Publications by authors named "Jef D Boeke"

100Publications

Sc3.0: revamping and minimizing the yeast genome.

Genome Biol 2020 08 13;21(1):205. Epub 2020 Aug 13.

CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics. Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.

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http://dx.doi.org/10.1186/s13059-020-02130-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7425127PMC
August 2020

Synthetic Genomes.

Annu Rev Biochem 2020 06;89:77-101

Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY 10016, USA; email:

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http://dx.doi.org/10.1146/annurev-biochem-013118-110704DOI Listing
June 2020

CRISPR-Cas12a system in fission yeast for multiplex genomic editing and CRISPR interference.

Authors:
Yu Zhao Jef D Boeke

Nucleic Acids Res 2020 06;48(10):5788-5798

Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA.

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http://dx.doi.org/10.1093/nar/gkaa329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7261154PMC
June 2020

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

Philos Trans R Soc Lond B Biol Sci 2020 03 10;375(1795):20190335. Epub 2020 Feb 10.

Department of Pathology, Johns Hopkins University School of Medicine, 733N Broadway, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1098/rstb.2019.0335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7061987PMC
March 2020

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

Nat Struct Mol Biol 2020 02 10;27(2):179-191. Epub 2020 Feb 10.

Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.

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http://dx.doi.org/10.1038/s41594-020-0374-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7082080PMC
February 2020

Widespread Transcriptional Scanning in the Testis Modulates Gene Evolution Rates.

Cell 2020 01;180(2):248-262.e21

Institute for Computational Medicine, NYU Langone Health, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.12.015DOI Listing
January 2020

Phylogenetic debugging of a complete human biosynthetic pathway transplanted into yeast.

Nucleic Acids Res 2020 01;48(1):486-499

Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.

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http://dx.doi.org/10.1093/nar/gkz1098DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145547PMC
January 2020

Structure and function of the Orc1 BAH-nucleosome complex.

Nat Commun 2019 07 1;10(1):2894. Epub 2019 Jul 1.

Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA.

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http://dx.doi.org/10.1038/s41467-019-10609-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602975PMC
July 2019

Superloser: A Plasmid Shuffling Vector for with Exceedingly Low Background.

G3 (Bethesda) 2019 08 8;9(8):2699-2707. Epub 2019 Aug 8.

Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, 10016 and

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http://dx.doi.org/10.1534/g3.119.400325DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6686923PMC
August 2019

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

Nat Commun 2019 02 14;10(1):839. Epub 2019 Feb 14.

Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.

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http://www.nature.com/articles/s41467-019-08474-w
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http://dx.doi.org/10.1038/s41467-019-08474-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6376008PMC
February 2019

A scalable peptide-GPCR language for engineering multicellular communication.

Nat Commun 2018 11 29;9(1):5057. Epub 2018 Nov 29.

Department of Chemistry, Columbia University, New York, New York, 10027, USA.

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http://dx.doi.org/10.1038/s41467-018-07610-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6265332PMC
November 2018

Meeting report: mobile genetic elements and genome plasticity 2018.

Mob DNA 2018 22;9:21. Epub 2018 Jun 22.

9Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892 USA.

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http://dx.doi.org/10.1186/s13100-018-0126-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6015446PMC
June 2018

Karyotype engineering by chromosome fusion leads to reproductive isolation in yeast.

Nature 2018 08 1;560(7718):392-396. Epub 2018 Aug 1.

Institute for Systems Genetics, NYU Langone Health, New York, NY, USA.

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http://dx.doi.org/10.1038/s41586-018-0374-xDOI Listing
August 2018

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

PLoS Genet 2018 05 24;14(5):e1007418. Epub 2018 May 24.

Department of Biomolecular Chemistry, School of Medicine and Public Health, Madison, WI, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1007418DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5991416PMC
May 2018

In vitro DNA SCRaMbLE.

Nat Commun 2018 05 22;9(1):1935. Epub 2018 May 22.

Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, 10016, USA.

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http://dx.doi.org/10.1038/s41467-018-03743-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5964173PMC
May 2018

Heterozygous diploid and interspecies SCRaMbLEing.

