2024

45. Kang H, Park D, Kim J*, Logical regulation of endogenous gene expression using programmable, multi-input processing CRISPR guide RNAs. Nucleic Acids Research, 2024.

44. Kim J, Seo M, Lim Y, Kim J*, START: A Versatile Platform for Bacterial Ligand Sensing with Programmable Performances. Advanced Science, 2024.

2022

43. Kim J*, Simmel FC*, Scaling up genelet circuits, Nature Chemistry 14:1210-1211, 2022. *, co-corresponding authors. – News & Views article
42. Ryan J, Hong S, Foo M, Kim J, Tang X, Model-based investigation of the relationship between regulation level and pulse property of I1-FFL gene circuits, ACS Synthetic Biology 11:2417–2428, 2022.
41. Choi S, Lee G, Kim J*, Cellular computational logic using toehold switches, International Journal of Molecular Sciences 23:4265, 2022.
40. van der Linden AJ, Pieters PA, Bartelds MV, Nathalia BL, Yin P, Huck WTS*, Kim J*, de Greef TFA*, DNA input classification by a riboregulator-based cell-free perceptron, ACS Synthetic Biology 11:1510-1520, 2022. *, co-corresponding authors.
39. Kim J, Quijano JF, Kim J, Yeung E, Murray RM, Synthetic logic circuits using RNA aptamer against T7 RNA polymerase, Biotechnology Journal 17:2000449, 2022.

2021

38. Heo T†, Kang H†, Choi S†, Kim J*, Detection of pks island mRNAs using toehold sensors in Escherichia coli, Life 11:1280, 2021. †, co-first authors.
37. Yeung E, Kim J, Yuan Y, Gonçalves J, Murray RM, Data-driven network models for genetic circuits from time-series data with incomplete measurements, Journal of the Royal Society Interface 18:20210413, 2021.
36. Hong S†, Jeong D†, Ryan J†, Foo M*, Tang X*, Kim J*, Design and evaluation of synthetic RNA-based incoherent feed-forward loop circuits, Biomolecules 11:1182, 2021. †, co-first authors. *, co-corresponding authors.
35. Pieters PA, Nathalia BL, van der Linden AJ, Yin P, Kim J*, Huck WTS*, de Greef TFA*, Cell-free characterization of coherent feed-forward loop-based synthetic genetic circuits, ACS Synthetic Biology 10:1406-1416, 2021. *, co-corresponding authors.
34. Hong S†, Kim J†, Kim J*, Multilevel gene regulation using switchable transcription terminator and toehold switch in Escherichia coli, Applied Sciences 11:4532, 2021. †, co-first authors.
33. Hwang Y, Kim SG, Jang S, Kim J*, Jung GY*, Signal amplification and optimization of riboswitch-based hybrid inputs by modular and titratable toehold switches, Journal of Biological Engineering  15:11, 2021. *, co-corresponding authors.

2020

32. Paulino NMG, Foo M, Kim J, Bates DG, On the stability of nucleic acid feedback control systems, Automatica  119:109103, 2020.
31. Kim J, Franco E, RNA nanotechnology in synthetic biology, Current Opinion in Biotechnology 63:135–141, 2020.

