1932

Abstract

Measurement of biological systems containing biomolecules and bioparticles is a key task in the fields of analytical chemistry, biology, and medicine. Driven by the complex nature of biological systems and unprecedented amounts of measurement data, artificial intelligence (AI) in measurement science has rapidly advanced from the use of silicon-based machine learning (ML) for data mining to the development of molecular computing with improved sensitivity and accuracy. This review presents an overview of fundamental ML methodologies and discusses their applications in disease diagnostics, biomarker discovery, and imaging analysis. We next provide the working principles of molecular computing using logic gates and arithmetical devices, which can be employed for in situ detection, computation, and signal transduction for biological systems. This review concludes by summarizing the strengths and limitations of AI-involved biological measurement in fundamental and applied research.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-anchem-091520-091450
2021-07-27
2024-04-18
Loading full text...

Full text loading...

/deliver/fulltext/anchem/14/1/annurev-anchem-091520-091450.html?itemId=/content/journals/10.1146/annurev-anchem-091520-091450&mimeType=html&fmt=ahah

Literature Cited

  1. 1. 
    Zhang J, Arbault S, Sojic N, Jiang D. 2019. Electrochemiluminescence imaging for bioanalysis. Annu. Rev. Anal. Chem. 12:275–95
    [Google Scholar]
  2. 2. 
    Luo F, Qin G, Xia T, Fang X. 2020. Single-molecule imaging of protein interactions and dynamics. Annu. Rev. Anal. Chem. 13:337–61
    [Google Scholar]
  3. 3. 
    Ye D, Zuo X, Fan C. 2018. DNA nanotechnology-enabled interfacial engineering for biosensor development. Annu. Rev. Anal. Chem. 11:171–95
    [Google Scholar]
  4. 4. 
    Lian H, He S, Chen C, Yan X 2019. Flow cytometric analysis of nanoscale biological particles and organelles. Annu. Rev. Anal. Chem. 12:389–409
    [Google Scholar]
  5. 5. 
    Chen Z, Chen JJ, Fan R 2019. Single-cell protein secretion detection and profiling. Annu. Rev. Anal. Chem. 12:431–49
    [Google Scholar]
  6. 6. 
    Zhang J, Lin B, Wu L, Huang M, Li X et al. 2020. DNA nanolithography enables a highly ordered recognition interface in a microfluidic chip for the efficient capture and release of circulating tumor cells. Angew. Chem. Int. Ed. 59:14115–19
    [Google Scholar]
  7. 7. 
    Li Y, Liu C, Bai X, Tian F, Hu G, Sun J. 2020. Enantiomorphic microvortex-enabled supramolecular sensing of racemic amino acids by using achiral building blocks. Angew. Chem. Int. Ed. 59:3486–90
    [Google Scholar]
  8. 8. 
    Benenson Y, Gil B, Ben-Dor U, Adar R, Shapiro E. 2004. An autonomous molecular computer for logical control of gene expression. Nature 429:423–29
    [Google Scholar]
  9. 9. 
    Sormanni P, Aprile FA, Vendruscolo M. 2018. Third generation antibody discovery methods: in silico rational design. Chem. Soc. Rev. 47:9137–57
    [Google Scholar]
  10. 10. 
    Nam AS, Kim K-T, Chaligne R, Izzo F, Ang C et al. 2019. Somatic mutations and cell identity linked by Genotyping of Transcriptomes. Nature 571:355–60
    [Google Scholar]
  11. 11. 
    Zhang M, Zou Y, Xu X, Zhang X, Gao M et al. 2020. Highly parallel and efficient single cell mRNA sequencing with paired picoliter chambers. Nat. Commun. 11: 2118.
    [Google Scholar]
  12. 12. 
    Beam AL, Kohane IS. 2018. Big data and machine learning in health care. JAMA 319:1317–18
    [Google Scholar]
  13. 13. 
    Eraslan G, Avsec Ž, Gagneur J, Theis FJ. 2019. Deep learning: new computational modelling techniques for genomics. Nat. Rev. Genet. 20:389–403
    [Google Scholar]
  14. 14. 
    Nam AS, Chaligne R, Landau DA. 2021. Integrating genetic and non-genetic determinants of cancer evolution by single-cell multi-omics. Nat. Rev. Genet. 22:3–18
    [Google Scholar]
  15. 15. 