Nat Commun 2018 05 22;9(1):1934. Epub 2018 May 22.

Department of Biochemistry Molecular Pharmacology and Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA.

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http://www.nature.com/articles/s41467-018-04157-0
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http://dx.doi.org/10.1038/s41467-018-04157-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5964232PMC
May 2018

Precise control of SCRaMbLE in synthetic haploid and diploid yeast.

Nat Commun 2018 05 22;9(1):1933. Epub 2018 May 22.

Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.

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http://www.nature.com/articles/s41467-018-03084-4
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http://dx.doi.org/10.1038/s41467-018-03084-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5964104PMC
May 2018

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

SLAS Discov 2018 Jul 3;23(6):491-494. Epub 2018 May 3.

1 Institute for Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.

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http://dx.doi.org/10.1177/2472555218767842DOI Listing
July 2018

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

Cell 2018 02;172(5):952-965.e18

St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris 75015, France; Paris Descartes University, Imagine Institute, Paris 75015, France; Howard Hughes Medical Institute, New York, NY 10065, USA; Pediatric Immunology-Hematology Unit, Necker Hospital for Sick Children, Paris 75015, France.

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http://dx.doi.org/10.1016/j.cell.2018.02.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5886375PMC
February 2018

Stress response factors drive regrowth of quiescent cells.

Curr Genet 2018 Aug 17;64(4):807-810. Epub 2018 Feb 17.

Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York City, NY, 10016, USA.

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http://dx.doi.org/10.1007/s00294-018-0813-0DOI Listing
August 2018

Gibson Deletion: a novel application of isothermal in vitro recombination.

Biol Proced Online 2018 19;20. Epub 2018 Jan 19.

Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, Institute of Systems Genetics (ISG), New York, NY 10016 USA.

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http://dx.doi.org/10.1186/s12575-018-0068-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5774033PMC
January 2018

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

Nucleic Acids Res 2018 01;46(1):e2

Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1093/nar/gkx905DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5758894PMC
January 2018

Construction of Designer Selectable Marker Deletions with a CRISPR-Cas9 Toolbox in and New Design of Common Entry Vectors.

Authors:
Yu Zhao Jef D Boeke

G3 (Bethesda) 2018 03 2;8(3):789-796. Epub 2018 Mar 2.

Institute for Systems Genetics, NYU Langone Health, New York 10016

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http://dx.doi.org/10.1534/g3.117.300363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5844300PMC
March 2018

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

Elife 2018 01 8;7. Epub 2018 Jan 8.

Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States.

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http://dx.doi.org/10.7554/eLife.30058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5821460PMC
January 2018

Resetting the Yeast Epigenome with Human Nucleosomes.

Cell 2017 Dec 30;171(7):1508-1519.e13. Epub 2017 Nov 30.

Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674173126
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http://dx.doi.org/10.1016/j.cell.2017.10.043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5732057PMC
December 2017

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

Methods Mol Biol 2018 ;1671:211-225

Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, 10016, USA.

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http://dx.doi.org/10.1007/978-1-4939-7295-1_14DOI Listing
July 2018

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

G3 (Bethesda) 2018 01 4;8(1):173-183. Epub 2018 Jan 4.

Department of Biochemistry and Molecular Pharmacology NYU Langone Health, New York 10016

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http://dx.doi.org/10.1534/g3.117.300347DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5765346PMC
January 2018

Construction of Comprehensive Dosage-Matching Core Histone Mutant Libraries for .

Genetics 2017 12 30;207(4):1263-1273. Epub 2017 Oct 30.

MOE Key laboratory of Bioinformatics and Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, PR China

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http://dx.doi.org/10.1534/genetics.117.300450DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5714446PMC
December 2017

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

G3 (Bethesda) 2017 12 4;7(12):3857-3866. Epub 2017 Dec 4.

Ministry of Education Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, PR China

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http://dx.doi.org/10.1534/g3.117.300252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5714483PMC
December 2017

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

Elife 2017 09 26;6. Epub 2017 Sep 26.

Institute for Systems Genetics, NYU Langone Medical Center, New York, United States.

