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

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, Zimmer B, Sakata S, Dinis A, Ohara O, Garcia Reino EJ, Dobbs K, Hasek M, Holloway SP, McCammon K, Hussong SA, DeRosa N, Van Skike CE, Katolik A, Lorenzo L, Hyodo M, Faria E, Halwani R, Fukuhara R, Smith GA, Galvan V, Damha MJ, Al-Muhsen S, Itan Y, Boeke JD, Notarangelo LD, Studer L, Kobayashi M, Diogo L, Fairbrother WG, Abel L, Rosenberg BR, Hart PJ, Etzioni A, Casanova JL.

Cell. 2018 Feb 22;172(5):952-965.e18. doi: 10.1016/j.cell.2018.02.019.


Stress response factors drive regrowth of quiescent cells.

Kuang Z, Ji H, Boeke JD.

Curr Genet. 2018 Feb 17. doi: 10.1007/s00294-018-0813-0. [Epub ahead of print] Review.


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

Kalva S, Boeke JD, Mita P.

Biol Proced Online. 2018 Jan 19;20:2. doi: 10.1186/s12575-018-0068-7. eCollection 2018.


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

Mita P, Wudzinska A, Sun X, Andrade J, Nayak S, Kahler DJ, Badri S, LaCava J, Ueberheide B, Yun CY, Fenyö D, Boeke JD.

Elife. 2018 Jan 8;7. pii: e30058. doi: 10.7554/eLife.30058.


Dissection of affinity captured LINE-1 macromolecular complexes.

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, LaCava J.

Elife. 2018 Jan 8;7. pii: e30094. doi: 10.7554/eLife.30094.


Resetting the Yeast Epigenome with Human Nucleosomes.

Truong DM, Boeke JD.

Cell. 2017 Dec 14;171(7):1508-1519.e13. doi: 10.1016/j.cell.2017.10.043. Epub 2017 Nov 30.


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

Chuang J, Boeke JD, Mitchell LA.

Methods Mol Biol. 2018;1671:211-225. doi: 10.1007/978-1-4939-7295-1_14.


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

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.

G3 (Bethesda). 2018 Jan 4;8(1):173-183. doi: 10.1534/g3.117.300347.


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

Jiang S, Liu Y, Wang A, Qin Y, Luo M, Wu Q, Boeke JD, Dai J.

Genetics. 2017 Dec;207(4):1263-1273. doi: 10.1534/genetics.117.300450. Epub 2017 Oct 30.


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

Jiang S, Liu Y, Xu C, Wang Y, Gong J, Shen Y, Wu Q, Boeke JD, Dai J.

G3 (Bethesda). 2017 Dec 4;7(12):3857-3866. doi: 10.1534/g3.117.300252.


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

Kuang Z, Pinglay S, Ji H, Boeke JD.

Elife. 2017 Sep 26;6. pii: e29938. doi: 10.7554/eLife.29938.


Intact piRNA pathway prevents L1 mobilization in male meiosis.

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.

Proc Natl Acad Sci U S A. 2017 Jul 11;114(28):E5635-E5644. doi: 10.1073/pnas.1701069114. Epub 2017 Jun 19.


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

Kannan M, Li J, Fritz SE, Husarek KE, Sanford JC, Sullivan TL, Tiwary PK, An W, Boeke JD, Symer DE.

Mob DNA. 2017 May 10;8:8. doi: 10.1186/s13100-017-0091-2. eCollection 2017.


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

Payer LM, Steranka JP, Yang WR, Kryatova M, Medabalimi S, Ardeljan D, Liu C, Boeke JD, Avramopoulos D, Burns KH.

Proc Natl Acad Sci U S A. 2017 May 16;114(20):E3984-E3992. doi: 10.1073/pnas.1704117114. Epub 2017 May 2.


Design of a synthetic yeast genome.

Richardson SM, Mitchell LA, Stracquadanio G, Yang K, Dymond JS, DiCarlo JE, Lee D, Huang CL, Chandrasegaran S, Cai Y, Boeke JD, Bader JS.

Science. 2017 Mar 10;355(6329):1040-1044. doi: 10.1126/science.aaf4557.


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

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, Cai Y, Heguy A, Ueberheide B, Fenyö D, Dai J, Bader JS, Boeke JD.

Science. 2017 Mar 10;355(6329). pii: eaaf4831. doi: 10.1126/science.aaf4831.


Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome.

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, Mitchell LA, Luo Z, Fan Y, Zhou B, Wen B, Tan F, Wang Y, Zi J, Xie Z, Li B, Yang K, Richardson SM, Jiang H, French CE, Nieduszynski CA, Koszul R, Marston AL, Yuan Y, Wang J, Bader JS, Dai J, Boeke JD, Xu X, Cai Y, Yang H.

Science. 2017 Mar 10;355(6329). pii: eaaf4791. doi: 10.1126/science.aaf4791.


Bug mapping and fitness testing of chemically synthesized chromosome X.

