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John Dennis Aach, PH.D.

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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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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. 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. Corrigendum: Engineering and optimising deaminase fusions for genome editing. Nat Commun. 2017 10 09; 8:16169. PMID: 28991237.
    Citations:    Fields:    
  2. Kuznetsov G, Goodman DB, Filsinger GT, Landon M, Rohland N, Aach J, Lajoie MJ, Church GM. Optimizing complex phenotypes through model-guided multiplex genome engineering. Genome Biol. 2017 05 25; 18(1):100. PMID: 28545477.
    Citations: 2     Fields:    Translation:Cells
  3. Aach J, Lunshof J, Iyer E, Church GM. Correction: Addressing the ethical issues raised by synthetic human entities with embryo-like features. Elife. 2017 04 13; 6. PMID: 28494857.
    Citations:    Fields:    
  4. Aach J, Lunshof J, Iyer E, Church GM. Addressing the ethical issues raised by synthetic human entities with embryo-like features. Elife. 2017 03 21; 6. PMID: 28494856.
    Citations: 8     Fields:    Translation:Humans
  5. 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. Engineering and optimising deaminase fusions for genome editing. Nat Commun. 2016 11 02; 7:13330. PMID: 27804970.
    Citations: 12     Fields:    Translation:HumansCells
  6. 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. Genome-wide inactivation of porcine endogenous retroviruses (PERVs). Science. 2015 Nov 27; 350(6264):1101-4. PMID: 26456528.
    Citations: 88     Fields:    Translation:HumansAnimalsCells
  7. 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. Highly efficient Cas9-mediated transcriptional programming. Nat Methods. 2015 Apr; 12(4):326-8. PMID: 25730490.
    Citations: 133     Fields:    Translation:HumansCells
  8. Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Ferrante TC, Terry R, Turczyk BM, Yang JL, Lee HS, Aach J, Zhang K, Church GM. Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. Nat Protoc. 2015 Mar; 10(3):442-58. PMID: 25675209.
    Citations: 55     Fields:    
  9. 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. Targeted and genome-wide sequencing reveal single nucleotide variations impacting specificity of Cas9 in human stem cells. Nat Commun. 2014 Nov 26; 5:5507. PMID: 25425480.
    Citations: 43     Fields:    Translation:HumansCells
  10. Byrne SM, Ortiz L, Mali P, Aach J, Church GM. Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells. Nucleic Acids Res. 2015 Feb 18; 43(3):e21. PMID: 25414332.
    Citations: 37     Fields:    Translation:HumansCells
  11. Gu L, Li C, Aach J, Hill DE, Vidal M, Church GM. Multiplex single-molecule interaction profiling of DNA-barcoded proteins. Nature. 2014 Nov 27; 515(7528):554-7. PMID: 25252978.
    Citations: 11     Fields:    Translation:Cells
  12. Li J, Gu L, Aach J, Church GM. Improved cell-free RNA and protein synthesis system. PLoS One. 2014; 9(9):e106232. PMID: 25180701.
    Citations: 13     Fields:    Translation:Cells
  13. 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. Highly multiplexed subcellular RNA sequencing in situ. Science. 2014 Mar 21; 343(6177):1360-3. PMID: 24578530.
    Citations: 153     Fields:    Translation:HumansCells
  14. Gregg CJ, Lajoie MJ, Napolitano MG, Mosberg JA, Goodman DB, Aach J, Isaacs FJ, Church GM. Rational optimization of tolC as a powerful dual selectable marker for genome engineering. Nucleic Acids Res. 2014 Apr; 42(7):4779-90. PMID: 24452804.
    Citations: 11     Fields:    Translation:Cells
  15. 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. PMID: 23907171.
    Citations: 516     Fields:    Translation:HumansCells
  16. 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; 31(8):688-91. PMID: 23929339.
    Citations: 226     Fields:    Translation:AnimalsCells
  17. 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; 41(19):9049-61. PMID: 23907390.
    Citations: 121     Fields:    Translation:HumansCells
  18. 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. PMID: 23503053.
    Citations: 11     Fields:    Translation:Cells
  19. 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; 41(7):4336-43. PMID: 23460208.
    Citations: 311     Fields:    Translation:AnimalsCells
  20. 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. PMID: 23287722.
    Citations: 2153     Fields:    Translation:HumansCells
  21. Lo C, Liu R, Lee J, Robasky K, Byrne S, Lucchesi C, Aach J, Church G, Bafna V, Zhang K. On the design of clone-based haplotyping. Genome Biol. 2013; 14(9):R100. PMID: 24028704.
    Citations: 11     Fields:    Translation:HumansCells
  22. 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. PMID: 22797899.
    Citations: 60     Fields:    Translation:HumansCells
  23. 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. PMID: 21245846.
    Citations: 25     Fields:    Translation:Cells
  24. 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. PMID: 20373666.
    Citations: 17     Fields:    Translation:Humans
  25. 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. PMID: 19620972.
    Citations: 84     Fields:    Translation:HumansCells
  26. 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. PMID: 19525355.
    Citations: 34     Fields:    Translation:HumansAnimalsCells
  27. 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. PMID: 19478186.
    Citations: 218     Fields:    Translation:HumansAnimalsCells
  28. 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. PMID: 18260140.
    Citations: 54     Fields:    Translation:AnimalsCells
  29. 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. PMID: 17588932.
    Citations: 97     Fields:    Translation:AnimalsCells
  30. 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. PMID: 17016519.
    Citations: 44     Fields:    Translation:CellsPHPublic Health
  31. 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. PMID: 16493423.
    Citations: 22     Fields:    Translation:HumansCells
  32. Aach J, Church GM. Accommodation or prediction? Science. 2005 Jun 03; 308(5727):1409-12; author reply 1409-12. PMID: 15938023.
    Citations:    Fields:    
  33. 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 07; 228(1):31-46. PMID: 15064081.
    Citations: 2     Fields:    Translation:Cells
  34. 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. PMID: 12769849.
    Citations: 106     Fields:    Translation:AnimalsCells
  35. Steffen M, Petti A, Aach J, D'haeseleer P, Church G. Automated modelling of signal transduction networks. BMC Bioinformatics. 2002 Nov 01; 3:34. PMID: 12413400.
    Citations: 67     Fields:    Translation:AnimalsCells
  36. 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. PMID: 12032321.
    Citations: 78     Fields:    Translation:AnimalsCells
  37. 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. PMID: 11726920.
    Citations: 1047     Fields:    
  38. Aach J, Church GM. Aligning gene expression time series with time warping algorithms. Bioinformatics. 2001 Jun; 17(6):495-508. PMID: 11395426.
    Citations: 45     Fields:    Translation:Animals
  39. 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. PMID: 11237010.
    Citations: 16     Fields:    Translation:HumansCells
  40. Aach J, Rindone W, Church GM. Systematic management and analysis of yeast gene expression data. Genome Res. 2000 Apr; 10(4):431-45. PMID: 10779484.
    Citations: 31     Fields:    Translation:Animals
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Funded by the NIH/NCATS Clinical and Translational Science Award (CTSA) program, grant number UL1TR001102, and through institutional support from Harvard University, Harvard Medical School, Harvard T.H. Chan School of Public Health, Beth Israel Deaconess Medical Center, Boston Children's Hospital, Brigham and Women's Hospital, Massachusetts General Hospital and the Dana Farber Cancer Institute.