Our publications may be tracked on Google Scholar.

Research Articles ( * denotes equal contribution)

  1. Lopatkin AJ, Stokes JM, Zheng EJ, Yang JH, Takahashi MK, You L, Collins JJ. Bacterial metabolic state more accurately predicts antibiotic lethality than growth rateNat Microbiol. 2019; 4(12):2109-2117.

  2. Yang JH, Wright SN*, Hamblin M*, McCloskey D, Alcantar MA, Schrübbers L, Lopatkin AJ, Satish S, Nili A, Palsson BO, Walker GC, Collins JJ. A white-box machine learning approach for revealing antibiotic mechanisms of action. Cell. 2019; 177(6):1649-1661.

  3. Yang JH*, Bhargava P*, McCloskey D, Mao N, Palsson BO, Collins JJ. Antibiotic-induced changes to the host metabolic environment inhibit drug efficacy and alter immune function. Cell Host Microbe. 2017; 22(6):757-765.

  4. Takahashi N*, Gruber CC*, Yang JH, Liu X, Braff D, Yashaswini C, Bhubhani S, Furuta Y, Andreescu S, Collins JJ, Walker GC. Lethality of MalE-LacZ hybrid protein shares mechanistic attributes with oxidative component of antibiotic lethality. Proc Natl Acad Sci U S A. 2017; 114(34):9164-9169.

  5. Meylan S, Porter CB*, Yang JH*, Belenky P, Gutierrez A, Lobritz MA, Park J, Kim S, Moskowitz S, Collins JJ. Carbon sources tune antibiotic susceptibility in Pseudomonas aeruginosa via Tricarboxylic acid cycle control. Cell Chem Biol. 2017; 24(2):195-206.

  6. Lobritz MA*, Belenky P*, Porter CBM, Gutierrez A, Yang JH, Schwarz EG, Dwyer DJ, Khalil AS, Collins JJ. Antibiotic efficacy is linked to bacterial cellular respirationProc Natl Acad Sci U S A. 2015; 112(27):8173-80.

  7. Dwyer DJ*, Belenky PA*, Yang JH*, MacDonald IC, Martell JD, Takahashi N, Chan CT, Lobritz MA, Braff D, Schwarz EG, Ye JD, Pati M, Vercruysse M, Ralifo PS, Allison KR, Khalil AS, Ting AY, Walker GC, Collins JJ. Antibiotics induce redox-related physiological alterations as part of their lethalityProc Natl Acad Sci U S A. 2014; 111(20):E2100-9.

  8. Yang JH, Polanowska-Grabowska RK, Smith JS, Shields CW, Saucerman JJ. PKA catalytic subunit compartmentation regulates contractile and hypertrophic responses to β-adrenergic signaling. J Mol Cell Cardiol. 2014; 66:83-93.

  9. Yang JH, Saucerman JJ. Phospholemman is a negative feed-forward regulator of Ca2+ in β-adrenergic signaling, accelerating β-adrenergic inotropy. J Mol Cell Cardiol. 2012; 52(5):1048-55.

  10. Sample V*, DiPilato LM*, Yang JH*, Ni Q, Saucerman JJ, Zhang J. Regulation of nuclear PKA revealed by spatiotemporal manipulation of cAMP. Nat Chem Biol. 2012; 8(4):375-82.

  11. Benedict KF, Mac Gabhann F*, Amanfu RK*, Chavali AK*, Gianchandani EP*, Glaw LS*, Oberhardt MA*, Thorne BC*, Yang JH*, Papin JA, Peirce SM, Saucerman JJ, Skalak TC. Systems analysis of bounded signaling modules generates experimental roadmap for eight major diseases. Ann Biomed Eng. 2011; 39(2):621-35.

  12. Gurewitsch ED, Kim EJ, Yang JH, Outland KE, McDonald MK, Allen RH. Comparing McRoberts’ and Rubin’s maneuvers for initial management of shoulder dystocia: An objective evaluation. Am J Obstet Gynecol. 2005; 192(1):153-160.



  1. Yang JH*, Bening SC*, Collins JJ. Antibiotic efficacy – context matters. Curr Opin Microbiol. 2017; 39:73-80.

  2. Yang JH, Saucerman JJ. Computational models reduce complexity and accelerate insight into cardiac signaling networks. Circ Res. 2011; 108(01):85-97.


Conference Proceedings

  1. Kim EJ, Allen RH, Yang JH, McDonald MK, Tam W, Gurewitsch ED. Simulating complicated human birth for research and training. Conf Proc IEEE Eng Med Biol Soc. 2004; 4:2762-6.


  1. Gurewitsch E, Kim E, Yang J, Outland K, Allen R. An objective evaluation of McRoberts’ and Rubin’s maneuvers for shoulder dystocia. Am J Obstet Gynecol. 2003; 189(6):S208.


  1. Yang J. Science Careers: Where does advocacy fit? Science. 2009; 323(5911):208-209.