Jef D. Boeke Department of Biochemistry and Molecular Pharmacology Institute for Systems Genetics Biography Publications Institution JoVE Articles Jef D. Boeke has not added a biography. If you are Jef D. Boeke and would like to personalize this page please email our Author Liaison for assistance. Publications Versatile Genetic Assembly System (VEGAS) to Assemble Pathways for Expression in S. Cerevisiae Nucleic Acids Research. May, 2015 | Pubmed ID: 25956652 Interplay Between Histone H3 Lysine 56 Deacetylation and Chromatin Modifiers in Response to DNA Damage Genetics. May, 2015 | Pubmed ID: 25786853 Yeast Golden Gate (yGG) for the Efficient Assembly of S. Cerevisiae Transcription Units ACS Synthetic Biology. Mar, 2015 | Pubmed ID: 25756291 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. Feb, 2015 | Pubmed ID: 25624482 RADOM, an Efficient in Vivo Method for Assembling Designed DNA Fragments Up to 10 Kb Long in Saccharomyces Cerevisiae ACS Synthetic Biology. Mar, 2015 | Pubmed ID: 24895839 Human Genomics. Sleeping Dogs of the Genome Science (New York, N.Y.). Dec, 2014 | Pubmed ID: 25477445 Circular Permutation of a Synthetic Eukaryotic Chromosome with the Telomerator Proceedings of the National Academy of Sciences of the United States of America. Dec, 2014 | Pubmed ID: 25378705 High-temporal-resolution View of Transcription and Chromatin States Across Distinct Metabolic States in Budding Yeast Nature Structural & Molecular Biology. Oct, 2014 | Pubmed ID: 25173176 Expression and Detection of LINE-1 ORF-encoded Proteins Mobile Genetic Elements. 2014 | Pubmed ID: 25054082 Characterisation of Cytoplasmic DNA Complementary to Non-retroviral RNA Viruses in Human Cells Scientific Reports. 2014 | Pubmed ID: 24875540 Total Synthesis of a Functional Designer Eukaryotic Chromosome Science (New York, N.Y.). Apr, 2014 | Pubmed ID: 24674868 Long Interspersed Element-1 Protein Expression is a Hallmark of Many Human Cancers The American Journal of Pathology. May, 2014 | Pubmed ID: 24607009 TRNA Genes Rapidly Change in Evolution to Meet Novel Translational Demands ELife. 2013 | Pubmed ID: 24363105 TE-array--a High Throughput Tool to Study Transposon Transcription BMC Genomics. 2013 | Pubmed ID: 24325565 Affinity Proteomics Reveals Human Host Factors Implicated in Discrete Stages of LINE-1 Retrotransposition Cell. Nov, 2013 | Pubmed ID: 24267889 Genome-wide Consequences of Deleting Any Single Gene Molecular Cell. Nov, 2013 | Pubmed ID: 24211263 Architectural Organization of the Metabolic Regulatory Enzyme Ghrelin O-acyltransferase The Journal of Biological Chemistry. Nov, 2013 | Pubmed ID: 24045953 Kinetochore Function and Chromosome Segregation Rely on Critical Residues in Histones H3 and H4 in Budding Yeast Genetics. Nov, 2013 | Pubmed ID: 24037263 Influence of RNA Structural Elements on Ty1 Retrotransposition Mobile Genetic Elements. Mar, 2013 | Pubmed ID: 23914314 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. Jul, 2013 | Pubmed ID: 23818630 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. May, 2013 | Pubmed ID: 23674285 Multichange Isothermal Mutagenesis: a New Strategy for Multiple Site-directed Mutations in Plasmid DNA ACS Synthetic Biology. Aug, 2013 | Pubmed ID: 23654272 Using Functional Proteome Microarrays to Study Protein Lysine Acetylation Methods in Molecular Biology (Clifton, N.J.). 