Jef D. Boeke - Publications

Affiliations: 
Johns Hopkins University, Baltimore, MD 
Area:
Molecular Biology, Genetics, Microbiology Biology

317 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Steranka JP, Tang Z, Grivainis M, Huang CRL, Payer LM, Rego FOR, Miller TLA, Galante PAF, Ramaswami S, Heguy A, Fenyö D, Boeke JD, Burns KH. Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome. Mobile Dna. 10: 8. PMID 30899333 DOI: 10.1186/s13100-019-0148-5  0.44
2019 Jia B, Wu Y, Li BZ, Mitchell LA, Liu H, Pan S, Wang J, Zhang HR, Jia N, Li B, Shen M, Xie ZX, Liu D, Cao YX, Li X, ... ... Boeke JD, et al. Author Correction: Precise control of SCRaMbLE in synthetic haploid and diploid yeast. Nature Communications. 10: 839. PMID 30765692 DOI: 10.1038/s41467-019-08474-w  0.36
2019 Billerbeck S, Brisbois J, Agmon N, Jimenez M, Temple J, Shen M, Boeke JD, Cornish VW. Author Correction: A scalable peptide-GPCR language for engineering multicellular communication. Nature Communications. 10: 554. PMID 30696846 DOI: 10.1038/s41467-019-08545-y  0.4
2018 Billerbeck S, Brisbois J, Agmon N, Jimenez M, Temple J, Shen M, Boeke JD, Cornish VW. A scalable peptide-GPCR language for engineering multicellular communication. Nature Communications. 9: 5057. PMID 30498215 DOI: 10.1038/s41467-018-07610-2  0.4
2018 Luo J, Sun X, Cormack BP, Boeke JD. Karyotype engineering by chromosome fusion leads to reproductive isolation in yeast. Nature. PMID 30069047 DOI: 10.1038/s41586-018-0374-x  0.36
2018 Sun X, Wang X, Tang Z, Grivainis M, Kahler D, Yun C, Mita P, Fenyö D, Boeke JD. Transcription factor profiling reveals molecular choreography and key regulators of human retrotransposon expression. Proceedings of the National Academy of Sciences of the United States of America. PMID 29802231 DOI: 10.1073/pnas.1722565115  1
2018 Hoggard TA, Chang F, Perry KR, Subramanian S, Kenworthy J, Chueng J, Shor E, Hyland EM, Boeke JD, Weinreich M, Fox CA. Yeast heterochromatin regulators Sir2 and Sir3 act directly at euchromatic DNA replication origins. Plos Genetics. 14: e1007418. PMID 29795547 DOI: 10.1371/journal.pgen.1007418  0.6
2018 Wu Y, Zhu RY, Mitchell LA, Ma L, Liu R, Zhao M, Jia B, Xu H, Li YX, Yang ZM, Ma Y, Li X, Liu H, Liu D, Xiao WH, ... ... Boeke JD, et al. In vitro DNA SCRaMbLE. Nature Communications. 9: 1935. PMID 29789594 DOI: 10.1038/s41467-018-03743-6  0.52
2018 Shen MJ, Wu Y, Yang K, Li Y, Xu H, Zhang H, Li BZ, Li X, Xiao WH, Zhou X, Mitchell LA, Bader JS, Yuan Y, Boeke JD. Heterozygous diploid and interspecies SCRaMbLEing. Nature Communications. 9: 1934. PMID 29789590 DOI: 10.1038/s41467-018-04157-0  0.76
2018 Jia B, Wu Y, Li BZ, Mitchell LA, Liu H, Pan S, Wang J, Zhang HR, Jia N, Li B, Shen M, Xie ZX, Liu D, Cao YX, Li X, ... ... Boeke JD, et al. Precise control of SCRaMbLE in synthetic haploid and diploid yeast. Nature Communications. 9: 1933. PMID 29789567 DOI: 10.1038/s41467-018-03084-4  0.36
2018 Mita P, Boeke JD. Cycling to Maintain and Improve Fitness: Line-1 Modes of Nuclear Entrance and Retrotransposition. Slas Discovery : Advancing Life Sciences R & D. 2472555218767842. PMID 29724131 DOI: 10.1177/2472555218767842  1
2018 Venkataraman A, Yang K, Irizarry J, Mackiewicz M, Mita P, Kuang Z, Xue L, Ghosh D, Liu S, Ramos P, Hu S, Bayron Kain D, Keegan S, Saul R, Colantonio S, ... ... Boeke JD, et al. A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors. Nature Methods. PMID 29638227 DOI: 10.1038/nmeth.4632  1
2018 Zhang SY, Clark NE, Freije CA, Pauwels E, Taggart AJ, Okada S, Mandel H, Garcia P, Ciancanelli MJ, Biran A, Lafaille FG, Tsumura M, Cobat A, Luo J, Volpi S, ... ... Boeke JD, et al. Inborn Errors of RNA Lariat Metabolism in Humans with Brainstem Viral Infection. Cell. 172: 952-965.e18. PMID 29474921 DOI: 10.1016/j.cell.2018.02.019  0.36
2018 Kalva S, Boeke JD, Mita P. Gibson Deletion: a novel application of isothermal in vitro recombination. Biological Procedures Online. 20: 2. PMID 29375275 DOI: 10.1186/s12575-018-0068-7  1
2018 Mita P, Wudzinska A, Sun X, Andrade J, Nayak S, Kahler DJ, Badri S, LaCava J, Ueberheide B, Yun CY, Fenyö D, Boeke JD. LINE-1 protein localization and functional dynamics during the cell cycle. Elife. 7. PMID 29309036 DOI: 10.7554/eLife.30058  1
2018 Taylor MS, Altukhov I, Molloy KR, Mita P, Jiang H, Adney EM, Wudzinska A, Badri S, Ischenko D, Eng G, Burns KH, Fenyö D, Chait BT, Alexeev D, Rout MP, ... Boeke JD, et al. Dissection of affinity captured LINE-1 macromolecular complexes. Elife. 7. PMID 29309035 DOI: 10.7554/eLife.30094  1
2018 Chuang J, Boeke JD, Mitchell LA. Coupling Yeast Golden Gate and VEGAS for Efficient Assembly of the Violacein Pathway in Saccharomyces cerevisiae. Methods in Molecular Biology (Clifton, N.J.). 1671: 211-225. PMID 29170962 DOI: 10.1007/978-1-4939-7295-1_14  0.32
2017 Xie ZX, Mitchell LA, Liu HM, Li BZ, Liu D, Agmon N, Wu Y, Li X, Zhou X, Li B, Xiao WH, Ding MZ, Wang Y, Yuan YJ, Boeke JD. Rapid and Efficient CRISPR/Cas9-Based Mating-Type Switching of Saccharomyces cerevisiae. G3 (Bethesda, Md.). PMID 29150593 DOI: 10.1534/g3.117.300347  0.64
2017 Jiang S, Liu Y, Wang A, Qin Y, Luo M, Wu Q, Boeke JD, Dai J. Construction of Comprehensive Dosage-Matching Core Histone Mutant Libraries for Saccharomyces cerevisiae. Genetics. PMID 29084817 DOI: 10.1534/genetics.117.300450  0.64
2017 Jiang S, Liu Y, Xu C, Wang Y, Gong J, Shen Y, Wu Q, Boeke JD, Dai J. Dissecting Nucleosome Function with a Comprehensive Histone H2A and H2B Mutant Library. G3 (Bethesda, Md.). PMID 29038170 DOI: 10.1534/g3.117.300252  0.64
2017 Newkirk SJ, Lee S, Grandi FC, Gaysinskaya V, Rosser JM, Vanden Berg N, Hogarth CA, Marchetto MCN, Muotri AR, Griswold MD, Ye P, Bortvin A, Gage FH, Boeke JD, An W. Intact piRNA pathway prevents L1 mobilization in male meiosis. Proceedings of the National Academy of Sciences of the United States of America. PMID 28630288 DOI: 10.1073/pnas.1701069114  0.52
2017 Kannan M, Li J, Fritz SE, Husarek KE, Sanford JC, Sullivan TL, Tiwary PK, An W, Boeke JD, Symer DE. Dynamic silencing of somatic L1 retrotransposon insertions reflects the developmental and cellular contexts of their genomic integration. Mobile Dna. 8: 8. PMID 28491150 DOI: 10.1186/s13100-017-0091-2  0.48
2017 Payer LM, Steranka JP, Yang WR, Kryatova M, Medabalimi S, Ardeljan D, Liu C, Boeke JD, Avramopoulos D, Burns KH. Structural variants caused by Alu insertions are associated with risks for many human diseases. Proceedings of the National Academy of Sciences of the United States of America. PMID 28465436 DOI: 10.1073/pnas.1704117114  0.44
2017 Richardson SM, Mitchell LA, Stracquadanio G, Yang K, Dymond JS, DiCarlo JE, Lee D, Huang CL, Chandrasegaran S, Cai Y, Boeke JD, Bader JS. Design of a synthetic yeast genome. Science (New York, N.Y.). 355: 1040-1044. PMID 28280199 DOI: 10.1126/science.aaf4557  0.76
2017 Mitchell LA, Wang A, Stracquadanio G, Kuang Z, Wang X, Yang K, Richardson S, Martin JA, Zhao Y, Walker R, Luo Y, Dai H, Dong K, Tang Z, Yang Y, ... ... Boeke JD, et al. Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond. Science (New York, N.Y.). 355. PMID 28280154 DOI: 10.1126/science.aaf4831  0.76
2017 Shen Y, Wang Y, Chen T, Gao F, Gong J, Abramczyk D, Walker R, Zhao H, Chen S, Liu W, Luo Y, Müller CA, Paul-Dubois-Taine A, Alver B, Stracquadanio G, ... ... Boeke JD, et al. Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome. Science (New York, N.Y.). 355. PMID 28280153 DOI: 10.1126/science.aaf4791  0.76
2017 Wu Y, Li BZ, Zhao M, Mitchell LA, Xie ZX, Lin QH, Wang X, Xiao WH, Wang Y, Zhou X, Liu H, Li X, Ding MZ, Liu D, Zhang L, ... ... Boeke JD, et al. Bug mapping and fitness testing of chemically synthesized chromosome X. Science (New York, N.Y.). 355. PMID 28280152 DOI: 10.1126/science.aaf4706  0.76
2017 Xie ZX, Li BZ, Mitchell LA, Wu Y, Qi X, Jin Z, Jia B, Wang X, Zeng BX, Liu HM, Wu XL, Feng Q, Zhang WZ, Liu W, Ding MZ, ... ... Boeke JD, et al. "Perfect" designer chromosome V and behavior of a ring derivative. Science (New York, N.Y.). 355. PMID 28280151 DOI: 10.1126/science.aaf4704  0.76
2017 Mercy G, Mozziconacci J, Scolari VF, Yang K, Zhao G, Thierry A, Luo Y, Mitchell LA, Shen M, Shen Y, Walker R, Zhang W, Wu Y, Xie ZX, Luo Z, ... ... Boeke JD, et al. 3D organization of synthetic and scrambled chromosomes. Science (New York, N.Y.). 355. PMID 28280150 DOI: 10.1126/science.aaf4597  0.76
2017 Zhang W, Zhao G, Luo Z, Lin Y, Wang L, Guo Y, Wang A, Jiang S, Jiang Q, Gong J, Wang Y, Hou S, Huang J, Li T, Qin Y, ... ... Boeke JD, et al. Engineering the ribosomal DNA in a megabase synthetic chromosome. Science (New York, N.Y.). 355. PMID 28280149 DOI: 10.1126/science.aaf3981  0.76
2017 Agmon N, Tang Z, Yang K, Sutter B, Ikushima S, Cai Y, Caravelli K, Martin JA, Sun X, Choi WJ, Zhang A, Stracquadanio G, Hao H, Tu BP, Fenyo D, ... ... Boeke JD, et al. Low escape-rate genome safeguards with minimal molecular perturbation of Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America. PMID 28174266 DOI: 10.1073/pnas.1621250114  0.76