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http://dx.doi.org/10.7554/eLife.29938DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5634782PMC
September 2017

Dynamic silencing of somatic L1 retrotransposon insertions reflects the developmental and cellular contexts of their genomic integration.

Mob DNA 2017 10;8. Epub 2017 May 10.

Laboratory of Immunobiology, Mouse Cancer Genetics Program and Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA.

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http://dx.doi.org/10.1186/s13100-017-0091-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5424313PMC
May 2017

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

Proc Natl Acad Sci U S A 2017 05 2;114(20):E3984-E3992. Epub 2017 May 2.

Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205;

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http://dx.doi.org/10.1073/pnas.1704117114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5441760PMC
May 2017

Design of a synthetic yeast genome.

Science 2017 03;355(6329):1040-1044

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1126/science.aaf4557DOI Listing
March 2017

A high throughput mutagenic analysis of yeast sumo structure and function.

PLoS Genet 2017 02 6;13(2):e1006612. Epub 2017 Feb 6.

Department of Biochemistry and Molecular Biology, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1006612DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5319795PMC
February 2017

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

ACS Synth Biol 2017 03 22;6(3):497-506. Epub 2016 Dec 22.

High Throughput Biology Center and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine , Baltimore, Maryland 21205, United States.

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http://dx.doi.org/10.1021/acssynbio.6b00205DOI Listing
March 2017

The dynamic landscape of fission yeast meiosis alternative-splice isoforms.

Genome Res 2017 01 17;27(1):145-156. Epub 2016 Nov 17.

Toyota Technological Institute at Chicago, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1101/gr.208041.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5204338PMC
January 2017

Somatic retrotransposition is infrequent in glioblastomas.

Mob DNA 2016 11;7:22. Epub 2016 Nov 11.

Department of Pathology, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA.

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http://dx.doi.org/10.1186/s13100-016-0077-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5105304PMC
November 2016

A map of mobile DNA insertions in the NCI-60 human cancer cell panel.

Mob DNA 2016 31;7:20. Epub 2016 Oct 31.

Department of Pathology, Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA ; McKusick-Nathans Institute of Genetic Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA ; High Throughput (HiT) Biology Center, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA ; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA.

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http://dx.doi.org/10.1186/s13100-016-0078-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5087121PMC
October 2016

Fluorescence ImmunoPrecipitation (FLIP): a Novel Assay for High-Throughput IP.

Biol Proced Online 2016 15;18:16. Epub 2016 Aug 15.

Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, ACLSW Room 560, 430 East 29th Street, New York, NY 10016 USA ; High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA.

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http://dx.doi.org/10.1186/s12575-016-0046-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4983793PMC
August 2016

Meeting Report: The Role of the Mobilome in Cancer.

Cancer Res 2016 08 18;76(15):4316-9. Epub 2016 Jul 18.

Division of Cancer Biology, NCI, NIH, Rockville, Maryland.

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http://dx.doi.org/10.1158/0008-5472.CAN-15-3421DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4991632PMC
August 2016

BioPartsDB: a synthetic biology workflow web-application for education and research.

Bioinformatics 2016 11 13;32(22):3519-3521. Epub 2016 Jul 13.

Department of Biomedical Engineering and High-Throughput Biology Center, Johns Hopkins University, Baltimore, MD 21218, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5181553PMC
November 2016

Characterization of L1-Ribonucleoprotein Particles.

Methods Mol Biol 2016 ;1400:311-38

Department of Biochemistry and Molecular Pharmacology and Institute for Systems Genetics, New York University Langone School of Medicine, 550 First Avenue, New York, NY, 10016, USA.

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http://dx.doi.org/10.1007/978-1-4939-3372-3_20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5084692PMC
December 2016

How retrotransposons shape genome regulation.

Curr Opin Genet Dev 2016 04 6;37:90-100. Epub 2016 Feb 6.

Institute for Systems Genetics, Department of Biochemistry & Molecular Pharmacology, NYU Langone Medical Center, 430 East 29 Street, NY, NY 10016, USA.

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http://dx.doi.org/10.1016/j.gde.2016.01.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4914423PMC
April 2016

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

G3 (Bethesda) 2016 04 7;6(4):881-92. Epub 2016 Apr 7.