    Esteva A, Kuprel B, Novoa RA, Ko J, Swetter SM et al. 2017. Dermatologist-level classification of skin cancer with deep neural networks. Nature 542:115–18
    [Google Scholar]
  16. 16. 
    Silver D, Schrittwieser J, Simonyan K, Antonoglou I, Huang A et al. 2017. Mastering the game of Go without human knowledge. Nature 550:354–59
    [Google Scholar]
  17. 17. 
    He J, Baxter SL, Xu J, Xu J, Zhou X, Zhang K. 2019. The practical implementation of artificial intelligence technologies in medicine. Nat. Med. 25:30–36
    [Google Scholar]
  18. 18. 
    Jordan MI, Mitchell TM. 2015. Machine learning: trends, perspectives, and prospects. Science 349:255–60
    [Google Scholar]
  19. 19. 
    Kalinin SV, Sumpter BG, Archibald RK. 2015. Big–deep–smart data in imaging for guiding materials design. Nat. Mater. 14:973–80
    [Google Scholar]
  20. 20. 
    Lee EY, Fulan BM, Wong GCL Ferguson AL. 2016. Mapping membrane activity in undiscovered peptide sequence space using machine learning italicPNAS 113:13588–93
    [Google Scholar]
  21. 21. 
    Butler KT, Davies DW, Cartwright H, Isayev O, Walsh A. 2018. Machine learning for molecular and materials science. Nature 559:547–55
    [Google Scholar]
  22. 22. 
    Sanchez-Lengeling B, Aspuru-Guzik A. 2018. Inverse molecular design using machine learning: generative models for matter engineering. Science 361:360–65
    [Google Scholar]
  23. 23. 
    Segler MHS, Preuss M, Waller MP. 2018. Planning chemical syntheses with deep neural networks and symbolic AI. Nature 555:604–10
    [Google Scholar]
  24. 24. 
    Bath J, Turberfield AJ. 2007. DNA nanomachines. Nat. Nanotechnol. 2:275–84
    [Google Scholar]
  25. 25. 
    Ruben AJ, Landweber LF. 2000. The past, present and future of molecular computing. Nat. Rev. Mol. Cell Biol. 1:69–72
    [Google Scholar]
  26. 26. 
    Benenson Y. 2012. Biomolecular computing systems: principles, progress and potential. Nat. Rev. Genet. 13:455–68
    [Google Scholar]
  27. 27. 
    Yang F, Zuo X, Fan C, Zhang X-E. 2018. Biomacromolecular nanostructures-based interfacial engineering: from precise assembly to precision biosensing. Natl. Sci. Rev. 5:740–55
    [Google Scholar]
  28. 28. 
    Song P, Shen J, Ye D, Dong B, Wang F et al. 2020. Programming bulk enzyme heterojunctions for biosensor development with tetrahedral DNA framework. Nat. Commun. 11:838
    [Google Scholar]
  29. 29. 
    Shaoning P, Ozawa S, Kasabov N. 2005. Incremental linear discriminant analysis for classification of data streams. IEEE Trans. Syst. Man Cybern. B 35:905–14
    [Google Scholar]
  30. 30. 
    Suykens JAK, Vandewalle J. 1999. Least squares support vector machine classifiers. Neural Process. Lett. 9:293–300
    [Google Scholar]
  31. 31. 
    Díaz-Uriarte R, Alvarez de Andrés S. 2006. Gene selection and classification of microarray data using random forest. BMC Bioinform. 7:3
    [Google Scholar]
  32. 32. 
    Schmidhuber J. 2015. Deep learning in neural networks: an overview. Neural Netw 61:85–117
    [Google Scholar]
  33. 33. 
    Mai Q. 2013. A review of discriminant analysis in high dimensions. WIREs Comput. Stat. 5:190–97
    [Google Scholar]
  34. 34. 
    Noble WS. 2006. What is a support vector machine?. Nat. Biotechnol. 24:1565–67
    [Google Scholar]
  35. 35. 
    Altman N, Krzywinski M. 2017. Ensemble methods: bagging and random forests. Nat. Methods 14:933–34
    [Google Scholar]
  36. 36. 
    Krogh A. 2008. What are artificial neural networks?. Nat. Biotechnol. 26:195–97
    [Google Scholar]
  37. 37. 