2017 Newman HA, Meluh PB, Lu J, Vidal J, Carson C, Lagesse E, Gray JJ, Boeke JD, Matunis MJ. A high throughput mutagenic analysis of yeast sumo structure and function. Plos Genetics. 13: e1006612. PMID 28166236 DOI: 10.1371/journal.pgen.1006612  0.52
2017 Tang Z, Steranka JP, Ma S, Grivainis M, Rodić N, Huang CR, Shih IM, Wang TL, Boeke JD, Fenyö D, Burns KH. Human transposon insertion profiling: Analysis, visualization and identification of somatic LINE-1 insertions in ovarian cancer. Proceedings of the National Academy of Sciences of the United States of America. PMID 28096347 DOI: 10.1073/pnas.1619797114  0.44
2016 Achanta P, Steranka JP, Tang Z, Rodić N, Sharma R, Yang WR, Ma S, Grivainis M, Huang CR, Schneider AM, Gallia GL, Riggins GJ, Quinones-Hinojosa A, Fenyö D, Boeke JD, et al. Somatic retrotransposition is infrequent in glioblastomas. Mobile Dna. 7: 22. PMID 27843500 DOI: 10.1186/s13100-016-0077-5  0.44
2016 Zampella JG, Rodić N, Yang WR, Huang CR, Welch J, Gnanakkan VP, Cornish TC, Boeke JD, Burns KH. A map of mobile DNA insertions in the NCI-60 human cancer cell panel. Mobile Dna. 7: 20. PMID 27807467 DOI: 10.1186/s13100-016-0078-4  0.44
2016 Mita P, Savas JN, Briggs EM, Ha S, Gnanakkan V, Yates JR, Robins DM, David G, Boeke JD, Garabedian MJ, Logan SK. URI Regulates KAP1 Phosphorylation and Transcriptional Repression Via PP2A Phosphatase in Prostate Cancer Cells. The Journal of Biological Chemistry. PMID 27780869 DOI: 10.1074/jbc.M116.741660  1
2016 Mita P, Lhakhang T, Li D, Eichinger DJ, Fenyo D, Boeke JD. Fluorescence ImmunoPrecipitation (FLIP): a Novel Assay for High-Throughput IP. Biological Procedures Online. 18: 16. PMID 27528826 DOI: 10.1186/s12575-016-0046-x  1
2016 Ardeljan D, Taylor MS, Burns KH, Boeke JD, Espey MG, Woodhouse EC, Howcroft TK. Meeting Report: The Role of the Mobilome in Cancer. Cancer Research. 76: 4316-9. PMID 27527733 DOI: 10.1158/0008-5472.CAN-15-3421  1
2016 Stracquadanio G, Yang K, Boeke JD, Bader JS. BioPartsDB: a synthetic biology workflow web-application for education and research. Bioinformatics (Oxford, England). PMID 27412090 DOI: 10.1093/bioinformatics/btw394  0.76
2016 Boeke JD, Church G, Hessel A, Kelley NJ, Arkin A, Cai Y, Carlson R, Chakravarti A, Cornish VW, Holt L, Isaacs FJ, Kuiken T, Lajoie M, Lessor T, Lunshof J, et al. The Genome Project-Write. Science (New York, N.Y.). PMID 27256881 DOI: 10.1126/science.aaf6850  1
2016 Taylor MS, LaCava J, Dai L, Mita P, Burns KH, Rout MP, Boeke JD. Characterization of L1-Ribonucleoprotein Particles. Methods in Molecular Biology (Clifton, N.J.). 1400: 311-38. PMID 26895062 DOI: 10.1007/978-1-4939-3372-3_20  1
2016 Mita P, Boeke JD. How retrotransposons shape genome regulation. Current Opinion in Genetics & Development. 37: 90-100. PMID 26855260 DOI: 10.1016/j.gde.2016.01.001  1
2016 Sliva A, Kuang Z, Meluh PB, Boeke JD. Barcode Sequencing Screen Identifies SUB1 as a Regulator of Yeast Pheromone Inducible Genes. G3 (Bethesda, Md.). PMID 26837954 DOI: 10.1534/g3.115.026757  0.52
2015 Yang K, Stracquadanio G, Luo J, Boeke JD, Bader JS. BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts. Bioinformatics (Oxford, England). PMID 26568632 DOI: 10.1093/bioinformatics/btv664  1
2015 Shen Y, Stracquadanio G, Wang Y, Yang K, Mitchell LA, Xue Y, Cai Y, Chen T, Dymond JS, Kang K, Gong J, Zeng X, Zhang Y, Li Y, Feng Q, ... ... Boeke JD, et al. SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes. Genome Research. PMID 26566658 DOI: 10.1101/gr.193433.115  1
2015 Sliva A, Yang H, Boeke JD, Mathews DJ. Freedom and Responsibility in Synthetic Genomics: The Synthetic Yeast Project. Genetics. 200: 1021-8. PMID 26272997 DOI: 10.1534/genetics.115.176370  1
2015 Rodić N, Steranka JP, Makohon-Moore A, Moyer A, Shen P, Sharma R, Kohutek ZA, Huang CR, Ahn D, Mita P, Taylor MS, Barker NJ, Hruban RH, Iacobuzio-Donahue CA, Boeke JD, et al. Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma. Nature Medicine. PMID 26259033 DOI: 10.1038/nm.3919  1
2015 Taylor MS, Dempsey DR, Hwang Y, Chen Z, Chu N, Boeke JD, Cole PA. Mechanistic analysis of ghrelin-O-acyltransferase using substrate analogs. Bioorganic Chemistry. 62: 64-73. PMID 26246082 DOI: 10.1016/j.bioorg.2015.07.003  1
2015 Ikushima S, Zhao Y, Boeke JD. Development of a Tightly Controlled Off Switch for Saccharomyces cerevisiae Regulated by Camphor, a Low-Cost Natural Product. G3 (Bethesda, Md.). PMID 26206350 DOI: 10.1534/g3.114.012765  1
2015 Sen P, Dang W, Donahue G, Dai J, Dorsey J, Cao X, Liu W, Cao K, Perry R, Lee JY, Wasko BM, Carr DT, He C, Robison B, Wagner J, ... ... Boeke JD, et al. H3K36 methylation promotes longevity by enhancing transcriptional fidelity. Genes & Development. 29: 1362-1376. PMID 26159996 DOI: 10.1101/gad.263707.115  1
2015 Mitchell LA, Phillips NA, Lafont A, Martin JA, Cutting R, Boeke JD. qPCRTag Analysis - A High Throughput, Real Time PCR Assay for Sc2.0 Genotyping. Journal of Visualized Experiments : Jove. PMID 26067760 DOI: 10.3791/52941  1
2015 Mitchell LA, Chuang J, Agmon N, Khunsriraksakul C, Phillips NA, Cai Y, Truong DM, Veerakumar A, Wang Y, Mayorga M, Blomquist P, Sadda P, Trueheart J, Boeke JD. Versatile genetic assembly system (VEGAS) to assemble pathways for expression in S. cerevisiae. Nucleic Acids Research. PMID 25956652 DOI: 10.1093/nar/gkv466  1
2015 Simoneau A, Delgoshaie N, Celic I, Dai J, Abshiru N, Costantino S, Thibault P, Boeke JD, Verreault A, Wurtele H. Interplay between histone H3 lysine 56 deacetylation and chromatin modifiers in response to DNA damage. Genetics. 200: 185-205. PMID 25786853 DOI: 10.1534/genetics.115.175919  1
2015 Agmon N, Mitchell LA, Cai Y, Ikushima S, Chuang J, Zheng A, Choi WJ, Martin JA, Caravelli K, Stracquadanio G, Boeke JD. Yeast Golden Gate (yGG) for the Efficient Assembly of S. cerevisiae Transcription Units. Acs Synthetic Biology. 4: 853-9. PMID 25756291 DOI: 10.1021/sb500372z  1
2015 Cai Y, Agmon N, Choi WJ, Ubide A, Stracquadanio G, Caravelli K, Hao H, Bader JS, Boeke JD. 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. 112: 1803-8. PMID 25624482 DOI: 10.1073/pnas.1424704112  1
2015 Lin Q, Jia B, Mitchell LA, Luo J, Yang K, Zeller KI, Zhang W, Xu Z, Stracquadanio G, Bader JS, Boeke JD, Yuan YJ. RADOM, an efficient in vivo method for assembling designed DNA fragments up to 10 kb long in Saccharomyces cerevisiae. Acs Synthetic Biology. 4: 213-20. PMID 24895839 DOI: 10.1021/sb500241e  1
2014 Gorbunova V, Boeke JD, Helfand SL, Sedivy JM. Human Genomics. Sleeping dogs of the genome. Science (New York, N.Y.). 346: 1187-8. PMID 25477445 DOI: 10.1126/science.aaa3177  1
2014 Mitchell LA, Boeke JD. Circular permutation of a synthetic eukaryotic chromosome with the telomerator. Proceedings of the National Academy of Sciences of the United States of America. 111: 17003-10. PMID 25378705 DOI: 10.1073/pnas.1414399111  1
2014 Kuang Z, Cai L, Zhang X, Ji H, Tu BP, Boeke JD. High-temporal-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast. Nature Structural & Molecular Biology. 21: 854-63. PMID 25173176 DOI: 10.1038/nsmb.2881  1
2014 Dai L, LaCava J, Taylor MS, Boeke JD. Expression and detection of LINE-1 ORF-encoded proteins. Mobile Genetic Elements. 4: e29319. PMID 25054082 DOI: 10.4161/mge.29319  0.44
2014 Shimizu A, Nakatani Y, Nakamura T, Jinno-Oue A, Ishikawa O, Boeke JD, Takeuchi Y, Hoshino H. Characterisation of cytoplasmic DNA complementary to non-retroviral RNA viruses in human cells. Scientific Reports. 4: 5074. PMID 24875540 DOI: 10.1038/srep05074  1
2014 Annaluru N, Muller H, Mitchell LA, Ramalingam S, Stracquadanio G, Richardson SM, Dymond JS, Kuang Z, Scheifele LZ, Cooper EM, Cai Y, Zeller K, Agmon N, Han JS, Hadjithomas M, ... ... Boeke JD, et al. Total synthesis of a functional designer eukaryotic chromosome. Science (New York, N.Y.). 344: 55-8. PMID 24674868 DOI: 10.1126/science.1249252  1
2014 Rodić N, Sharma R, Sharma R, Zampella J, Dai L, Taylor MS, Hruban RH, Iacobuzio-Donahue CA, Maitra A, Torbenson MS, Goggins M, Shih IeM, Duffield AS, Montgomery EA, Gabrielson E, ... ... Boeke JD, et al. Long interspersed element-1 protein expression is a hallmark of many human cancers. The American Journal of Pathology. 184: 1280-6. PMID 24607009 DOI: 10.1016/j.ajpath.2014.01.007  1
2013 Yona AH, Bloom-Ackermann Z, Frumkin I, Hanson-Smith V, Charpak-Amikam Y, Feng Q, Boeke JD, Dahan O, Pilpel Y. tRNA genes rapidly change in evolution to meet novel translational demands. Elife. 2: e01339. PMID 24363105 DOI: 10.7554/eLife.01339  1
2013 Gnanakkan VP, Jaffe AE, Dai L, Fu J, Wheelan SJ, Levitsky HI, Boeke JD, Burns KH. TE-array--a high throughput tool to study transposon transcription. Bmc Genomics. 14: 869. PMID 24325565 DOI: 10.1186/1471-2164-14-869  1
