Jef D. Boeke

ZATELLITE enables real-time visualization and manipulation of human centromeres in live cells using synthetic zinc fingers without causing DNA damage.

The paper identifies a disrupted CCR5-like immunoglobulin gene in black-footed ferrets linked to increased susceptibility to plague caused by Yersinia pestis.

This study inserts a human RET haplotype into mice to model Hirschsprung disease, finding that regulatory variants reduce RET expression and contribute to disease.

The paper introduces an improved plasmid toolkit to streamline the mSwAP-In method for large-scale genome writing in mammalian cells.

The paper identifies proto-point centromeres in Saccharomycodales yeast, showing they evolved from retrotransposon LTRs, supporting the hypothesis that point centromeres originated from ancestral retrotransposons.

The paper demonstrates somatic L1 retrotransposition in adult mouse liver using an intrahepatic reporter assay and identifies distinct regulatory mechanisms in tumor versus normal cells.

This paper introduces a method to deliver synthetic haplotypes containing T2D GWAS variants to hiPSCs to study their functional impact on differentiation.

The paper uses Nanopore long-read DNA sequencing to analyze retrotransposon activation in aged and Alzheimer's disease brains, identifying somatic insertions and epigenetic changes.

The paper identifies enhancer-like elements on ecDNA in colorectal cancer that are derived from transposable elements and are functionally active in cancer cell fitness.

This study introduces a humanized mouse model of XDP with SVA_F insertion in TAF1, revealing myelin loss and oligodendrocyte dysfunction as key pathogenic features.

The paper genomically rewrote a mouse Taf1 allele with a human XDP patient-derived TAF1 allele, revealing that intronic SVA retrotransposons reduce TAF1 levels and cause neurodegeneration.

The paper analyzes ORF1p expression across cancers, finding it correlates with immune suppression in some tumors and activation in others, linked to copy number alterations.

Chromnitron predicts protein-DNA binding landscapes across cell types and proteins using multimodal learning, revealing new regulators of T cell exhaustion and dynamic shifts during neurogenesis.

The paper identifies context-dependent enhancer synergy in mouse embryonic stem cells, showing that enhancers can significantly boost neighboring DHS activity and that this synergy depends on distance and specific transcription factor sequences.

The paper observes that lentiviral infection selectively depletes cells containing extrachromosomal DNA (ecDNA), suggesting potential therapeutic strategies for ecDNA-driven cancers.

This paper introduces SGE, a method for screening metabolic pathways in mammalian cells, and finds that mitochondrial localization and large synthetic DNA constructs are key for successful pathway engineering.

The paper introduces an automated workflow for high-throughput assembly of large DNA libraries using yeast-based methods, achieving high success rates in assembling diverse DNA constructs.

This paper introduces a method to temporally control Cas9 DNA targeting by coupling it with transcription through engineered RNA binding, enabling selective gene editing in yeast and human cells.

This study replaces human variant histones in yeast, showing macroH2A1 disrupts chromatin organization and causes genome instability.

The paper investigates how genomic context affects enhancer function by analyzing the murine Igf2/H19 locus and shows that regulatory elements depend on their native surroundings.

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.

This paper introduces mSwAP-In, a method for efficient genome rewriting in mouse embryonic stem cells, demonstrating its use for Trp53 and ACE2 locus modifications to create more accurate disease models.

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.

A de novo yeast neochromosome carrying all 275 tRNA genes was built and characterized; it imposes a growth burden, with genome doubling and deletions in haploids possibly reflecting compensation.

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 analyzes multi-omic data from two pig heart xenografts in human decedents to identify immune and metabolic responses associated with rejection and injury.

This study demonstrates that genomic rearrangements in yeast can be efficiently induced using SCRaMbLE, leading to diverse genetic changes and phenotypic effects.

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