    Libbrecht MW, Noble WS. 2015. Machine learning applications in genetics and genomics. Nat. Rev. Genet. 16:321–32
    [Google Scholar]
  38. 38. 
    Käll L, Canterbury JD, Weston J, Noble WS, MacCoss MJ. 2007. Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat. Methods 4:923–25
    [Google Scholar]
  39. 39. 
    Yu K-H, Beam AL, Kohane IS. 2018. Artificial intelligence in healthcare. Nat. Biomed. Eng. 2:719–31
    [Google Scholar]
  40. 40. 
    Ko J, Baldassano SN, Loh P-L, Kording K, Litt B, Issadore D. 2018. Machine learning to detect signatures of disease in liquid biopsies—a user's guide. Lab Chip 18:395–405
    [Google Scholar]
  41. 41. 
    Liu C, Zhao J, Tian F, Chang J, Zhang W, Sun J. 2019. λ-DNA- and aptamer-mediated sorting and analysis of extracellular vesicles. J. Am. Soc. Chem. 141:3817–21
    [Google Scholar]
  42. 42. 
    Zhang P, Wu X, Gardashova G, Yang Y, Zhang Y et al. 2020. Molecular and functional extracellular vesicle analysis using nanopatterned microchips monitors tumor progression and metastasis. Sci. Transl. Med. 12:eaaz2878
    [Google Scholar]
  43. 43. 
    Liu C, Zhao J, Tian F, Cai L, Zhang W et al. 2019. Low-cost thermophoretic profiling of extracellular-vesicle surface proteins for the early detection and classification of cancers. Nat. Biomed. Eng. 3:183–93
    [Google Scholar]
  44. 44. 
    Ko J, Bhagwat N, Yee SS, Ortiz N, Sahmoud A et al. 2017. Combining machine learning and nanofluidic technology to diagnose pancreatic cancer using exosomes. ACS Nano 11:11182–93
    [Google Scholar]
  45. 45. 
    Carter L, Rothwell DG, Mesquita B, Smowton C, Leong HS et al. 2017. Molecular analysis of circulating tumor cells identifies distinct copy-number profiles in patients with chemosensitive and chemorefractory small-cell lung cancer. Nat. Med. 23:114–19
    [Google Scholar]
  46. 46. 
    Ramaswamy S, Tamayo P, Rifkin R, Mukherjee S, Yeang C-H et al. 2001. Multiclass cancer diagnosis using tumor gene expression signatures italicPNAS 9815149–54
    [Google Scholar]
  47. 47. 
    Zviran A, Schulman RC, Shah M, Hill STK, Deochand S et al. 2020. Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring. Nat. Med. 26:1114–24
    [Google Scholar]
  48. 48. 
    Nassiri F, Chakravarthy A, Feng S, Shen SY, Nejad R et al. 2020. Detection and discrimination of intracranial tumors using plasma cell-free DNA methylomes. Nat. Med. 26:1044–47
    [Google Scholar]
  49. 49. 
    Cohen JD, Li L, Wang Y, Thoburn C, Afsari B et al. 2018. Detection and localization of surgically resectable cancers with a multi-analyte blood test. Science 359:926–30
    [Google Scholar]
  50. 50. 
    Titano JJ, Badgeley M, Schefflein J, Pain M, Su A et al. 2018. Automated deep-neural-network surveillance of cranial images for acute neurologic events. Nat. Med. 24:1337–41
    [Google Scholar]
  51. 51. 
    Kermany DS, Goldbaum M, Cai W, Valentim CCS, Liang H et al. 2018. Identifying medical diagnoses and treatable diseases by image-based deep learning. Cell 172:1122–31.e9
    [Google Scholar]
  52. 52. 
    Nam JG, Park S, Hwang EJ, Lee JH, Jin K-N et al. 2019. Development and validation of deep learning–based automatic detection algorithm for malignant pulmonary nodules on chest radiographs. Radiology 290:218–28
    [Google Scholar]
  53. 53. 
    Gulshan V, Peng L, Coram M, Stumpe MC, Wu D et al. 2016. Development and validation of a deep learning algorithm for detection of diabetic retinopathy in retinal fundus photographs. JAMA 316:2402–10
    [Google Scholar]
  54. 54. 