2019

30. Kim J*, Zhou Y*, Carlson PD, Teichmann M, Chaudhary S, Simmel FC, Silver PA, Collins JJ, Yin P, Green AA, De novo-designed translation-repressing riboregulators for multi-input cellular logic, Nature Chemical Biology 15:1173–1182, 2019. *, co-first authors. – Cover article [Link]
29. Jin M, Garreau N, Kim Y, Kim J*, Yin P*, Programmable CRISPR-Cas repression, activation, and computation with sequence-independent targets and triggers, ACS Synthetic Biology  8:1583-1589, 2019. *, co-corresponding authors.
28. Paulino NMG, Foo M, Kim J, Bates DG, PID and state feedback controllers using DNA strand displacement reactions, IEEE Control Systems Letters  3:805-810, 2019. [PDF]
27. Paulino NMG, Foo M, Kim J, Bates DG, Robustness analysis of a nucleic acid controller for a dynamic biomolecular process using the structured singular value, Journal of Process Control  78:34-44, 2019. [PDF]
26. Jeong D*, Klocke M*, Agarwal S, Kim J, Choi S, Franco E, Kim J, Cell-Free Synthetic Biology Platform for Engineering Synthetic Biological Circuits and Systems, Methods and Protocols 2:39, 2019. *, co-first authors. [PDF]
25. Green LN, Subramanian HKK, Mardanlou V, Kim J, Hariadi R, Franco E, Autonomous dynamic control of DNA nanostructure self-assembly, Nature Chemistry 11:510-520, 2019. [PDF] – News & Views by Tim Liedl in Nature Chemistry 11:497-499.

