Jef D. Boeke

Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics

Affiliated withInstitute for Systems Genetics

Research Area

Biography

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 18	2015

Other Publications

Article	Year
A nucleocapsid functionality contained within the amino terminus of the Ty1 protease that is distinct and separable from proteolytic activity. Journal of virology\| PubMed ID: 11739699	2002
Telomeric and rDNA silencing in Saccharomyces cerevisiae are dependent on a nuclear NAD(+) salvage pathway. Genetics\| PubMed ID: 11901108	2002
Ty1 defect in proteolysis at high temperature. Journal of virology\| PubMed ID: 11932388	2002
Inhibition of reverse transcription in vivo by elevated manganese ion concentration. Molecular cell\| PubMed ID: 11983178	2002
Tn7-mediated mutagenesis of Saccharomyces cerevisiae genomic DNA in vitro. Methods in enzymology\| PubMed ID: 12073315	2002
SIR2 family of NAD(+)-dependent protein deacetylases. Methods in enzymology\| PubMed ID: 12078503	2002
Functional profiling of the Saccharomyces cerevisiae genome. Nature\| PubMed ID: 12140549	2002
Human l1 retrotransposition is associated with genetic instability in vivo. Cell\| PubMed ID: 12176320	2002
A core nucleosome surface crucial for transcriptional silencing. Nature genetics\| PubMed ID: 12244315	2002
Molecular archeology of L1 insertions in the human genome. Genome biology\| PubMed ID: 12372140	2002
SIRT3, a human SIR2 homologue, is an NAD-dependent deacetylase localized to mitochondria. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 12374852	2002
Structure of a Sir2 enzyme bound to an acetylated p53 peptide. Molecular cell\| PubMed ID: 12408821	2002
Human L1 element target-primed reverse transcription in vitro. The EMBO journal\| PubMed ID: 12411507	2002
Transcriptional interactions between yeast tRNA genes, flanking genes and Ty elements: a genomic point of view. Genome research\| PubMed ID: 12566403	2003
Short-chain fatty acid activation by acyl-coenzyme A synthetases requires SIR2 protein function in Salmonella enterica and Saccharomyces cerevisiae. Genetics\| PubMed ID: 12618394	2003
Identifying related L1 retrotransposons by analyzing 3' transduced sequences. Genome biology\| PubMed ID: 12734010	2003
The unusual phylogenetic distribution of retrotransposons: a hypothesis. Genome research\| PubMed ID: 12952870	2003
DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray. Nature genetics\| PubMed ID: 14566339	2003
Molecular biology. Ring around the retroelement. Science (New York, N.Y.)\| PubMed ID: 14716001	2004
Structural basis for the mechanism and regulation of Sir2 enzymes. Molecular cell\| PubMed ID: 15023335	2004
Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature\| PubMed ID: 15152245	2004
A highly active synthetic mammalian retrotransposon. Nature\| PubMed ID: 15152256	2004
Local definition of Ty1 target preference by long terminal repeats and clustered tRNA genes. Genome research\| PubMed ID: 15197163	2004
Evolution: A is for adaptation. Nature\| PubMed ID: 15385995	2004
FKBP12 controls aspartate pathway flux in Saccharomyces cerevisiae to prevent toxic intermediate accumulation. Eukaryotic cell\| PubMed ID: 15470257	2004
Ty1 mobilizes subtelomeric Y' elements in telomerase-negative Saccharomyces cerevisiae survivors. Molecular and cellular biology\| PubMed ID: 15509791	2004
Regulated nucleosome mobility and the histone code. Nature structural & molecular biology\| PubMed ID: 15523479	2004
A robust toolkit for functional profiling of the yeast genome. Molecular cell\| PubMed ID: 15525520	2004
An evaluation of detection methods for large lariat RNAs. RNA (New York, N.Y.)\| PubMed ID: 15661842	2005
Identification and characterization of critical cis-acting sequences within the yeast Ty1 retrotransposon. RNA (New York, N.Y.)\| PubMed ID: 15661848	2005
Reconstitution of papillomavirus E2-mediated plasmid maintenance in Saccharomyces cerevisiae by the Brd4 bromodomain protein. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 15710895	2005
Genome-wide identification of Isw2 chromatin-remodeling targets by localization of a catalytically inactive mutant. Genes & development\| PubMed ID: 15833917	2005
TFIIIB subunit Bdp1p is required for periodic integration of the Ty1 retrotransposon and targeting of Isw2p to S. cerevisiae tDNAs. Genes & development\| PubMed ID: 15833918	2005
Improved microarray methods for profiling the Yeast Knockout strain collection. Nucleic acids research\| PubMed ID: 15994458	2005
LINE-1 retrotransposons: modulators of quantity and quality of mammalian gene expression? BioEssays : news and reviews in molecular, cellular and developmental biology\| PubMed ID: 16015595	2005
