References
-
Cameron, D. E., Bashor, C. J. & Collins, J. J. A brief history of synthetic biology. Nat. Rev. Microbiol. 12, 381–390 (2014).
-
Brophy, J. A. N. & Voigt, C. A. Principles of genetic circuit design. Nat. Methods 11, 508–520 (2014).
-
Way, J. C., Collins, J. J., Keasling, J. D. & Silver, P. A. Integrating biological redesign: where synthetic biology came from and where it needs to go. Cell 157, 151–161 (2014).
-
Nielsen, J. & Keasling, J. D. Engineering cellular metabolism. Cell 164, 1185–1197 (2016).
-
Nielsen, A. A. K. et al. Genetic circuit design automation. Science 352, aac7341 (2016).
-
Jones, T. S., Oliveira, S. M. D., Myers, C. J., Voigt, C. A. & Densmore, D. Genetic circuit design automation with Cello 2.0. Nat. Protoc. 17, 1097–1113 (2022).
-
Angermueller, C., Pärnamaa, T., Parts, L. & Stegle, O. Deep learning for computational biology. Mol. Syst. Biol. 12, 878 (2016).
-
Shetty, R. P., Endy, D. & Knight, T. F. Jr. Engineering BioBrick vectors from BioBrick parts. J. Biol. Eng. 2, 5 (2008).
-
Purnick, P. E. M. & Weiss, R. The second wave of synthetic biology: from modules to systems. Nat. Rev. Mol. Cell Biol. 10, 410–422 (2009).
-
Kwok, R. Five hard truths for synthetic biology. Nature 463, 288–290 (2010).
-
Lee, S. Y. et al. A comprehensive metabolic map for production of bio-based chemicals. Nat. Catal. 2, 18–33 (2019).
-
Keasling, J. D. Manufacturing molecules through metabolic engineering. Science 330, 1355–1358 (2010).
-
Khalil, A. S. & Collins, J. J. Synthetic biology: applications come of age. Nat. Rev. Genet. 11, 367–379 (2010).
-
Pei, L., Garfinkel, M. & Schmidt, M. Bottlenecks and opportunities for synthetic biology biosafety standards. Nat. Commun. 13, 2175 (2022).
-
Whitesides, G. M. The origins and the future of microfluidics. Nature 442, 368–373 (2006).
-
Lan, F., Demaree, B., Ahmed, N. & Abate, A. R. Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding. Nat. Biotechnol. 35, 640–646 (2017).
-
Abate, A. R., Hung, T., Mary, P., Agresti, J. J. & Weitz, D. A. High-throughput injection with microfluidics using picoinjectors. Proc. Natl Acad. Sci. USA 107, 19163–19166 (2010).
-
Selberg, J., Gomez, M. & Rolandi, M. The potential for convergence between synthetic biology and bioelectronics. Cell Syst. 7, 231–244 (2018).
-
Rivnay, J. et al. Integrating bioelectronics with cell-based synthetic biology. Nat. Rev. Bioeng. 3, 317–332 (2025).
-
Aghlmand, F. et al. A 65-nm CMOS fluorescence sensor for dynamic monitoring of living cells. IEEE J. Solid-State Circuits 58, 3003–3019 (2023).
-
Lee, H., Liu, Y., Westervelt, R. M. & Ham, D. IC/microfluidic hybrid system for magnetic manipulation of biological cells. IEEE J. Solid-State Circuits 41, 1471–1480 (2006).
-
Ghafar-Zadeh, E., Sawan, M., Chodavarapu, V. P. & Hosseini-Nia, T. Bacteria growth monitoring through a differential CMOS capacitive sensor. IEEE Trans. Biomed. Circuits Syst. 4, 232–238 (2010).
-
Manickam, A. et al. A fully integrated CMOS fluorescence biochip for DNA and RNA testing. IEEE J. Solid-State Circuits 52, 2857–2870 (2017).
-
Zhu, C., Maldonado, J. & Sengupta, K. CMOS-based electrokinetic microfluidics with multi-modal cellular and bio-molecular sensing for end-to-end point-of-care system. IEEE Trans. Biomed. Circuits Syst. 15, 1250–1267 (2021).
-
Inda-Webb, M. E. et al. Sub-1.4 cm3 capsule for detecting labile inflammatory biomarkers in situ. Nature 620, 386–392 (2023).
-
Tschirhart, T. et al. Electronic control of gene expression and cell behaviour in Escherichia coli through redox signalling. Nat. Commun. 8, 14030 (2017).
-
Eddie, B. J., Malanoski, A. P., Onderko, E. L., Phillips, D. A. & Glaven, S. M. Marinobacter atlanticus electrode biofilms differentially regulate gene expression depending on electrode potential and lifestyle. Biofilm 3, 100051 (2021).
-
Riglar, D. T. & Silver, P. A. Engineering bacteria for diagnostic and therapeutic applications. Nat. Rev. Microbiol. 16, 214–225 (2018).
-
Rothschild, L. J. et al. Building synthetic cells—from the technology infrastructure to cellular entities. ACS Synth. Biol. 13, 974–997 (2024).
-
Jung, J. K. et al. Cell-free biosensors for rapid detection of water contaminants. Nat. Biotechnol. 38, 1451–1459 (2020).
-
Takahashi, M. K. et al. A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers. Nat. Commun. 9, 3347 (2018).
-
Chen, Y. et al. Genetic circuit design automation for yeast. Nat. Microbiol. 5, 1349–1360 (2020).