2013 Taylor MS, Lacava J, Mita P, Molloy KR, Huang CR, Li D, Adney EM, Jiang H, Burns KH, Chait BT, Rout MP, Boeke JD, Dai L. Affinity proteomics reveals human host factors implicated in discrete stages of LINE-1 retrotransposition. Cell. 155: 1034-48. PMID 24267889 DOI: 10.1016/j.cell.2013.10.021  1
2013 Teng X, Dayhoff-Brannigan M, Cheng WC, Gilbert CE, Sing CN, Diny NL, Wheelan SJ, Dunham MJ, Boeke JD, Pineda FJ, Hardwick JM. Genome-wide consequences of deleting any single gene. Molecular Cell. 52: 485-94. PMID 24211263 DOI: 10.1016/j.molcel.2013.09.026  1
2013 Taylor MS, Ruch TR, Hsiao PY, Hwang Y, Zhang P, Dai L, Huang CR, Berndsen CE, Kim MS, Pandey A, Wolberger C, Marmorstein R, Machamer C, Boeke JD, Cole PA. Architectural organization of the metabolic regulatory enzyme ghrelin O-acyltransferase. The Journal of Biological Chemistry. 288: 32211-28. PMID 24045953 DOI: 10.1074/jbc.M113.510313  1
2013 Ng TM, Lenstra TL, Duggan N, Jiang S, Ceto S, Holstege FC, Dai J, Boeke JD, Biggins S. Kinetochore function and chromosome segregation rely on critical residues in histones H3 and H4 in budding yeast. Genetics. 195: 795-807. PMID 24037263 DOI: 10.1534/genetics.113.152082  1
2013 Purzycka KJ, Garfinkel DJ, Boeke JD, Le Grice SF. Influence of RNA structural elements on Ty1 retrotransposition. Mobile Genetic Elements. 3: e25060. PMID 23914314 DOI: 10.4161/mge.25060  0.56
2013 O'Donnell KA, An W, Schrum CT, Wheelan SJ, Boeke JD. 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. 110: E2706-13. PMID 23818630 DOI: 10.1073/pnas.1302504110  1
2013 Fiedler KL, Bheda P, Dai J, Boeke JD, Wolberger C, Cotter RJ. 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. 48: 608-15. PMID 23674285 DOI: 10.1002/jms.3198  1
2013 Mitchell LA, Cai Y, Taylor M, Noronha AM, Chuang J, Dai L, Boeke JD. Multichange isothermal mutagenesis: a new strategy for multiple site-directed mutations in plasmid DNA. Acs Synthetic Biology. 2: 473-7. PMID 23654272 DOI: 10.1021/sb300131w  1
2013 Lu JY, Lin YY, Boeke JD, Zhu H. Using functional proteome microarrays to study protein lysine acetylation. Methods in Molecular Biology (Clifton, N.J.). 981: 151-65. PMID 23381860 DOI: 10.1007/978-1-62703-305-3_12  1
2013 Benachenhou F, Sperber GO, Bongcam-Rudloff E, Andersson G, Boeke JD, Blomberg J. Conserved structure and inferred evolutionary history of long terminal repeats (LTRs). Mobile Dna. 4: 5. PMID 23369192 DOI: 10.1186/1759-8753-4-5  1
2013 Huang Q, Purzycka KJ, Lusvarghi S, Li D, Legrice SF, Boeke JD. Retrotransposon Ty1 RNA contains a 5'-terminal long-range pseudoknot required for efficient reverse transcription. Rna (New York, N.Y.). 19: 320-32. PMID 23329695 DOI: 10.1261/rna.035535.112  1
2013 Boeke JD. Fungal, Plant and Animal Retrotransposon Elements Handbook of Proteolytic Enzymes. 1: 248-253. DOI: 10.1016/B978-0-12-382219-2.00059-4  1
2012 Huang CR, Burns KH, Boeke JD. Active transposition in genomes. Annual Review of Genetics. 46: 651-75. PMID 23145912 DOI: 10.1146/annurev-genet-110711-155616  1
2012 Taylor MS, Hwang Y, Hsiao PY, Boeke JD, Cole PA. Ghrelin O-acyltransferase assays and inhibition. Methods in Enzymology. 514: 205-28. PMID 22975055 DOI: 10.1016/B978-0-12-381272-8.00013-1  1
2012 Dancy BM, Crump NT, Peterson DJ, Mukherjee C, Bowers EM, Ahn YH, Yoshida M, Zhang J, Mahadevan LC, Meyers DJ, Boeke JD, Cole PA. Live-cell studies of p300/CBP histone acetyltransferase activity and inhibition. Chembiochem : a European Journal of Chemical Biology. 13: 2113-21. PMID 22961914 DOI: 10.1002/cbic.201200381  1
2012 Burns KH, Boeke JD. Human transposon tectonics. Cell. 149: 740-52. PMID 22579280 DOI: 10.1016/j.cell.2012.04.019  1
2012 O'Donnell KA, Keng VW, York B, Reineke EL, Seo D, Fan D, Silverstein KA, Schrum CT, Xie WR, Mularoni L, Wheelan SJ, Torbenson MS, O'Malley BW, Largaespada DA, Boeke JD. 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. 109: E1377-86. PMID 22556267 DOI: 10.1073/pnas.1115433109  1
2012 Bheda P, Swatkoski S, Fiedler KL, Boeke JD, Cotter RJ, Wolberger C. 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. 109: E916-25. PMID 22474337 DOI: 10.1073/pnas.1121471109  1
2012 Darby MM, Serebreni L, Pan X, Boeke JD, Corden JL. The Saccharomyces cerevisiae Nrd1-Nab3 transcription termination pathway acts in opposition to Ras signaling and mediates response to nutrient depletion. Molecular and Cellular Biology. 32: 1762-75. PMID 22431520 DOI: 10.1128/MCB.00050-12  1
2012 Xie Z, Dai J, Dai L, Tan M, Cheng Z, Wu Y, Boeke JD, Zhao Y. Lysine succinylation and lysine malonylation in histones. Molecular & Cellular Proteomics : McP. 11: 100-7. PMID 22389435 DOI: 10.1074/mcp.M111.015875  1
2012 Cooper EM, Müller H, Chandrasegaran S, Bader JS, Boeke JD. The Build-a-Genome course. Methods in Molecular Biology (Clifton, N.J.). 852: 273-83. PMID 22328440 DOI: 10.1007/978-1-61779-564-0_20  1
2012 Richardson SM, Liu S, Boeke JD, Bader JS. Design-A-Gene with GeneDesign. Methods in Molecular Biology (Clifton, N.J.). 852: 235-47. PMID 22328438 DOI: 10.1007/978-1-61779-564-0_18  1
2012 Muller H, Annaluru N, Schwerzmann JW, Richardson SM, Dymond JS, Cooper EM, Bader JS, Boeke JD, Chandrasegaran S. Assembling large DNA segments in yeast. Methods in Molecular Biology (Clifton, N.J.). 852: 133-50. PMID 22328431 DOI: 10.1007/978-1-61779-564-0_11  1
2012 Annaluru N, Muller H, Ramalingam S, Kandavelou K, London V, Richardson SM, Dymond JS, Cooper EM, Bader JS, Boeke JD, Chandrasegaran S. Assembling DNA fragments by USER fusion. Methods in Molecular Biology (Clifton, N.J.). 852: 77-95. PMID 22328427 DOI: 10.1007/978-1-61779-564-0_7  1
2012 Lin YY, Kiihl S, Suhail Y, Liu SY, Chou YH, Kuang Z, Lu JY, Khor CN, Lin CL, Bader JS, Irizarry R, Boeke JD. Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. Nature. 482: 251-5. PMID 22318606 DOI: 10.1038/nature10804  0.32
2012 Jeong JS, Jiang L, Albino E, Marrero J, Rho HS, Hu J, Hu S, Vera C, Bayron-Poueymiroy D, Rivera-Pacheco ZA, Ramos L, Torres-Castro C, Qian J, Bonaventura J, Boeke JD, et al. Rapid identification of monospecific monoclonal antibodies using a human proteome microarray. Molecular & Cellular Proteomics : McP. 11: O111.016253. PMID 22307071 DOI: 10.1074/mcp.O111.016253  0.36
2012 Sims JJ, Scavone F, Cooper EM, Kane LA, Youle RJ, Boeke JD, Cohen RE. Polyubiquitin-sensor proteins reveal localization and linkage-type dependence of cellular ubiquitin signaling. Nature Methods. 9: 303-9. PMID 22306808 DOI: 10.1038/nmeth.1888  1
2012 Mularoni L, Zhou Y, Bowen T, Gangadharan S, Wheelan SJ, Boeke JD. Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots. Genome Research. 22: 693-703. PMID 22219510 DOI: 10.1101/gr.129460.111  1
2012 Dai J, Boeke JD. Strain construction and screening methods for a yeast histone H3/H4 mutant library. Methods in Molecular Biology (Clifton, N.J.). 833: 1-14. PMID 22183584 DOI: 10.1007/978-1-61779-477-3_1  1
2012 Yarrington RM, Richardson SM, Lisa Huang CR, Boeke JD. Novel transcript truncating function of Rap1p revealed by synthetic codon-optimized Ty1 retrotransposon. Genetics. 190: 523-35. PMID 22135353 DOI: 10.1534/genetics.111.136648  1
2011 Lu JY, Lin YY, Zhu H, Chuang LM, Boeke JD. Protein acetylation and aging. Aging. 3: 911-2. PMID 22067362  1
2011 Dymond JS, Richardson SM, Coombes CE, Babatz T, Muller H, Annaluru N, Blake WJ, Schwerzmann JW, Dai J, Lindstrom DL, Boeke AC, Gottschling DE, Chandrasegaran S, Bader JS, Boeke JD. Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature. 477: 471-6. PMID 21918511 DOI: 10.1038/nature10403  1
2011 Lu JY, Lin YY, Sheu JC, Wu JT, Lee FJ, Chen Y, Lin MI, Chiang FT, Tai TY, Berger SL, Zhao Y, Tsai KS, Zhu H, Chuang LM, Boeke JD. Acetylation of yeast AMPK controls intrinsic aging independently of caloric restriction. Cell. 146: 969-79. PMID 21906795 DOI: 10.1016/j.cell.2011.07.044  1
2011 Cai Y, Boeke JD. Genome remodeling. Nature Biotechnology. 29: 807-8. PMID 21904325 DOI: 10.1038/nbt.1964  1
2011 Hyland EM, Molina H, Poorey K, Jie C, Xie Z, Dai J, Qian J, Bekiranov S, Auble DT, Pandey A, Boeke JD. An evolutionarily 'young' lysine residue in histone H3 attenuates transcriptional output in Saccharomyces cerevisiae. Genes & Development. 25: 1306-19. PMID 21685365 DOI: 10.1101/gad.2050311  1
2011 Dai L, Huang Q, Boeke JD. Effect of reverse transcriptase inhibitors on LINE-1 and Ty1 reverse transcriptase activities and on LINE-1 retrotransposition. Bmc Biochemistry. 12: 18. PMID 21545744 DOI: 10.1186/1471-2091-12-18  1
2011 Yu Q, Olsen L, Zhang X, Boeke JD, Bi X. Differential contributions of histone H3 and H4 residues to heterochromatin structure. Genetics. 188: 291-308. PMID 21441216 DOI: 10.1534/genetics.111.127886  1
2011 An W, Dai L, Niewiadomska AM, Yetil A, O'Donnell KA, Han JS, Boeke JD. Characterization of a synthetic human LINE-1 retrotransposon ORFeus-Hs. Mobile Dna. 2: 2. PMID 21320307 DOI: 10.1186/1759-8753-2-2  1