    Poplin R, Varadarajan AV, Blumer K, Liu Y, McConnell MV et al. 2018. Prediction of cardiovascular risk factors from retinal fundus photographs via deep learning. Nat. Biomed. Eng. 2:158–64
    [Google Scholar]
  55. 55. 
    De Fauw J, Ledsam JR, Romera-Paredes B, Nikolov S, Tomasev N et al. 2018. Clinically applicable deep learning for diagnosis and referral in retinal disease. Nat. Med. 24:1342–50
    [Google Scholar]
  56. 56. 
    Coudray N, Ocampo PS, Sakellaropoulos T, Narula N, Snuderl M et al. 2018. Classification and mutation prediction from non–small cell lung cancer histopathology images using deep learning. Nat. Med. 24:1559–67
    [Google Scholar]
  57. 57. 
    Kather JN, Pearson AT, Halama N, Jäger D, Krause J et al. 2019. Deep learning can predict microsatellite instability directly from histology in gastrointestinal cancer. Nat. Med. 25:1054–56
    [Google Scholar]
  58. 58. 
    Chen PHC, Gadepalli K, MacDonald R, Liu Y, Kadowaki S et al. 2019. An augmented reality microscope with real-time artificial intelligence integration for cancer diagnosis. Nat. Med. 25:1453–57
    [Google Scholar]
  59. 59. 
    Hollon TC, Pandian B, Adapa AR, Urias E, Save AV et al. 2020. Near real-time intraoperative brain tumor diagnosis using stimulated Raman histology and deep neural networks. Nat. Med. 26:52–58
    [Google Scholar]
  60. 60. 
    Lever J, Krzywinski M, Altman N. 2017. Principal component analysis. Nat. Methods 14:641–42
    [Google Scholar]
  61. 61. 
    Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J et al. 2005. MicroRNA expression profiles classify human cancers. Nature 435:834–38
    [Google Scholar]
  62. 62. 
    D'Haeseleer P. 2005. How does gene expression clustering work?. Nat. Biotechnol. 23:1499–501
    [Google Scholar]
  63. 63. 
    Belkina AC, Ciccolella CO, Anno R, Halpert R, Spidlen J, Snyder-Cappione JE. 2019. Automated optimized parameters for T-distributed stochastic neighbor embedding improve visualization and analysis of large datasets. Nat. Commun. 10:5415
    [Google Scholar]
  64. 64. 
    Abdi H, Williams LJ. 2010. Principal component analysis. WIREs Comput. Stat. 2:433–59
    [Google Scholar]
  65. 65. 
    Daxin J, Chun T, Aidong Z 2004. Cluster analysis for gene expression data: a survey. IEEE Trans. Knowl. Data Eng. 16:1370–86
    [Google Scholar]
  66. 66. 
    Altman N, Krzywinski M. 2017. Clustering. Nat. Methods 14:545–46
    [Google Scholar]
  67. 67. 
    Alshawaqfeh M, Bashaireh A, Serpedin E, Suchodolski J. 2017. Consistent metagenomic biomarker detection via robust PCA. Biol. Direct 12:4
    [Google Scholar]
  68. 68. 
    Veyel D, Wenger K, Broermann A, Bretschneider T, Luippold AH et al. 2020. Biomarker discovery for chronic liver diseases by multi-omics—a preclinical case study. Sci. Rep. 10:1314
    [Google Scholar]
  69. 69. 
    Sinkala M, Mulder N, Martin D. 2020. Machine learning and network analyses reveal disease subtypes of pancreatic cancer and their molecular characteristics. Sci. Rep. 10:1212
    [Google Scholar]
  70. 70. 
    Kobak D, Berens P. 2019. The art of using t-SNE for single-cell transcriptomics. Nat. Commun. 10:5416
    [Google Scholar]
  71. 71. 
    Cao J, Spielmann M, Qiu X, Huang X, Ibrahim DM et al. 2019. The single-cell transcriptional landscape of mammalian organogenesis. Nature 566:496–502
    [Google Scholar]
  72. 72. 
    Papalexi E, Satija R. 2018. Single-cell RNA sequencing to explore immune cell heterogeneity. Nat. Rev. Immunol. 18:35–45
    [Google Scholar]
  73. 73. 
    de Silva AP, Uchiyama S. 2007. Molecular logic and computing. Nat. Nanotechnol. 2:399–410
    [Google Scholar]
  74. 74. 