-
Fedorec, A. J. H. et al. Emergent digital bio-computation through spatial diffusion and engineered bacteria. Nat. Commun. 15, 4896 (2024).
-
Sun, G. L., Reynolds, E. E. & Belcher, A. M. Designing yeast as plant-like hyperaccumulators for heavy metals. Nat. Commun. 10, 5080 (2019).
-
van der Meer, J. R. & Belkin, S. Where microbiology meets microengineering: design and applications of reporter bacteria. Nat. Rev. Microbiol. 8, 511–522 (2010).
-
Go´mez, R. et al. Microfluidic biochip for impedance spectroscopy of biological species. Biomed. Microdevices 3, 201–209 (2001).
-
Petchakup, C., Li, K. & Hou, H. Advances in single cell impedance cytometry for biomedical applications. Micromachines 8, 87 (2017).
-
Kang, J., Kim, T., Tak, Y., Lee, J.-H. & Yoon, J. Cyclic voltammetry for monitoring bacterial attachment and biofilm formation. J. Ind. Eng. Chem. 18, 800–807 (2012).
-
Zadeh, E. G., Sawan, M., Jalali, M. & Therriault, D. CMOS-based capacitive sensor array dedicated to microfluidic studies. In 2006 International Workshop on Computer Architecture for Machine Perception and Sensing 42–43 (IEEE, 2006).
-
Valijam, S. et al. Fabricating a dielectrophoretic microfluidic device using 3D-printed moulds and silver conductive paint. Sci. Rep. 13, 9560 (2023).
-
Akabuogu, E. U., Zhang, L., Krašovec, R., Roberts, I. S. & Waigh, T. A. Electrical impedance spectroscopy with bacterial biofilms: neuronal-like behavior. Nano Lett. 24, 2234–2241 (2024).
-
Arduini, F. et al. Origami multiple paper-based electrochemical biosensors for pesticide detection. Biosens. Bioelectron. 126, 346–354 (2019).
-
Yi, C., Li, C.-W., Ji, S. & Yang, M. Microfluidics technology for manipulation and analysis of biological cells. Anal. Chim. Acta 560, 1–23 (2006).
-
Gach, P. C. et al. A droplet microfluidic platform for automating genetic engineering. ACS Synth. Biol. 5, 426–433 (2016).
-
Iwai, K. et al. Scalable and automated CRISPR-based strain engineering using droplet microfluidics. Microsyst. Nanoeng. 8, 31 (2022).
-
Fu, A. Y., Spence, C., Scherer, A., Arnold, F. H. & Quake, S. R. A microfabricated fluorescence-activated cell sorter. Nat. Biotechnol. 17, 1109–1111 (1999).
-
Hatch, A. C. et al. 1-Million droplet array with wide-field fluorescence imaging for digital PCR. Lab Chip 11, 3838–3845 (2011).
-
Bhargava, K. C., Thompson, B. & Malmstadt, N. Discrete elements for 3D microfluidics. Proc. Natl Acad. Sci. USA 111, 15013–15018 (2014).
-
Zeng, Y., Novak, R., Shuga, J., Smith, M. T. & Mathies, R. A. High-performance single cell genetic analysis using microfluidic emulsion generator arrays. Anal. Chem. 82, 3183–3190 (2010).
-
Bennett, M. R. & Hasty, J. Microfluidic devices for measuring gene network dynamics in single cells. Nat. Rev. Genet. 10, 628–638 (2009).
-
Toriello, N. M. et al. Integrated microfluidic bioprocessor for single-cell gene expression analysis. Proc. Natl Acad. Sci. USA 105, 20173–20178 (2008).
-
Leung, K. et al. A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities. Proc. Natl Acad. Sci. USA 109, 7665–7670 (2012).
-
Churski, K. et al. Rapid screening of antibiotic toxicity in an automated microdroplet system. Lab Chip 12, 1629–1637 (2012).
-
Oblath, E. A., Henley, W. H., Alarie, J. P. & Ramsey, J. M. A microfluidic chip integrating DNA extraction and real-time PCR for the detection of bacteria in saliva. Lab Chip 13, 1325–1332 (2013).
-
Lashkaripour, A. et al. Machine learning enables design automation of microfluidic flow-focusing droplet generation. Nat. Commun. 12, 25 (2021).
-
Linshiz, G. et al. End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis. J. Biol. Eng. 10, 3 (2016).
-
Fracassi, C., Postiglione, L., Fiore, G. & di Bernardo, D. Automatic control of gene expression in mammalian cells. ACS Synth. Biol. 5, 296–302 (2015).
-
Wu, L. L., Babikian, S., Li, G.-P. & Bachman, M. Microfluidic printed circuit boards. In 2011 IEEE 61st Electronic Components and Technology Conference (ECTC) 1576–1581 (IEEE, 2011).
-
Husser, M. C., Vo, P. Q. N., Sinha, H., Ahmadi, F. & Shih, S. C. C. An automated induction microfluidics system for synthetic biology. ACS Synth. Biol. 7, 933–944 (2018).
-
Howell, J., Hammarton, T. C., Altmann, Y. & Jimenez, M. High-speed particle detection and tracking in microfluidic devices using event-based sensing. Lab Chip 20, 3024–3035 (2020).
-
de Cesare, I. et al. ChipSeg: an automatic tool to segment bacterial and mammalian cells cultured in microfluidic devices. ACS Omega 6, 2473–2476 (2021).