2011 Xie Y, Rosser JM, Thompson TL, Boeke JD, An W. Characterization of L1 retrotransposition with high-throughput dual-luciferase assays. Nucleic Acids Research. 39: e16. PMID 21071410 DOI: 10.1093/nar/gkq1076  1
2010 Barnett BP, Hwang Y, Taylor MS, Kirchner H, Pfluger PT, Bernard V, Lin YY, Bowers EM, Mukherjee C, Song WJ, Longo PA, Leahy DJ, Hussain MA, Tschöp MH, Boeke JD, et al. Glucose and weight control in mice with a designed ghrelin O-acyltransferase inhibitor. Science (New York, N.Y.). 330: 1689-92. PMID 21097901 DOI: 10.1126/science.1196154  1
2010 Ben-Aroya S, Pan X, Boeke JD, Hieter P. Making temperature-sensitive mutants. Methods in Enzymology. 470: 181-204. PMID 20946811 DOI: 10.1016/S0076-6879(10)70008-2  1
2010 Dai J, Hyland EM, Norris A, Boeke JD. Yin and Yang of histone H2B roles in silencing and longevity: a tale of two arginines. Genetics. 186: 813-28. PMID 20713692 DOI: 10.1534/genetics.110.118489  1
2010 Pan X, Reissman S, Douglas NR, Huang Z, Yuan DS, Wang X, McCaffery JM, Frydman J, Boeke JD. Trivalent arsenic inhibits the functions of chaperonin complex. Genetics. 186: 725-34. PMID 20660648 DOI: 10.1534/genetics.110.117655  1
2010 Huang CR, Schneider AM, Lu Y, Niranjan T, Shen P, Robinson MA, Steranka JP, Valle D, Civin CI, Wang T, Wheelan SJ, Ji H, Boeke JD, Burns KH. Mobile interspersed repeats are major structural variants in the human genome. Cell. 141: 1171-82. PMID 20602999 DOI: 10.1016/j.cell.2010.05.026  1
2010 Matecic M, Smith DL, Pan X, Maqani N, Bekiranov S, Boeke JD, Smith JS. A microarray-based genetic screen for yeast chronological aging factors. Plos Genetics. 6: e1000921. PMID 20421943 DOI: 10.1371/journal.pgen.1000921  1
2010 Lee PA, Dymond JS, Scheifele LZ, Richardson SM, Foelber KJ, Boeke JD, Bader JS. CLONEQC: lightweight sequence verification for synthetic biology. Nucleic Acids Research. 38: 2617-23. PMID 20211841 DOI: 10.1093/nar/gkq093  1
2010 Richardson SM, Nunley PW, Yarrington RM, Boeke JD, Bader JS. GeneDesign 3.0 is an updated synthetic biology toolkit. Nucleic Acids Research. 38: 2603-6. PMID 20211837 DOI: 10.1093/nar/gkq143  1
2010 Norris A, Boeke JD. Silent information regulator 3: the Goldilocks of the silencing complex. Genes & Development. 24: 115-22. PMID 20080949 DOI: 10.1101/gad.1865510  1
2010 Cooper EM, Boeke JD, Cohen RE. Specificity of the BRISC deubiquitinating enzyme is not due to selective binding to Lys63-linked polyubiquitin. The Journal of Biological Chemistry. 285: 10344-52. PMID 20032457 DOI: 10.1074/jbc.M109.059667  1
2010 Luo J, Xu X, Hall H, Hyland EM, Boeke JD, Hazbun T, Kuo MH. Histone h3 exerts a key function in mitotic checkpoint control. Molecular and Cellular Biology. 30: 537-49. PMID 19917722 DOI: 10.1128/MCB.00980-09  1
2009 Scheifele LZ, Cost GJ, Zupancic ML, Caputo EM, Boeke JD. Retrotransposon overdose and genome integrity. Proceedings of the National Academy of Sciences of the United States of America. 106: 13927-32. PMID 19666515 DOI: 10.1073/pnas.0906552106  1
2009 An W, Davis ES, Thompson TL, O'Donnell KA, Lee CY, Boeke JD. Plug and play modular strategies for synthetic retrotransposons. Methods (San Diego, Calif.). 49: 227-35. PMID 19481606 DOI: 10.1016/j.ymeth.2009.05.013  1
2009 Ivics Z, Li MA, Mátés L, Boeke JD, Nagy A, Bradley A, Izsvák Z. Transposon-mediated genome manipulation in vertebrates. Nature Methods. 6: 415-22. PMID 19478801 DOI: 10.1038/nmeth.1332  1
2009 Lin YY, Lu JY, Zhang J, Walter W, Dang W, Wan J, Tao SC, Qian J, Zhao Y, Boeke JD, Berger SL, Zhu H. Protein acetylation microarray reveals that NuA4 controls key metabolic target regulating gluconeogenesis. Cell. 136: 1073-84. PMID 19303850 DOI: 10.1016/j.cell.2009.01.033  1
2009 Huang H, Maertens AM, Hyland EM, Dai J, Norris A, Boeke JD, Bader JS. HistoneHits: a database for histone mutations and their phenotypes. Genome Research. 19: 674-81. PMID 19218532 DOI: 10.1101/gr.083402.108  1
2009 Dymond JS, Scheifele LZ, Richardson S, Lee P, Chandrasegaran S, Bader JS, Boeke JD. Teaching synthetic biology, bioinformatics and engineering to undergraduates: the interdisciplinary Build-a-Genome course. Genetics. 181: 13-21. PMID 19015540 DOI: 10.1534/genetics.108.096784  1
2008 Norris A, Bianchet MA, Boeke JD. Compensatory interactions between Sir3p and the nucleosomal LRS surface imply their direct interaction. Plos Genetics. 4: e1000301. PMID 19079580 DOI: 10.1371/journal.pgen.1000301  1
2008 Qi Y, Suhail Y, Lin YY, Boeke JD, Bader JS. 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. 18: 1991-2004. PMID 18832443 DOI: 10.1101/gr.077693.108  1
2008 Dai J, Hyland EM, Yuan DS, Huang H, Bader JS, Boeke JD. Probing nucleosome function: a highly versatile library of synthetic histone H3 and H4 mutants. Cell. 134: 1066-78. PMID 18805098 DOI: 10.1016/j.cell.2008.07.019  1
2008 Scheifele LZ, Boeke JD. From the shards of a shattered genome, diversity. Proceedings of the National Academy of Sciences of the United States of America. 105: 11593-4. PMID 18701721 DOI: 10.1073/pnas.0805812105  1
2008 O'Donnell KA, Burns KH, Boeke JD. A descent into the nuage: the maelstrom of transposon control. Developmental Cell. 15: 179-81. PMID 18694557 DOI: 10.1016/j.devcel.2008.07.016  1
2008 Han Y, Lin YB, An W, Xu J, Yang HC, O'Connell K, Dordai D, Boeke JD, Siliciano JD, Siliciano RF. Orientation-dependent regulation of integrated HIV-1 expression by host gene transcriptional readthrough. Cell Host & Microbe. 4: 134-46. PMID 18692773 DOI: 10.1016/j.chom.2008.06.008  1
2008 Lin YY, Qi Y, Lu JY, Pan X, Yuan DS, Zhao Y, Bader JS, Boeke JD. A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation. Genes & Development. 22: 2062-74. PMID 18676811 DOI: 10.1101/gad.1679508  1
2008 An W, Han JS, Schrum CM, Maitra A, Koentgen F, Boeke JD. Conditional activation of a single-copy L1 transgene in mice by Cre. Genesis (New York, N.Y. : 2000). 46: 373-83. PMID 18615728 DOI: 10.1002/dvg.20407  1
2008 Celic I, Verreault A, Boeke JD. Histone H3 K56 hyperacetylation perturbs replisomes and causes DNA damage. Genetics. 179: 1769-84. PMID 18579506 DOI: 10.1534/genetics.108.088914  1
2008 Wheelan SJ, Martínez Murillo F, Boeke JD. The incredible shrinking world of DNA microarrays. Molecular Biosystems. 4: 726-32. PMID 18563246 DOI: 10.1039/b706237k  1
2008 Li F, Dong J, Pan X, Oum JH, Boeke JD, Lee SE. Microarray-based genetic screen defines SAW1, a gene required for Rad1/Rad10-dependent processing of recombination intermediates. Molecular Cell. 30: 325-35. PMID 18471978 DOI: 10.1016/j.molcel.2008.02.028  1
2008 Ben-Aroya S, Coombes C, Kwok T, O'Donnell KA, Boeke JD, Hieter P. Toward a comprehensive temperature-sensitive mutant repository of the essential genes of Saccharomyces cerevisiae. Molecular Cell. 30: 248-58. PMID 18439903 DOI: 10.1016/j.molcel.2008.02.021  1
2008 Meluh PB, Pan X, Yuan DS, Tiffany C, Chen O, Sookhai-Mahadeo S, Wang X, Peyser BD, Irizarry R, Spencer FA, Boeke JD. 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.). 416: 221-47. PMID 18392971 DOI: 10.1007/978-1-59745-321-9_15  1
2008 O'Donnell KA, Boeke JD. Domesticated DNA transposon proteins mediate retrotransposon control. Cell Research. 18: 331-3. PMID 18311163 DOI: 10.1038/cr.2008.34  1
2008 Burns KH, Boeke JD. Great exaptations. Journal of Biology. 7: 5. PMID 18279541 DOI: 10.1186/jbiol66  1
2008 Huang Z, Sucgang RS, Lin YY, Shi X, Boeke JD, Pan X. Plasmid-chromosome shuffling for non-deletion alleles in yeast. Nature Methods. 5: 167-9. PMID 18193055 DOI: 10.1038/nmeth.1173  1
2008 Pan X, Yuan D, Ye P, Bader J, Boeke JD. Response to Dr Stephen Cooper's 'On the use of metaphor to understand, explain, or rationalize redundant genes in yeast' Fems Yeast Research. 8: 349-350. DOI: 10.1111/j.1567-1364.2008.00357.x  1
2007 Sulek M, Yarrington R, McGibbon G, Boeke JD, Junop M. A critical role for the C-terminus of Nej1 protein in Lif1p association, DNA binding and non-homologous end-joining. Dna Repair. 6: 1805-18. PMID 17765666 DOI: 10.1016/j.dnarep.2007.07.009  1
2007 Zurita-Martinez SA, Puria R, Pan X, Boeke JD, Cardenas ME. Efficient Tor signaling requires a functional class C Vps protein complex in Saccharomyces cerevisiae. Genetics. 176: 2139-50. PMID 17565946 DOI: 10.1534/genetics.107.072835  1
2007 Yarrington RM, Chen J, Bolton EC, Boeke JD. Mn2+ suppressor mutations and biochemical communication between Ty1 reverse transcriptase and RNase H domains. Journal of Virology. 81: 9004-12. PMID 17537863 DOI: 10.1128/JVI.02502-06  1
2007 O'Donnell KA, Boeke JD. Mighty Piwis defend the germline against genome intruders. Cell. 129: 37-44. PMID 17418784 DOI: 10.1016/j.cell.2007.03.028  1
2007 Pan X, Yuan DS, Ooi SL, Wang X, Sookhai-Mahadeo S, Meluh P, Boeke JD. dSLAM analysis of genome-wide genetic interactions in Saccharomyces cerevisiae. Methods (San Diego, Calif.). 41: 206-21. PMID 17189863 DOI: 10.1016/j.ymeth.2006.07.033  1
