Synthetic Biology and Microbiome Engineering

Journal Publications

  1. Ernlund A., Moffatt L, Timm C, Zudock K, Howser C, Blount K, Alkhalil, A, Shupp J, Karig DK. Examining the effect of wound cleansing on the microbiome of venous stasis ulcers. 2021. Wound Repair and Regeneration 29(5):766-776.
  2. Weissman JL, Dogra S, Javadi K, Bolten S, Flint R, Davati C, Beattie J, Dixit K, Peesay T, Awan S, Thielen P, Breitwieser F, Johnson PLF, Karig D, Fagan WF, Bewick S. Exploring the Functional Composition of the Human Microbiome Using a Hand-Curated Microbial Trait Database. 2021. BMC Bioinformatics, 22(1).
  3. Loomis K, Wu S, Ernlund A, Zudock K, Reno A, Blount K & Karig D. A mixed community of skin microbiome representatives influences cutaneous processes more than individual members. 2021. Microbiome 9:22.
  4. Timm C, Loomis K, Stone W, Mehoke T, Brensinger B, Pellicore M, Staniczenko P, Charles C, Nayak S, Karig D. Isolation and characterization of diverse microbial representatives from the human skin microbiome. 2020. Microbiome 8:1-12.
  5. Mainali KP, Bewick S, Vecchio-Pagan B, Karig D, Fagan W. Detecting interaction networks in the human microbiome with conditional Granger causality. 2019. PLOS Comp Biol 15(5):e1007037.
  6. Bewick S, Gurarie E, Beattie J, Daviti C, Flint R, Mehoke T, Thielen P, Breitweiser F, Karig D, and Fagan W. Trait-Based Analysis of the Human Skin Microbiome. 2019. Microbiome 7(1):101.
  7. Karig D*, Martini KM*, Lu T*, DeLateur N, Goldenfeld N, Weiss R. Stochastic Turing patterns in a synthetic bacterial population. 2018. Proc Natl Acad Sci USA 201720770. (*equal contribution authors).
  8. Tsoi R, Wu F, Zhang C, Bewick S, Karig D, You L. Metabolic Division of Labor In Microbial Systems. 2018. Proc Natl Acad Sci USA
  9. Timm CM, Lloyd EP, Egan A, Mariner R, Karig D. Direct Growth of Bacteria in Headspace Vials Allows for Screening of Volatiles by Gas Chromatography Mass Spectrometry. Frontiers in microbiology 9 (2018): 491.
  10. Vecchio-Pagan B, Bewick S, Mainali K, Karig D, Fagan WF. Ecological Stoichiometry of the Human Microbiome. 2017. Frontiers in Microbiology 8:1119.
  11. Karig DK, Bessling S, Thielen P, Zhang S, Wolfe J. Heat-stable preservation of protein expression systems for portable therapeutics production. 2017. Journal of the Royal Society Interface 14(129):20161039.
  12. Karig DK. Cell-free synthetic biology for environmental sensing and remediation. 2017. Current Opinion in Biotechnology 45:69-75.
  13. Bewick S, Thielen P, Mehoke T, Karig D, and Fagan W. Sampling, Sequencing, and the SAD. 2017. Ecological Complexity.
  14. Bewick S, Staniczenko PA, Li B, Karig D, and Fagan W. Invasion Speeds in Microbial Systems with Toxin Production and Quorum Sensing. 2017. Journal of Theoretical Biology 420:290-303.
  15. Lopatkin AJ, Huang S, Smith RP, Srimani JK, Sysoeva TA, Bewick S, Karig DK, You L. Antibiotics as a selective driver for conjugation dynamics. 2016. Nature Microbiology 16044.
  16. Karimi A, Karig D, Kumar A, Ardekani AM. Interplay of physical mechanisms and biofilm processes: review of microfluidic methods. 2015. Lab Chip 15 (1):23-42.
  17. Iyer S*, Karig DK*, Norred SE, Simpson ML, Doktycz MJ. Multi-input regulation and logic with T7 promoters in cells and cell-free systems. 2013. PLOS One 8(10):78442. (*equal contribution authors)
  18. Karig DK, Jung SY, Srijanto B, Collier CP, Simpson ML. Probing cell-free gene expression noise in femtoliter volumes. 2013. ACS Synth Biol 2(9):497-505.
  19. Kumar A, Karig D, Acharya R, Neethirajan S, Mukherjee PP, Retterer S, Doktycz MJ. Microscale confinement features can affect biofilm formation. 2013. Microfluidics and Nanofluidics 14(5):895-902.
  20. Karig DK, Iyer S, Simpson ML, Doktycz MJ. Expression optimization and synthetic gene networks in cell-free systems. 2012. Nucleic Acids Research 40(8):3763-3774.
  21. Karig DK, Siuti P, Dar RD, Retterer ST, Doktycz MJ, Simpson ML. Model for biological communication in a nanofabricated cell-mimic driven by stochastic resonance. 2011. Nano Communication Networks 2(1):39-49.
  22. Dar RD, Karig DK, Cooke JF, Cox CD, Simpson ML. Distribution and regulation of stochasticity and plasticity in Saccharomyces cerevisiae. 2010. Chaos 20:037106.
  23. Simpson ML, Cox CD, Allen MS, McCollum JM, Dar RD, Karig DK, and Cooke JF. Noise in biological circuits. 2009. WIREs Nanomed Nanobiotechnol 1:214–225.
  24. Karig DK and Simpson ML. Tying new knots in synthetic biology. 2008. HFSP Journal 2:124-128.
  25. Brenner K*, Karig DK*, Weiss R, Arnold FH. Engineered bidirectional communication mediates a consensus in a microbial biofilm consortium. 2007. Proc Natl Acad Sci USA 104:17300-17304. (*equal contribution authors)
  26. Andrianantoandro E*, Basu S*, Karig DK*, and Weiss R. Synthetic biology: new engineering rules for an emerging discipline. 2006. Mol Syst Biol 2:2006.0028. (*equal contribution authors)
  27. Karig D and Weiss R. Signal-amplifying genetic circuit enables in vivo observation of weak promoter activation in the Rhl quorum sensing system. 2005. Biotechnol Bioeng 89(6):709-18.
  28. Weiss R, Basu S, Hooshangi S, Kalmbach A, Karig D, Mehreja R and Netravali I. Genetic circuit building blocks for cellular computation, communications, and signal processing. 2003. Natural Computing 2(1): 47-84.
  29. Basu S, Karig D, and Weiss R. Engineering signal processing in cells: towards molecular concentration band detection. 2003. Natural Computing 2(4): 463-478.