2013 | Pubmed ID: 23381860 Conserved Structure and Inferred Evolutionary History of Long Terminal Repeats (LTRs) Mobile DNA. 2013 | Pubmed ID: 23369192 Retrotransposon Ty1 RNA Contains a 5'-terminal Long-range Pseudoknot Required for Efficient Reverse Transcription RNA (New York, N.Y.). Mar, 2013 | Pubmed ID: 23329695 Active Transposition in Genomes Annual Review of Genetics. 2012 | Pubmed ID: 23145912 Ghrelin O-acyltransferase Assays and Inhibition Methods in Enzymology. 2012 | Pubmed ID: 22975055 Live-cell Studies of P300/CBP Histone Acetyltransferase Activity and Inhibition Chembiochem : a European Journal of Chemical Biology. Sep, 2012 | Pubmed ID: 22961914 Poly(A) Binding Protein C1 is Essential for Efficient L1 Retrotransposition and Affects L1 RNP Formation Molecular and Cellular Biology. Nov, 2012 | Pubmed ID: 22907758 Human Transposon Tectonics Cell. May, 2012 | Pubmed ID: 22579280 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. May, 2012 | Pubmed ID: 22556267 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. Apr, 2012 | Pubmed ID: 22474337 The Saccharomyces Cerevisiae Nrd1-Nab3 Transcription Termination Pathway Acts in Opposition to Ras Signaling and Mediates Response to Nutrient Depletion Molecular and Cellular Biology. May, 2012 | Pubmed ID: 22431520 Lysine Succinylation and Lysine Malonylation in Histones Molecular & Cellular Proteomics : MCP. May, 2012 | Pubmed ID: 22389435 The Build-a-Genome Course Methods in Molecular Biology (Clifton, N.J.). 2012 | Pubmed ID: 22328440 Design-A-Gene with GeneDesign Methods in Molecular Biology (Clifton, N.J.). 2012 | Pubmed ID: 22328438 Assembling Large DNA Segments in Yeast Methods in Molecular Biology (Clifton, N.J.). 2012 | Pubmed ID: 22328431 Assembling DNA Fragments by USER Fusion Methods in Molecular Biology (Clifton, N.J.). 2012 | Pubmed ID: 22328427 Functional Dissection of Lysine Deacetylases Reveals That HDAC1 and P300 Regulate AMPK Nature. Feb, 2012 | Pubmed ID: 22318606 Rasche Ermittlung Monospezifischen Monoklonaler Antikörper Mit Einem Menschlichen Proteom-Microarray Molecular & Cellular Proteomics : MCP. Feb, 2012 | Pubmed ID: 22307071 Polyubiquitin-sensor Proteins Reveal Localization and Linkage-type Dependence of Cellular Ubiquitin Signaling Nature Methods. Mar, 2012 | Pubmed ID: 22306808 Retrotransposon Ty1 Integration Targets Specifically Positioned Asymmetric Nucleosomal DNA Segments in TRNA Hotspots Genome Research. Apr, 2012 | Pubmed ID: 22219510 Strain Construction and Screening Methods for a Yeast Histone H3/H4 Mutant Library Methods in Molecular Biology (Clifton, N.J.). 2012 | Pubmed ID: 22183584 Novel Transcript Truncating Function of Rap1p Revealed by Synthetic Codon-optimized Ty1 Retrotransposon Genetics. Feb, 2012 | Pubmed ID: 22135353 Protein Acetylation and Aging Aging. Oct, 2011 | Pubmed ID: 22067362 Synthetic Chromosome Arms Function in Yeast and Generate Phenotypic Diversity by Design Nature. Sep, 2011 | Pubmed ID: 21918511 Acetylation of Yeast AMPK Controls Intrinsic Aging Independently of Caloric Restriction Cell. Sep, 2011 | Pubmed ID: 21906795 Genome Remodeling Nature Biotechnology. Sep, 2011 | Pubmed ID: 21904325 An Evolutionarily 'young' Lysine Residue in Histone H3 Attenuates Transcriptional Output in Saccharomyces Cerevisiae Genes & Development. Jun, 2011 | Pubmed ID: 21685365 Effect of Reverse Transcriptase Inhibitors on LINE-1 and Ty1 Reverse Transcriptase Activities and on LINE-1 Retrotransposition BMC Biochemistry. 