Gene-breaking: a new paradigm for human retrotransposon-mediated gene evolution. Genome research\| PubMed ID: 16024818	2005
Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools. Nucleic acids research\| PubMed ID: 16166654	2005
Insights into the role of histone H3 and histone H4 core modifiable residues in Saccharomyces cerevisiae. Molecular and cellular biology\| PubMed ID: 16260619	2005
Global synthetic-lethality analysis and yeast functional profiling. Trends in genetics : TIG\| PubMed ID: 16309778	2006
Transposon technology and vertebrate functional genomics. Genome biology\| PubMed ID: 16356279	2005
GeneDesign: rapid, automated design of multikilobase synthetic genes. Genome research\| PubMed ID: 16481661	2006
A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell\| PubMed ID: 16487579	2006
Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nature genetics\| PubMed ID: 16501559	2006
Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae. Genome research\| PubMed ID: 16510898	2006
Use of mixture models in a microarray-based screening procedure for detecting differentially represented yeast mutants. Statistical applications in genetics and molecular biology\| PubMed ID: 16646779	2003
Gene function prediction from congruent synthetic lethal interactions in yeast. Molecular systems biology\| PubMed ID: 16729061	2005
The biochemistry of sirtuins. Annual review of biochemistry\| PubMed ID: 16756498	2006
The sirtuins hst3 and Hst4p preserve genome integrity by controlling histone h3 lysine 56 deacetylation. Current biology : CB\| PubMed ID: 16815704	2006
Nucleocytosolic acetyl-coenzyme a synthetase is required for histone acetylation and global transcription. Molecular cell\| PubMed ID: 16857587	2006
The LRS and SIN domains: two structurally equivalent but functionally distinct nucleosomal surfaces required for transcriptional silencing. Molecular and cellular biology\| PubMed ID: 17015465	2006
Stacking the deck: double-tiled DNA microarrays. Nature methods\| PubMed ID: 17060914	2006
Transposon insertion site profiling chip (TIP-chip). Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 17101968	2006
Active retrotransposition by a synthetic L1 element in mice. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 17124176	2006
dSLAM analysis of genome-wide genetic interactions in Saccharomyces cerevisiae. Methods (San Diego, Calif.)\| PubMed ID: 17189863	2007
Mighty Piwis defend the germline against genome intruders. Cell\| PubMed ID: 17418784	2007
Mn2+ suppressor mutations and biochemical communication between Ty1 reverse transcriptase and RNase H domains. Journal of virology\| PubMed ID: 17537863	2007
Efficient Tor signaling requires a functional class C Vps protein complex in Saccharomyces cerevisiae. Genetics\| PubMed ID: 17565946	2007
Plasmid-chromosome shuffling for non-deletion alleles in yeast. Nature methods\| PubMed ID: 18193055	2008
Great exaptations. Journal of biology\| PubMed ID: 18279541	2008
Domesticated DNA transposon proteins mediate retrotransposon control. Cell research\| PubMed ID: 18311163	2008
Analysis of genetic interactions on a genome-wide scale in budding yeast: diploid-based synthetic lethality analysis by microarray. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 18392971	2008
Toward a comprehensive temperature-sensitive mutant repository of the essential genes of Saccharomyces cerevisiae. Molecular cell\| PubMed ID: 18439903	2008
Microarray-based genetic screen defines SAW1, a gene required for Rad1/Rad10-dependent processing of recombination intermediates. Molecular cell\| PubMed ID: 18471978	2008
The incredible shrinking world of DNA microarrays. Molecular bioSystems\| PubMed ID: 18563246	2008
Histone H3 K56 hyperacetylation perturbs replisomes and causes DNA damage. Genetics\| PubMed ID: 18579506	2008
Conditional activation of a single-copy L1 transgene in mice by Cre. Genesis (New York, N.Y. : 2000)\| PubMed ID: 18615728	2008
A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation. Genes & development\| PubMed ID: 18676811	2008
Orientation-dependent regulation of integrated HIV-1 expression by host gene transcriptional readthrough. Cell host & microbe\| PubMed ID: 18692773	2008
A descent into the nuage: the maelstrom of transposon control. Developmental cell\| PubMed ID: 18694557	2008
From the shards of a shattered genome, diversity. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 18701721	2008
Probing nucleosome function: a highly versatile library of synthetic histone H3 and H4 mutants. Cell\| PubMed ID: 18805098	2008
