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Predispositional genome sequencing in healthy adults: design, participant characteristics, and early outcomes of the PeopleSeq Consortium.

Zoltick ES, Linderman MD, McGinniss MA, Ramos E, Ball MP, Church GM, Leonard DGB, Pereira S, McGuire AL, Caskey CT, Sanderson SC, Schadt EE, Nielsen DE, Crawford SD, Green RC; PeopleSeq Consortium.

Genome Med. 2019 Feb 27;11(1):10. doi: 10.1186/s13073-019-0619-9.


REST and Neural Gene Network Dysregulation in iPSC Models of Alzheimer's Disease.

Meyer K, Feldman HM, Lu T, Drake D, Lim ET, Ling KH, Bishop NA, Pan Y, Seo J, Lin YT, Su SC, Church GM, Tsai LH, Yankner BA.

Cell Rep. 2019 Jan 29;26(5):1112-1127.e9. doi: 10.1016/j.celrep.2019.01.023.


Significant abundance of cis configurations of coding variants in diploid human genomes.

Hoehe MR, Herwig R, Mao Q, Peters BA, Drmanac R, Church GM, Huebsch T.

Nucleic Acids Res. 2019 Jan 30. doi: 10.1093/nar/gkz031. [Epub ahead of print]


Crystal structure of the Redβ C-terminal domain in complex with λ Exonuclease reveals an unexpected homology with λ Orf and an interaction with Escherichia coli single stranded DNA binding protein.

Caldwell BJ, Zakharova E, Filsinger GT, Wannier TM, Hempfling JP, Chun-Der L, Pei D, Church GM, Bell CE.

Nucleic Acids Res. 2019 Feb 28;47(4):1950-1963. doi: 10.1093/nar/gky1309.


CRISPR-C: circularization of genes and chromosome by CRISPR in human cells.

Møller HD, Lin L, Xiang X, Petersen TS, Huang J, Yang L, Kjeldsen E, Jensen UB, Zhang X, Liu X, Xu X, Wang J, Yang H, Church GM, Bolund L, Regenberg B, Luo Y.

Nucleic Acids Res. 2018 Dec 14;46(22):e131. doi: 10.1093/nar/gky767.


CRISPR Guide RNA Cloning for Mammalian Systems.

Nageshwaran S, Chavez A, Cher Yeo N, Guo X, Lance-Byrne A, Tung A, Collins JJ, Church GM.

J Vis Exp. 2018 Oct 2;(140). doi: 10.3791/57998.


Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow.

Brunk E, Chang RL, Xia J, Hefzi H, Yurkovich JT, Kim D, Buckmiller E, Wang HH, Cho BK, Yang C, Palsson BO, Church GM, Lewis NE.

Proc Natl Acad Sci U S A. 2018 Oct 23;115(43):11096-11101. doi: 10.1073/pnas.1811971115. Epub 2018 Oct 9.


Establishing a Cell-Free Vibrio natriegens Expression System.

Wiegand DJ, Lee HH, Ostrov N, Church GM.

ACS Synth Biol. 2018 Oct 19;7(10):2475-2479. doi: 10.1021/acssynbio.8b00222. Epub 2018 Sep 12.


Developmental barcoding of whole mouse via homing CRISPR.

Kalhor R, Kalhor K, Mejia L, Leeper K, Graveline A, Mali P, Church GM.

Science. 2018 Aug 31;361(6405). pii: eaat9804. doi: 10.1126/science.aat9804. Epub 2018 Aug 9.


Inter-homologue repair in fertilized human eggs?

Egli D, Zuccaro MV, Kosicki M, Church GM, Bradley A, Jasin M.

Nature. 2018 Aug;560(7717):E5-E7. doi: 10.1038/s41586-018-0379-5. Epub 2018 Aug 8. No abstract available.


Biosensor libraries harness large classes of binding domains for construction of allosteric transcriptional regulators.

Juárez JF, Lecube-Azpeitia B, Brown SL, Johnston CD, Church GM.

Nat Commun. 2018 Aug 6;9(1):3101. doi: 10.1038/s41467-018-05525-6.


An enhanced CRISPR repressor for targeted mammalian gene regulation.

Yeo NC, Chavez A, Lance-Byrne A, Chan Y, Menn D, Milanova D, Kuo CC, Guo X, Sharma S, Tung A, Cecchi RJ, Tuttle M, Pradhan S, Lim ET, Davidsohn N, Ebrahimkhani MR, Collins JJ, Lewis NE, Kiani S, Church GM.

Nat Methods. 2018 Aug;15(8):611-616. doi: 10.1038/s41592-018-0048-5. Epub 2018 Jul 16.


