The CCV Center has ended. As of 10/28/2015 this website will no longer be updated.

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Publications

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Yang L, Güell M, Niu D, George H, Lesha E, Grishin D, Aach J, Shrock E, Xu W, Poci J, Cortazio R, Wilkinson RA, Fishman JA, Church G. (2015) Genome-wide inactivation of porcine endogenous retroviruses (PERVs). Science [Epub ahead of print] PubMed
PubmedCentral pending
Kiani S, Chavez A, Tuttle M, Hall RN, Chari R, Ter-Ovanesyan D, Qian J, Pruitt BW, Beal J, Vora S, Buchthal J, Kowal EJ, Ebrahimkhani MR, Collins JJ, Weiss R, Church GM. (2015) Cas9 gRNA engineering for genome editing, activation and repression. Nat. Methods [Epub ahead of print] PubMed
PubmedCentral pending
Hinson JT, Chopra A, Nafissi N, Polacheck WJ, Benson CC, Swist S, Gorham J, Yang L6, Schafer S7, Sheng CC, Haghighi A, Homsy J, Hubner N, Church G, Cook SA, Linke WA, Chen CS, Seidman JG, Seidman CE. (2015) Titin mutations in iPS cells define sarcomere insufficiency as a cause of dilated cardiomyopathy. Science 349:982 PubMed
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Baltimore BD, Berg P, Botchan M, Carroll D, Charo RA, Church G, Corn JE, Daley GQ, Doudna JA, Fenner M, Greely HT, Jinek M, Martin GS, Penhoet E, Puck J, Sternberg SH, Weissman JS, Yamamoto KR. (2015) A prudent path forward for genomic engineering and germline gene modification. Science 348:36 PubMed
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Tsai SQ, Zheng Z, Nguyen NT, Liebers M, Topkar VV, Thapar V, Wyvekens N, Khayter C, Iafrate AJ, Le LP, Aryee MJ, Joung JK. (2015) GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol. 33(2):187-97. PubMed
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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. PubMed
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Hoehe MR, Church GM, Lehrach H, Kroslak T, Palczewski S, Nowick K, Schulz S, Suk EK, Huebsch T. (2014) Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes. Nat Commun. 5:5569. PubMed
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Yang L, Grishin D, Wang G, Aach J, Zhang CZ, Chari R, Homsy J, Cai X, Zhao Y, Fan JB, Seidman C, Seidman J, Pu W, Church G. (2014) Targeted and genome-wide sequencing reveal single nucleotide variations impacting specificity of Cas9 in human stem cells. Nat Commun. 5:5507. PubMed
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Morris SA, Cahan P, Li H, Zhao AM, San Roman AK, Shivdasani RA, Collins JJ, Daley GQ. (2014) Dissecting engineered cell types and enhancing cell fate conversion via CellNet. Cell 158(4):889-902. PubMed
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Cahan P, Li H, Morris SA, Lummertz da Rocha E, Daley GQ, Collins JJ. (2014) CellNet: network biology applied to stem cell engineering. Cell 158(4):903-15 PubMed
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Busskamp V, Lewis NE, Guye P, Ng AH, Shipman SL, Byrne SM, Sanjana NE, Murn J, Li Y, Li S, Stadler M, Weiss R, Church GM. (2014) Rapid neurogenesis through transcriptional activation in human stem cells. Mol Syst Biol. 10:760 PubMed
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Stern JN, Yaari G, Vander Heiden JA, Church G, Donahue WF, Hintzen RQ, Huttner AJ, Laman JD, Nagra RM, Nylander A, Pitt D, Ramanan S, Siddiqui BA, Vigneault F, Kleinstein SH, Hafler DA, O'Connor KC. (2014) B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes. Sci Transl Med. 6(248):248ra107. PubMed
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Güell M, Yang L, Church GM. (2014) Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA). Bioinformatics 30(20):2968-70. PubMed
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Montague TG, Cruz JM, Gagnon JA, Church GM, Valen E.(2014) CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res. 42(Web Server issue):W401-7. PubMed
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Wang G, McCain ML, Yang L, He A, Pasqualini FS, Agarwal A, Yuan H, Jiang D, Zhang D, Zangi L, Geva J, Roberts AE, Ma Q, Ding J, Chen J, Wang DZ, Li K, Wang J, Wanders RJ, Kulik W, Vaz FM, Laflamme MA, Murry CE, Chien KR, Kelley RI, Church GM, Parker KK, Pu WT.(2014) Modeling the mitochondrial cardiomyopathy of Barth syndrome with induced pluripotent stem cell and heart-on-chip technologies. Nat Med. 20(6):616-23. PubMed
PubmedCentral
Aach J, Mali P, Church GM. (2014) CasFinder: Flexible algorithm for identifying specific Cas9 targets in genomes bioRxiv doi:10.1101/005074 open access article
Tsai SQ, Wyvekens N, Khayter C, Foden JA, Thapar V, Reyon D, Goodwin MJ, Aryee MJ, Joung JK. (2014) Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nat. Biotechnol. 32(6):569-7 PubMed
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Church GM, Elowitz MB, Smolke CD, Voigt CA, Weiss R. (2014) Realizing the potential of synthetic biology. Nat Rev Mol Cell Biol. 15(4):289-94 PubMed
(PubmedCentral pending)
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):1360-3 PubMed
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Fu Y, Sander JD, Reyon D, Cascio VM, Joung JK. (2014) Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat. Biotechnol. 32(3):279-84 PubMed
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Robasky K, Lewis NE, Church GM. (2014) The role of replicates for error mitigation in next-generation sequencing. Nat Rev Genet. 15(1):56-62 PubMed
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Maeder ML, Angstman JF, Richardson ME, Linder SJ, Cascio VM, Tsai SQ, Ho QH, Sander JD, Reyon D, Bernstein BE, Costello JF, Wilkinson MF, Joung JK. (2013) Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins. Nat. Biotechnol. 31(12):1137 PubMed