2011 | Pubmed ID: 21545744 Differential Contributions of Histone H3 and H4 Residues to Heterochromatin Structure Genetics. Jun, 2011 | Pubmed ID: 21441216 Characterization of a Synthetic Human LINE-1 Retrotransposon ORFeus-Hs Mobile DNA. 2011 | Pubmed ID: 21320307 Characterization of L1 Retrotransposition with High-throughput Dual-luciferase Assays Nucleic Acids Research. Feb, 2011 | Pubmed ID: 21071410 Glucose and Weight Control in Mice with a Designed Ghrelin O-acyltransferase Inhibitor Science (New York, N.Y.). Dec, 2010 | Pubmed ID: 21097901 Making Temperature-sensitive Mutants Methods in Enzymology. 2010 | Pubmed ID: 20946811 Yin and Yang of Histone H2B Roles in Silencing and Longevity: a Tale of Two Arginines Genetics. Nov, 2010 | Pubmed ID: 20713692 Trivalent Arsenic Inhibits the Functions of Chaperonin Complex Genetics. Oct, 2010 | Pubmed ID: 20660648 Mobile Interspersed Repeats Are Major Structural Variants in the Human Genome Cell. Jun, 2010 | Pubmed ID: 20602999 A Microarray-based Genetic Screen for Yeast Chronological Aging Factors PLoS Genetics. Apr, 2010 | Pubmed ID: 20421943 CLONEQC: Lightweight Sequence Verification for Synthetic Biology Nucleic Acids Research. May, 2010 | Pubmed ID: 20211841 GeneDesign 3.0 is an Updated Synthetic Biology Toolkit Nucleic Acids Research. May, 2010 | Pubmed ID: 20211837 Silent Information Regulator 3: the Goldilocks of the Silencing Complex Genes & Development. Jan, 2010 | Pubmed ID: 20080949 Specificity of the BRISC Deubiquitinating Enzyme is Not Due to Selective Binding to Lys63-linked Polyubiquitin The Journal of Biological Chemistry. Apr, 2010 | Pubmed ID: 20032457 Histone H3 Exerts a Key Function in Mitotic Checkpoint Control Molecular and Cellular Biology. Jan, 2010 | Pubmed ID: 19917722 Retrotransposon Overdose and Genome Integrity Proceedings of the National Academy of Sciences of the United States of America. Aug, 2009 | Pubmed ID: 19666515 Plug and Play Modular Strategies for Synthetic Retrotransposons Methods (San Diego, Calif.). Nov, 2009 | Pubmed ID: 19481606 Transposon-mediated Genome Manipulation in Vertebrates Nature Methods. Jun, 2009 | Pubmed ID: 19478801 Protein Acetylation Microarray Reveals That NuA4 Controls Key Metabolic Target Regulating Gluconeogenesis Cell. Mar, 2009 | Pubmed ID: 19303850 HistoneHits: a Database for Histone Mutations and Their Phenotypes Genome Research. Apr, 2009 | Pubmed ID: 19218532 Teaching Synthetic Biology, Bioinformatics and Engineering to Undergraduates: the Interdisciplinary Build-a-Genome Course Genetics. Jan, 2009 | Pubmed ID: 19015540 Compensatory Interactions Between Sir3p and the Nucleosomal LRS Surface Imply Their Direct Interaction PLoS Genetics. Dec, 2008 | Pubmed ID: 19079580 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. Dec, 2008 | Pubmed ID: 18832443 Probing Nucleosome Function: a Highly Versatile Library of Synthetic Histone H3 and H4 Mutants Cell. Sep, 2008 | Pubmed ID: 18805098 From the