Jef D. Boeke

A nucleocapsid functionality contained within the amino terminus of the Ty1 protease that is distinct and separable from proteolytic activity.

Telomeric and rDNA silencing in Saccharomyces cerevisiae are dependent on a nuclear NAD(+) salvage pathway.

Ty1 defect in proteolysis at high temperature.

Inhibition of reverse transcription in vivo by elevated manganese ion concentration.

Tn7-mediated mutagenesis of Saccharomyces cerevisiae genomic DNA in vitro.

SIR2 family of NAD(+)-dependent protein deacetylases.

Functional profiling of the Saccharomyces cerevisiae genome.

Human l1 retrotransposition is associated with genetic instability in vivo.

A core nucleosome surface crucial for transcriptional silencing.

Molecular archeology of L1 insertions in the human genome.

SIRT3, a human SIR2 homologue, is an NAD-dependent deacetylase localized to mitochondria.

Structure of a Sir2 enzyme bound to an acetylated p53 peptide.

Human L1 element target-primed reverse transcription in vitro.

Transcriptional interactions between yeast tRNA genes, flanking genes and Ty elements: a genomic point of view.

Short-chain fatty acid activation by acyl-coenzyme A synthetases requires SIR2 protein function in Salmonella enterica and Saccharomyces cerevisiae.

Identifying related L1 retrotransposons by analyzing 3' transduced sequences.

The unusual phylogenetic distribution of retrotransposons: a hypothesis.

DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray.

Molecular biology. Ring around the retroelement.

Structural basis for the mechanism and regulation of Sir2 enzymes.

Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes.

A highly active synthetic mammalian retrotransposon.

Local definition of Ty1 target preference by long terminal repeats and clustered tRNA genes.

Evolution: A is for adaptation.

FKBP12 controls aspartate pathway flux in Saccharomyces cerevisiae to prevent toxic intermediate accumulation.

Ty1 mobilizes subtelomeric Y' elements in telomerase-negative Saccharomyces cerevisiae survivors.

Regulated nucleosome mobility and the histone code.

A robust toolkit for functional profiling of the yeast genome.

An evaluation of detection methods for large lariat RNAs.

Identification and characterization of critical cis-acting sequences within the yeast Ty1 retrotransposon.

Reconstitution of papillomavirus E2-mediated plasmid maintenance in Saccharomyces cerevisiae by the Brd4 bromodomain protein.

Genome-wide identification of Isw2 chromatin-remodeling targets by localization of a catalytically inactive mutant.

TFIIIB subunit Bdp1p is required for periodic integration of the Ty1 retrotransposon and targeting of Isw2p to S. cerevisiae tDNAs.

Improved microarray methods for profiling the Yeast Knockout strain collection.

LINE-1 retrotransposons: modulators of quantity and quality of mammalian gene expression?

Gene-breaking: a new paradigm for human retrotransposon-mediated gene evolution.

Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools.

Insights into the role of histone H3 and histone H4 core modifiable residues in Saccharomyces cerevisiae.

Global synthetic-lethality analysis and yeast functional profiling.

Transposon technology and vertebrate functional genomics.

GeneDesign: rapid, automated design of multikilobase synthetic genes.

A DNA integrity network in the yeast Saccharomyces cerevisiae.

Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets.

Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae.

Use of mixture models in a microarray-based screening procedure for detecting differentially represented yeast mutants.

Gene function prediction from congruent synthetic lethal interactions in yeast.

The biochemistry of sirtuins.

The sirtuins hst3 and Hst4p preserve genome integrity by controlling histone h3 lysine 56 deacetylation.

Nucleocytosolic acetyl-coenzyme a synthetase is required for histone acetylation and global transcription.

The LRS and SIN domains: two structurally equivalent but functionally distinct nucleosomal surfaces required for transcriptional silencing.

Stacking the deck: double-tiled DNA microarrays.

Transposon insertion site profiling chip (TIP-chip).

Active retrotransposition by a synthetic L1 element in mice.

dSLAM analysis of genome-wide genetic interactions in Saccharomyces cerevisiae.

Mighty Piwis defend the germline against genome intruders.

Mn2+ suppressor mutations and biochemical communication between Ty1 reverse transcriptase and RNase H domains.

Efficient Tor signaling requires a functional class C Vps protein complex in Saccharomyces cerevisiae.

Plasmid-chromosome shuffling for non-deletion alleles in yeast.

Great exaptations.

Domesticated DNA transposon proteins mediate retrotransposon control.

Analysis of genetic interactions on a genome-wide scale in budding yeast: diploid-based synthetic lethality analysis by microarray.

Toward a comprehensive temperature-sensitive mutant repository of the essential genes of Saccharomyces cerevisiae.

Microarray-based genetic screen defines SAW1, a gene required for Rad1/Rad10-dependent processing of recombination intermediates.

The incredible shrinking world of DNA microarrays.

Histone H3 K56 hyperacetylation perturbs replisomes and causes DNA damage.

Conditional activation of a single-copy L1 transgene in mice by Cre.

A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation.

Orientation-dependent regulation of integrated HIV-1 expression by host gene transcriptional readthrough.

A descent into the nuage: the maelstrom of transposon control.

From the shards of a shattered genome, diversity.

Probing nucleosome function: a highly versatile library of synthetic histone H3 and H4 mutants.

Finding friends and enemies in an enemies-only network: a graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions.