Book and Monographs

  1. Karig D, Reno A, Franklin LE, Timm A. Cell-Free Synthetic Biology Biosensors. 2022. Handbook of Cell Biosensors, Editor: Gerald Thouand. Springer, U.K. pp. 319-338.
  2. Bewick S, Karig D and Fagan WF. Contamination Issues in Microbiome Sequencing Studies. from: Microbial Ecology: Current Advances from Genomics, Metagenomics and Other Omics (Edited by: Diana Marco). 2019. Caister Academic Press, U.K. Pages: 13-26.
  3. Neethirajan S, Karig D, Kumar A, Mukherjee PP, Retterer ST, Doktycz MJ. 2012. Biofilms in microfluidic devices. 2012. Encyclopedia of Nanotechnology, Ed: B. Bhushan, Springer, New York.

Conference Proceedings

  1. Kumar A, Karig D, Neethirijan S, Suresh AK, Srijanto BR, Mukherjee PP, Retterer S, Doktycz MJ. Adhesion and formation of microbial biofilms in complex microfluidic devices. 2012. Proceedings of the 3rd ASME Micro/Nanoscale Heat and Mass Transfer International Conference.
  2. Hsu A, Vijayan V, Fomundam L, Gerchman Y, Karig D, Hooshangi S, Basu S, and Weiss R. Dynamic control in a coordinated multi-cellular maze solving system. 2005. American Controls Conference.
  3. Basu S, Karig D, and Weiss R. Engineering signal processing in cells: towards molecular concentration band detection. 2002. Eighth International Meeting on DNA Based Computers, pp. 61-72.
  4. McGregor JP, Karig DK, Shi Z, and Lee RB. A processor architecture defense against buffer overflow attacks. 2003. Proceedings of the IEEE International Conference on Information Technology: Research and Education (ITRE), pp. 243-250.
  5. Lee RB, Karig DK, McGregor JP, and Shi Z. Enlisting hardware architecture to thwart malicious code injection. 2003. Proceedings of the International Conference on Security in Pervasive Computing (SPC-2003), pp. 237-252.

Research Reports

  1. Karig D and Lee RB. Remote denial of service attacks and countermeasures. 2001. Princeton University Department of Electrical Engineering Technical Report CE-L2001-002.