Institute for Systems Genetics, New York University Langone School of Medicine, New York 10016

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http://dx.doi.org/10.1534/g3.115.026757DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4825658PMC
April 2016

BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts.

Bioinformatics 2016 03 14;32(6):937-9. Epub 2015 Nov 14.

Department of Biomedical Engineering, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA and.

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http://dx.doi.org/10.1093/bioinformatics/btv664DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4803390PMC
March 2016

SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes.

Genome Res 2016 Jan 13;26(1):36-49. Epub 2015 Nov 13.

High-Throughput Biology Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA; Department of Biomedical Engineering, School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA;

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http://dx.doi.org/10.1101/gr.193433.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691749PMC
January 2016

Much ado about zero.

Cell 2015 Oct 22;163(3):534-5. Epub 2015 Oct 22.

Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA.

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http://dx.doi.org/10.1016/j.cell.2015.10.033DOI Listing
October 2015

Freedom and Responsibility in Synthetic Genomics: The Synthetic Yeast Project.

Genetics 2015 Aug;200(4):1021-8

Berman Institute of Bioethics, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205

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http://dx.doi.org/10.1534/genetics.115.176370DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4574254PMC
August 2015

Mechanistic analysis of ghrelin-O-acyltransferase using substrate analogs.

Bioorg Chem 2015 Oct 13;62:64-73. Epub 2015 Jul 13.

Department of Pharmacology & Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, USA. Electronic address:

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http://dx.doi.org/10.1016/j.bioorg.2015.07.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4567917PMC
October 2015

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

G3 (Bethesda) 2015 Jul 22;5(10):1983-90. Epub 2015 Jul 22.

High Throughput Biology Center and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, New York, New York 10011

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http://dx.doi.org/10.1534/g3.114.012765DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4592980PMC
July 2015

qPCRTag Analysis--A High Throughput, Real Time PCR Assay for Sc2.0 Genotyping.

J Vis Exp 2015 May 25(99):e52941. Epub 2015 May 25.

Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics;

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http://www.jove.com/video/52941/qpcrtag-analysis-high-throug
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http://dx.doi.org/10.3791/52941DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542976PMC
May 2015

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

Nucleic Acids Res 2015 Jul 8;43(13):6620-30. Epub 2015 May 8.

Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York City, NY 10016, USA Institute for Systems Genetics, New York University Langone School of Medicine, New York City, NY 10016, USA High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA

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http://dx.doi.org/10.1093/nar/gkv466DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4513848PMC
July 2015

Interplay between histone H3 lysine 56 deacetylation and chromatin modifiers in response to DNA damage.

Genetics 2015 May 18;200(1):185-205. Epub 2015 Mar 18.

Centre de recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, QC, Canada H1T 2M4 Département de Médecine, Université de Montréal, Succursale Centre-Ville, Montreal, QC, Canada H3C 3J7

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http://www.genetics.org/content/genetics/200/1/185.full.pdf
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http://www.genetics.org/cgi/doi/10.1534/genetics.115.175919
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http://dx.doi.org/10.1534/genetics.115.175919DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4423362PMC
May 2015

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

ACS Synth Biol 2015 Jul 23;4(7):853-9. Epub 2015 Mar 23.

†Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, New York 10016, United States.

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http://dx.doi.org/10.1021/sb500372zDOI Listing
July 2015

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

Proc Natl Acad Sci U S A 2015 Feb 26;112(6):1803-8. Epub 2015 Jan 26.

School of Medicine, The Johns Hopkins University, Baltimore, MD 21205; Institute for Systems Genetics, NYU Langone Medical Center, New York, NY 10016; and

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http://dx.doi.org/10.1073/pnas.1424704112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330768PMC
February 2015

Human Genomics. Sleeping dogs of the genome.

Science 2014 Dec;346(6214):1187-8

Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.

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http://dx.doi.org/10.1126/science.aaa3177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4312280PMC
December 2014

Circular permutation of a synthetic eukaryotic chromosome with the telomerator.

Proc Natl Acad Sci U S A 2014 Dec 5;111(48):17003-10. Epub 2014 Nov 5.