Shards of a Shattered Genome, Diversity Proceedings of the National Academy of Sciences of the United States of America. Aug, 2008 | Pubmed ID: 18701721 A Descent into the Nuage: the Maelstrom of Transposon Control Developmental Cell. Aug, 2008 | Pubmed ID: 18694557 Orientation-dependent Regulation of Integrated HIV-1 Expression by Host Gene Transcriptional Readthrough Cell Host & Microbe. Aug, 2008 | Pubmed ID: 18692773 A Comprehensive Synthetic Genetic Interaction Network Governing Yeast Histone Acetylation and Deacetylation Genes & Development. Aug, 2008 | Pubmed ID: 18676811 Conditional Activation of a Single-copy L1 Transgene in Mice by Cre Genesis (New York, N.Y. : 2000). Jul, 2008 | Pubmed ID: 18615728 Histone H3 K56 Hyperacetylation Perturbs Replisomes and Causes DNA Damage Genetics. Aug, 2008 | Pubmed ID: 18579506 The Incredible Shrinking World of DNA Microarrays Molecular BioSystems. Jul, 2008 | Pubmed ID: 18563246 Microarray-based Genetic Screen Defines SAW1, a Gene Required for Rad1/Rad10-dependent Processing of Recombination Intermediates Molecular Cell. May, 2008 | Pubmed ID: 18471978 Toward a Comprehensive Temperature-sensitive Mutant Repository of the Essential Genes of Saccharomyces Cerevisiae Molecular Cell. Apr, 2008 | Pubmed ID: 18439903 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.). 2008 | Pubmed ID: 18392971 Domesticated DNA Transposon Proteins Mediate Retrotransposon Control Cell Research. Mar, 2008 | Pubmed ID: 18311163 Great Exaptations Journal of Biology. 2008 | Pubmed ID: 18279541 Plasmid-chromosome Shuffling for Non-deletion Alleles in Yeast Nature Methods. Feb, 2008 | Pubmed ID: 18193055 Efficient Tor Signaling Requires a Functional Class C Vps Protein Complex in Saccharomyces Cerevisiae Genetics. Aug, 2007 | Pubmed ID: 17565946 Mn2+ Suppressor Mutations and Biochemical Communication Between Ty1 Reverse Transcriptase and RNase H Domains Journal of Virology. Sep, 2007 | Pubmed ID: 17537863 Mighty Piwis Defend the Germline Against Genome Intruders Cell. Apr, 2007 | Pubmed ID: 17418784 DSLAM Analysis of Genome-wide Genetic Interactions in Saccharomyces Cerevisiae Methods (San Diego, Calif.). Feb, 2007 | Pubmed ID: 17189863 Active Retrotransposition by a Synthetic L1 Element in Mice Proceedings of the National Academy of Sciences of the United States of America. Dec, 2006 | Pubmed ID: 17124176 Transposon Insertion Site Profiling Chip (TIP-chip) Proceedings of the National Academy of Sciences of the United States of America. Nov, 2006 | Pubmed ID: 17101968 Stacking the Deck: Double-tiled DNA Microarrays Nature Methods. Nov, 2006 | Pubmed ID: 17060914 The LRS and SIN Domains: Two Structurally Equivalent but Functionally Distinct Nucleosomal Surfaces Required for Transcriptional Silencing Molecular and Cellular Biology. Dec, 2006 | Pubmed ID: 17015465 Nucleocytosolic Acetyl-coenzyme a Synthetase is Required for Histone Acetylation and Global Transcription Molecular Cell. Jul, 2006 | Pubmed ID: 16857587 The Sirtuins Hst3 and Hst4p Preserve Genome Integrity by Controlling Histone H3 Lysine 56 Deacetylation Current Biology : CB. Jul, 2006 | Pubmed ID: 16815704 The Biochemistry of Sirtuins Annual Review of Biochemistry. 