse and human to identify candidate genes for glial fate specification and optimize astrocyte differentiation protocols.

EUAdb is a database that standardizes information about FDA-authorized SARS-CoV-2 diagnostic tests to improve comparability and reproducibility.

The paper uses synthetic genomic reconstitution to study Hox cluster regulation, finding that distal enhancers are required for full transcriptional output while chromatin remodeling can occur without them.

The paper identifies an alternative splicing mechanism that regulates hTERT expression during development, linking it to telomerase activity and disease.

This study engineers the biosynthesis of the polyketide bikaverin in yeast by enhancing enzyme expression and using enzyme fusion to increase yield.

The paper transplants the human adenine de novo pathway into yeast to study regulatory mechanisms, finding that PPAT/ADE4 is a central regulatory node influenced by metabolites and mutations.

The paper identifies functionally important regions in ORF1p and ORF2p of human LINE-1 through trialanine mutagenesis, showing most mutants lose retrotransposition activity.

The paper introduces Superloser, a plasmid shuffling vector for yeast that enables efficient gene pathway replacement with low background.

The paper describes a pipeline for de novo assembly, delivery, and expression of a 101 kb human gene in mouse cells, demonstrating functional evaluation of a full-length gene.

The paper introduces a method to assemble synthetic haplotypes for functional analysis of AMD-associated variants, demonstrating its application to the 10q26 risk region.

The paper shows that yeast heterochromatin regulators Sir2 and Sir3 directly affect euchromatic DNA replication origins by modifying chromatin structure and suppressing MCM loading defects.

The paper identifies distinct nuclear and cytoplasmic intermediates of LINE-1 retrotransposition using mass spectrometry and affinity purification.

This paper introduces human nucleosomes into yeast, showing adaptation through mutations and histone residue changes, revealing chromatin dynamics and transcriptional effects.