-
Bachler, S., Haidas, D., Ort, M., Duncombe, T. A. & Dittrich, P. S. Microfluidic platform enables tailored translocation and reaction cascades in nanoliter droplet networks. Commun. Biol. 3, 769 (2020).
-
van Sluijs, B., Maas, R. J. M., van der Linden, A. J., de Greef, T. F. A. & Huck, W. T. S. A microfluidic optimal experimental design platform for forward design of cell-free genetic networks. Nat. Commun. 13, 3626 (2022).
-
Zhao, S. et al. A new design for living cell-based biosensors: microgels with a selectively permeable shell that can harbor bacterial species. Sens. Actuators B Chem. 334, 129648 (2021).
-
Khazim, M., Pedone, E., Postiglione, L., di Bernardo, D. & Marucci, L. A microfluidic/microscopy-based platform for on-chip controlled gene expression in mammalian cells. Methods Mol. Biol. 2229, 205–219 (2021).
-
Ren, Y. et al. A three-in-one microfluidic droplet digital PCR platform for absolute quantitative analysis of DNA. Lab Chip 23, 2521–2530 (2023).
-
Sun, Y. et al. Two-layered microfluidic devices for high-throughput dynamic analysis of synthetic gene circuits in E. coli. ACS Synth. Biol. 11, 3954–3965 (2022).
-
Rahman, K. M. T. & Butzin, N. C. Counter-on-chip for bacterial cell quantification, growth, and live–dead estimations. Sci. Rep. 14, 782 (2024).
-
Pardee, K. et al. Paper-based synthetic gene networks. Cell 159, 940–954 (2014).
-
Dou, M., Dominguez, D. C., Li, X., Sanchez, J. & Scott, G. A versatile PDMS/paper hybrid microfluidic platform for sensitive infectious disease diagnosis. Anal. Chem. 86, 7978–7986 (2014).
-
Delamarche, E., Juncker, D. & Schmid, H. Microfluidics for processing surfaces and miniaturizing biological assays. Adv. Mater. 17, 2911–2933 (2005).
-
Gulati, S. et al. Opportunities for microfluidic technologies in synthetic biology. J. R. Soc. Interface 6, S493–S506 (2009).
-
Xian, Z. et al. A novel microfluidics PMMA/paper hybrid bioimmunosensor for laser-induced fluorescence detection in the determination of α-fetoprotein from serum. Microchem. J. 195, 109476 (2023).
-
Srinivasan, V., Pamula, V., Pollack, M. & Fair, R. A digital microfluidic biosensor for multianalyte detection. In the Sixteenth Annual International Conference on Micro Electro Mechanical Systems 327–330 (IEEE, 2003).
-
Hamedi, M. M. et al. Integrating electronics and microfluidics on paper. Adv. Mater. 28, 5054–5063 (2016).
-
Lee, H., Sun, E., Ham, D. & Weissleder, R. Chip–NMR biosensor for detection and molecular analysis of cells. Nat. Med. 14, 869–874 (2008).
-
Zhou, A. Y., Baruch, M., Ajo-Franklin, C. M. & Maharbiz, M. M. A portable bioelectronic sensing system (BESSY) for environmental deployment incorporating differential microbial sensing in miniaturized reactors. PLoS ONE 12, e0184994 (2017).
-
Madhvapathy, S. R. et al. Miniaturized implantable temperature sensors for the long-term monitoring of chronic intestinal inflammation. Nat. Biomed. Eng. 8, 1040–1052 (2024).
-
Stephenson, A. et al. PurpleDrop: a digital microfluidics-based platform for hybrid molecular–electronics applications. IEEE Micro 40, 76–86 (2020).
-
Cai, R. et al. Creation of a point-of-care therapeutics sensor using protein engineering, electrochemical sensing and electronic integration. Nat. Commun. 15, 1689 (2024).
-
Coelho, B. et al. Hybrid digital-droplet microfluidic chip for applications in droplet digital nucleic acid amplification: design, fabrication and characterization. Sensors 23, 4927 (2023).
-
Bouzid, K., Greener, J., Carrara, S. & Gosselin, B. Portable impedance-sensing device for microorganism characterization in the field. Sci. Rep. 13, 10526 (2023).
-
Jafari, H., Soleymani, L. & Genov, R. 16-Channel CMOS impedance spectroscopy DNA analyzer with dual-slope multiplying ADCs. IEEE Trans. Biomed. Circuits Syst. 6, 468–478 (2012).
-
Manaresi, N. et al. A CMOS chip for individual cell manipulation and detection. IEEE J. Solid-State Circuits 38, 2297–2305 (2003).
-
Luan, L., Evans, R. D., Jokerst, N. M. & Fair, R. B. Integrated optical sensor in a digital microfluidic platform. IEEE Sens. J. 8, 628–635 (2008).
-
Hunt, T. P., Issadore, D. & Westervelt, R. M. Integrated circuit/microfluidic chip to programmably trap and move cells and droplets with dielectrophoresis. Lab Chip 8, 81–87 (2008).
-
Lai, K. Y.-T., Yang, Y.-T. & Lee, C.-Y. An intelligent digital microfluidic processor for biomedical detection. J. Signal Process. Syst. 78, 85–93 (2014).
-
Park, J. et al. Microscale biosensor array based on flexible polymeric platform toward lab-on-a-needle: real-time multiparameter biomedical assays on curved needle surfaces. ACS Sens. 5, 1363–1373 (2020).
