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List of works by Jef D Boeke

"Perfect" designer chromosome V and behavior of a ring derivative

scientific article

3D organization of synthetic and scrambled chromosomes.

scientific article published in March 2017

A DNA integrity network in the yeast Saccharomyces cerevisiae

scientific article (publication date: 10 March 2006)

A DNA microarray-based genetic screen for nonhomologous end-joining mutants in Saccharomyces cerevisiae

scientific article

A Robust Toolkit for Functional Profiling of the Yeast Genome

scientific article published on 01 November 2004

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

scientific article

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

scientific article

A core nucleosome surface crucial for transcriptional silencing

scientific article published on 16 September 2002

A critical role for the C-terminus of Nej1 protein in Lif1p association, DNA binding and non-homologous end-joining

scientific article published on 31 August 2007

A highly active synthetic mammalian retrotransposon

scientific article published on May 2004

A human nuclear shuttling protein that interacts with human immunodeficiency virus type 1 matrix is packaged into virions.

scientific article

A microarray-based genetic screen for yeast chronological aging factors

scientific article

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

scientific article published on January 2002

A scalable peptide-GPCR language for engineering multicellular communication

scientific article published in Nature Communications

A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors

scientific article published on 19 March 2018

Acetylation of yeast AMPK controls intrinsic aging independently of caloric restriction

scientific article

Active Transposition in Genomes ⬇️

scientific article published on January 1, 2012

Active retrotransposition by a synthetic L1 element in mice

scholarly article

An evaluation of detection methods for large lariat RNAs

scientific article published on 20 January 2005

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 17 September 2013

Assembling DNA fragments by USER fusion

scientific article

Assembling large DNA segments in yeast

scientific article published in January 2012

Author Correction: A scalable peptide-GPCR language for engineering multicellular communication

scientific article published in Nature Communications

Author Correction: L1 drives IFN in senescent cells and promotes age-associated inflammation

scientific article published on 01 August 2019

Author Correction: Precise control of SCRaMbLE in synthetic haploid and diploid yeast

scientific article published in Nature Communications

BRCA1 and S phase DNA repair pathways restrict LINE-1 retrotransposition in human cells

scientific article published on 10 February 2020

Barcode Sequencing Screen Identifies SUB1 as a Regulator of Yeast Pheromone Inducible Genes

scientific article

Big DNA as a tool to dissect an age-related macular degeneration haplotype

article

Big DNA as a tool to dissect an age-related macular degeneration-associated haplotype

article

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

scientific article

Bug mapping and fitness testing of chemically synthesized chromosome X.

scientific article

CLONEQC: lightweight sequence verification for synthetic biology

scientific article

Cell fitness screens reveal a conflict between LINE-1 retrotransposition and DNA replication

scientific article published on 10 February 2020

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

scientific article (publication date: 14 February 2011)

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

scientific article (publication date: December 2008)

Comprehensive Scanning Mutagenesis of Human Retrotransposon LINE-1 Identifies Motifs Essential for Function

scientific article published on 30 October 2019

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

scientific article published on July 2008

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

scientific article published on February 2013

Construction of Comprehensive Dosage-Matching Core Histone Mutant Libraries for Saccharomyces cerevisiae

scientific article published on 30 October 2017

Construction of Designer Selectable Marker Deletions with CRISPR-Cas9 Toolbox in Schizosaccharomyces pombe and Optimized Design of Common Entry Vectors

scientific article published on 10 January 2018

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

scientific article published on July 2013

Coupling Yeast Golden Gate and VEGAS for Efficient Assembly of the Violacein Pathway in Saccharomyces cerevisiae

scientific article published in January 2018

Cycling to Maintain and Improve Fitness: Line-1 Modes of Nuclear Entrance and Retrotransposition

scientific article published on 03 May 2018

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

scientific article published on 19 October 2003

DNA repair. A little help for my ends

scientific article published in October 1996

Design of a synthetic yeast genome.

scientific article

Design-A-Gene with GeneDesign

article

Development of a Tightly Controlled Off Switch for Saccharomyces cerevisiae Regulated by Camphor, a Low-Cost Natural Product

scientific article

Differential Contributions of Histone H3 and H4 Residues to Heterochromatin Structure ⬇️

scientific article published on March 24, 2011

Dissecting Nucleosome Function with a Comprehensive Histone H2A and H2B Mutant Library.

scientific article published on 16 October 2017

Dissection of affinity captured LINE-1 macromolecular complexes.