2006 | Pubmed ID: 16756498 Functional Genomics of Genes with Small Open Reading Frames (sORFs) in S. Cerevisiae Genome Research. Mar, 2006 | Pubmed ID: 16510898 Analysis of the Human Protein Interactome and Comparison with Yeast, Worm and Fly Interaction Datasets Nature Genetics. Mar, 2006 | Pubmed ID: 16501559 A DNA Integrity Network in the Yeast Saccharomyces Cerevisiae Cell. Mar, 2006 | Pubmed ID: 16487579 GeneDesign: Rapid, Automated Design of Multikilobase Synthetic Genes Genome Research. Apr, 2006 | Pubmed ID: 16481661 Global Synthetic-lethality Analysis and Yeast Functional Profiling Trends in Genetics : TIG. Jan, 2006 | Pubmed ID: 16309778 Gene Function Prediction from Congruent Synthetic Lethal Interactions in Yeast Molecular Systems Biology. 2005 | Pubmed ID: 16729061 Transposon Technology and Vertebrate Functional Genomics Genome Biology. 2005 | Pubmed ID: 16356279 Insights into the Role of Histone H3 and Histone H4 Core Modifiable Residues in Saccharomyces Cerevisiae Molecular and Cellular Biology. Nov, 2005 | Pubmed ID: 16260619 Improved Statistical Analysis of Budding Yeast TAG Microarrays Revealed by Defined Spike-in Pools Nucleic Acids Research. 2005 | Pubmed ID: 16166654 Gene-breaking: a New Paradigm for Human Retrotransposon-mediated Gene Evolution Genome Research. Aug, 2005 | Pubmed ID: 16024818 LINE-1 Retrotransposons: Modulators of Quantity and Quality of Mammalian Gene Expression? BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology. Aug, 2005 | Pubmed ID: 16015595 Improved Microarray Methods for Profiling the Yeast Knockout Strain Collection Nucleic Acids Research. 2005 | Pubmed ID: 15994458 TFIIIB Subunit Bdp1p is Required for Periodic Integration of the Ty1 Retrotransposon and Targeting of Isw2p to S. Cerevisiae TDNAs Genes & Development. Apr, 2005 | Pubmed ID: 15833918 Genome-wide Identification of Isw2 Chromatin-remodeling Targets by Localization of a Catalytically Inactive Mutant Genes & Development. Apr, 2005 | Pubmed ID: 15833917 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. Feb, 2005 | Pubmed ID: 15710895 Identification and Characterization of Critical Cis-acting Sequences Within the Yeast Ty1 Retrotransposon RNA (New York, N.Y.). Mar, 2005 | Pubmed ID: 15661848 An Evaluation of Detection Methods for Large Lariat RNAs RNA (New York, N.Y.). Mar, 2005 | Pubmed ID: 15661842 A Robust Toolkit for Functional Profiling of the Yeast Genome Molecular Cell. Nov, 2004 | Pubmed ID: 15525520 Regulated Nucleosome Mobility and the Histone Code Nature Structural & Molecular Biology. Nov, 2004 | Pubmed ID: 15523479 Ty1 Mobilizes Subtelomeric Y' Elements in Telomerase-negative Saccharomyces Cerevisiae Survivors Molecular and Cellular Biology. Nov, 2004 | Pubmed ID: 15509791 FKBP12 Controls Aspartate Pathway Flux in Saccharomyces Cerevisiae to Prevent Toxic Intermediate Accumulation Eukaryotic Cell. Oct, 2004 | Pubmed ID: 15470257 Evolution: A is for Adaptation Nature. Sep, 2004 | Pubmed ID: 15385995 Local Definition of Ty1 Target Preference by Long Terminal Repeats and Clustered TRNA Genes Genome Research. Jul, 2004 | Pubmed ID: 15197163 A Highly Active Synthetic Mammalian Retrotransposon Nature. May, 2004 | Pubmed ID: 15152256 Transcriptional Disruption by the L1 Retrotransposon and Implications for Mammalian Transcriptomes Nature. May, 2004 | Pubmed ID: 15152245 Structural Basis for the Mechanism and Regulation of Sir2 Enzymes Molecular Cell. Mar, 2004 | Pubmed ID: 15023335 Molecular Biology. Ring Around the Retroelement Science (New York, N.Y.). Jan, 2004 | Pubmed ID: 14716001 Use of Mixture Models in a Microarray-based Screening Procedure for Detecting Differentially Represented Yeast Mutants Statistical Applications in Genetics and Molecular Biology. 