Department of Biochemistry and Molecular Pharmacology and Institute for Systems Genetics, New York University Langone School of Medicine, New York, NY 10016

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http://dx.doi.org/10.1073/pnas.1414399111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4260612PMC
December 2014

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

Nat Struct Mol Biol 2014 Oct 31;21(10):854-63. Epub 2014 Aug 31.

1] High Throughput Biology Center, Johns Hopkins University, Baltimore, Maryland, USA. [2] Department of Molecular Biology &Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. [3] Institute for Systems Genetics, NYU Langone Medical Center, New York, New York, USA. [4] Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, New York, USA.

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http://dx.doi.org/10.1038/nsmb.2881DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4190017PMC
October 2014

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

Mob Genet Elements 2014 22;4:e29319. Epub 2014 May 22.

Institute for Systems Genetics; New York University School of Medicine; New York, NY USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4091050PMC
May 2014

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

ACS Synth Biol 2015 Mar 4;4(3):213-20. Epub 2014 Jun 4.

†Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, PR China.

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http://dx.doi.org/10.1021/sb500241eDOI Listing
March 2015

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

Sci Rep 2014 May 30;4:5074. Epub 2014 May 30.

Department of Virology and Preventive Medicine, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, JAPAN.

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http://dx.doi.org/10.1038/srep05074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4038843PMC
May 2014

Total synthesis of a functional designer eukaryotic chromosome.

Science 2014 04 27;344(6179):55-8. Epub 2014 Mar 27.

Department of Environmental Health Sciences, Johns Hopkins University (JHU) School of Public Health, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1126/science.1249252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4033833PMC
April 2014

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

Am J Pathol 2014 May 6;184(5):1280-6. Epub 2014 Mar 6.

Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland. Electronic address:

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http://dx.doi.org/10.1016/j.ajpath.2014.01.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4005969PMC
May 2014

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

Elife 2013 Dec 20;2:e01339. Epub 2013 Dec 20.

Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3868979PMC
December 2013

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

BMC Genomics 2013 Dec 10;14:869. Epub 2013 Dec 10.

The Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building (MRB) Room 469, Baltimore, MD 21205, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3878892PMC
December 2013

Genome-wide consequences of deleting any single gene.

Mol Cell 2013 Nov 7;52(4):485-94. Epub 2013 Nov 7.

Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1016/j.molcel.2013.09.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3975072PMC
November 2013

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

Genetics 2013 Nov 13;195(3):795-807. Epub 2013 Sep 13.

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109.

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http://dx.doi.org/10.1534/genetics.113.152082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813865PMC
November 2013

Influence of RNA structural elements on Ty1 retrotransposition.

Mob Genet Elements 2013 Mar;3(2):e25060

RNA Structure and Function Laboratory; Institute of Bioorganic Chemistry; Polish Academy of Sciences; Poznań, Poland ; HIV Drug Resistance Program; National Cancer Institute; Frederick, MD USA.

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http://dx.doi.org/10.4161/mge.25060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3681743PMC
March 2013

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

Proc Natl Acad Sci U S A 2013 Jul 1;110(29):E2706-13. Epub 2013 Jul 1.

Department of Molecular Biology and Genetics, and High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1073/pnas.1302504110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3718180PMC
July 2013

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

J Mass Spectrom 2013 May;48(5):608-15

Middle Atlantic Mass Spectrometry Laboratory, Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1002/jms.3198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784001PMC
May 2013

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

ACS Synth Biol 2013 Aug 11;2(8):473-7. Epub 2013 Mar 11.

Department of Molecular Biology and Genetics and High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

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http://dx.doi.org/10.1021/sb300131wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4040258PMC
August 2013

Using functional proteome microarrays to study protein lysine acetylation.

Methods Mol Biol 2013 ;981:151-65

Department of Laboratory Medicine, National Taiwan University Hospital, Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.

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http://dx.doi.org/10.1007/978-1-62703-305-3_12DOI Listing
July 2013

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

Mob DNA 2013 Feb 1;4(1). Epub 2013 Feb 1.

Section of Virology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3601003PMC
February 2013