scientific article published on 8 January 2018

Dynamic motif occupancy (DynaMO) analysis identifies transcription factors and their binding sites driving dynamic biological processes

scientific article published in January 2018

EUAdb: a resource for COVID-19 test development

scientific article published on 30 July 2020

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

scientific article

Engineered dual selection for directed evolution of SpCas9 PAM specificity

scientific article published on 13 January 2021

Engineering the ribosomal DNA in a megabase synthetic chromosome

scientific article published in March 2017

Evolution: A is for adaptation

scientific article published in Nature

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

scientific article published on 2 October 2008

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

retracted paper

Functional profiling of the Saccharomyces cerevisiae genome

scientific article (publication date: 25 July 2002)

Gene function prediction from congruent synthetic lethal interactions in yeast

scientific article published on 22 November 2005

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

scientific article published on 15 July 2005

GeneDesign 3.0 is an updated synthetic biology toolkit

scientific article

GeneDesign: rapid, automated design of multikilobase synthetic genes

scientific article

Genetic interaction mapping informs integrative structure determination of protein complexes

scientific article published on 01 December 2020

Genome remodeling ⬇️

scientific article published on September 8, 2011

Genome-wide consequences of deleting any single gene

scientific article

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

scientific article published on April 2005

Ghrelin O-acyltransferase assays and inhibition

scientific article published on January 2012

Gibson Deletion: a novel application of isothermal in vitro recombination

scientific article

Global synthetic-lethality analysis and yeast functional profiling

scientific article

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

scientific article

Great exaptations.

scientific article published on January 2008

Heterozygous diploid and interspecies SCRaMbLEing.

scientific article

Histone h3 exerts a key function in mitotic checkpoint control

scientific article

HistoneHits: a database for histone mutations and their phenotypes

scientific article published on 13 February 2009

Human RNA lariat debranching enzyme cDNA complements the phenotypes of Saccharomyces cerevisiae dbr1 and Schizosaccharomyces pombe dbr1 mutants

scientific article

Human l1 retrotransposition is associated with genetic instability in vivo

scientific article published on 01 August 2002

Human transposon insertion profiling by sequencing (TIPseq) to map LINE-1 insertions in single cells

scientific article published on 10 February 2020

Human transposon insertion profiling: Analysis, visualization and identification of somatic LINE-1 insertions in ovarian cancer

scientific article published on 17 January 2017

Human transposon tectonics

scientific article

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

scientific article published on 20 January 2005

Identifying related L1 retrotransposons by analyzing 3' transduced sequences

scientific article

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

scientific article

In vitro DNA SCRaMbLE.

scientific article

Inborn Errors of RNA Lariat Metabolism in Humans with Brainstem Viral Infection

scientific article published in February 2018

Inhibition of Ty1 transposition by mating pheromones in Saccharomyces cerevisiae

scientific article published on May 1991

Inhibition of reverse transcription in vivo by elevated manganese ion concentration

scientific article

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

scientific article published in November 2005

Intact piRNA pathway prevents L1 mobilization in male meiosis

scientific article

Intronic snoRNA biosynthesis in Saccharomyces cerevisiae depends on the lariat-debranching enzyme: intron length effects and activity of a precursor snoRNA

scientific article

Karyotype engineering by chromosome fusion leads to reproductive isolation in yeast

scientific article published in Nature

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

scientific article

L1 drives IFN in senescent cells and promotes age-associated inflammation

scientific article published on 06 February 2019

LINE-1 protein localization and functional dynamics during the cell cycle.

scientific article published on 8 January 2018

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

scientific article

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

scientific article

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

scientific article published on 14 June 2004

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

scientific article published on 06 March 2014

Low escape-rate genome safeguards with minimal molecular perturbation of Saccharomyces cerevisiae

scientific article

Lysine succinylation and lysine malonylation in histones.

scientific article

Making temperature-sensitive mutants

scientific article published on March 2010

Mapping of DBR1 and YPK1 suggests a major revision of the genetic map of the left arm of Saccharomyces cerevisiae Chromosome XI

scientific article

Meeting report: mobile genetic elements and genome plasticity 2018.

scientific article

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

scientific article

Mighty Piwis defend the germline against genome intruders

scientific article

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

scientific article (publication date: September 2007)

Mobile interspersed repeats are major structural variants in the human genome

scientific article published on June 2010

Molecular archeology of L1 insertions in the human genome.

scientific article

Molecular biology. Ring around the retroelement

scientific article

Msn2/4 regulate expression of glycolytic enzymes and control transition from quiescence to growth

scientific article published on 26 September 2017

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

scientific article

New Orthogonal Transcriptional Switches Derived from Tet Repressor Homologues for Saccharomyces cerevisiae Regulated by 2,4-Diacetylphloroglucinol and Other Ligands

scientific article published on 22 December 2016

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

scientific article published on 30 November 2011

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

scientific article published in August 2008

Pathway engineering in yeast for synthesizing the complex polyketide bikaverin

scientific article published on 03 December 2020

Phylogenetic debugging of a complete human biosynthetic pathway transplanted into yeast

scientific article published on 01 January 2020

Plug and play modular strategies for synthetic retrotransposons.