Prior to POSTECH

24. Kim J, Green AA, Yin P, Ribocomputing: Cellular logic computation using RNA devices, Biochemistry 57:883–885, 2018. [PDF]
23. Mardanlou V, Yaghoubi KC, Green LN, Subramanian HK, Hariadi RF, Kim J, Franco E, A coarse-grained model captures the temporal evolution of DNA nanotube length distributions, Natural Computing 17:183–199, 2018.
22. Green AA*, Kim J*, Ma D, Silver PA, Collins JJ, Yin P, Complex cellular logic computation using ribocomputing devices, Nature 548:117–121, 2017. *, co-first authors. [PDF]
21. Foo M, Kim J, Kim J, Bates DG, Proportional-integral degradation (PI-Deg) control allows accurate tracking of biomolecular concentrations with fewer chemical reactions, IEEE Life Sciences Letters 2:55–58, 2016. [PDF]
20. Cuba C, Giordano G, Kim J, Blanchini F, Franco E, Molecular titration promotes oscillations and bistability in minimal network models with monomeric regulators, ACS Synthetic Biology 5:321–333, 2016. [PDF]
19. Takahashi M, Chappell J, Hayes C, Sun ZZ, Kim J, Singhal V, Spring K, Al-Khabouri S, Fall C, Noireaux V, Murray RM, Lucks J, Rapidly characterizing the fast dynamics of RNA genetic circuitry with cell-free transcription-translation (TX-TL) systems, ACS Synthetic Biology 4:503–515, 2015. [PDF]
18. Yordanov B, Kim J, Petersen R, Shudy A, Kulkarni VV, Phillips A, Computational design of nucleic acid feedback control circuits, ACS Synthetic Biology 3:600–616, 2014. [PDF]
17. Kim J, Khetarpal I, Sen S, Murray RM, Synthetic circuit for exact adaptation and fold-change detection, Nucleic Acids Research 42:6078–6089, 2014. [PDF]
16. Siegal-Gaskins D*, Tuza ZA*, Kim J*, Noireaux V, Murray RM, Resource usage and gene circuit performance characterization in a cell-free ‘breadboard’, ACS Synthetic Biology 3:416–425, 2014. *, co-first authors. [PDF]
15. Kulkarni VV, Kharisov E, Hovakimyan N, Kim J, Load capacity improvements in nucleic acid based systems using partially open feedback control, ACS Synthetic Biology 3:617–626, 2014. [PDF]
14. Weitz M, Kim J, Kapsner K, Winfree E, Franco E, Simmel FC, Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator, Nature Chemistry 6:295–302, 2014. [PDF] – Cover article [Link]
13. Subsoontorn P*, Kim J*, Winfree E, Ensemble Bayesian analysis of bistability in a synthetic transcriptional switch, ACS Synthetic Biology 1:299–316, 2012. *, co-first authors. [PDF]
12. Lee D, Do IG, Choi K, Sung CO, Jang KT, Choi D, Heo JS, Choi SH, Kim J, Park JY, Cha HJ, Joh JW, Choi KY, Kim DS, The expression of phospho-AKT1 and phospho-mTOR is associated with a favorable prognosis independent of PTEN expression in intrahepatic cholangiocarcinomas, Modern Pathology 25:131–139, 2012. [PDF]
11. Cha HJ, Kim J, Hong SJ, Hong SM, Park JH, Kim ES, Choi YJ, Do IG, Joh JW, Kim DS, Choi KY, Overexpression of renal tumor antigen is associated with tumor invasion and poor prognosis of hepatocellular carcinoma, Annals of Surgical Oncology Suppl 3:S404–11, 2012. [PDF]
10. Franco E, Friedrichs E, Kim J, Jungmann R, Murray RM, Winfree E, Simmel FC, Timing molecular motion and production with a synthetic transcriptional clock, Proceedings of the National Academy of Sciences USA 108:E784–E793, 2011. [PDF] – Highlights in Biopolymers
9. Kim J, Winfree E, Synthetic in vitro transcriptional oscillators, Molecular Systems Biology 7:465, 2011. [PDF]
8. Kwon JH*, Kim J*, Park JY, Hong SM, Park CW, Hong SJ, Park SY, Choi YJ, Do IG, Joh JW, Kim DS, Choi KY, Overexpression of HMGB2 is associated with tumor aggressiveness and prognosis of hepatocellular carcinoma, Clinical Cancer Research 16:5511–21, 2010. *, co-first authors. [PDF] – Highlights in Clinical Cancer Research
7. Kim J, Hong SJ, Park JY, Park JH, Yu YS, Park SY, Lim EK, Choi KY, Lee EK, Paik SS, Lee KG, Wang HJ, Do IG, Joh JW, Kim DS, Epithelial-mesenchymal transition gene signature to predict clinical outcome of hepatocellular carcinoma, Cancer Science 101:1521–28, 2010. [PDF] – A prognostic test (OncoHepaTest) based on this study is licensed as new health technology by Ministry of Health and Welfare in Korea (Ministry of Health and Welfare Notice 2010-83)
6. Kim J*, Kim JM*, Hong SJ, Park JH, Park SY, Hwang T, Yi GS, Kim SH, Cho EY, Joh JW, Park JY, Kim DS, Increased expression of autophagy protein Beclin1 and LC3 in high-grade hepatocellular carcinoma and metastatic carcinoma, Biochip Journal 3:316–25, 2009. *, co-first authors.
5. Hong SJ*, Kim J*, Park JH, Lim EK, Kim J, Choi YJ, Gu H, Kim SW, Choi KY, Joh JW, Kim DS, Proteomic profiling of human hepatocellular carcinoma tissues by two-dimensional electrophoresis and mass spectrometry, Biochip Journal 3:237–48, 2009. *, co-first authors.
4. Kim J, Hong SJ, Park JH, Lee CB, Kim SW, Gu H, Choi GS, Kwon CHD, Joh JW, Kim DS, Real-time reverse transcription PCR analysis for validation of transketolase gene in hepatocellular carcinoma tissues, Biochip Journal 3:130–8, 2009.
3. Kim J, Hong SJ, Park JH, Park SY, Kim SW, Cho EY, Do IG, Joh JW, Kim DS, Expression of cystathionine betasynthase is downregulated in hepatocellular carcinoma and associated with poor prognosis, Oncology Reports 21:1449–54, 2009. [PDF]
2. Kim J, Hong SJ, Lim EK, Yu YS, Kim SW, Roh JH, Do IG, Joh JW, Kim DS, Expression of nicotinamide N-methyltransferase in hepatocellular carcinoma is associated with poor prognosis, Journal of Experimental and Clinical Cancer Research 28:20, 2009. [PDF]
1. Kim J, White KS, Winfree E, Construction of an in vitro bistable circuit from synthetic transcriptional switches, Molecular Systems Biology 2:68, 2006. [PDF] – News & Views by Michael Simpson in Molecular Systems Biology 2:69.