Directed differentiation of human induced pluripotent stem cells into mature kidney podocytes and establishment of a Glomerulus Chip.

Musah S, Dimitrakakis N, Camacho DM, Church GM, Ingber DE.

Nat Protoc. 2018 Jul;13(7):1662-1685. doi: 10.1038/s41596-018-0007-8.


Enhanced Bacterial Immunity and Mammalian Genome Editing via RNA-Polymerase-Mediated Dislodging of Cas9 from Double-Strand DNA Breaks.

Clarke R, Heler R, MacDougall MS, Yeo NC, Chavez A, Regan M, Hanakahi L, Church GM, Marraffini LA, Merrill BJ.

Mol Cell. 2018 Jul 5;71(1):42-55.e8. doi: 10.1016/j.molcel.2018.06.005.


Characterizing Protein Kinase Substrate Specificity Using the Proteomic Peptide Library (ProPeL) Approach.

Lubner JM, Balsbaugh JL, Church GM, Chou MF, Schwartz D.

Curr Protoc Chem Biol. 2018 Jun;10(2):e38. doi: 10.1002/cpch.38.


Current CRISPR gene drive systems are likely to be highly invasive in wild populations.

Noble C, Adlam B, Church GM, Esvelt KM, Nowak MA.

Elife. 2018 Jun 19;7. pii: e33423. doi: 10.7554/eLife.33423.


High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR-Cas9 in yeast.

Guo X, Chavez A, Tung A, Chan Y, Kaas C, Yin Y, Cecchi R, Garnier SL, Kelsic ED, Schubert M, DiCarlo JE, Collins JJ, Church GM.

Nat Biotechnol. 2018 Jul;36(6):540-546. doi: 10.1038/nbt.4147. Epub 2018 May 21.


Codon usage of highly expressed genes affects proteome-wide translation efficiency.

Frumkin I, Lajoie MJ, Gregg CJ, Hornung G, Church GM, Pilpel Y.

Proc Natl Acad Sci U S A. 2018 May 22;115(21):E4940-E4949. doi: 10.1073/pnas.1719375115. Epub 2018 May 7.


High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing.

de Paz AM, Cybulski TR, Marblestone AH, Zamft BM, Church GM, Boyden ES, Kording KP, Tyo KEJ.

Nucleic Acids Res. 2018 Jul 27;46(13):e78. doi: 10.1093/nar/gky296.


Simultaneous Discovery of Cell-Free DNA and the Nucleosome Ladder.

Henikoff S, Church GM.

Genetics. 2018 May;209(1):27-29. doi: 10.1534/genetics.118.300775. No abstract available.


The ethics of experimenting with human brain tissue.

Farahany NA, Greely HT, Hyman S, Koch C, Grady C, Pașca SP, Sestan N, Arlotta P, Bernat JL, Ting J, Lunshof JE, Iyer EPR, Hyun I, Capestany BH, Church GM, Huang H, Song H.

Nature. 2018 Apr;556(7702):429-432. doi: 10.1038/d41586-018-04813-x. No abstract available.


An Integrated Genome-wide CRISPRa Approach to Functionalize lncRNAs in Drug Resistance.

Bester AC, Lee JD, Chavez A, Lee YR, Nachmani D, Vora S, Victor J, Sauvageau M, Monteleone E, Rinn JL, Provero P, Church GM, Clohessy JG, Pandolfi PP.

Cell. 2018 Apr 19;173(3):649-664.e20. doi: 10.1016/j.cell.2018.03.052.


Enabling multiplexed testing of pooled donor cells through whole-genome sequencing.

Chan Y, Chan YK, Goodman DB, Guo X, Chavez A, Lim ET, Church GM.

Genome Med. 2018 Apr 19;10(1):31. doi: 10.1186/s13073-018-0541-6.


Response to "Unexpected mutations after CRISPR-Cas9 editing in vivo".

Wilson CJ, Fennell T, Bothmer A, Maeder ML, Reyon D, Cotta-Ramusino C, Fernandez CA, Marco E, Barrera LA, Jayaram H, Albright CF, Cox GF, Church GM, Myer VE.

Nat Methods. 2018 Apr;15(4):236-237. doi: 10.1038/nmeth.4552. Epub 2018 Mar 30. No abstract available.


Precise Cas9 targeting enables genomic mutation prevention.

Chavez A, Pruitt BW, Tuttle M, Shapiro RS, Cecchi RJ, Winston J, Turczyk BM, Tung M, Collins JJ, Church GM.

Proc Natl Acad Sci U S A. 2018 Apr 3;115(14):3669-3673. doi: 10.1073/pnas.1718148115. Epub 2018 Mar 19.


Adaptive evolution of genomically recoded Escherichia coli.