2006 An W, Han JS, Wheelan SJ, Davis ES, Coombes CE, Ye P, Triplett C, Boeke JD. Active retrotransposition by a synthetic L1 element in mice. Proceedings of the National Academy of Sciences of the United States of America. 103: 18662-7. PMID 17124176 DOI: 10.1073/pnas.0605300103  1
2006 Wheelan SJ, Scheifele LZ, Martínez-Murillo F, Irizarry RA, Boeke JD. Transposon insertion site profiling chip (TIP-chip). Proceedings of the National Academy of Sciences of the United States of America. 103: 17632-7. PMID 17101968 DOI: 10.1073/pnas.0605450103  1
2006 Wheelan SJ, Martínez-Murillo F, Irizarry RA, Boeke JD. Stacking the deck: double-tiled DNA microarrays. Nature Methods. 3: 903-7. PMID 17060914 DOI: 10.1038/nmeth951  1
2006 Fry CJ, Norris A, Cosgrove M, Boeke JD, Peterson CL. The LRS and SIN domains: two structurally equivalent but functionally distinct nucleosomal surfaces required for transcriptional silencing. Molecular and Cellular Biology. 26: 9045-59. PMID 17015465 DOI: 10.1128/MCB.00248-06  1
2006 Takahashi H, McCaffery JM, Irizarry RA, Boeke JD. Nucleocytosolic acetyl-coenzyme a synthetase is required for histone acetylation and global transcription. Molecular Cell. 23: 207-17. PMID 16857587 DOI: 10.1016/j.molcel.2006.05.040  1
2006 Celic I, Masumoto H, Griffith WP, Meluh P, Cotter RJ, Boeke JD, Verreault A. The sirtuins hst3 and Hst4p preserve genome integrity by controlling histone h3 lysine 56 deacetylation. Current Biology : Cb. 16: 1280-9. PMID 16815704 DOI: 10.1016/j.cub.2006.06.023  1
2006 Sauve AA, Wolberger C, Schramm VL, Boeke JD. The biochemistry of sirtuins. Annual Review of Biochemistry. 75: 435-65. PMID 16756498 DOI: 10.1146/annurev.biochem.74.082803.133500  1
2006 Kastenmayer JP, Ni L, Chu A, Kitchen LE, Au WC, Yang H, Carter CD, Wheeler D, Davis RW, Boeke JD, Snyder MA, Basrai MA. Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae. Genome Research. 16: 365-73. PMID 16510898 DOI: 10.1101/gr.4355406  1
2006 Gandhi TK, Zhong J, Mathivanan S, Karthick L, Chandrika KN, Mohan SS, Sharma S, Pinkert S, Nagaraju S, Periaswamy B, Mishra G, Nandakumar K, Shen B, Deshpande N, Nayak R, ... ... Boeke JD, et al. Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nature Genetics. 38: 285-93. PMID 16501559 DOI: 10.1038/ng1747  1
2006 Pan X, Ye P, Yuan DS, Wang X, Bader JS, Boeke JD. A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell. 124: 1069-81. PMID 16487579 DOI: 10.1016/j.cell.2005.12.036  1
2006 Richardson SM, Wheelan SJ, Yarrington RM, Boeke JD. GeneDesign: rapid, automated design of multikilobase synthetic genes. Genome Research. 16: 550-6. PMID 16481661 DOI: 10.1101/gr.4431306  1
2006 Ooi SL, Pan X, Peyser BD, Ye P, Meluh PB, Yuan DS, Irizarry RA, Bader JS, Spencer FA, Boeke JD. Global synthetic-lethality analysis and yeast functional profiling. Trends in Genetics : Tig. 22: 56-63. PMID 16309778 DOI: 10.1016/j.tig.2005.11.003  1
2005 Ye P, Peyser BD, Pan X, Boeke JD, Spencer FA, Bader JS. Gene function prediction from congruent synthetic lethal interactions in yeast. Molecular Systems Biology. 1: 2005.0026. PMID 16729061 DOI: 10.1038/msb4100034  1
2005 An W, Boeke JD. Transposon technology and vertebrate functional genomics. Genome Biology. 6: 361. PMID 16356279 DOI: 10.1186/gb-2005-6-12-361  1
2005 Hyland EM, Cosgrove MS, Molina H, Wang D, Pandey A, Cottee RJ, Boeke JD. Insights into the role of histone H3 and histone H4 core modifiable residues in Saccharomyces cerevisiae. Molecular and Cellular Biology. 25: 10060-70. PMID 16260619 DOI: 10.1128/MCB.25.22.10060-10070.2005  1
2005 Peyser BD, Irizarry RA, Tiffany CW, Chen O, Yuan DS, Boeke JD, Spencer FA. Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools. Nucleic Acids Research. 33: e140. PMID 16166654 DOI: 10.1093/nar/gni138  1
2005 Wheelan SJ, Aizawa Y, Han JS, Boeke JD. Gene-breaking: a new paradigm for human retrotransposon-mediated gene evolution. Genome Research. 15: 1073-8. PMID 16024818 DOI: 10.1101/gr.3688905  1
2005 Han JS, Boeke JD. LINE-1 retrotransposons: modulators of quantity and quality of mammalian gene expression? Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 27: 775-84. PMID 16015595 DOI: 10.1002/bies.20257  1
2005 Yuan DS, Pan X, Ooi SL, Peyser BD, Spencer FA, Irizarry RA, Boeke JD. Improved microarray methods for profiling the Yeast Knockout strain collection. Nucleic Acids Research. 33: e103. PMID 15994458 DOI: 10.1093/nar/gni105  1
2005 Bachman N, Gelbart ME, Tsukiyama T, Boeke JD. TFIIIB subunit Bdp1p is required for periodic integration of the Ty1 retrotransposon and targeting of Isw2p to S. cerevisiae tDNAs. Genes & Development. 19: 955-64. PMID 15833918 DOI: 10.1101/gad.1299105  1
2005 Gelbart ME, Bachman N, Delrow J, Boeke JD, Tsukiyama T. Genome-wide identification of Isw2 chromatin-remodeling targets by localization of a catalytically inactive mutant. Genes & Development. 19: 942-54. PMID 15833917 DOI: 10.1101/gad.1298905  1
2005 Brannon AR, Maresca JA, Boeke JD, Basrai MA, McBride AA. 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. 102: 2998-3003. PMID 15710895 DOI: 10.1073/pnas.0407818102  1
2005 Bolton EC, Coombes C, Eby Y, Cardell M, Boeke JD. Identification and characterization of critical cis-acting sequences within the yeast Ty1 retrotransposon. Rna (New York, N.Y.). 11: 308-22. PMID 15661848 DOI: 10.1261/rna.7860605  1
2005 Coombes CE, Boeke JD. An evaluation of detection methods for large lariat RNAs. Rna (New York, N.Y.). 11: 323-31. PMID 15661842 DOI: 10.1261/rna.7124405  1
2004 Pan X, Yuan DS, Xiang D, Wang X, Sookhai-Mahadeo S, Bader JS, Hieter P, Spencer F, Boeke JD. A robust toolkit for functional profiling of the yeast genome. Molecular Cell. 16: 487-96. PMID 15525520 DOI: 10.1016/j.molcel.2004.09.035  1
2004 Cosgrove MS, Boeke JD, Wolberger C. Regulated nucleosome mobility and the histone code. Nature Structural & Molecular Biology. 11: 1037-43. PMID 15523479 DOI: 10.1038/nsmb851  1
2004 Maxwell PH, Coombes C, Kenny AE, Lawler JF, Boeke JD, Curcio MJ. Ty1 mobilizes subtelomeric Y' elements in telomerase-negative Saccharomyces cerevisiae survivors. Molecular and Cellular Biology. 24: 9887-98. PMID 15509791 DOI: 10.1128/MCB.24.22.9887-9898.2004  1
2004 Arévalo-Rodríguez M, Pan X, Boeke JD, Heitman J. FKBP12 controls aspartate pathway flux in Saccharomyces cerevisiae to prevent toxic intermediate accumulation. Eukaryotic Cell. 3: 1287-96. PMID 15470257 DOI: 10.1128/EC.3.5.1287-1296.2004  1
2004 Boeke JD. Evolution: A is for adaptation. Nature. 431: 408-9. PMID 15385995 DOI: 10.1038/431408a  1
2004 Bachman N, Eby Y, Boeke JD. Local definition of Ty1 target preference by long terminal repeats and clustered tRNA genes. Genome Research. 14: 1232-47. PMID 15197163 DOI: 10.1101/gr.2052904  1
2004 Han JS, Boeke JD. A highly active synthetic mammalian retrotransposon. Nature. 429: 314-8. PMID 15152256 DOI: 10.1038/nature02535  1
2004 Han JS, Szak ST, Boeke JD. Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature. 429: 268-74. PMID 15152245 DOI: 10.1038/nature02536  1
2004 Starai VJ, Takahashi H, Boeke JD, Escalante-Semerena JC. A link between transcription and intermediary metabolism: a role for Sir2 in the control of acetyl-coenzyme A synthetase. Current Opinion in Microbiology. 7: 115-9. PMID 15063846 DOI: 10.1016/j.mib.2004.02.005  1
2004 Avalos JL, Boeke JD, Wolberger C. Structural basis for the mechanism and regulation of Sir2 enzymes. Molecular Cell. 13: 639-48. PMID 15023335 DOI: 10.1016/S1097-2765(04)00082-6  1
2004 Perlman PS, Boeke JD. Molecular biology. Ring around the retroelement. Science (New York, N.Y.). 303: 182-4. PMID 14716001 DOI: 10.1126/science.1093514  1
2003 Irizarry RA, Ooi SL, Wu Z, Boeke JD. Use of mixture models in a microarray-based screening procedure for detecting differentially represented yeast mutants. Statistical Applications in Genetics and Molecular Biology. 2: Article1. PMID 16646779 DOI: 10.2202/1544-6115.1002  0.56
2003 Ooi SL, Shoemaker DD, Boeke JD. DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray. Nature Genetics. 35: 277-86. PMID 14566339 DOI: 10.1038/ng1258  1
2003 Boeke JD. The unusual phylogenetic distribution of retrotransposons: a hypothesis. Genome Research. 13: 1975-83. PMID 12952870 DOI: 10.1101/gr.1392003  1
2003 Szak ST, Pickeral OK, Landsman D, Boeke JD. Identifying related L1 retrotransposons by analyzing 3' transduced sequences. Genome Biology. 4: R30. PMID 12734010  1
2003 Starai VJ, Takahashi H, Boeke JD, Escalante-Semerena JC. Short-chain fatty acid activation by acyl-coenzyme A synthetases requires SIR2 protein function in Salmonella enterica and Saccharomyces cerevisiae. Genetics. 163: 545-55. PMID 12618394  1
2003 Bolton EC, Boeke JD. Transcriptional interactions between yeast tRNA genes, flanking genes and Ty elements: a genomic point of view. Genome Research. 13: 254-63. PMID 12566403 DOI: 10.1101/gr.612203  1
2002 Starai VJ, Celic I, Cole RN, Boeke JD, Escalante-Semerena JC. Sir2-dependent activation of acetyl-CoA synthetase by deacetylation of active lysine. Science (New York, N.Y.). 298: 2390-2. PMID 12493915 DOI: 10.1126/science.1077650  1