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Gole J, Gore A, Richards A, Chiu YJ, Fung HL, Bushman D, Chiang HI, Chun J, Lo YH, Zhang K. (2013) Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. Nat. Biotechnol. 31(12):1126 PubMed
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Video
Eroshenko N, Church GM. (2013) Mutants of Cre recombinase with improved accuracy. Nat. Commun. 4:2509 PubMed
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Esvelt KM, Mali P, Braff JL, Moosburner M, Yaung SJ, Church GM. (2013) Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat. Methods. 10(11):1116 PubMed
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Mali P, Esvelt KM, Church GM. (2013) Cas9 as a versatile tool for engineering biology. Nat. Methods. 10(10):957 PubMed
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Mendenhall EM, Williamson KE, Reyon D, Zou JY, Ram O, Joung JK, Bernstein BE. (2013) Locus-specific editing of histone modifications at endogenous enhancers. Nat. Biotechnol. 31(12):1133 PubMed
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Lo C, Liu R, Lee J, Robasky K, Byrne S, Lucchesi C, Aach J, Church GM, Bafna V, Zhang K. (2013) On the design of clone-based haplotyping. Genome Biol. 14(9):R100 PubMed
open access article
Sander JD, Ramirez CL, Linder SJ, Pattanayak V, Shoresh N, Ku M, Foden JA, Reyon D, Bernstein BE, Liu DR, Joung JK. (2013) In silico abstraction of zinc finger nuclease cleavage profiles reveals an expanded landscape of off-target sites. Nucleic Acids Res. 41(19):e181 PubMed
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Konermann S, Brigham MD, Trevino AE, Hsu PD, Heidenreich M, Cong L, Platt RJ, Scott DA, Church GM, Zhang F. (2013) Optical control of mammalian endogenous transcription and epigenetic states. Nature. 500(7463):472-6 PubMed
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Yang L, Guell M, Byrne S, Yang JL, De Los Angeles A, Mali P, Aach J, Kim-Kiselak C, Briggs AW, Rios X, Huang PY, Daley G, Church G. (2013) Optimization of scarless human stem cell genome editing. Nucleic Acids Res. 41(19):9049 PubMed
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Friedland AE, Tzur YB, Esvelt KM, Colaiácovo MP, Church GM, Calarco JA (2013) Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nat. Methods. 10(8):741 PubMed
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Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM. (2013) CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat. Biotechnol. 31(9):822 PubMed
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Fu Y, Foden JA, Khayter C, Maeder ML, Reyon D, Joung JK, Sander JD (2013) High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat. Biotechnol. 31(9):822 PubMed
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Mali P, Aach J, Lee JH, Levner D, Nip L, Church GM (2013) Barcoding cells using cell-surface programmable DNA-binding domains. Nat. Methods. 10(5):403 PubMed
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Dicarlo JE, Norville JE, Mali P, Rios X, Aach J, Church GM (2013) Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res. 41(7):4336 PubMed
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Maeder ML, Linder SJ, Reyon D, Angstman JF, Fu Y, Sander JD, Joung JK (2013) Robust, synergistic regulation of human gene expression using TALE activators. Nat. Methods. 10(3):243 PubMed
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Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ, Sander JD, Peterson RT, Yeh JR, Joung JK (2013) Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat. Biotechnol. 31(3):227 PubMed
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Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM (2013) RNA-guided human genome engineering via Cas9. Science. 39(6121):823 PubMed
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Joung JK, Sander J (2012) TALENs: a widely applicable technology for targeted genome editing. Nat Rev Mol Cell Biol 14(1):49 PubMed
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Briggs AW, Rios X, Chari R, Yang L, Zhang F, Mali P, Church GM (2012) Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers. Nucleic Acids Research 40(15):e117 PubMed
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Ramirez CL, Certo MT, Mussolino C, Goodwin MJ, Cradick TJ, McCaffrey AP, Cathomen T, Scharenberg AM, Joung JK (2012) Engineered zinc finger nickases induce homology-directed repair with reduced mutagenic effects. Nucleic Acids Research 40(12):5560 PubMed
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Reyon D, Tsai SQ, Khayter C, Foden JA, Sander JD, Joung JK (2012) FLASH assembly of TALENs for high-throughput genome editing. Nat. Biotechnol. 30:460 PubMed
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Rios X, Briggs AW, Christodoulou D, Gorham JM, Seidman JG, Church, GM (2012) Stable gene targeting in human cells using single-strand oligonucleotides with modified bases. PLoS One. 7:e36697 PubMed
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Peters BA, Kermani BG, Sparks AB, Alferov O, Hong P, Alexeev A, Jiang Y, Dahl F, Tang YT, Haas J, Robasky K, Zaranek AW, Lee J-H, Ball MP, Peterson JE, Perazich H, Yeung G, Liu J, Chen L, Kennemer MI, Pothuraju K, Konvicka K, Tsoupko-Sitnikov M, Pant KP, Ebert JC, Nilsen GB, Baccash J, Halpern AL, Church GM, Drmanac R (2012) Accurate whole genome sequencing and haplotyping from 10-20 human cells. Nature. 487(7406):190 PubMed
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