-
Khorasani, M., Behnam, M., van den Berg, L., Backhouse, C. J. & Elliott, D. G. High-voltage CMOS controller for microfluidics. IEEE Trans. Biomed. Circuits Syst. 3, 89–96 (2009).
-
Issadore, D., Franke, T., Brown, K. A. & Westervelt, R. M. A microfluidic microprocessor: controlling biomimetic containers and cells using hybrid integrated circuit/microfluidic chips. Lab Chip 10, 2937–2943 (2010).
-
Manickam, A., Chevalier, A., McDermott, M., Ellington, A. D. & Hassibi, A. A CMOS electrochemical impedance spectroscopy (EIS) biosensor array. IEEE Trans. Biomed. Circuits Syst. 4, 379–390 (2010).
-
Bounik, R. et al. A CMOS microelectrode array integrated into an open, continuously perfused microfluidic system. In 2022 IEEE Biomedical Circuits and Systems Conference (BioCAS) 491–494 (IEEE, 2022).
-
Ding, Z., Xu, C., Wang, Y. & Pellegrini, G. Ultra-low-light CMOS biosensor complements microfluidics to achieve portable diagnostics. Procedia Technol. 27, 39–41 (2017).
-
Frey, U. et al. Switch-matrix-based high-density microelectrode array in CMOS technology. IEEE J. Solid-State Circuits 45, 467–482 (2010).
-
Liu, Q. et al. 17.7 Droplet microfluidics co-designed with real-time CMOS luminescence sensing and impedance spectroscopy of 4nl droplets at a 67mm/s velocity. In 2024 IEEE International Solid-State Circuits Conference (ISSCC) 326–328 (IEEE, 2024).
-
Jin, X., Liu, Z., Li, T., Guo, Q. & Yang, J. Online monitoring and portable analytical system with CMOS sensor and microfluidic technology for cell cultivation applications. In 2010 Symposium on Photonics and Optoelectronics 1–4 (IEEE, 2010).
-
Issadore, D., Franke, T., Brown, K. A., Hunt, T. P. & Westervelt, R. M. High-voltage dielectrophoretic and magnetophoretic hybrid integrated circuit/microfluidic chip. J. Microelectromech. Syst. 18, 1220–1225 (2009).
-
Li, R. et al. A flexible and physically transient electrochemical sensor for real-time wireless nitric oxide monitoring. Nat. Commun. 11, 3207 (2020).
-
Uguz, I. et al. Flexible switch matrix addressable electrode arrays with organic electrochemical transistor and pn diode technology. Nat. Commun. 15, 533 (2024).
-
Sawan, M., Miled, M. A. & Ghafar-Zadeh, E. CMOS/microfluidic lab-on-chip for cells-based diagnostic tools. In 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology 5334–5337 (IEEE, 2010).
-
Cornelis, S. et al. Silicon µPCR chip for forensic STR profiling with hybeacon probe melting curves. Sci. Rep. 9, 7341 (2019).
-
Mimee, M. et al. An ingestible bacterial–electronic system to monitor gastrointestinal health. Science 360, 915–918 (2018).
-
Lee, H., Liu, Y., Ham, D. & Westervelt, R. M. Integrated cell manipulation system—CMOS/microfluidic hybrid. Lab Chip 7, 331–337 (2007).
-
Zhou, Q. et al. Miniature magnetic resonance imaging system for in situ monitoring of bacterial growth and biofilm formation. In IEEE Transactions on Biomedical Circuits and Systems 990–1000 (IEEE, 2024).
-
Hall, D. A. et al. A scalable CMOS molecular electronics chip for single-molecule biosensing. IEEE Trans. Biomed. Circuits Syst. 16, 1030–1043 (2022).
-
Huang, Y. & Mason, A. J. Lab-on-CMOS integration of microfluidics and electrochemical sensors. Lab Chip 13, 3929–3934 (2013).
-
Ghafar-Zadeh, E., Sawan, M. & Therriault, D. Novel direct-write CMOS-based laboratory-on-chip: design, assembly and experimental results. Sens. Actuators A Phys. 134, 27–36 (2007).
-
Lee, H., Xu, L., Koh, D., Nyayapathi, N. & Oh, K. Various on-chip sensors with microfluidics for biological applications. Sensors 14, 17008–17036 (2014).
-
Toumazou, C. et al. Simultaneous DNA amplification and detection using a pH-sensing semiconductor system. Nat. Methods 10, 641–646 (2013).
-
Chien, J.-C. et al. A high-throughput flow cytometry-on-a-CMOS platform for single-cell dielectric spectroscopy at microwave frequencies. Lab Chip 18, 2065–2076 (2018).
-
Levine, P. M., Gong, P., Levicky, R. & Shepard, K. L. Active CMOS sensor array for electrochemical biomolecular detection. IEEE J. Solid-State Circuits 43, 1859–1871 (2008).
-
Rosenstein, J. K., Wanunu, M., Merchant, C. A., Drndic, M. & Shepard, K. L. Integrated nanopore sensing platform with sub-microsecond temporal resolution. Nat. Methods 9, 487–492 (2012).
-
Hong, L., Li, H., Yang, H. & Sengupta, K. Fully integrated fluorescence biosensors on-chip employing multi-functional nanoplasmonic optical structures in CMOS. IEEE J. Solid-State Circuits 52, 2388–2406 (2017).