    Culler SJ, Hoff KG, Smolke CD. 2010. Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science 330:1251–55
    [Google Scholar]
  75. 75. 
    Elbaz J, Lioubashevski O, Wang F, Remacle F, Levine RD, Willner I. 2010. DNA computing circuits using libraries of DNAzyme subunits. Nat. Nanotechnol. 5:417–22
    [Google Scholar]
  76. 76. 
    Chen Z, Kibler RD, Hunt A, Busch F, Pearl J et al. 2020. De novo design of protein logic gates. Science 368:78–84
    [Google Scholar]
  77. 77. 
    Basu S, Gerchman Y, Collins CH, Arnold FH, Weiss R. 2005. A synthetic multicellular system for programmed pattern formation. Nature 434:1130–34
    [Google Scholar]
  78. 78. 
    Isaacs FJ, Dwyer DJ, Collins JJ. 2006. RNA synthetic biology. Nat. Biotechnol. 24:545–54
    [Google Scholar]
  79. 79. 
    Davidson EA, Ellington AD. 2007. Synthetic RNA circuits. Nat. Chem. Biol. 3:23–28
    [Google Scholar]
  80. 80. 
    Rinaudo K, Bleris L, Maddamsetti R, Subramanian S, Weiss R, Benenson Y. 2007. A universal RNAi-based logic evaluator that operates in mammalian cells. Nat. Biotechnol. 25:795–801
    [Google Scholar]
  81. 81. 
    Win MN, Smolke CD. 2008. Higher-order cellular information processing with synthetic RNA devices. Science 322:456–60
    [Google Scholar]
  82. 82. 
    Skerker JM, Perchuk BS, Siryaporn A, Lubin EA, Ashenberg O et al. 2008. Rewiring the specificity of two-component signal transduction systems. Cell 133:1043–54
    [Google Scholar]
  83. 83. 
    Ye D, Li M, Zhai T, Song P, Song L et al. 2020. Encapsulation and release of living tumor cells using hydrogels with the hybridization chain reaction. Nat. Protoc. 15:2163–85
    [Google Scholar]
  84. 84. 
    Adleman L. 1994. Molecular computation of solutions to combinatorial problems. Science 266:1021–24
    [Google Scholar]
  85. 85. 
    Seelig G, Soloveichik D, Zhang DY, Winfree E. 2006. Enzyme-free nucleic acid logic circuits. Science 314:1585–88
    [Google Scholar]
  86. 86. 
    Zhang DY, Turberfield AJ, Yurke B, Winfree E. 2007. Engineering entropy-driven reactions and networks catalyzed by DNA. Science 318:1121–25
    [Google Scholar]
  87. 87. 
    Lipton R. 1995. DNA solution of hard computational problems. Science 268:542–45
    [Google Scholar]
  88. 88. 
    Faulhammer D, Cukras AR, Lipton RJ Landweber LF. 2000. Molecular computation: RNA solutions to chess problems PNAS 97:1385–89
    [Google Scholar]
  89. 89. 
    You M, Lyu Y, Han D, Qiu L, Liu Q et al. 2017. DNA probes for monitoring dynamic and transient molecular encounters on live cell membranes. Nat. Nanotechnol. 12:453–59
    [Google Scholar]
  90. 90. 
    Rudchenko M, Taylor S, Pallavi P, Dechkovskaia A, Khan S et al. 2013. Autonomous molecular cascades for evaluation of cell surfaces. Nat. Nanotechnol. 8:580–86
    [Google Scholar]
  91. 91. 
    Morihiro K, Ankenbruck N, Lukasak B, Deiters A. 2017. Small molecule release and activation through DNA computing. J. Am. Soc. Chem. 139:13909–15
    [Google Scholar]
  92. 92. 
    Li J, Mo L, Lu C-H, Fu T, Yang H-H, Tan W 2016. Functional nucleic acid-based hydrogels for bioanalytical and biomedical applications. Chem. Soc. Rev. 45:1410–31
    [Google Scholar]
  93. 93. 
    Han D, Qi X, Myhrvold C, Wang B, Dai M et al. 2017. Single-stranded DNA and RNA origami. Science 358:eaao2648
    [Google Scholar]
  94. 94. 
    Mao C, LaBean TH, Reif JH, Seeman NC. 2000. Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature 407:493–96
    [Google Scholar]
  95. 95. 