2002 Cost GJ, Feng Q, Jacquier A, Boeke JD. Human L1 element target-primed reverse transcription in vitro. The Embo Journal. 21: 5899-910. PMID 12411507 DOI: 10.1093/emboj/cdf592  1
2002 Avalos JL, Celic I, Muhammad S, Cosgrove MS, Boeke JD, Wolberger C. Structure of a Sir2 enzyme bound to an acetylated p53 peptide. Molecular Cell. 10: 523-35. PMID 12408821 DOI: 10.1016/S1097-2765(02)00628-7  1
2002 Onyango P, Celic I, McCaffery JM, Boeke JD, Feinberg AP. 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. 99: 13653-8. PMID 12374852 DOI: 10.1073/pnas.222538099  1
2002 Szak ST, Pickeral OK, Makalowski W, Boguski MS, Landsman D, Boeke JD. Molecular archeology of L1 insertions in the human genome. Genome Biology. 3: research0052. PMID 12372140  1
2002 Park JH, Cosgrove MS, Youngman E, Wolberger C, Boeke JD. A core nucleosome surface crucial for transcriptional silencing. Nature Genetics. 32: 273-9. PMID 12244315 DOI: 10.1038/ng982  1
2002 Symer DE, Connelly C, Szak ST, Caputo EM, Cost GJ, Parmigiani G, Boeke JD. Human l1 retrotransposition is associated with genetic instability in vivo. Cell. 110: 327-38. PMID 12176320 DOI: 10.1016/S0092-8674(02)00839-5  1
2002 Giaever G, Chu AM, Ni L, Connelly C, Riles L, Véronneau S, Dow S, Lucau-Danila A, Anderson K, André B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R, ... ... Boeke JD, et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature. 418: 387-91. PMID 12140549 DOI: 10.1038/nature00935  1
2002 Smith JS, Avalos J, Celic I, Muhammad S, Wolberger C, Boeke JD. SIR2 family of NAD(+)-dependent protein deacetylases. Methods in Enzymology. 353: 282-300. PMID 12078503 DOI: 10.1016/S0076-6879(02)53056-1  1
2002 Bachman N, Biery MC, Boeke JD, Craig NL. Tn7-mediated mutagenesis of Saccharomyces cerevisiae genomic DNA in vitro Methods in Enzymology. 350: 230-247. PMID 12073315 DOI: 10.1016/S0076-6879(02)50966-6  1
2002 Bolton EC, Mildvan AS, Boeke JD. Inhibition of reverse transcription in vivo by elevated manganese ion concentration. Molecular Cell. 9: 879-89. PMID 11983178 DOI: 10.1016/S1097-2765(02)00495-1  1
2002 Lawler JF, Haeusser DP, Dull A, Boeke JD, Keeney JB. Ty1 defect in proteolysis at high temperature. Journal of Virology. 76: 4233-40. PMID 11932388 DOI: 10.1128/JVI.76.9.4233-4240.2002  1
2002 Sandmeier JJ, Celic I, Boeke JD, Smith JS. Telomeric and rDNA silencing in Saccharomyces cerevisiae are dependent on a nuclear NAD(+) salvage pathway. Genetics. 160: 877-89. PMID 11901108  1
2002 Lawler JF, Merkulov GV, Boeke JD. A nucleocapsid functionality contained within the amino terminus of the Ty1 protease that is distinct and separable from proteolytic activity. Journal of Virology. 76: 346-54. PMID 11739699 DOI: 10.1128/JVI.76.1.346-354.2002  1
2001 Sauve AA, Celic I, Avalos J, Deng H, Boeke JD, Schramm VL. Chemistry of gene silencing: the mechanism of NAD+-dependent deacetylation reactions. Biochemistry. 40: 15456-63. PMID 11747420 DOI: 10.1021/bi011858j  1
2001 Ooi SL, Shoemaker DD, Boeke JD. A DNA microarray-based genetic screen for nonhomologous end-joining mutants in Saccharomyces cerevisiae. Science (New York, N.Y.). 294: 2552-6. PMID 11701889 DOI: 10.1126/science.1065672  1
2001 Ooi SL, Dann C, Nam K, Leahy DJ, Damha MJ, Boeke JD. RNA lariat debranching enzyme. Methods in Enzymology. 342: 233-48. PMID 11586896 DOI: 10.1016/S0076-6879(01)42548-1  1
2001 Schumann G, Hermankova M, Cannon K, Mankowski JL, Boeke JD. Therapeutic effect of a Gag-nuclease fusion protein against retroviral infection in vivo. Journal of Virology. 75: 7030-41. PMID 11435583 DOI: 10.1128/JVI.75.15.7030-7041.2001  1
2001 Lawler JF, Merkulov GV, Boeke JD. Frameshift signal transplantation and the unambiguous analysis of mutations in the yeast retrotransposon Ty1 Gag-Pol overlap region. Journal of Virology. 75: 6769-75. PMID 11435555 DOI: 10.1128/JVI.75.15.6769-6775.2001  1
2001 Loewith R, Smith JS, Meijer M, Williams TJ, Bachman N, Boeke JD, Young D. Pho23 is associated with the Rpd3 histone deacetylase and is required for its normal function in regulation of gene expression and silencing in Saccharomyces cerevisiae. The Journal of Biological Chemistry. 276: 24068-74. PMID 11306585 DOI: 10.1074/jbc.M102176200  1
2001 Smith JS, Boeke JD. Transcription. Is S phase important for transcriptional silencing? Science (New York, N.Y.). 291: 608-9. PMID 11158666 DOI: 10.1126/science.291.5504.608  1
2001 Carbrey JM, Bonhivers M, Boeke JD, Agre P. Aquaporins in Saccharomyces: Characterization of a second functional water channel protein. Proceedings of the National Academy of Sciences of the United States of America. 98: 1000-5. PMID 11158584 DOI: 10.1073/pnas.98.3.1000  1
2001 Wei W, Gilbert N, Ooi SL, Lawler JF, Ostertag EM, Kazazian HH, Boeke JD, Moran JV. Human L1 retrotransposition: cis preference versus trans complementation. Molecular and Cellular Biology. 21: 1429-39. PMID 11158327 DOI: 10.1128/MCB.21.4.1429-1439.2001  1
2001 Cost GJ, Golding A, Schlissel MS, Boeke JD. Target DNA chromatinization modulates nicking by L1 endonuclease. Nucleic Acids Research. 29: 573-7. PMID 11139628  1
2001 Merkulov GV, Lawler JF, Eby Y, Boeke JD. Ty1 proteolytic cleavage sites are required for transposition: all sites are not created equal. Journal of Virology. 75: 638-44. PMID 11134277 DOI: 10.1128/JVI.75.2.638-644.2001  1
2000 Gupta K, Ott D, Hope TJ, Siliciano RF, Boeke JD. A human nuclear shuttling protein that interacts with human immunodeficiency virus type 1 matrix is packaged into virions. Journal of Virology. 74: 11811-24. PMID 11090181 DOI: 10.1128/JVI.74.24.11811-11824.2000  1
2000 Smith JS, Brachmann CB, Celic I, Kenna MA, Muhammad S, Starai VJ, Avalos JL, Escalante-Semerena JC, Grubmeyer C, Wolberger C, Boeke JD. A phylogenetically conserved NAD+-dependent protein deacetylase activity in the Sir2 protein family. Proceedings of the National Academy of Sciences of the United States of America. 97: 6658-63. PMID 10841563 DOI: 10.1073/pnas.97.12.6658  1
2000 Pickeral OK, Makałowski W, Boguski MS, Boeke JD. Frequent human genomic DNA transduction driven by LINE-1 retrotransposition. Genome Research. 10: 411-5. PMID 10779482 DOI: 10.1101/gr.10.4.411  1
1999 Ke N, Gao X, Keeney JB, Boeke JD, Voytas DF. The yeast retrotransposon Ty5 uses the anticodon stem-loop of the initiator methionine tRNA as a primer for reverse transcription. Rna (New York, N.Y.). 5: 929-38. PMID 10411136 DOI: 10.1017/S1355838299990015  1
1999 Boeke JD, Pickeral OK. Retroshuffling the genomic deck. Nature. 398: 108-9, 111. PMID 10086353 DOI: 10.1038/18118  1
1999 Smith JS, Caputo E, Boeke JD. A genetic screen for ribosomal DNA silencing defects identifies multiple DNA replication and chromatin-modulating factors Molecular and Cellular Biology. 19: 3184-3197. PMID 10082585  1
1998 Cost GJ, Boeke JD. Targeting of human retrotransposon integration is directed by the specificity of the L1 endonuclease for regions of unusual DNA structure. Biochemistry. 37: 18081-93. PMID 9922177 DOI: 10.1021/bi981858s  1
1998 Merkulov GV, Boeke JD. Libraries of green fluorescent protein fusions generated by transposition in vitro Gene. 222: 213-222. PMID 9831655 DOI: 10.1016/S0378-1119(98)00503-4  1
1998 Hoff EF, Levin HL, Boeke JD. Schizosaccharomyces pombe retrotransposon Tf2 mobilizes primarily through homologous cDNA recombination. Molecular and Cellular Biology. 18: 6839-52. PMID 9774697  1
1998 Ooi SL, Samarsky DA, Fournier MJ, Boeke JD. Intronic snoRNA biosynthesis in Saccharomyces cerevisiae depends on the lariat-debranching enzyme: intron length effects and activity of a precursor snoRNA. Rna (New York, N.Y.). 4: 1096-110. PMID 9740128 DOI: 10.1017/S1355838298980785  1
1998 Dej KJ, Gerasimova T, Corces VG, Boeke JD. A hotspot for the Drosophila gypsy retroelement in the ovo locus. Nucleic Acids Research. 26: 4019-25. PMID 9705514  1
1998 Boeke JD, Devine SE. Yeast retrotransposons: Finding a nice quiet neighborhood Cell. 93: 1087-1089. PMID 9657139 DOI: 10.1016/S0092-8674(00)81450-6  1
1998 Smith JS, Brachmann CB, Pillus L, Boeke JD. Distribution of a limited Sir2 protein pool regulates the strength of yeast rDNA silencing and is modulated by Sir4p Genetics. 149: 1205-1219. PMID 9649515  1
1998 Kim JM, Vanguri S, Boeke JD, Gabriel A, Voytas DF. Transposable elements and genome organization: A comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence Genome Research. 8: 464-478. PMID 9582191  1
1998 Cannon K, Qin L, Schumann G, Boeke JD. Moloney murine leukemia virus protease expressed in bacteria is enzymatically active. Archives of Virology. 143: 381-8. PMID 9541621 DOI: 10.1007/s007050050294  1
1998 Brachmann RK, Yu K, Eby Y, Pavletich NP, Boeke JD. Genetic selection of intragenic suppressor mutations that reverse the effect of common p53 cancer mutations Embo Journal. 17: 1847-1859. PMID 9524109 DOI: 10.1093/emboj/17.7.1847  1