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, Liu BL, Wu XL, Li FF, Dong XT, Jia B, Zhang WZ, Jiang GZ, Liu Y, Bai X, Song TQ, Chen Y, Zhou SJ, Zhu RY, Gao F, Kuang Z, Wang X, Shen M, Yang K, Stracquadanio G, Richardson SM, Lin Y, Wang L, Walker R, Luo Y, Ma PS, Yang H, Cai Y, Dai J, Bader JS, Boeke JD, Yuan YJ.

Science. 2017 Mar 10;355(6329). pii: eaaf4706. doi: 10.1126/science.aaf4706.


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

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, Li X, Zhao GR, Qiao JJ, Cheng JS, Zhao M, Kuang Z, Wang X, Martin JA, Stracquadanio G, Yang K, Bai X, Zhao J, Hu ML, Lin QH, Zhang WQ, Shen MH, Chen S, Su W, Wang EX, Guo R, Zhai F, Guo XJ, Du HX, Zhu JQ, Song TQ, Dai JJ, Li FF, Jiang GZ, Han SL, Liu SY, Yu ZC, Yang XN, Chen K, Hu C, Li DS, Jia N, Liu Y, Wang LT, Wang S, Wei XT, Fu MQ, Qu LM, Xin SY, Liu T, Tian KR, Li XN, Zhang JH, Song LX, Liu JG, Lv JF, Xu H, Tao R, Wang Y, Zhang TT, Deng YX, Wang YR, Li T, Ye GX, Xu XR, Xia ZB, Zhang W, Yang SL, Liu YL, Ding WQ, Liu ZN, Zhu JQ, Liu NZ, Walker R, Luo Y, Wang Y, Shen Y, Yang H, Cai Y, Ma PS, Zhang CT, Bader JS, Boeke JD, Yuan YJ.

Science. 2017 Mar 10;355(6329). pii: eaaf4704. doi: 10.1126/science.aaf4704.


3D organization of synthetic and scrambled chromosomes.

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, Cai Y, Dai J, Yang H, Yuan YJ, Boeke JD, Bader JS, Muller H, Koszul R.

Science. 2017 Mar 10;355(6329). pii: eaaf4597. doi: 10.1126/science.aaf4597.


Engineering the ribosomal DNA in a megabase synthetic chromosome.

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, Dong J, Qin Q, Zhang J, Zou X, He X, Zhao L, Xiao Y, Xu M, Cheng E, Huang N, Zhou T, Shen Y, Walker R, Luo Y, Kuang Z, Mitchell LA, Yang K, Richardson SM, Wu Y, Li BZ, Yuan YJ, Yang H, Lin J, Chen GQ, Wu Q, Bader JS, Cai Y, Boeke JD, Dai J.

Science. 2017 Mar 10;355(6329). pii: eaaf3981. doi: 10.1126/science.aaf3981.


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

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, Bader JS, Boeke JD.

Proc Natl Acad Sci U S A. 2017 Feb 21;114(8):E1470-E1479. doi: 10.1073/pnas.1621250114. Epub 2017 Feb 7.


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

Newman HA, Meluh PB, Lu J, Vidal J, Carson C, Lagesse E, Gray JJ, Boeke JD, Matunis MJ.

PLoS Genet. 2017 Feb 6;13(2):e1006612. doi: 10.1371/journal.pgen.1006612. eCollection 2017 Feb.


The State of Systems Genetics in 2017.

Baliga NS, Björkegren JL, Boeke JD, Boutros M, Crawford NP, Dudley AM, Farber CR, Jones A, Levey AI, Lusis AJ, Mak HC, Nadeau JH, Noyes MB, Petretto E, Seyfried NT, Steinmetz LM, Vonesch SC.

Cell Syst. 2017 Jan 25;4(1):7-15. doi: 10.1016/j.cels.2017.01.005.


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

Tang Z, Steranka JP, Ma S, Grivainis M, Rodić N, Huang CR, Shih IM, Wang TL, Boeke JD, Fenyö D, Burns KH.

Proc Natl Acad Sci U S A. 2017 Jan 31;114(5):E733-E740. doi: 10.1073/pnas.1619797114. Epub 2017 Jan 17.


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

Ikushima S, Boeke JD.

ACS Synth Biol. 2017 Mar 17;6(3):497-506. doi: 10.1021/acssynbio.6b00205. Epub 2016 Dec 22.


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

Kuang Z, Boeke JD, Canzar S.

Genome Res. 2017 Jan;27(1):145-156. doi: 10.1101/gr.208041.116. Epub 2016 Nov 17.


Somatic retrotransposition is infrequent in glioblastomas.

Achanta P, Steranka JP, Tang Z, Rodić N, Sharma R, Yang WR, Ma S, Grivainis M, Huang CRL, Schneider AM, Gallia GL, Riggins GJ, Quinones-Hinojosa A, Fenyö D, Boeke JD, Burns KH.