Wannier TM, Kunjapur AM, Rice DP, McDonald MJ, Desai MM, Church GM.

Proc Natl Acad Sci U S A. 2018 Mar 20;115(12):3090-3095. doi: 10.1073/pnas.1715530115. Epub 2018 Feb 13.


Spontaneous CRISPR loci generation in vivo by non-canonical spacer integration.

Nivala J, Shipman SL, Church GM.

Nat Microbiol. 2018 Mar;3(3):310-318. doi: 10.1038/s41564-017-0097-z. Epub 2018 Jan 29.


From Designing the Molecules of Life to Designing Life: Future Applications Derived from Advances in DNA Technologies.

Kohman RE, Kunjapur AM, Hysolli E, Wang Y, Church GM.

Angew Chem Int Ed Engl. 2018 Apr 9;57(16):4313-4328. doi: 10.1002/anie.201707976. Epub 2018 Feb 23. Review.


Engineering posttranslational proofreading to discriminate nonstandard amino acids.

Kunjapur AM, Stork DA, Kuru E, Vargas-Rodriguez O, Landon M, Söll D, Church GM.

Proc Natl Acad Sci U S A. 2018 Jan 16;115(3):619-624. doi: 10.1073/pnas.1715137115. Epub 2018 Jan 4.


The Future of Multiplexed Eukaryotic Genome Engineering.

Thompson DB, Aboulhouda S, Hysolli E, Smith CJ, Wang S, Castanon O, Church GM.

ACS Chem Biol. 2018 Feb 16;13(2):313-325. doi: 10.1021/acschembio.7b00842. Epub 2017 Dec 28.


Efficient in situ barcode sequencing using padlock probe-based BaristaSeq.

Chen X, Sun YC, Church GM, Lee JH, Zador AM.

Nucleic Acids Res. 2018 Feb 28;46(4):e22. doi: 10.1093/nar/gkx1206.


A CRISPR-Cas9-based gene drive platform for genetic interaction analysis in Candida albicans.

Shapiro RS, Chavez A, Porter CBM, Hamblin M, Kaas CS, DiCarlo JE, Zeng G, Xu X, Revtovich AV, Kirienko NV, Wang Y, Church GM, Collins JJ.

Nat Microbiol. 2018 Jan;3(1):73-82. doi: 10.1038/s41564-017-0043-0. Epub 2017 Oct 23.


Mature induced-pluripotent-stem-cell-derived human podocytes reconstitute kidney glomerular-capillary-wall function on a chip.

Musah S, Mammoto A, Ferrante TC, Jeanty SSF, Hirano-Kobayashi M, Mammoto T, Roberts K, Chung S, Novak R, Ingram M, Fatanat-Didar T, Koshy S, Weaver JC, Church GM, Ingber DE.

Nat Biomed Eng. 2017;1. pii: 0069. doi: 10.1038/s41551-017-0069. Epub 2017 May 10.


DNA sequencing at 40: past, present and future.

Shendure J, Balasubramanian S, Church GM, Gilbert W, Rogers J, Schloss JA, Waterston RH.

Nature. 2017 Oct 19;550(7676):345-353. doi: 10.1038/nature24286. Epub 2017 Oct 11. Review.


Corrigendum: An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes.

Cho YS, Kim H, Kim HM, Jho S, Jun J, Lee YJ, Chae KS, Kim CG, Kim S, Eriksson A, Edwards JS, Lee S, Kim BC, Manica A, Oh TK, Church GM, Bhak J.

Nat Commun. 2017 Oct 9;8:16168. doi: 10.1038/ncomms16168.


Heterologous erythromycin production across strain and plasmid construction.

Fang L, Guell M, Church GM, Pfeifer BA.

Biotechnol Prog. 2018 Jan;34(1):271-276. doi: 10.1002/btpr.2567. Epub 2017 Oct 13.


Rapid Sequential in Situ Multiplexing with DNA Exchange Imaging in Neuronal Cells and Tissues.

Wang Y, Woehrstein JB, Donoghue N, Dai M, Avendaño MS, Schackmann RCJ, Zoeller JJ, Wang SSH, Tillberg PW, Park D, Lapan SW, Boyden ES, Brugge JS, Kaeser PS, Church GM, Agasti SS, Jungmann R, Yin P.

Nano Lett. 2017 Oct 11;17(10):6131-6139. doi: 10.1021/acs.nanolett.7b02716. Epub 2017 Oct 2.


A systematic comparison of error correction enzymes by next-generation sequencing.

Lubock NB, Zhang D, Sidore AM, Church GM, Kosuri S.

Nucleic Acids Res. 2017 Sep 6;45(15):9206-9217. doi: 10.1093/nar/gkx691.