1998 Brachmann CB, Davies A, Cost GJ, Caputo E, Li J, Hieter P, Boeke JD. Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast (Chichester, England). 14: 115-32. PMID 9483801 DOI: 10.1002/(SICI)1097-0061(19980130)14:2<115::AID-YEA204>3.0.CO;2-2  1
1998 Feng Q, Schumann G, Boeke JD. Retrotransposon R1Bm endonuclease cleaves the target sequence Proceedings of the National Academy of Sciences of the United States of America. 95: 2083-2088. PMID 9482842 DOI: 10.1073/pnas.95.5.2083  1
1998 Kenna MA, Brachmann CB, Devine SE, Boeke JD. Invading the yeast nucleus: A nuclear localization signal at the C terminus of Ty1 integrase is required for transposition in vivo Molecular and Cellular Biology. 18: 1115-1124. PMID 9448009  1
1997 Brachmann RK, Boeke JD. Tag games in yeast: The two-hybrid system and beyond Current Opinion in Biotechnology. 8: 561-568. PMID 9353226 DOI: 10.1016/S0958-1669(97)80029-8  1
1997 Lauermann V, Boeke JD. Plus strand strong-stop DNA transfer in yeast Ty retrotransposons Embo Journal. 16: 6603-6612. PMID 9351840 DOI: 10.1093/emboj/16.21.6603  1
1997 Basrai MA, Hieter P, Boeke JD. Small open reading frames: Beautiful needles in the haystack Genome Research. 7: 768-771. PMID 9267801  1
1997 Schumann G, Cannon K, Ma WP, Crouch RJ, Boeke JD. Antiretroviral effect of a gag-RNase HI fusion gene. Gene Therapy. 4: 593-9. PMID 9231076 DOI: 10.1038/sj.gt.3300421  1
1997 Song SU, Kurkulos M, Boeke JD, Corces VG. Infection of the germ line by retroviral particles produced in the follicle cells: a possible mechanism for the mobilization of the gypsy retroelement of Drosophila. Development (Cambridge, England). 124: 2789-98. PMID 9226450  1
1997 Boeke JD. LINEs and Alus--the polyA connection Nature Genetics. 16: 6-7. PMID 9140383  1
1997 Lauermann V, Hermankova M, Boeke JD. Increased length of long terminal repeats inhibits Ty1 transposition and leads to the formation of tandem multimers. Genetics. 145: 911-22. PMID 9093846  1
1997 Smith JS, Boeke JD. An unusual form of transcriptional silencing in yeast ribosomal DNA. Genes & Development. 11: 241-54. PMID 9009206  1
1997 Nam K, Lee G, Trambley J, Devine SE, Boeke JD. Severe growth defect in a Schizosaccharomyces pombe mutant defective in intron lariat degradation Molecular and Cellular Biology. 17: 809-818. PMID 9001235  1
1997 Brachmann CB, Boeke JD. Mapping the multimerization domains of the Gag protein of yeast retrotransposon Ty1. Journal of Virology. 71: 812-7. PMID 8985422  1
1996 Lauermann V, Peden K, Boeke JD. Alternative tRNA primers for HIV [3] Aids. 10: 1738-1740. PMID 8970697  1
1996 Boeke JD, Hahn B. Destroying retroviruses from within Trends in Microbiology. 4: 421-426. PMID 8950810 DOI: 10.1016/0966-842X(96)10065-2  1
1996 Feng Q, Moran JV, Kazazian HH, Boeke JD. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition Cell. 87: 905-916. PMID 8945517 DOI: 10.1016/S0092-8674(00)81997-2  1
1996 Cost GJ, Boeke JD. A useful colony colour phenotype associated with the yeast selectable/counter-selectable marker MET15. Yeast (Chichester, England). 12: 939-41. PMID 8873447 DOI: 10.1002/(SICI)1097-0061(199608)12:10<939::AID-YEA988>3.0.CO;2-L  1
1996 Boeke JD. DNA repair. A little help for my ends Nature. 383. PMID 8857529  1
1996 Vidal M, Braun P, Chen E, Boeke JD, Harlow E. Genetic characterization of a mammalian protein-protein interaction domain by using a yeast reverse two-hybrid system. Proceedings of the National Academy of Sciences of the United States of America. 93: 10321-6. PMID 8816798 DOI: 10.1073/pnas.93.19.10321  1
1996 Vidal M, Brachmann RK, Fattaey A, Harlow E, Boeke JD. Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions. Proceedings of the National Academy of Sciences of the United States of America. 93: 10315-20. PMID 8816797 DOI: 10.1073/pnas.93.19.10315  1
1996 Merkulov GV, Swiderek KM, Baker Brachmann C, Boeke JD. A critical proteolytic cleavage site near the C terminus of the yeast retrotransposon Ty1 Gag protein Journal of Virology. 70: 5548-5556. PMID 8764068  1
1996 Gabriel A, Willems M, Mules EH, Boeke JD. Replication infidelity during a single cycle of Ty1 retrotransposition Proceedings of the National Academy of Sciences of the United States of America. 93: 7767-7771. PMID 8755550 DOI: 10.1073/pnas.93.15.7767  1
1996 Schumann G, Qin L, Rein A, Natsoulis G, Boeke JD. Therapeutic effect of Gag-nuclease fusion protein on retrovirus-infected cell cultures Journal of Virology. 70: 4329-4337. PMID 8676455  1
1996 Brachmann RK, Vidal M, Boeke JD. Dominant-negative p53 mutations selected in yeast hit cancer hot spots Proceedings of the National Academy of Sciences of the United States of America. 93: 4091-4095. PMID 8633021 DOI: 10.1073/pnas.93.9.4091  1
1996 Devine SE, Boeke JD. Integration of the yeast retrotransposon Ty1 is targeted to regions upstream of genes transcribed by RNA polymerase III Genes and Development. 10: 620-633. PMID 8598291  1
1996 Boeke JD. A little help for my ends Nature. 383: 579-580. DOI: 10.1038/383579a0  1
1995 Natsoulis G, Seshaiah P, Federspiel MJ, Rein A, Hughes SH, Boeke JD. Targeting of a nuclease to murine leukemia virus capsids inhibits viral multiplication. Proceedings of the National Academy of Sciences of the United States of America. 92: 364-8. PMID 7831291 DOI: 10.1073/pnas.92.2.364  1
1995 Lauermann V, Nam K, Trambley J, Boeke JD. Plus-strand strong-stop DNA synthesis in retrotransposon Ty1 Journal of Virology. 69: 7845-7850. PMID 7494296  1
1994 Natsoulis G, Winston F, Boeke JD. The SPT10 and SPT21 genes of Saccharomyces cerevisiae. Genetics. 136: 93-105. PMID 8138180  1
1994 Monokian GM, Braiterman LT, Boeke JD. In-frame linker insertion mutagenesis of yeast transposon Ty1: mutations, transposition and dominance Gene. 139: 9-18. PMID 8112595 DOI: 10.1016/0378-1119(94)90517-7  1
1994 Braiterman LT, Boeke JD. In vitro integration of retrotransposon Ty1: A direct physical assay Molecular and Cellular Biology. 14: 5719-5730. PMID 8065307  1
1994 Dollard C, Ricupero-Hovasse SL, Natsoulis G, Boeke JD, Winston F. SPT10 and SPT21 are required for transcription of particular histone genes in Saccharomyces cerevisiae Molecular and Cellular Biology. 14: 5223-5228. PMID 8035801  1
1994 Tugendreich S, Feng Q, Kroll J, Sears DD, Boeke JD, Hieter P. Alu sequences in RMSA-1 protein? Nature. 370: 106. PMID 8022478 DOI: 10.1038/370106a0  1
1994 Keeney JB, Boeke JD. Efficient targeted integration at leu1-32 and ura4-294 in Schizosaccharomyces pombe. Genetics. 136: 849-56. PMID 8005439  1
1994 Song SU, Gerasimova T, Kurkulos M, Boeke JD, Corces VG. An env-like protein encoded by a Drosophila retroelement: evidence that gypsy is an infectious retrovirus. Genes & Development. 8: 2046-57. PMID 7958877  1
1994 Lauermann V, Boeke JD. The primer tRNA sequence is not inherited during Ty1 retrotransposition Proceedings of the National Academy of Sciences of the United States of America. 91: 9847-9851. PMID 7937903 DOI: 10.1073/pnas.91.21.9847  1
1994 Devine SE, Boeke JD. Efficient integration of artificial transposons into plasmid targets in vitro: A useful tool for DNA mapping, sequencing and genetic analysis Nucleic Acids Research. 22: 3765-3772. PMID 7937090 DOI: 10.1093/nar/22.18.3765  1
1994 Braiterman LT, Boeke JD. Ty1 in vitro integration: Effects of mutations in cis and in trans Molecular and Cellular Biology. 14: 5731-5740. PMID 7520525  1
1994 Baker Brachmann C, Boeke JD. Overview: Fusion proteins: Fundamental and therapeutic applications Expert Opinion On Therapeutic Patents. 4: 1037-1051. DOI: 10.1517/13543776.4.9.1037  1
1994 Levin HL, Weaver DC, Boeke JD. Novel gene expression mechanism in a fission yeast retroelement: Tf1 proteins are derived from a single primary translation product (The EMBO Journal (1993) 12 (4885-4895)) Embo Journal. 13: 1494.  1
1993 Voytas DF, Boeke JD. Yeast retrotransposons and tRNAs Trends in Genetics. 9: 421-427. PMID 8122309 DOI: 10.1016/0168-9525(93)90105-Q  1
1992 Chapman KB, Solomon SD, Boeke JD. SDH1, the gene encoding the succinate dehydrogenase flavoprotein subunit from Saccharomyces cerevisiae Gene. 118: 131-136. PMID 1511876 DOI: 10.1016/0378-1119(92)90260-V  1
1992 Voytas DF, Boeke JD. Yeast retrotransposon revealed [8] Nature. 358: 717. PMID 1324434  1
1992 Chapman KB, Byström AS, Boeke JD. Initiator methionine tRNA is essential for Ty1 transposition in yeast Proceedings of the National Academy of Sciences of the United States of America. 89: 3236-3240. PMID 1314382  1
1992 Levin HL, Boeke JD. Demonstration of retrotransposition of the Tf1 element in fission yeast Embo Journal. 11: 1145-1153. PMID 1312461  1
1991 Berlin V, Brill JA, Trueheart J, Boeke JD, Fink GR. Genetic screens and selections for cell and nuclear fusion mutants. Methods in Enzymology. 194: 774-92. PMID 2005824 DOI: 10.1016/0076-6879(91)94058-K  1