-
Zhu, C., Wen, Y., Liu, T., Yang, H. & Sengupta, K. An ingestible pill with CMOS fluorescence sensor array, bi-directional wireless interface and packaged optics for in-vivo bio-molecular sensing. IEEE Trans. Biomed. Circuits Syst. 17, 257–272 (2023).
-
Bustillo, J., Fife, K., Merriman, B. & Rothberg, J. Development of the ion torrent CMOS chip for DNA sequencing. In 2013 IEEE International Electron Devices Meeting 8.1.1–8.1.4 (IEEE, 2013).
-
Lai, K. Y.-T. et al. A field-programmable lab-on-a-chip with built-in self-test circuit and low-power sensor-fusion solution in 0.35μm standard CMOS process. In 2015 IEEE Asian Solid-State Circuits Conference (A-SSCC) 1–4 (IEEE, 2015).
-
Murali, P. et al. 24.6 A CMOS micro-flow cytometer for magnetic label detection and classification. In 2014 IEEE International Solid-State Circuits Conference Digest of Technical Papers (ISSCC) 422–423 (IEEE, 2014).
-
Singh, R. R., Leng, L., Guenther, A. & Genov, R. A CMOS–microfluidic chemiluminescence contact imaging microsystem. IEEE J. Solid-State Circuits 47, 2822–2833 (2012).
-
Kumashi, S. et al. A CMOS multi-modal electrochemical and impedance cellular sensing array for massively paralleled exoelectrogen screening. IEEE Trans. Biomed. Circuits Syst. 15, 221–234 (2021).
-
Lee, D. et al. A multi-functional CMOS biosensor array with on-chip DEP-assisted sensing for rapid low-concentration analyte detection and close-loop particle manipulation with no external electrodes. IEEE Trans. Biomed. Circuits Syst. 17, 1214–1226 (2023).
-
Kuo, Y.-H., Chen, Y.-S., Huang, P.-C. & Lee, G.-B. A CMOS-based capacitive biosensor for detection of a breast cancer microRNA biomarker. IEEE Open J. Nanotechnol. 1, 157–162 (2020).
-
Murari, K., Etienne-Cummings, R., Thakor, N. V. & Cauwenberghs, G. A CMOS in-pixel CTIA high-sensitivity fluorescence imager. IEEE Trans. Biomed. Circuits Syst. 5, 449–458 (2011).
-
Forouhi, S., Dehghani, R. & Ghafar-Zadeh, E. CMOS based capacitive sensors for life science applications: a review. Sens. Actuators A Phys. 297, 111531 (2019).
-
Vallero, A. et al. Memristive biosensors integration with microfluidic platform. IEEE Trans. Circuits Syst. I Regul. Pap. 63, 2120–2127 (2016).
-
Sun, A. C., Alvarez-Fontecilla, E., Venkatesh, A. G., Aronoff-Spencer, E. & Hall, D. A. High-density redox amplified coulostatic discharge-based biosensor array. IEEE J. Solid-State Circuits 53, 2054–2064 (2018).
-
Tang, H. et al. 2D magnetic sensor array for real-time cell tracking and multi-site detection with increased robustness and flow-rate. In 2019 IEEE Custom Integrated Circuits Conference (CICC) 1–4 (IEEE, 2019).
-
Spyropoulos, G. D., Gelinas, J. N. & Khodagholy, D. Internal ion-gated organic electrochemical transistor: a building block for integrated bioelectronics. Sci. Adv. 5, eaau7378 (2019).
-
Linder, V. et al. Microfluidics/CMOS orthogonal capabilities for cell biology. Biomed. Microdevices 8, 159–166 (2006).
-
Atkinson, J. T. et al. Real-time bioelectronic sensing of environmental contaminants. Nature 611, 548–553 (2022).
-
Hall, D. A., Gaster, R. S., Makinwa, K. A. A., Wang, S. X. & Murmann, B. A 256 pixel magnetoresistive biosensor microarray in 0.18 µm CMOS. IEEE J. Solid-State Circuits 48, 1290–1301 (2013).
-
Fuller, C. W. et al. Molecular electronics sensors on a scalable semiconductor chip: a platform for single-molecule measurement of binding kinetics and enzyme activity. Proc. Natl Acad. Sci. USA 119, e2112812119 (2022).
-
Manickam, A. et al. A fully-electronic charge-based DNA sequencing CMOS biochip. In 2012 Symposium on VLSI Circuits (VLSIC) 126–127 (IEEE, 2012).
-
Manickam, A. et al. A CMOS electrochemical biochip with 32 × 32 three-electrode voltammetry pixels. IEEE J. Solid-State Circuits 54, 2980–2990 (2019).
-
Dragas, J. et al. In vitro multi-functional microelectrode array featuring 59760 electrodes, 2048 electrophysiology channels, stimulation, impedance measurement, and neurotransmitter detection channels. IEEE J. Solid-State Circuits 52, 1576–1590 (2017).
-
Rothe, J., Frey, O., Stettler, A., Chen, Y. & Hierlemann, A. Fully integrated CMOS microsystem for electrochemical measurements on 32 × 32 working electrodes at 90 frames per second. Anal. Chem. 86, 6425–6432 (2014).
-
Wang, H., Mahdavi, A., Tirrell, D. A. & Hajimiri, A. A magnetic cell-based sensor. Lab Chip 12, 4465–4471 (2012).
