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John Dennis Aach, PH.D.

TitleLecturer on Genetics
InstitutionHarvard Medical School
DepartmentGenetics
AddressHarvard Medical School
Genetics NRB Room 238
77 Avenue Louis Pasteur
Boston MA 02115
Phone617/432-0061
Fax617/432-6513

 Bibliographic 
 selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Li JF, Norville JE, Aach J, McCormack M, Zhang D, Bush J, Church GM, Sheen J. Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat Biotechnol. 2013 Aug 8; 31(8):688-91.
    View in: PubMed
  2. Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol. 2013 Sep; 31(9):833-8.
    View in: PubMed
  3. 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. Optimization of scarless human stem cell genome editing. Nucleic Acids Res. 2013 Oct 1; 41(19):9049-61.
    View in: PubMed
  4. Mali P, Aach J, Lee JH, Levner D, Nip L, Church GM. Barcoding cells using cell-surface programmable DNA-binding domains. Nat Methods. 2013 May; 10(5):403-6.
    View in: PubMed
  5. Dicarlo JE, Norville JE, Mali P, Rios X, Aach J, Church GM. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res. 2013 Apr 1; 41(7):4336-43.
    View in: PubMed
  6. Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. RNA-guided human genome engineering via Cas9. Science. 2013 Feb 15; 339(6121):823-6.
    View in: PubMed
  7. 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. A public resource facilitating clinical use of genomes. Proc Natl Acad Sci U S A. 2012 Jul 24; 109(30):11920-7.
    View in: PubMed
  8. Tolonen AC, Haas W, Chilaka AC, Aach J, Gygi SP, Church GM. Proteome-wide systems analysis of a cellulosic biofuel-producing microbe. Mol Syst Biol. 2011 Jan 18; 7:461.
    View in: PubMed
  9. Lunshof JE, Bobe J, Aach J, Angrist M, Thakuria JV, Vorhaus DB, Hoehe MR, Church GM. Personal genomes in progress: from the human genome project to the personal genome project. Dialogues Clin Neurosci. 2010; 12(1):47-60.
    View in: PubMed
  10. Zhang K, Li JB, Gao Y, Egli D, Xie B, Deng J, Li Z, Lee JH, Aach J, Leproust EM, Eggan K, Church GM. Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human. Nat Methods. 2009 Aug; 6(8):613-8.
    View in: PubMed
  11. 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. Multiplex padlock targeted sequencing reveals human hypermutable CpG variations. Genome Res. 2009 Sep; 19(9):1606-15.
    View in: PubMed
  12. Li JB, Levanon EY, Yoon JK, Aach J, Xie B, Leproust E, Zhang K, Gao Y, Church GM. Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science. 2009 May 29; 324(5931):1210-3.
    View in: PubMed
  13. Kim DS, Ross SE, Trimarchi JM, Aach J, Greenberg ME, Cepko CL. Identification of molecular markers of bipolar cells in the murine retina. J Comp Neurol. 2008 Apr 10; 507(5):1795-810.
    View in: PubMed
  14. Bakal C, Aach J, Church G, Perrimon N. Quantitative morphological signatures define local signaling networks regulating cell morphology. Science. 2007 Jun 22; 316(5832):1753-6.
    View in: PubMed
  15. Tolonen AC, Aach J, Lindell D, Johnson ZI, Rector T, Steen R, Church GM, Chisholm SW. Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability. Mol Syst Biol. 2006; 2:53.
    View in: PubMed
  16. Zhang K, Zhu J, Shendure J, Porreca GJ, Aach JD, Mitra RD, Church GM. Long-range polony haplotyping of individual human chromosome molecules. Nat Genet. 2006 Mar; 38(3):382-7.
    View in: PubMed
  17. Aach J, Church GM. Accommodation or prediction? Science. 2005 Jun 3; 308(5727):1409-12; author reply 1409-12.
    View in: PubMed
  18. Aach J, Church GM. Mathematical models of diffusion-constrained polymerase chain reactions: basis of high-throughput nucleic acid assays and simple self-organizing systems. J Theor Biol. 2004 May 7; 228(1):31-46.
    View in: PubMed
  19. Grad Y, Aach J, Hayes GD, Reinhart BJ, Church GM, Ruvkun G, Kim J. Computational and experimental identification of C. elegans microRNAs. Mol Cell. 2003 May; 11(5):1253-63.
    View in: PubMed
  20. Steffen M, Petti A, Aach J, D'haeseleer P, Church G. Automated modelling of signal transduction networks. BMC Bioinformatics. 2002 Nov 1; 3:34.
    View in: PubMed
  21. Dudley AM, Aach J, Steffen MA, Church GM. Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc Natl Acad Sci U S A. 2002 May 28; 99(11):7554-9.
    View in: PubMed
  22. 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. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001 Dec; 29(4):365-71.
    View in: PubMed
  23. Aach J, Church GM. Aligning gene expression time series with time warping algorithms. Bioinformatics. 2001 Jun; 17(6):495-508.
    View in: PubMed
  24. Aach J, Bulyk ML, Church GM, Comander J, Derti A, Shendure J. Computational comparison of two draft sequences of the human genome. Nature. 2001 Feb 15; 409(6822):856-9.
    View in: PubMed
  25. Aach J, Rindone W, Church GM. Systematic management and analysis of yeast gene expression data. Genome Res. 2000 Apr; 10(4):431-45.
    View in: PubMed
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