Mob DNA. 2016 Nov 11;7:22. doi: 10.1186/s13100-016-0077-5. eCollection 2016.


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

Zampella JG, Rodić N, Yang WR, Huang CR, Welch J, Gnanakkan VP, Cornish TC, Boeke JD, Burns KH.

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


URI Regulates KAP1 Phosphorylation and Transcriptional Repression via PP2A Phosphatase in Prostate Cancer Cells.

Mita P, Savas JN, Briggs EM, Ha S, Gnanakkan V, Yates JR 3rd, Robins DM, David G, Boeke JD, Garabedian MJ, Logan SK.

J Biol Chem. 2016 Dec 2;291(49):25516-25528. Epub 2016 Oct 25.


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

Mita P, Lhakhang T, Li D, Eichinger DJ, Fenyo D, Boeke JD.

Biol Proced Online. 2016 Aug 15;18:16. doi: 10.1186/s12575-016-0046-x. eCollection 2016.


Meeting Report: The Role of the Mobilome in Cancer.

Ardeljan D, Taylor MS, Burns KH, Boeke JD, Espey MG, Woodhouse EC, Howcroft TK.

Cancer Res. 2016 Aug 1;76(15):4316-9. doi: 10.1158/0008-5472.CAN-15-3421. Epub 2016 Jul 18.


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

Stracquadanio G, Yang K, Boeke JD, Bader JS.

Bioinformatics. 2016 Nov 15;32(22):3519-3521. Epub 2016 Jul 13.


GENOME ENGINEERING. The Genome Project-Write.

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, Maurano MT, Mitchell LA, Rine J, Rosser S, Sanjana NE, Silver PA, Valle D, Wang H, Way JC, Yang L.

Science. 2016 Jul 8;353(6295):126-7. doi: 10.1126/science.aaf6850. Epub 2016 Jun 2. No abstract available.


Characterization of L1-Ribonucleoprotein Particles.

Taylor MS, LaCava J, Dai L, Mita P, Burns KH, Rout MP, Boeke JD.

Methods Mol Biol. 2016;1400:311-38. doi: 10.1007/978-1-4939-3372-3_20.


How retrotransposons shape genome regulation.

Mita P, Boeke JD.

Curr Opin Genet Dev. 2016 Apr;37:90-100. doi: 10.1016/j.gde.2016.01.001. Epub 2016 Feb 6. Review.


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

Sliva A, Kuang Z, Meluh PB, Boeke JD.

G3 (Bethesda). 2016 Apr 7;6(4):881-92. doi: 10.1534/g3.115.026757.


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

Yang K, Stracquadanio G, Luo J, Boeke JD, Bader JS.

Bioinformatics. 2016 Mar 15;32(6):937-9. doi: 10.1093/bioinformatics/btv664. Epub 2015 Nov 14.


SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes.

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, Xu X, Wang J, Wang J, Yang H, Boeke JD, Bader JS.

Genome Res. 2016 Jan;26(1):36-49. doi: 10.1101/gr.193433.115. Epub 2015 Nov 13.


Much ado about zero.

Boeke JD, Fenyo D.

Cell. 2015 Oct 22;163(3):534-5. doi: 10.1016/j.cell.2015.10.033. Epub 2015 Oct 22.


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

Sliva A, Yang H, Boeke JD, Mathews DJ.

Genetics. 2015 Aug;200(4):1021-8. doi: 10.1534/genetics.115.176370.


Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma.

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, Burns KH.

Nat Med. 2015 Sep;21(9):1060-4. doi: 10.1038/nm.3919. Epub 2015 Aug 10.


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

Taylor MS, Dempsey DR, Hwang Y, Chen Z, Chu N, Boeke JD, Cole PA.

Bioorg Chem. 2015 Oct;62:64-73. doi: 10.1016/j.bioorg.2015.07.003. Epub 2015 Jul 13.


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

Ikushima S, Zhao Y, Boeke JD.

G3 (Bethesda). 2015 Jul 22;5(10):1983-90. doi: 10.1534/g3.114.012765.


H3K36 methylation promotes longevity by enhancing transcriptional fidelity.

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, Gregory BD, Kaeberlein M, Kennedy BK, Boeke JD, Berger SL.

Genes Dev. 2015 Jul 1;29(13):1362-76. doi: 10.1101/gad.263707.115.


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

Mitchell LA, Phillips NA, Lafont A, Martin JA, Cutting R, Boeke JD.

J Vis Exp. 2015 May 25;(99):e52941. doi: 10.3791/52941.


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

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.

Nucleic Acids Res. 2015 Jul 27;43(13):6620-30. doi: 10.1093/nar/gkv466. Epub 2015 May 8.


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

Simoneau A, Delgoshaie N, Celic I, Dai J, Abshiru N, Costantino S, Thibault P, Boeke JD, Verreault A, Wurtele H.

Genetics. 2015 May;200(1):185-205. doi: 10.1534/genetics.115.175919. Epub 2015 Mar 18.

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