-
Lee, D. et al. 17.6 Fully integrated CMOS ferrofluidic biomolecular processing platform with on-chip droplet-based manipulation, multiplexing and sensing. In 2024 IEEE International Solid-State Circuits Conference (ISSCC) 324–326 (IEEE, 2024).
-
Hierlemann, A., Frey, U., Hafizovic, S. & Heer, F. Growing cells atop microelectronic chips: interfacing electrogenic cells in vitro with CMOS-based microelectrode arrays. Proc. IEEE 99, 252–284 (2011).
-
Welch, D. & Christen, J. B. Seamless integration of CMOS and microfluidics using flip chip bonding. J. Micromech. Microeng. 23, 035009 (2013).
-
Dong, R., Liu, Y., Mou, L., Deng, J. & Jiang, X. Microfluidics‐based biomaterials and biodevices. Adv. Mater. 31, e1805033 (2018).
-
van Erp, R., Soleimanzadeh, R., Nela, L., Kampitsis, G. & Matioli, E. Co-designing electronics with microfluidics for more sustainable cooling. Nature 585, 211–216 (2020).
-
Sun, T. & Morgan, H. Single-cell microfluidic impedance cytometry: a review. Microfluid. Nanofluid. 8, 423–443 (2010).
-
Ostrov, N. et al. A modular yeast biosensor for low-cost point-of-care pathogen detection. Sci. Adv. 3, e1603221 (2017).
-
Carpenter, A. C., Paulsen, I. T. & Williams, T. C. Blueprints for biosensors: design, limitations, and applications. Genes 9, 375 (2018).
-
Au, A. K., Bhattacharjee, N., Horowitz, L. F., Chang, T. C. & Folch, A. 3D-printed microfluidic automation. Lab Chip 15, 1934–1941 (2015).
-
Paguirigan, A. L. & Beebe, D. J. Microfluidics meet cell biology: bridging the gap by validation and application of microscale techniques for cell biological assays. BioEssays 30, 811–821 (2008).
-
Yan, S., Zhang, J., Yuan, D. & Li, W. Hybrid microfluidics combined with active and passive approaches for continuous cell separation. Electrophoresis 38, 238–249 (2016).
-
Battat, S., Weitz, D. A. & Whitesides, G. M. An outlook on microfluidics: the promise and the challenge. Lab Chip 22, 530–536 (2022).
-
Atkinson, J. T., Chavez, M. S., Niman, C. M. & El‐Naggar, M. Y. Living electronics: a catalogue of engineered living electronic components. Microb. Biotechnol. 16, 507–533 (2022).
-
Diorio, C., Hsu, D. & Figueroa, M. Adaptive CMOS: from biological inspiration to systems-on-a-chip. Proc. IEEE 90, 345–357 (2002).
-
Mosadegh, B., Bersano-Begey, T., Park, J. Y., Burns, M. A. & Takayama, S. Next-generation integrated microfluidic circuits. Lab Chip 11, 2813–2818 (2011).
-
Lashkaripour, A., Silva, R. & Densmore, D. Desktop micromilled microfluidics. Microfluid. Nanofluid. 22, 31 (2018).
-
Khan, S. M., Gumus, A., Nassar, J. M. & Hussain, M. M. CMOS enabled microfluidic systems for healthcare based applications. Adv. Mater. 30, e1705759 (2018).
-
Karim, A. S. et al. Deconstructing synthetic biology across scales: a conceptual approach for training synthetic biologists. Nat. Commun. 15, 5425 (2024).
-
Ma, Y. et al. A review of electrochemical electrodes and readout interface designs for biosensors. IEEE Open J. Solid-State Circuits Soc. 3, 76–88 (2023).
-
Dixon, T. A., Williams, T. C. & Pretorius, I. S. Sensing the future of bio-informational engineering. Nat. Commun. 12, 388 (2021).
-
Datta-Chaudhuri, T., Smela, E. & Abshire, P. A. System-on-chip considerations for heterogeneous integration of CMOS and fluidic bio-interfaces. IEEE Trans. Biomed. Circuits Syst. 10, 1129–1142 (2016).
-
Brooks, S. M. & Alper, H. S. Applications, challenges, and needs for employing synthetic biology beyond the lab. Nat. Commun. 12, 1390 (2021).
-
Steiger, C. et al. Ingestible electronics for diagnostics and therapy. Nat. Rev. Mater. 4, 83–98 (2018).
-
Nadeau, P. et al. Prolonged energy harvesting for ingestible devices. Nat. Biomed. Eng. 1, 0022 (2017).
-
Muluneh, M. & Issadore, D. A multi-scale PDMS fabrication strategy to bridge the size mismatch between integrated circuits and microfluidics. Lab Chip 14, 4552–4558 (2014).
-
Zargaryan, A., Farhoudi, N., Haworth, G., Ashby, J. F. & Au, S. H. Hybrid 3D printed-paper microfluidics. Sci. Rep. 10, 18379 (2020).
-
Huang, H. & Densmore, D. Fluigi. ACM J. Emerg. Technol. Comput. Syst. 11, 1–19 (2014).
-
Kim, S. J. et al. The bottom of the memory hierarchy: semiconductor and DNA data storage. MRS Bull. 48, 547–559 (2023).
-
Ros, P. M., Miccoli, B., Sanginario, A. & Demarchi, D. Low-power architecture for integrated CMOS bio-sensing. In 2017 IEEE Biomedical Circuits and Systems Conference (BioCAS) 1–4 (IEEE, 2017).
