Center for Genomically Engineered Organs


Saka SK, Wang Y, Kishi JY, Zhu A, Zeng Y, Xie W, Kirli K, Yapp C, Cicconet M, Beliveau BJ, Lapan SW, Yin S, Lin M, Boyden ES, Kaeser PS, Pihan G, Church GM, Yin P (2019) Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues.  Nat Biotechnol 37:1080

Kalhor R, Kalhor K, Mejia L, Leeper K, Graveline A, Mali P, Church GM. (2018) Developmental barcoding of whole mouse via homing CRISPR. Science. 361:eaat9804

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.  (2018) High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR-Cas9 in yeast. Nat Biotechnol. 36:540

Chavez A, Pruitt BW, Tuttle M, Shapiro RS, Cecchi RJ, Winston J, Turczyk BM, Tung M, Collins JJ, Church GM. (2018) Precise Cas9 targeting enables genomic mutation prevention. Proc Natl Acad Sci U S A. 115:3669

Nivala J, Shipman SL, Church GM. (2018) Spontaneous CRISPR loci generation in vivo by non-canonical spacer integration. Nat Microbiol. 3:310

Iyer EPR, Punthambaker S, Liu S, Jindal K, Farrell M, Murn J, Ferrante T, Rudnicki S, Kohman RE, Wassie AT, Goodwin D, Chen F, Alon S, Sinha A, Milanova D, Aron L, Camplisson C, Skrynnyk A, Reginato PL, Conway N, Aach J, Yankner B, Boyden ES, Church GM (2018) Barcoded oligonucleotides ligated on RNA amplified for multiplex and parallel in-situ analyses

Wang Y, Xie W, Kohman RE, Church GM. (2018) Multiplexed imaging using same species primary antibodies with signal amplification.

Thompson DB, Aboulhouda S, Hysolli E, Smith CJ, Wang S, Castanon O, Church GM. (2018) The Future of Multiplexed Eukaryotic Genome Engineering. ACS Chem Biol. 16;13:313

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. (2018) A CRISPR-Cas9-based gene drive platform for genetic interaction analysis in Candida albicans. Nat Microbiol. 3:73

Carter AC, Chang HY, Church G, Dombkowski A, Ecker JR, Gil E, Giresi PG, Greely H, Greenleaf WJ, Hacohen N, He C, Hill D, Ko J, Kohane I, Kundaje A, Palmer M, Snyder MP, Tung J, Urban A, Vidal M, Wong W.  (2017) Challenges and recommendations for epigenomics in precision health. Nat Biotechnol. 35:1128

Chari R, Church GM. (2017) Beyond editing to writing large genomes. Nat Rev Genet 18:749

Yoon YG, Dai P, Wohlwend J, Chang JB, Marblestone AH, Boyden ES. (2017) Feasibility of 3D Reconstruction of Neural Morphology Using Expansion Microscopy and Barcode-Guided Agglomeration. Front Comput Neurosci. 11:97

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. (2017) Rapid Sequential in Situ Multiplexing with DNA Exchange Imaging in Neuronal Cells and Tissues. Nano Lett. 17:6131

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. (2017) Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9. Science 357:1303

Shipman SL, Nivala J, Macklis JD, Church GM. (2016) Molecular recordings by directed CRISPR spacer acquisition. Science 353:463

Chari R, Yeo NC, Chavez A, Church GM. (2017) sgRNA Scorer 2.0: A Species-Independent Model To Predict CRISPR/Cas9 Activity. ACS Synth Biol 6:902

Adamala KP, Martin-Alarcon DA, Guthrie-Honea KR, Boyden ES. (2017) Engineering genetic circuit interactions within and between synthetic minimal cells. Nat Chem. 9:43

Aach J, Lunshof J, Iyer E, Church G, M. (2017) Addressing the ethical issues raised by synthetic human entities with embryo-like features. eLife pii: e20674. doi: 10.7554/eLife.20674.

Kalhor R, Mali P, Church GM. (2017) Rapidly evolving homing CRISPR barcodes. Nat Methods. 14:195

Kowal EJK, Ter-Ovanesyan D, Regev A, Church GM. (2017) Extracellular Vesicle Isolation and Analysis by Western Blotting. Methods Mol Biol. 1660:143

Wang G, Yang L, Grishin D, Rios X, Ye LY, Hu Y, Li K, Zhang D, Church GM, Pu WT. (2017) Efficient, footprint-free human iPSC genome editing by consolidation of Cas9/CRISPR and piggyBac technologies. Nat Protoc 12:88

Chen F, Wassie AT, Cote AJ, Sinha A, Alon S, Asano S, Daugharthy ER, Chang JB, Marblestone A, Church GM, Raj A4 Boyden ES. (2016) Nanoscale imaging of RNA with expansion microscopy. Nat Methods 13:679

Shipman SL, Nivala J, Macklis JD, Church GM. (2017) CRISPR-Cas encoding of a digital movie into the genomes of a population of living bacteria. Nature 547:345

Chavez A, Tuttle M, Pruitt BW, Ewen-Campen B, Chari R, Ter-Ovanesyan D, Haque SJ, Cecchi RJ, Kowal EJ, Buchthal J, Housden BE, Perrimon N, Collins JJ, Church G. (2016) Comparison of Cas9 activators in multiple species. Nat Methods 13:563

Foundational Publications

Beliveau BJ, Boettiger AN, Avendaño MS, Jungmann R, McCole RB, Joyce EF, Kim-Kiselak C, Bantignies F, Fonseka CY, Erceg J, Hannan MA, Hoang HG, Colognori D, Lee JT, Shih WM, Yin P, Zhuang X, Wu CT. (2015) Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes. Nat Commun. 6:7147

Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Ferrante TC, Terry R, Turczyk BM, Yang JL, Lee HS, Aach J, Zhang K, Church GM. (2015) Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. Nat Protoc. 10(3):442-58.

Chen F, Tillberg PW, Boyden ES. (2015) Optical imaging. Expansion microscopy. Science 347(6221):543

Kolesky DB, Truby RL, Gladman AS, Busbee TA, Homan KA, Lewis JA. (2014) 3D bioprinting of vascularized, heterogeneous cell-laden tissue constructs. Adv Mater. 26(19):3124

Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Yang JL, Ferrante TC, Terry R, Jeanty SS, Li C, Amamoto R, Peters DT, Turczyk BM, Marblestone AH, Inverso SA, Bernard A, Mali P, Rios X, Aach J, Church GM. (2014) Highly multiplexed subcellular RNA sequencing in situ. Science 343(6177):1360