2003 | Pubmed ID: 16646779 DNA Helicase Gene Interaction Network Defined Using Synthetic Lethality Analyzed by Microarray Nature Genetics. Nov, 2003 | Pubmed ID: 14566339 The Unusual Phylogenetic Distribution of Retrotransposons: a Hypothesis Genome Research. Sep, 2003 | Pubmed ID: 12952870 Identifying Related L1 Retrotransposons by Analyzing 3' Transduced Sequences Genome Biology. 2003 | Pubmed ID: 12734010 Short-chain Fatty Acid Activation by Acyl-coenzyme A Synthetases Requires SIR2 Protein Function in Salmonella Enterica and Saccharomyces Cerevisiae Genetics. Feb, 2003 | Pubmed ID: 12618394 Transcriptional Interactions Between Yeast TRNA Genes, Flanking Genes and Ty Elements: a Genomic Point of View Genome Research. Feb, 2003 | Pubmed ID: 12566403 Human L1 Element Target-primed Reverse Transcription in Vitro The EMBO Journal. Nov, 2002 | Pubmed ID: 12411507 Structure of a Sir2 Enzyme Bound to an Acetylated P53 Peptide Molecular Cell. Sep, 2002 | Pubmed ID: 12408821 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. Oct, 2002 | Pubmed ID: 12374852 Molecular Archeology of L1 Insertions in the Human Genome Genome Biology. Sep, 2002 | Pubmed ID: 12372140 A Core Nucleosome Surface Crucial for Transcriptional Silencing Nature Genetics. Oct, 2002 | Pubmed ID: 12244315 Human L1 Retrotransposition is Associated with Genetic Instability in Vivo Cell. Aug, 2002 | Pubmed ID: 12176320 Funktionelle Profilierung Des Saccharomyces Cerevisiae Genom Nature. Jul, 2002 | Pubmed ID: 12140549 SIR2 Family of NAD(+)-dependent Protein Deacetylases Methods in Enzymology. 2002 | Pubmed ID: 12078503 Tn7-mediated Mutagenesis of Saccharomyces Cerevisiae Genomic DNA in Vitro Methods in Enzymology. 2002 | Pubmed ID: 12073315 Inhibition of Reverse Transcription in Vivo by Elevated Manganese Ion Concentration Molecular Cell. Apr, 2002 | Pubmed ID: 11983178 Ty1 Defect in Proteolysis at High Temperature Journal of Virology. May, 2002 | Pubmed ID: 11932388 Telomeric and RDNA Silencing in Saccharomyces Cerevisiae Are Dependent on a Nuclear NAD(+) Salvage Pathway Genetics. Mar, 2002 | Pubmed ID: 11901108 A Nucleocapsid Functionality Contained Within the Amino Terminus of the Ty1 Protease That is Distinct and Separable from Proteolytic Activity Journal of Virology. Jan, 2002 | Pubmed ID: 11739699 qPCRTag Analyse - ein hoher Durchsatz, Echtzeit-PCR-Assay für Sc2.0 Genotyping Leslie A. Mitchell1, Nick A. Phillips1, Andrea Lafont2, James A. Martin1, Rupal Cutting2, Jef D. Boeke1 1Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, 2Roche Life Science, USA Biology
qPCRTag Analyse - ein hoher Durchsatz, Echtzeit-PCR-Assay für Sc2.0 Genotyping Leslie A. Mitchell1, Nick A. Phillips1, Andrea Lafont2, James A. Martin1, Rupal Cutting2, Jef D. Boeke1 1Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, 2Roche Life Science, USA Biology