-
Perry, J. M., Soffer, G., Jain, R. & Shih, S. C. C. Expanding the limits towards ‘one-pot’ DNA assembly and transformation on a rapid-prototype microfluidic device. Lab Chip 21, 3730–3741 (2021).
-
Ahrar, S., Raje, M., Lee, I. C. & Hui, E. E. Pneumatic computers for embedded control of microfluidics. Sci. Adv. 9, eadg0201 (2023).
-
Iyer, V., Murali, P., Paredes, J., Liepmann, D. & Boser, B. Encapsulation of integrated circuits in plastic microfluidic systems using hot embossing. In 2015 Transducers — 2015 18th International Conference on Solid-State Sensors, Actuators and Microsystems (TRANSDUCERS) 1822–1825 (IEEE, 2015).
-
Gopinathan, K. A., Mishra, A., Mutlu, B. R., Edd, J. F. & Toner, M. A microfluidic transistor for automatic control of liquids. Nature 622, 735–741 (2023).
-
Jang, B. & Hassibi, A. Biosensor systems in standard CMOS processes: fact or fiction? In 2008 IEEE International Symposium on Industrial Electronics 2045–2050 (IEEE, 2008).
-
Singh, R., Manickam, A. & Hassibi, A. CMOS biochips for hypothesis-driven DNA analysis. In 2014 IEEE Biomedical Circuits and Systems Conference (BioCAS) Proceedings 484–487 (IEEE, 2014).
-
Olanrewaju, A., Beaugrand, M., Yafia, M. & Juncker, D. Capillary microfluidics in microchannels: from microfluidic networks to capillaric circuits. Lab Chip 18, 2323–2347 (2018).
-
Li, J., Ha, N. S., ‘Leo’ Liu, T., van Dam, R. M. & Kim, C.-J. ‘C. J. ’ Ionic-surfactant-mediated electro-dewetting for digital microfluidics. Nature 572, 507–510 (2019).
-
Pollack, M. G., Shenderov, A. D. & Fair, R. B. Electrowetting-based actuation of droplets for integrated microfluidics. Lab Chip 2, 96 (2002).
-
Moragues, T. et al. Droplet-based microfluidics. Nat. Rev. Methods Primers 3, 32 (2023).
-
Ding, Y., Howes, P. D. & deMello, A. J. Recent advances in droplet microfluidics. Anal. Chem. 92, 132–149 (2019).
-
Lenshof, A. & Laurell, T. Continuous separation of cells and particles in microfluidic systems. Chem. Soc. Rev. 39, 1203–1217 (2010).
-
Beebe, D. J., Mensing, G. A. & Walker, G. M. Physics and applications of microfluidics in biology. Annu. Rev. Biomed. Eng. 4, 261–286 (2002).
-
Nielsen, J. B. et al. Microfluidics: innovations in materials and their fabrication and functionalization. Anal. Chem. 92, 150–168 (2019).
-
Tsur, E. E. Computer-aided design of microfluidic circuits. Annu. Rev. Biomed. Eng. 22, 285–307 (2020).
-
Sanka, R., Lippai, J., Samarasekera, D., Nemsick, S. & Densmore, D. 3DμF — interactive design environment for continuous flow microfluidic devices. Sci. Rep. 9, 9166 (2019).
-
Squires, T. M. & Quake, S. R. Microfluidics: fluid physics at the nanoliter scale. Rev. Mod. Phys. 77, 977–1026 (2005).
-
Sackmann, E. K., Fulton, A. L. & Beebe, D. J. The present and future role of microfluidics in biomedical research. Nature 507, 181–189 (2014).
-
Liu, Q. et al. A threshold-based bioluminescence detector with a CMOS-integrated photodiode array in 65 nm for a multi-diagnostic ingestible capsule. IEEE J. Solid-State Circuits 58, 838–851 (2023).
-
Gregor, C., Gwosch, K. C., Sahl, S. J. & Hell, S. W. Strongly enhanced bacterial bioluminescence with the ilux operon for single-cell imaging. Proc. Natl Acad. Sci. USA 115, 962–967 (2018).
-
Ying, D. & Hall, D. A. Current sensing front-ends: a review and design guidance. IEEE Sens. J. 21, 22329–22346 (2021).
-
Mulleti, S., Bhandari, A. & Eldar, Y. C. Power-aware analog to digital converters. In Applied and Numerical Harmonic Analysis 415–452 (Birkhäuser, 2023).
-
Yasar, A. & Yazicigil, R. T. Physical-layer security for energy-constrained integrated systems: challenges and design perspectives. IEEE Open J. Solid-State Circuits Soc. 3, 262–273 (2023).
-
De la Paz, E. et al. A self-powered ingestible wireless biosensing system for real-time in situ monitoring of gastrointestinal tract metabolites. Nat. Commun. 13, 7405 (2022).
-
Chandrakasan, A. P., Verma, N. & Daly, D. C. Ultralow-power electronics for biomedical applications. Annu. Rev. Biomed. Eng. 10, 247–274 (2008).
-
Mercier, P. P., Lysaght, A. C., Bandyopadhyay, S., Chandrakasan, A. P. & Stankovic, K. M. Energy extraction from the biologic battery in the inner ear. Nat. Biotechnol. 30, 1240–1243 (2012).
-
Wang, A., Highsmith Calhoun, B., & Chandrakasan, A. P. Sub-threshold design for ultra low-power systems. In Series on Integrated Circuits and Systems (Springer, 2006).