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. Genome research\| PubMed ID: 18832443	2008
Teaching synthetic biology, bioinformatics and engineering to undergraduates: the interdisciplinary Build-a-Genome course. Genetics\| PubMed ID: 19015540	2009
Compensatory interactions between Sir3p and the nucleosomal LRS surface imply their direct interaction. PLoS genetics\| PubMed ID: 19079580	2008
HistoneHits: a database for histone mutations and their phenotypes. Genome research\| PubMed ID: 19218532	2009
Protein acetylation microarray reveals that NuA4 controls key metabolic target regulating gluconeogenesis. Cell\| PubMed ID: 19303850	2009
Transposon-mediated genome manipulation in vertebrates. Nature methods\| PubMed ID: 19478801	2009
Plug and play modular strategies for synthetic retrotransposons. Methods (San Diego, Calif.)\| PubMed ID: 19481606	2009
Retrotransposon overdose and genome integrity. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 19666515	2009
Human Genomics. Sleeping dogs of the genome. Science (New York, N.Y.)\| PubMed ID: 25477445	2014
Histone h3 exerts a key function in mitotic checkpoint control. Molecular and cellular biology\| PubMed ID: 19917722	2010
Specificity of the BRISC deubiquitinating enzyme is not due to selective binding to Lys63-linked polyubiquitin. The Journal of biological chemistry\| PubMed ID: 20032457	2010
Silent information regulator 3: the Goldilocks of the silencing complex. Genes & development\| PubMed ID: 20080949	2010
GeneDesign 3.0 is an updated synthetic biology toolkit. Nucleic acids research\| PubMed ID: 20211837	2010
CLONEQC: lightweight sequence verification for synthetic biology. Nucleic acids research\| PubMed ID: 20211841	2010
A microarray-based genetic screen for yeast chronological aging factors. PLoS genetics\| PubMed ID: 20421943	2010
Mobile interspersed repeats are major structural variants in the human genome. Cell\| PubMed ID: 20602999	2010
Trivalent arsenic inhibits the functions of chaperonin complex. Genetics\| PubMed ID: 20660648	2010
Yin and Yang of histone H2B roles in silencing and longevity: a tale of two arginines. Genetics\| PubMed ID: 20713692	2010
Making temperature-sensitive mutants. Methods in enzymology\| PubMed ID: 20946811	2010
Characterization of L1 retrotransposition with high-throughput dual-luciferase assays. Nucleic acids research\| PubMed ID: 21071410	2011
Glucose and weight control in mice with a designed ghrelin O-acyltransferase inhibitor. Science (New York, N.Y.)\| PubMed ID: 21097901	2010
Characterization of a synthetic human LINE-1 retrotransposon ORFeus-Hs. Mobile DNA\| PubMed ID: 21320307	2011
Differential contributions of histone H3 and H4 residues to heterochromatin structure. Genetics\| PubMed ID: 21441216	2011
Effect of reverse transcriptase inhibitors on LINE-1 and Ty1 reverse transcriptase activities and on LINE-1 retrotransposition. BMC biochemistry\| PubMed ID: 21545744	2011
An evolutionarily 'young' lysine residue in histone H3 attenuates transcriptional output in Saccharomyces cerevisiae. Genes & development\| PubMed ID: 21685365	2011
Genome remodeling. Nature biotechnology\| PubMed ID: 21904325	2011
Acetylation of yeast AMPK controls intrinsic aging independently of caloric restriction. Cell\| PubMed ID: 21906795	2011
Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature\| PubMed ID: 21918511	2011
Protein acetylation and aging. Aging\| PubMed ID: 22067362	2011
Novel transcript truncating function of Rap1p revealed by synthetic codon-optimized Ty1 retrotransposon. Genetics\| PubMed ID: 22135353	2012
Strain construction and screening methods for a yeast histone H3/H4 mutant library. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 22183584	2012
Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots. Genome research\| PubMed ID: 22219510	2012
Polyubiquitin-sensor proteins reveal localization and linkage-type dependence of cellular ubiquitin signaling. Nature methods\| PubMed ID: 22306808	2012
Rapid identification of monospecific monoclonal antibodies using a human proteome microarray. Molecular & cellular proteomics : MCP\| PubMed ID: 22307071	2012
Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. Nature\| PubMed ID: 22318606	2012
Assembling DNA fragments by USER fusion. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 22328427	2012
Assembling large DNA segments in yeast. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 22328431	2012
Design-A-Gene with GeneDesign. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 22328438	2012
The Build-a-Genome course. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 22328440	2012