1991 Sikorski RS, Boeke JD. In vitro mutagenesis and plasmid shuffling: from cloned gene to mutant yeast. Methods in Enzymology. 194: 302-18. PMID 2005795 DOI: 10.1016/0076-6879(91)94023-6  1
1991 Chapman KB, Boeke JD. Isolation and characterization of the gene encoding yeast debranching enzyme Cell. 65: 483-492. PMID 1850323 DOI: 10.1016/0092-8674(91)90466-C  1
1991 Xu H, Boeke JD. Inhibition of Ty1 Transposition by Mating Pheromones in Saccharomyces cerevisiae Molecular and Cellular Biology. 11: 2736-2743. PMID 1850102  1
1991 Mathias SL, Scott AF, Kazazian HH, Boeke JD, Gabriel A. Reverse transcriptase encoded by a human transposable element. Science (New York, N.Y.). 254: 1808-10. PMID 1722352  1
1991 Gabriel A, Boeke JD. Reverse transcriptase encoded by a retrotransposon from the trypanosomatid Crithidia fasciculata Proceedings of the National Academy of Sciences of the United States of America. 88: 9794-9798. PMID 1719539  1
1991 Natsoulis G, Dollard C, Winston F, Boeke JD. The products of the SPT10 and SPT21 genes of Saccharomyces cerevisiae increase the amplitude of transcriptional regulation at a large number of unlinked loci New Biologist. 3: 1249-1259. PMID 1667480  1
1991 Boeke JD, Eichinger DJ, Natsoulis G. Doubling Ty1 element copy number in Saccharomyces cerevisiae: Host genome stability and phenotypic effects Genetics. 129: 1043-1052. PMID 1664403  1
1991 Boeke JD, Chapman KB. Retrotransposition mechanisms Current Opinion in Cell Biology. 3: 502-507. PMID 1654062 DOI: 10.1016/0955-0674(91)90079-E  1
1991 Natsoulis G, Boeke JD. New antiviral strategy using capsid-nuclease fusion proteins Nature. 352: 632-635. PMID 1650915  1
1990 Levin HL, Boeke JD. The absence of adenine methylation increases the ligation efficiency of partially filled staggered DNA ends Nucleic Acids Research. 18: 6146. PMID 2235512 DOI: 10.1093/nar/18.20.6146  1
1990 Sikorski RS, Michaud W, Levin HL, Boeke JD, Hieter P. Trans-kingdom promiscuity. Nature. 345: 581-2. PMID 2190092 DOI: 10.1038/345581b0  1
1990 Levin HL, Weaver DC, Boeke JD. Two related families of retrotransposons from Schizosaccharomyces pombe Molecular and Cellular Biology. 10: 6791-6798. PMID 2174117  1
1990 Xu H, Boeke JD. Host genes that influence transposition in yeast: The abundance of a rare tRNA regulates Ty1 transposition frequency Proceedings of the National Academy of Sciences of the United States of America. 87: 8360-8364. PMID 2172984  1
1990 Hu H, Boeke JD. Localization of Sequences Required in cis for Yeast Ty1 Element Transposition near the Long Terminal Repeats: Analysis of Mini-Ty1 Elements Molecular and Cellular Biology. 10: 2695-2702. PMID 2160583  1
1990 Eichinger DJ, Boeke JD. A specific terminal structure is required for Ty1 transposition Genes and Development. 4: 324-330. PMID 2159935  1
1990 Curcio MJ, Hedge AM, Boeke JD, Garfinkel DJ. Ty RNA levels determine the spectrum of retrotransposition events that activate gene expression in Saccharomyces cerevisiae. Molecular & General Genetics : Mgg. 220: 213-21. PMID 2157950 DOI: 10.1007/BF00260484  1
1990 Boeke JD. Reverse transcriptase, the end of the chromosome, and the end of life Cell. 61: 193-195. PMID 1691957 DOI: 10.1016/0092-8674(90)90797-I  1
1989 Natsoulis G, Thomas W, Roghmann MC, Winston F, Boeke JD. Ty1 transposition in Saccharomyces cerevisiae is nonrandom Genetics. 123: 269-279. PMID 2555252  1
1989 Boeke JD, Corces VG. Transcription and reverse transcription of retrotransposons. Annual Review of Microbiology. 43: 403-34. PMID 2552899 DOI: 10.1146/annurev.mi.43.100189.002155  1
1988 Eichinger DJ, Boeke JD. The DNA intermediate in yeast Ty1 element transposition copurifies with virus-like particles: Cell-free Ty1 transposition Cell. 54: 955-966. PMID 2843295 DOI: 10.1016/0092-8674(88)90110-9  1
1988 Boeke JD, Eichinger D, Castrillon D, Fink GR. The Saccharomyces cerevisiae genome contains functional and nonfunctional copies of transposon Ty1 Molecular and Cellular Biology. 8: 1432-1442. PMID 2837641  1
1988 Boeke JD, Xu H, Fink GR. A general method for the chromosomal amplification of genes in yeast. Science (New York, N.Y.). 239: 280-2. PMID 2827308  1
1988 Youngren SD, Boeke JD, Sanders NJ, Garfinkel DJ. Functional organization of the retrotransposon Ty from Saccharomyces cerevisiae: Ty protease is required for transposition. Molecular and Cellular Biology. 8: 1421-31. PMID 2454391  1
1988 Boeke JD. Transposition of copia elements in Drosophila [4] Nature. 332: 21.  1
1987 Boeke JD, Trueheart J, Natsoulis G, Fink GR. [10] 5-Fluoroorotic acid as a selective agent in yeast molecular genetics Methods in Enzymology. 154: 164-175. PMID 3323810 DOI: 10.1016/0076-6879(87)54076-9  1
1987 Trueheart J, Boeke JD, Fink GR. Two genes required for cell fusion during yeast conjugation: evidence for a pheromone-induced surface protein Molecular and Cellular Biology. 7: 2316-2328. PMID 3302672  1
1987 Xu H, Boeke JD. High-frequency deletion between homologous sequences during retrotransposition of Ty elements in Saccharomyces cerevisiae Proceedings of the National Academy of Sciences of the United States of America. 84: 8553-8557. PMID 2825195  1
1986 Boeke JD, Styles CA, Fink GR. Saccharomyces cerevisiae SPT3 gene is required for transposition and transpositional recombination of chromosomal Ty elements Molecular and Cellular Biology. 6: 3575-3581. PMID 3025601  1
1986 Fink GR, Boeke JD, Garfinkel DJ. The mechanism and consequences of retrotransposition Trends in Genetics. 2: 118-123. DOI: 10.1016/0168-9525(86)90200-3  1
1985 Davis NG, Boeke JD, Model P. Fine structure of a membrane anchor domain Journal of Molecular Biology. 181: 111-121. PMID 3872373 DOI: 10.1016/0022-2836(85)90329-8  1
1985 Boeke JD, Garfinkel DJ, Styles CA, Fink GR. Ty elements transpose through an RNA intermediate Cell. 40: 491-500. PMID 2982495 DOI: 10.1016/0092-8674(85)90197-7  1
1985 Garfinkel DJ, Boeke JD, Fink GR. Ty element transposition: Reverse transcriptase and virus-like particles Cell. 42: 507-517. PMID 2411424 DOI: 10.1016/0092-8674(85)90108-4  1
1984 Boeke JD, La Croute F, Fink GR. A positive selection for mutants lacking orotidine-5′-phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid resistance Mgg Molecular &Amp; General Genetics. 197: 345-346. PMID 6394957 DOI: 10.1007/BF00330984  1
1983 Wallach M, Boeke JD. In vitro translation and characterization of a unique histidine-rich protein mRNA in the avian malaria parasite Plasmodium lophurae. Proceedings of the National Academy of Sciences of the United States of America. 80: 1867-71. PMID 6572948  1
1983 Barany F, Boeke JD. Genetic transformation of Streptococcus pneumoniae by DNA cloned into the single-stranded bacteriophage f1. Journal of Bacteriology. 153: 200-10. PMID 6571728  1
1982 Boeke JD, Model P, Zinder ND. Effects of bacteriophage f1 gene III protein on the host cell membrane Mgg Molecular & General Genetics. 186: 185-192. PMID 6955583 DOI: 10.1007/BF00331849  1
1982 Zinder ND, Boeke JD. The filamentous phage (Ff) as vectors for recombinant DNA- a review Gene. 19: 1-10. PMID 6292041 DOI: 10.1016/0378-1119(82)90183-4  1
1982 Boeke JD, Model P. A prokaryotic membrane anchor sequence: Carboxyl terminus of bacteriophage F1 gene III protein retains it in the membrane Proceedings of the National Academy of Sciences of the United States of America. 79: 5200-5204. PMID 6291030  1
1982 Barany F, Boeke JD, Tomasz A. Staphylococcal plasmids that replicate and express erythromycin resistance in both Streptococcus pneumoniae and Escherichia coli Proceedings of the National Academy of Sciences of the United States of America. 79: 2991-2995. PMID 6283551  1
1981 Model P, Russel M, Boeke JD. Filamentous phage assembly: membrane insertion of the major coat protein. Progress in Clinical and Biological Research. 64: 389-400. PMID 7036184  1
1981 Boeke JD. One and two codon insertion mutants of bacteriophage f1 Mgg Molecular &Amp; General Genetics. 181: 288-291. PMID 6264271 DOI: 10.1007/BF00425599  1
1980 Moses PB, Boeke JD, Horiuchi K, Zinder ND. Restructuring the bacteriophage f1 genome: expression of gene VIII in the intergenic space. Virology. 104: 267-78. PMID 7395106  1
1980 Boeke JD, Russel M, Model P. Processing of filamentous phage pre-coat protein. Effect of sequence variations near the signal peptidase cleavage site Journal of Molecular Biology. 144: 103-116. PMID 7230262 DOI: 10.1016/0022-2836(80)90027-3  1
1979 Boeke JD, Model P. Molecular basis of the am8H1 lesion in bacteriophage M13 Virology. 96: 299-301. PMID 462808 DOI: 10.1016/0042-6822(79)90198-3  1
1979 Boeke JD, Vovis GF, Zinder ND. Insertion mutant of bacteriophage f1 sensitive to EcoRI Proceedings of the National Academy of Sciences of the United States of America. 76: 2699-2702. PMID 379863  1
1978 Boeke JD, Ortiz-Crespo FI. Avian pollination studies: A simple scanning electron microscopic technique Science. 201: 167-168.  1
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