    Friedland AE, Lu TK, Wang X, Shi D, Church G, Collins JJ. 2009. Synthetic gene networks that count. Science 324:1199–202
    [Google Scholar]
  96. 96. 
    Voigt CA, Keasling JD. 2005. Programming cellular function. Nat. Chem. Biol. 1:304–7
    [Google Scholar]
  97. 97. 
    Xie Z, Wroblewska L, Prochazka L, Weiss R, Benenson Y. 2011. Multi-input RNAi-based logic circuit for identification of specific cancer cells. Science 333:1307–11
    [Google Scholar]
  98. 98. 
    Adar R, Benenson Y, Linshiz G, Rosner A, Tishby N Shapiro E. 2004. Stochastic computing with biomolecular automata PNAS 101:9960–65
    [Google Scholar]
  99. 99. 
    Han D, Zhu G, Wu C, Zhu Z, Chen T et al. 2013. Engineering a cell-surface aptamer circuit for targeted and amplified photodynamic cancer therapy. ACS Nano 7:2312–19
    [Google Scholar]
  100. 100. 
    You M, Zhu G, Chen T, Donovan MJ, Tan W. 2015. Programmable and multiparameter DNA-based logic platform for cancer recognition and targeted therapy. J. Am. Soc. Chem. 137:667–74
    [Google Scholar]
  101. 101. 
    Mager MD, LaPointe V, Stevens MM. 2011. Exploring and exploiting chemistry at the cell surface. Nat. Chem. 3:582–89
    [Google Scholar]
  102. 102. 
    Chang X, Zhang C, Lv C, Sun Y, Zhang M et al. 2019. Construction of a multiple-aptamer-based DNA logic device on live cell membranes via associative toehold activation for accurate cancer cell identification. J. Am. Soc. Chem. 141:12738–43
    [Google Scholar]
  103. 103. 
    Li L, Chen X, Cui C, Pan X, Li X et al. 2019. Aptamer displacement reaction from live-cell surfaces and its applications. J. Am. Soc. Chem. 141:17174–79
    [Google Scholar]
  104. 104. 
    Dirks RM Pierce NA. 2004. Triggered amplification by hybridization chain reaction italicPNAS 101:15275–78
    [Google Scholar]
  105. 105. 
    Choi HMT, Chang JY, Trinh LA, Padilla JE, Fraser SE, Pierce NA. 2010. Programmable in situ amplification for multiplexed imaging of mRNA expression. Nat. Biotechnol. 28:1208–12
    [Google Scholar]
  106. 106. 
    You M, Peng L, Shao N, Zhang L, Qiu L et al. 2014. DNA “nano-claw”: logic-based autonomous cancer targeting and therapy. J. Am. Soc. Chem. 136:1256–59
    [Google Scholar]
  107. 107. 
    Meng H-M, Liu H, Kuai H, Peng R, Mo L, Zhang X-B. 2016. Aptamer-integrated DNA nanostructures for biosensing, bioimaging and cancer therapy. Chem. Soc. Rev. 45:2583–602
    [Google Scholar]
  108. 108. 
    Peng R, Zheng X, Lyu Y, Xu L, Zhang X et al. 2018. Engineering a 3D DNA-logic gate nanomachine for bispecific recognition and computing on target cell surfaces. J. Am. Soc. Chem. 140:9793–96
    [Google Scholar]
  109. 109. 
    Ren K, Xu Y, Liu Y, Yang M, Ju H 2018. A responsive “nano string light” for highly efficient mRNA imaging in living cells via accelerated DNA cascade reaction. ACS Nano 12:263–71
    [Google Scholar]
  110. 110. 
    Miyamoto T, DeRose R, Suarez A, Ueno T, Chen M et al. 2012. Rapid and orthogonal logic gating with a gibberellin-induced dimerization system. Nat. Chem. Biol. 8:465–70
    [Google Scholar]
  111. 111. 
    Liang H, Chen S, Li P, Wang L, Li J et al. 2018. Nongenetic approach for imaging protein dimerization by aptamer recognition and proximity-induced DNA assembly. J. Am. Soc. Chem. 140:4186–90
    [Google Scholar]
  112. 112. 
    Chen S, Xu Z, Yang W, Lin X, Li J et al. 2019. Logic-gate-actuated DNA-controlled receptor assembly for the programmable modulation of cellular signal transduction. Angew. Chem. Int. Ed. 58:18186–90
    [Google Scholar]
  113. 113. 