Lysine succinylation and lysine malonylation in histones. Molecular & cellular proteomics : MCP\| PubMed ID: 22389435	2012
The Saccharomyces cerevisiae Nrd1-Nab3 transcription termination pathway acts in opposition to Ras signaling and mediates response to nutrient depletion. Molecular and cellular biology\| PubMed ID: 22431520	2012
Biotinylation of lysine method identifies acetylated histone H3 lysine 79 in Saccharomyces cerevisiae as a substrate for Sir2. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 22474337	2012
A Sleeping Beauty mutagenesis screen reveals a tumor suppressor role for Ncoa2/Src-2 in liver cancer. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 22556267	2012
Human transposon tectonics. Cell\| PubMed ID: 22579280	2012
Poly(A) binding protein C1 is essential for efficient L1 retrotransposition and affects L1 RNP formation. Molecular and cellular biology\| PubMed ID: 22907758	2012
Live-cell studies of p300/CBP histone acetyltransferase activity and inhibition. Chembiochem : a European journal of chemical biology\| PubMed ID: 22961914	2012
Ghrelin O-acyltransferase assays and inhibition. Methods in enzymology\| PubMed ID: 22975055	2012
Active transposition in genomes. Annual review of genetics\| PubMed ID: 23145912	2012
Retrotransposon Ty1 RNA contains a 5'-terminal long-range pseudoknot required for efficient reverse transcription. RNA (New York, N.Y.)\| PubMed ID: 23329695	2013
Conserved structure and inferred evolutionary history of long terminal repeats (LTRs). Mobile DNA\| PubMed ID: 23369192	2013
Using functional proteome microarrays to study protein lysine acetylation. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 23381860	2013
Multichange isothermal mutagenesis: a new strategy for multiple site-directed mutations in plasmid DNA. ACS synthetic biology\| PubMed ID: 23654272	2013
A quantitative analysis of histone methylation and acetylation isoforms from their deuteroacetylated derivatives: application to a series of knockout mutants. Journal of mass spectrometry : JMS\| PubMed ID: 23674285	2013
Controlled insertional mutagenesis using a LINE-1 (ORFeus) gene-trap mouse model. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 23818630	2013
Influence of RNA structural elements on Ty1 retrotransposition. Mobile genetic elements\| PubMed ID: 23914314	2013
Kinetochore function and chromosome segregation rely on critical residues in histones H3 and H4 in budding yeast. Genetics\| PubMed ID: 24037263	2013
Architectural organization of the metabolic regulatory enzyme ghrelin O-acyltransferase. The Journal of biological chemistry\| PubMed ID: 24045953	2013
Genome-wide consequences of deleting any single gene. Molecular cell\| PubMed ID: 24211263	2013
Affinity proteomics reveals human host factors implicated in discrete stages of LINE-1 retrotransposition. Cell\| PubMed ID: 24267889	2013
TE-array--a high throughput tool to study transposon transcription. BMC genomics\| PubMed ID: 24325565	2013
tRNA genes rapidly change in evolution to meet novel translational demands. eLife\| PubMed ID: 24363105	2013
Long interspersed element-1 protein expression is a hallmark of many human cancers. The American journal of pathology\| PubMed ID: 24607009	2014
Total synthesis of a functional designer eukaryotic chromosome. Science (New York, N.Y.)\| PubMed ID: 24674868	2014
Characterisation of cytoplasmic DNA complementary to non-retroviral RNA viruses in human cells. Scientific reports\| PubMed ID: 24875540	2014
RADOM, an efficient in vivo method for assembling designed DNA fragments up to 10 kb long in Saccharomyces cerevisiae. ACS synthetic biology\| PubMed ID: 24895839	2015
Expression and detection of LINE-1 ORF-encoded proteins. Mobile genetic elements\| PubMed ID: 25054082	2014
High-temporal-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast. Nature structural & molecular biology\| PubMed ID: 25173176	2014
Circular permutation of a synthetic eukaryotic chromosome with the telomerator. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 25378705	2014
Intrinsic biocontainment: multiplex genome safeguards combine transcriptional and recombinational control of essential yeast genes. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 25624482	2015
Yeast Golden Gate (yGG) for the Efficient Assembly of S. cerevisiae Transcription Units. ACS synthetic biology\| PubMed ID: 25756291	2015
Interplay between histone h3 lysine 56 deacetylation and chromatin modifiers in response to DNA damage. Genetics\| PubMed ID: 25786853	2015
Versatile genetic assembly system (VEGAS) to assemble pathways for expression in S. cerevisiae. Nucleic acids research\| PubMed ID: 25956652	2015