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Items: 40

1.

Corrigendum: Engineering and optimising deaminase fusions for genome editing.

Yang L, Briggs AW, Chew WL, Mali P, Guell M, Aach J, Goodman DB, Cox D, Kan Y, Lesha E, Soundararajan V, Zhang F, Church G.

Nat Commun. 2017 Oct 9;8:16169. doi: 10.1038/ncomms16169.

2.

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.

3.

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.

4.

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

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

Elife. 2017 Mar 21;6. pii: e20674. doi: 10.7554/eLife.20674. Erratum in: Elife. 2017 Apr 13;6:.

5.

Engineering and optimising deaminase fusions for genome editing.

Yang L, Briggs AW, Chew WL, Mali P, Guell M, Aach J, Goodman DB, Cox D, Kan Y, Lesha E, Soundararajan V, Zhang F, Church G.

Nat Commun. 2016 Nov 2;7:13330. doi: 10.1038/ncomms13330. Erratum in: Nat Commun. 2017 Oct 09;8:16169.

6.

Genome-wide inactivation of porcine endogenous retroviruses (PERVs).

Yang L, G├╝ell 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.

Science. 2015 Nov 27;350(6264):1101-4. doi: 10.1126/science.aad1191. Epub 2015 Oct 11.

7.

Highly efficient Cas9-mediated transcriptional programming.

Chavez A, Scheiman J, Vora S, Pruitt BW, Tuttle M, P R Iyer E, Lin S, Kiani S, Guzman CD, Wiegand DJ, Ter-Ovanesyan D, Braff JL, Davidsohn N, Housden BE, Perrimon N, Weiss R, Aach J, Collins JJ, Church GM.

Nat Methods. 2015 Apr;12(4):326-8. doi: 10.1038/nmeth.3312. Epub 2015 Mar 2.

8.

Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues.

Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Ferrante TC, Terry R, Turczyk BM, Yang JL, Lee HS, Aach J, Zhang K, Church GM.

Nat Protoc. 2015 Mar;10(3):442-58. doi: 10.1038/nprot.2014.191. Epub 2015 Feb 12.

9.

Targeted and genome-wide sequencing reveal single nucleotide variations impacting specificity of Cas9 in human stem cells.

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.

Nat Commun. 2014 Nov 26;5:5507. doi: 10.1038/ncomms6507.

10.

Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells.

Byrne SM, Ortiz L, Mali P, Aach J, Church GM.

Nucleic Acids Res. 2015 Feb 18;43(3):e21. doi: 10.1093/nar/gku1246. Epub 2014 Nov 20.

11.

Multiplex single-molecule interaction profiling of DNA-barcoded proteins.

Gu L, Li C, Aach J, Hill DE, Vidal M, Church GM.

Nature. 2014 Nov 27;515(7528):554-7. doi: 10.1038/nature13761. Epub 2014 Sep 21.

12.

Improved cell-free RNA and protein synthesis system.

Li J, Gu L, Aach J, Church GM.

PLoS One. 2014 Sep 2;9(9):e106232. doi: 10.1371/journal.pone.0106232. eCollection 2014.

13.

Highly multiplexed subcellular RNA sequencing in situ.

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.

Science. 2014 Mar 21;343(6177):1360-3. doi: 10.1126/science.1250212. Epub 2014 Feb 27.

14.

Rational optimization of tolC as a powerful dual selectable marker for genome engineering.

Gregg CJ, Lajoie MJ, Napolitano MG, Mosberg JA, Goodman DB, Aach J, Isaacs FJ, Church GM.

Nucleic Acids Res. 2014 Apr;42(7):4779-90. doi: 10.1093/nar/gkt1374. Epub 2014 Jan 22.

15.

On the design of clone-based haplotyping.

Lo C, Liu R, Lee J, Robasky K, Byrne S, Lucchesi C, Aach J, Church G, Bafna V, Zhang K.

Genome Biol. 2013;14(9):R100.

16.

Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9.

Li JF, Norville JE, Aach J, McCormack M, Zhang D, Bush J, Church GM, Sheen J.

Nat Biotechnol. 2013 Aug;31(8):688-91. doi: 10.1038/nbt.2654. No abstract available.

17.

Optimization of scarless human stem cell genome editing.

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.

Nucleic Acids Res. 2013 Oct;41(19):9049-61. doi: 10.1093/nar/gkt555. Epub 2013 Jul 31.

18.

CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering.

Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM.

Nat Biotechnol. 2013 Sep;31(9):833-8. doi: 10.1038/nbt.2675. Epub 2013 Aug 1.

19.

Barcoding cells using cell-surface programmable DNA-binding domains.

Mali P, Aach J, Lee JH, Levner D, Nip L, Church GM.

Nat Methods. 2013 May;10(5):403-6. doi: 10.1038/nmeth.2407. Epub 2013 Mar 17.

20.

Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems.

DiCarlo JE, Norville JE, Mali P, Rios X, Aach J, Church GM.

Nucleic Acids Res. 2013 Apr;41(7):4336-43. doi: 10.1093/nar/gkt135. Epub 2013 Mar 4.

21.

RNA-guided human genome engineering via Cas9.

Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM.

Science. 2013 Feb 15;339(6121):823-6. doi: 10.1126/science.1232033. Epub 2013 Jan 3.

22.

A public resource facilitating clinical use of genomes.

Ball MP, Thakuria JV, Zaranek AW, Clegg T, Rosenbaum AM, Wu X, Angrist M, Bhak J, Bobe J, Callow MJ, Cano C, Chou MF, Chung WK, Douglas SM, Estep PW, Gore A, Hulick P, Labarga A, Lee JH, Lunshof JE, Kim BC, Kim JI, Li Z, Murray MF, Nilsen GB, Peters BA, Raman AM, Rienhoff HY, Robasky K, Wheeler MT, Vandewege W, Vorhaus DB, Yang JL, Yang L, Aach J, Ashley EA, Drmanac R, Kim SJ, Li JB, Peshkin L, Seidman CE, Seo JS, Zhang K, Rehm HL, Church GM.

Proc Natl Acad Sci U S A. 2012 Jul 24;109(30):11920-7. doi: 10.1073/pnas.1201904109. Epub 2012 Jul 13.

23.

Proteome-wide systems analysis of a cellulosic biofuel-producing microbe.

Tolonen AC, Haas W, Chilaka AC, Aach J, Gygi SP, Church GM.

Mol Syst Biol. 2011 Jan 18;7:461. doi: 10.1038/msb.2010.116.

24.

Personal genomes in progress: from the human genome project to the personal genome project.

Lunshof JE, Bobe J, Aach J, Angrist M, Thakuria JV, Vorhaus DB, Hoehe MR, Church GM.

Dialogues Clin Neurosci. 2010;12(1):47-60.

25.

Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human.

Zhang K, Li JB, Gao Y, Egli D, Xie B, Deng J, Li Z, Lee JH, Aach J, Leproust EM, Eggan K, Church GM.

Nat Methods. 2009 Aug;6(8):613-8. doi: 10.1038/nmeth.1357. Epub 2009 Jul 20.

26.

Multiplex padlock targeted sequencing reveals human hypermutable CpG variations.

Li JB, Gao Y, Aach J, Zhang K, Kryukov GV, Xie B, Ahlford A, Yoon JK, Rosenbaum AM, Zaranek AW, LeProust E, Sunyaev SR, Church GM.

Genome Res. 2009 Sep;19(9):1606-15. doi: 10.1101/gr.092213.109. Epub 2009 Jun 12.

27.

Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing.

Li JB, Levanon EY, Yoon JK, Aach J, Xie B, Leproust E, Zhang K, Gao Y, Church GM.

Science. 2009 May 29;324(5931):1210-3. doi: 10.1126/science.1170995.

28.

Identification of molecular markers of bipolar cells in the murine retina.

Kim DS, Ross SE, Trimarchi JM, Aach J, Greenberg ME, Cepko CL.

J Comp Neurol. 2008 Apr 10;507(5):1795-810. doi: 10.1002/cne.21639.

29.

Quantitative morphological signatures define local signaling networks regulating cell morphology.

Bakal C, Aach J, Church G, Perrimon N.

Science. 2007 Jun 22;316(5832):1753-6.

30.

Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability.

Tolonen AC, Aach J, Lindell D, Johnson ZI, Rector T, Steen R, Church GM, Chisholm SW.

Mol Syst Biol. 2006;2:53. Epub 2006 Oct 3.

31.

Long-range polony haplotyping of individual human chromosome molecules.

Zhang K, Zhu J, Shendure J, Porreca GJ, Aach JD, Mitra RD, Church GM.

Nat Genet. 2006 Mar;38(3):382-7. Epub 2006 Feb 19.

PMID:
16493423
32.

Accommodation or prediction?

Aach J, Church GM.

Science. 2005 Jun 3;308(5727):1409-12; author reply 1409-12. No abstract available.

PMID:
15938023
34.

Computational and experimental identification of C. elegans microRNAs.

Grad Y, Aach J, Hayes GD, Reinhart BJ, Church GM, Ruvkun G, Kim J.

Mol Cell. 2003 May;11(5):1253-63.

35.

Automated modelling of signal transduction networks.

Steffen M, Petti A, Aach J, D'haeseleer P, Church G.

BMC Bioinformatics. 2002 Nov 1;3:34.

36.

Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range.

Dudley AM, Aach J, Steffen MA, Church GM.

Proc Natl Acad Sci U S A. 2002 May 28;99(11):7554-9.

37.

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M.

Nat Genet. 2001 Dec;29(4):365-71.

PMID:
11726920
38.

Aligning gene expression time series with time warping algorithms.

Aach J, Church GM.

Bioinformatics. 2001 Jun;17(6):495-508.

PMID:
11395426
39.

Computational comparison of two draft sequences of the human genome.

Aach J, Bulyk ML, Church GM, Comander J, Derti A, Shendure J.

Nature. 2001 Feb 15;409(6822):856-9.

PMID:
11237010
40.

Systematic management and analysis of yeast gene expression data.

Aach J, Rindone W, Church GM.

Genome Res. 2000 Apr;10(4):431-45.

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