Beyond editing to writing large genomes.

Chari R, Church GM.

Nat Rev Genet. 2017 Dec;18(12):749-760. doi: 10.1038/nrg.2017.59. Epub 2017 Aug 30.


Imaging of Isolated Extracellular Vesicles Using Fluorescence Microscopy.

Ter-Ovanesyan D, Kowal EJK, Regev A, Church GM, Cocucci E.

Methods Mol Biol. 2017;1660:233-241. doi: 10.1007/978-1-4939-7253-1_19.


Extracellular Vesicle Isolation and Analysis by Western Blotting.

Kowal EJK, Ter-Ovanesyan D, Regev A, Church GM.

Methods Mol Biol. 2017;1660:143-152. doi: 10.1007/978-1-4939-7253-1_12.


Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9.

Niu D, Wei HJ, Lin L, George H, Wang T, Lee IH, Zhao HY, Wang Y, Kan Y, Shrock E, Lesha E, Wang G, Luo Y, Qing Y, Jiao D, Zhao H, Zhou X, Wang S, Wei H, Güell M, Church GM, Yang L.

Science. 2017 Sep 22;357(6357):1303-1307. doi: 10.1126/science.aan4187. Epub 2017 Aug 10.


Rates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder.

Lim ET, Uddin M, De Rubeis S, Chan Y, Kamumbu AS, Zhang X, D'Gama AM, Kim SN, Hill RS, Goldberg AP, Poultney C, Minshew NJ, Kushima I, Aleksic B, Ozaki N, Parellada M, Arango C, Penzol MJ, Carracedo A, Kolevzon A, Hultman CM, Weiss LA, Fromer M, Chiocchetti AG, Freitag CM; Autism Sequencing Consortium, Church GM, Scherer SW, Buxbaum JD, Walsh CA.

Nat Neurosci. 2017 Sep;20(9):1217-1224. doi: 10.1038/nn.4598. Epub 2017 Jul 17.


Dissecting limiting factors of the Protein synthesis Using Recombinant Elements (PURE) system.

Li J, Zhang C, Huang P, Kuru E, Forster-Benson ETC, Li T, Church GM.

Translation (Austin). 2017 May 9;5(1):e1327006. doi: 10.1080/21690731.2017.1327006. eCollection 2017.


CRISPR-Cas encoding of a digital movie into the genomes of a population of living bacteria.

Shipman SL, Nivala J, Macklis JD, Church GM.

Nature. 2017 Jul 20;547(7663):345-349. doi: 10.1038/nature23017. Epub 2017 Jul 12.


The promise of organ and tissue preservation to transform medicine.

Giwa S, Lewis JK, Alvarez L, Langer R, Roth AE, Church GM, Markmann JF, Sachs DH, Chandraker A, Wertheim JA, Rothblatt M, Boyden ES, Eidbo E, Lee WPA, Pomahac B, Brandacher G, Weinstock DM, Elliott G, Nelson D, Acker JP, Uygun K, Schmalz B, Weegman BP, Tocchio A, Fahy GM, Storey KB, Rubinsky B, Bischof J, Elliott JAW, Woodruff TK, Morris GJ, Demirci U, Brockbank KGM, Woods EJ, Ben RN, Baust JG, Gao D, Fuller B, Rabin Y, Kravitz DC, Taylor MJ, Toner M.

Nat Biotechnol. 2017 Jun 7;35(6):530-542. doi: 10.1038/nbt.3889. Review.


Scalable Device for Automated Microbial Electroporation in a Digital Microfluidic Platform.

Madison AC, Royal MW, Vigneault F, Chen L, Griffin PB, Horowitz M, Church GM, Fair RB.

ACS Synth Biol. 2017 Sep 15;6(9):1701-1709. doi: 10.1021/acssynbio.7b00007. Epub 2017 Jun 7.


Millstone: software for multiplex microbial genome analysis and engineering.

Goodman DB, Kuznetsov G, Lajoie MJ, Ahern BW, Napolitano MG, Chen KY, Chen C, Church GM.

Genome Biol. 2017 May 25;18(1):101. doi: 10.1186/s13059-017-1223-1.


Optimizing complex phenotypes through model-guided multiplex genome engineering.

Kuznetsov G, Goodman DB, Filsinger GT, Landon M, Rohland N, Aach J, Lajoie MJ, Church GM.

Genome Biol. 2017 May 25;18(1):100. doi: 10.1186/s13059-017-1217-z.


Correction: Addressing the ethical issues raised by synthetic human entities with embryo-like features.

Aach J, Lunshof J, Iyer E, Church GM.

Elife. 2017 Apr 13;6. pii: e27642. doi: 10.7554/eLife.27642. No abstract available.

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