-
Farrar, J. T., Berkley, C. & Zworykin, V. K. Telemetering of intraenteric pressure in man by an externally energized wireless capsule. Science 131, 1814 (1960).
-
Yeknami, A. F. et al. A 0.3-V CMOS biofuel-cell-powered wireless glucose/lactate biosensing system. IEEE J. Solid-State Circuits 53, 3126–3139 (2018).
-
Dong, K. et al. Microbial fuel cell as power supply for implantable medical devices: a novel configuration design for simulating colonic environment. Biosens. Bioelectron. 41, 916–919 (2013).
-
El-Damak, D. & Chandrakasan, A. P. Solar energy harvesting system with integrated battery management and startup using single inductor and 3.2nW quiescent power. In 2015 Symposium on VLSI Circuits (VLSI Circuits) C280–C281 (IEEE, 2015).
-
Kadirvel, K. et al. A 330nA energy-harvesting charger with battery management for solar and thermoelectric energy harvesting. In 2012 IEEE International Solid-State Circuits Conference – (ISSCC) 106–108 (IEEE, 2012).
-
Ramadass, Y. K. & Chandrakasan, A. P. A batteryless thermoelectric energy-harvesting interface circuit with 35mV startup voltage. In 2010 IEEE International Solid-State Circuits Conference — (ISSCC) 486–487 (IEEE, 2010).
-
Dagdeviren, C. et al. Conformal piezoelectric energy harvesting and storage from motions of the heart, lung, and diaphragm. Proc. Natl Acad. Sci. USA 111, 1927–1932 (2014).
-
Sadat Mousavi, P. et al. A multiplexed, electrochemical interface for gene-circuit-based sensors. Nat. Chem. 12, 48–55 (2019).
-
Amalfitano, E. et al. A glucose meter interface for point-of-care gene circuit-based diagnostics. Nat. Commun. 12, 724 (2021).
-
Sang, M., Kim, K., Shin, J. & Yu, K. J. Ultra‐thin flexible encapsulating materials for soft bio‐integrated electronics. Adv. Sci. 9, e2202980 (2022).
-
Yang, Y. & Gao, W. Wearable and flexible electronics for continuous molecular monitoring. Chem. Soc. Rev. 48, 1465–1491 (2019).
-
Iyer, V., Issadore, D. A. & Aflatouni, F. The next generation of hybrid microfluidic/integrated circuit chips: recent and upcoming advances in high-speed, high-throughput, and multifunctional lab-on-IC systems. Lab Chip 23, 2553–2576 (2023).
-
McClune, C. J., Alvarez-Buylla, A., Voigt, C. A. & Laub, M. T. Engineering orthogonal signalling pathways reveals the sparse occupancy of sequence space. Nature 574, 702–706 (2019).
-
Du, P. et al. De novo design of an intercellular signaling toolbox for multi-channel cell–cell communication and biological computation. Nat. Commun. 11, 4226 (2020).
-
Marken, J. P. & Murray, R. M. Addressable and adaptable intercellular communication via DNA messaging. Nat. Commun. 14, 2358 (2023).
-
Sexton, J. T. & Tabor, J. J. Multiplexing cell–cell communication. Mol. Syst. Biol. 16, e9618 (2020).
-
LaFleur, T. L., Hossain, A. & Salis, H. M. Automated model-predictive design of synthetic promoters to control transcriptional profiles in bacteria. Nat. Commun. 13, 5159 (2022).
-
Sun, M. G. F., Seo, M.-H., Nim, S., Corbi-Verge, C. & Kim, P. M. Protein engineering by highly parallel screening of computationally designed variants. Sci. Adv. 2, e1600692 (2016).
-
Roehner, N. et al. GOLDBAR: a framework for combinatorial biological design. ACS Synth. Biol. 13, 2899–2911 (2024).
-
Naseri, G. & Koffas, M. A. G. Application of combinatorial optimization strategies in synthetic biology. Nat. Commun. 11, 2446 (2020).
-
Salahuddin, S., Ni, K. & Datta, S. The era of hyper-scaling in electronics. Nat. Electron. 1, 442–450 (2018).
-
Castle, S. D., Stock, M. & Gorochowski, T. E. Engineering is evolution: a perspective on design processes to engineer biology. Nat. Commun. 15, 3640 (2024).
-
Oliveira, S. M. D. & Densmore, D. Hardware, software, and wetware codesign environment for synthetic biology. Biodes. Res. 2022, 9794510 (2022).
-
Yazicigil, R. T. et al. Beyond crypto: physical-layer security for internet of things devices. IEEE Solid-State Circuits Mag. 12, 66–78 (2020).
-
Vakhter, V., Soysal, B., Schaumont, P. & Guler, U. Threat modeling and risk analysis for miniaturized wireless biomedical devices. IEEE Internet Things J. 9, 13338–13352 (2022).
-
Vatambeti, R. et al. Prediction of DDoS attacks in Agriculture 4.0 with the help of prairie dog optimization algorithm with IDSNet. Sci. Rep. 13, 15371 (2023).
-
Maraveas, C., Rajarajan, M., Arvanitis, K. G. & Vatsanidou, A. Cybersecurity threats and mitigation measures in Agriculture 4.0 and 5.0. Smart Agric. Technol. 9, 100616 (2024).
-
Rettore de Araujo Zanella, A., da Silva, E. & Pessoa Albini, L. C. Security challenges to smart agriculture: current state, key issues, and future directions. Array 8, 100048 (2020).