scientific article published on 28 May 2009

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

scientific article

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

scientific article published on February 5, 2012

Precise control of SCRaMbLE in synthetic haploid and diploid yeast.

scientific article published on 22 May 2018

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

scientific article

Protein acetylation and aging

scientific article published on October 2011

RNA lariat debranching enzyme

scientific article published on 01 January 2001

Rapid Identification of Monospecific Monoclonal Antibodies Using a Human Proteome Microarray ⬇️

scientific article published on February 3, 2012

Rapid and Efficient CRISPR/Cas9-Based Mating-Type Switching of Saccharomyces cerevisiae

scientific article published on 17 November 2017

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

scientific article

Regulated nucleosome mobility and the histone code.

scientific article

Resetting the Yeast Epigenome with Human Nucleosomes

scientific article

Retrotransposon R1Bm endonuclease cleaves the target sequence.

scientific article published in March 1998

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

scientific article published on 4 January 2012

Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma

scientific article published on 10 August 2015

Retrotransposon overdose and genome integrity.

scientific article published on 04 August 2009

Reverse Transcriptase Encoded by a Human Transposable Element ⬇️

scientific article (publication date: 20 December 1991)

Reverse transcriptase encoded by a retrotransposon from the trypanosomatid Crithidia fasciculata

scientific article

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

scientific article

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

scientific article

Silent information regulator 3: the Goldilocks of the silencing complex

scientific article published on January 2010

Stacking the deck: double-tiled DNA microarrays

scientific article published on 01 November 2006

Staphylococcal plasmids that replicate and express erythromycin resistance in both Streptococcus pneumoniae and Escherichia coli.

scientific article

Strain Construction and Screening Methods for a Yeast Histone H3/H4 Mutant Library ⬇️

scientific article published on January 1, 2012

Stress response factors drive regrowth of quiescent cells

scientific article published on 17 February 2018

Structural basis for the mechanism and regulation of Sir2 enzymes.

scientific article published in March 2004

Structural variants caused by Alu insertions are associated with risks for many human diseases

scientific article published on 2 May 2017

Structure and function of the Orc1 BAH-nucleosome complex

scientific article published on 01 July 2019

Structure of a Sir2 enzyme bound to an acetylated p53 peptide

scientific article

Superloser: A Plasmid Shuffling Vector for Saccharomyces cerevisiae with Exceedingly Low Background

scientific article published on 08 August 2019

Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond.

scientific article

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

scientific article published on 14 September 2011

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

scientific article published on April 2005

Targeting of a nuclease to murine leukemia virus capsids inhibits viral multiplication

scientific article

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

scientific article

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

scientific article

The Build-a-Genome course

scientific article published in January 2012

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

scientific article published on 2 October 2006

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

scientific article

The Saccharomyces cerevisiae SCRaMbLE system and genome minimization

scientific article

The biochemistry of sirtuins.

scientific article

The filamentous phage (Ff) as vectors for recombinant DNA--a review

scientific article published on July 1982

The incredible shrinking world of DNA microarrays

scientific article

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

scientific article

The unusual phylogenetic distribution of retrotransposons: a hypothesis

scientific article

Tn7-mediated mutagenesis of Saccharomyces cerevisiae genomic DNA in vitro

scientific article published on 01 January 2002

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

scientific article

Trans-kingdom promiscuity

scientific article published in Nature

Transcription factor profiling reveals molecular choreography and key regulators of human retrotransposon expression.

scientific article

Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes

scientific article published on May 2004

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

scientific article

Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome

scientific article published on 08 March 2019

Transposon insertion site profiling chip (TIP-chip).

scholarly article

Transposon technology and vertebrate functional genomics.

scientific article published on 2 December 2005

Transposon-mediated genome manipulation in vertebrates

scientific article

Ty1 defect in proteolysis at high temperature

scientific article

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

scientific article

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

scientific article published on 18 March 2003

Using functional proteome microarrays to study protein lysine acetylation.

scientific article published in January 2013

Widespread Transcriptional Scanning in the Testis Modulates Gene Evolution Rates

scientific article published on 01 January 2020

Yeast 2.0-connecting the dots in the construction of the world's first functional synthetic eukaryotic genome.

scientific article published in June 2018

Yeast heterochromatin regulators Sir2 and Sir3 act directly at euchromatic DNA replication origins.

scientific article

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

scientific article published on 16 August 2010

dSLAM analysis of genome-wide genetic interactions in Saccharomyces cerevisiae

scientific article published on February 2007

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