    Wang L, Li W, Sun J, Zhang S-Y, Yang S et al. 2018. Imaging of receptor dimers in zebrafish and living cells via aptamer recognition and proximity-induced hybridization chain reaction. Anal. Chem. 90:14433–38
    [Google Scholar]
  114. 114. 
    Gong X, Wei J, Liu J, Li R, Liu X, Wang F. 2019. Programmable intracellular DNA biocomputing circuits for reliable cell recognitions. Chem. Sci. 10:2989–97
    [Google Scholar]
  115. 115. 
    Du Y, Peng P, Li T. 2019. DNA logic operations in living cells utilizing lysosome-recognizing framework nucleic acid nanodevices for subcellular imaging. ACS Nano 13:5778–84
    [Google Scholar]
  116. 116. 
    Wang H, Peng P, Wang Q, Du Y, Tian Z, Li T. 2020. Environment-recognizing DNA-computation circuits for the intracellular transport of molecular payloads for mRNA imaging. Angew. Chem. Int. Ed. 59:6099–107
    [Google Scholar]
  117. 117. 
    Tam DY, Dai Z, Chan MS, Liu LS, Cheung MC et al. 2016. A reversible DNA logic gate platform operated by one- and two-photon excitations. Angew. Chem. Int. Ed. 55:164–68
    [Google Scholar]
  118. 118. 
    Liang L, Li J, Li Q, Huang Q, Shi J et al. 2014. Single-particle tracking and modulation of cell entry pathways of a tetrahedral DNA nanostructure in live cells. Angew. Chem. Int. Ed. 53:7745–50
    [Google Scholar]
  119. 119. 
    Green AA, Kim J, Ma D, Silver PA, Collins JJ, Yin P. 2017. Complex cellular logic computation using ribocomputing devices. Nature 548:117–21
    [Google Scholar]
  120. 120. 
    Wang SS, Ellington AD. 2019. Pattern generation with nucleic acid chemical reaction networks. Chem. Rev. 119:6370–83
    [Google Scholar]
  121. 121. 
    Simmel FC, Yurke B, Singh HR. 2019. Principles and applications of nucleic acid strand displacement reactions. Chem. Rev. 119:6326–69
    [Google Scholar]
  122. 122. 
    Qian L, Winfree E, Bruck J. 2011. Neural network computation with DNA strand displacement cascades. Nature 475:368–72
    [Google Scholar]
  123. 123. 
    Lopez R, Wang R, Seelig G. 2018. A molecular multi-gene classifier for disease diagnostics. Nat. Chem. 10:746–54
    [Google Scholar]
  124. 124. 
    Su H, Xu J, Wang Q, Wang F, Zhou X 2019. High-efficiency and integrable DNA arithmetic and logic system based on strand displacement synthesis. Nat. Commun. 10:5390
    [Google Scholar]
  125. 125. 
    Moerman PG, Schulman R. 2020. DNA computation improves diagnostic workflows. Nat. Nanotechnol. 15:626–27
    [Google Scholar]
  126. 126. 
    Zhang C, Zhao Y, Xu X, Xu R, Li H et al. 2020. Cancer diagnosis with DNA molecular computation. Nat. Nanotechnol. 15:709–15
    [Google Scholar]
  127. 127. 
    Camacho DM, Collins KM, Powers RK, Costello JC, Collins JJ. 2018. Next-generation machine learning for biological networks. Cell 173:1581–92
    [Google Scholar]
  128. 128. 
    Wang M, Wang T, Cai P, Chen X 2019. Nanomaterials discovery and design through machine learning. Small Methods 3:1900025
    [Google Scholar]
  129. 129. 
    Topol EJ. 2019. High-performance medicine: the convergence of human and artificial intelligence. Nat. Med. 25:44–56
    [Google Scholar]
  130. 130. 
    Merritt CR, Ong GT, Church SE, Barker K, Danaher P et al. 2020. Multiplex digital spatial profiling of proteins and RNA in fixed tissue. Nat. Biotechnol. 38:586–99
    [Google Scholar]
/content/journals/10.1146/annurev-anchem-091520-091450
Loading
/content/journals/10.1146/annurev-anchem-091520-091450
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error