Teaching synthetic biology, bioinformatics and engineering to undergraduates: the interdisciplinary Build-a-Genome course.

Compensatory interactions between Sir3p and the nucleosomal LRS surface imply their direct interaction.

HistoneHits: a database for histone mutations and their phenotypes.

Protein acetylation microarray reveals that NuA4 controls key metabolic target regulating gluconeogenesis.

Transposon-mediated genome manipulation in vertebrates.

Plug and play modular strategies for synthetic retrotransposons.

Retrotransposon overdose and genome integrity.

Human Genomics. Sleeping dogs of the genome.

Histone h3 exerts a key function in mitotic checkpoint control.

Specificity of the BRISC deubiquitinating enzyme is not due to selective binding to Lys63-linked polyubiquitin.

Silent information regulator 3: the Goldilocks of the silencing complex.

GeneDesign 3.0 is an updated synthetic biology toolkit.

CLONEQC: lightweight sequence verification for synthetic biology.

A microarray-based genetic screen for yeast chronological aging factors.

Mobile interspersed repeats are major structural variants in the human genome.

Trivalent arsenic inhibits the functions of chaperonin complex.

Yin and Yang of histone H2B roles in silencing and longevity: a tale of two arginines.

Making temperature-sensitive mutants.

Characterization of L1 retrotransposition with high-throughput dual-luciferase assays.

Glucose and weight control in mice with a designed ghrelin O-acyltransferase inhibitor.

Characterization of a synthetic human LINE-1 retrotransposon ORFeus-Hs.

Differential contributions of histone H3 and H4 residues to heterochromatin structure.

Effect of reverse transcriptase inhibitors on LINE-1 and Ty1 reverse transcriptase activities and on LINE-1 retrotransposition.

An evolutionarily 'young' lysine residue in histone H3 attenuates transcriptional output in Saccharomyces cerevisiae.

Genome remodeling.

Acetylation of yeast AMPK controls intrinsic aging independently of caloric restriction.

Synthetic chromosome arms function in yeast and generate phenotypic diversity by design.

Protein acetylation and aging.

Novel transcript truncating function of Rap1p revealed by synthetic codon-optimized Ty1 retrotransposon.

Strain construction and screening methods for a yeast histone H3/H4 mutant library.

Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots.

Polyubiquitin-sensor proteins reveal localization and linkage-type dependence of cellular ubiquitin signaling.

Rapid identification of monospecific monoclonal antibodies using a human proteome microarray.

Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK.

Assembling DNA fragments by USER fusion.

Assembling large DNA segments in yeast.

Design-A-Gene with GeneDesign.

The Build-a-Genome course.

Lysine succinylation and lysine malonylation in histones.

The Saccharomyces cerevisiae Nrd1-Nab3 transcription termination pathway acts in opposition to Ras signaling and mediates response to nutrient depletion.

Biotinylation of lysine method identifies acetylated histone H3 lysine 79 in Saccharomyces cerevisiae as a substrate for Sir2.

A Sleeping Beauty mutagenesis screen reveals a tumor suppressor role for Ncoa2/Src-2 in liver cancer.

Human transposon tectonics.

Poly(A) binding protein C1 is essential for efficient L1 retrotransposition and affects L1 RNP formation.

Live-cell studies of p300/CBP histone acetyltransferase activity and inhibition.

Ghrelin O-acyltransferase assays and inhibition.

Active transposition in genomes.

Retrotransposon Ty1 RNA contains a 5'-terminal long-range pseudoknot required for efficient reverse transcription.

Conserved structure and inferred evolutionary history of long terminal repeats (LTRs).

Using functional proteome microarrays to study protein lysine acetylation.

Multichange isothermal mutagenesis: a new strategy for multiple site-directed mutations in plasmid DNA.

A quantitative analysis of histone methylation and acetylation isoforms from their deuteroacetylated derivatives: application to a series of knockout mutants.

Controlled insertional mutagenesis using a LINE-1 (ORFeus) gene-trap mouse model.

Influence of RNA structural elements on Ty1 retrotransposition.

Kinetochore function and chromosome segregation rely on critical residues in histones H3 and H4 in budding yeast.

Architectural organization of the metabolic regulatory enzyme ghrelin O-acyltransferase.

Genome-wide consequences of deleting any single gene.

Affinity proteomics reveals human host factors implicated in discrete stages of LINE-1 retrotransposition.

TE-array--a high throughput tool to study transposon transcription.

tRNA genes rapidly change in evolution to meet novel translational demands.

Long interspersed element-1 protein expression is a hallmark of many human cancers.

Total synthesis of a functional designer eukaryotic chromosome.

Characterisation of cytoplasmic DNA complementary to non-retroviral RNA viruses in human cells.

RADOM, an efficient in vivo method for assembling designed DNA fragments up to 10 kb long in Saccharomyces cerevisiae.

Expression and detection of LINE-1 ORF-encoded proteins.

High-temporal-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast.

Circular permutation of a synthetic eukaryotic chromosome with the telomerator.

Intrinsic biocontainment: multiplex genome safeguards combine transcriptional and recombinational control of essential yeast genes.

Yeast Golden Gate (yGG) for the Efficient Assembly of S. cerevisiae Transcription Units.

Interplay between histone h3 lysine 56 deacetylation and chromatin modifiers in response to DNA damage.

Versatile genetic assembly system (VEGAS) to assemble pathways for expression in S. cerevisiae.