Our publications may be tracked on Google Scholar. ( * denotes equal contribution, underline denotes Yang Lab members )


  1. Chitale P, Lemenze AD, Fogarty EC, Shah A, Grady CA, Odom-Mabey AR, Johnson WE, Yang JH, Eren AM, Brosch R, Kumar P, Alland P. A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genomebioRxiv. 2022.

  2. Bruiners N, Guerrini V, Ukey R, Dikdan RJ, Yang JH, Mishra PK, Onyuka A, Handler D, Vieth J, Carayannopoulos M, Guo S, Pollen M, Pinter A, Tyagi S, Feingold D, Philipp C, Libutti SK, Gennaro ML. Longitudinal Analysis of Biologic Correlates of COVID-19 Resolution: Case ReportFront Med. 2022; 9:91537.

  3. Yang JH. CRISP(e)R drug discoveryNat Chem Biol. 2022.

  4. Bruiners N, Guerrini V, Ukey R, Dikdan R, Yang J, Mishra PK, Onyuka A, Handler D, Vieth J, Carayannopulos M, Guo S, Pollen M, Pinter A, Tyagi S, Feingold D, Philipp C, Libutti S, Gennaro ML. Biologic correlates of beneficial convalescent plasma therapy in a COVID-19 patient reveal disease resolution mechanismsmedRxiv. 2022.


  1. Sanders LM, Yang JH, Scott RT, Qutub AA, Martin HG, Berrios DC, Hastings JJA, Rask J, Mackintosh G, Hoarfrost AL, Chalk S, Kalantari J, Khezeli K, Antonsen EL, Babdor J, Barker R, Baranzini SE, Beheshti A, Delgado-Aparicio GM, Glicksberg BS, Greene CS, Haendel M, Hamid AA, Heller P, Jamieson D, Jarvis KJ, Komarova SV, Komorowski M, Kothiyal P, Mahabal A, Manor U, Mason CE, Matar M, Mias GI, Miller J, Myers JG, Nelson C, Oribello J, Park S, Parsons-Wingerter P, Prabhu RK, Reynolds RJ, Saravia-Butler A, Saria S, Sawyer A, Singh NK, Soboczenski F, Snyder M, Soman K, Theriot CA, Van Valen D, Venkateswaran K, Warren L, Worthey L, Zitnik M, Costes SV. Beyond Low Earth Orbit: Biological Research, Artificial Intelligence, and Self-Driving LabsarXiv. 2021; 2112.12582.

  2. Scott RT, Antonsen EL, Sanders LM, Hastings JJA, Park S, Mackintosh G, Reynolds RJ, Hoarfrost AL, Sawyer A, Greene CS, Glicksberg BS, Theriot CA, Berrios DC, Miller J, Babdor J, Barker R, Baranzini SE, Beheshti A, Chalk S, Delgado-Aparicio GM, Haendel M, Hamid AA, Heller P, Jamieson D, Jarvis KJ, Kalantari J, Khezeli K, Komarova SV, Komorowski M, Kothiyal P, Mahabal A, Manor U, Martin HG, Mason CE, Matar M, Mias GI, Myers JG, Nelson C, Oribello J, Parsons-Wingerter P, Prabhu RK, Qutub AA, Rask J, Saravia-Butler A, Saria S, Singh NK, Soboczenski F, Snyder M, Soman K, Van Valen D, Venkateswaran K, Warren L, Worthey L, Yang JH, Zitnik M, Costes SV. Beyond Low Earth Orbit: Biomonitoring, Artificial Intelligence, and Precision Space Health. arXiv. 2021; 2112.12554.

  3. Kim GL, Hooven TA, Norambuena J, Li B, Boyd JM, Yang JH, Parker D. Growth and stress tolerance comprise independent metabolic strategies critical for Staphylococcus aureus infection. mBio. 2021; 12(3):e0081421.

  4. Lopatkin AJ*, Yang JH*. Digital insights into nucleotide metabolism and antibiotic treatment failure. Front Digit Health. 2021.

  5. León-Buitimea A, Morones-Ramírez JR, Yang JH, Peña-Miller R. Editorial: Facing the upcoming of multidrug-resistant and extensively drug-resistant bacteria: novel antimicrobial therapies (NATs). Front Bioeng Biotechnol. 2021; 9:636278.

  6. Lopatkin AJ, Bening SC, Manson AL, Stokes JM, Kohanski MA, Badran AH, Earl AM, Cheney NJYang JH, Collins JJ. Clinically relevant mutations in core metabolic genes confer antibiotic resistance. Science. 2021; 371(6531):eaba0862.

  7. Anahtar MN, Yang JH, Kanjilal S. Applications of machine learning to the problem of antimicrobial resistance: An emerging model for translational research. J Clin Microbiol. 2021; 59(7):e0126020.



  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.


  1. 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.

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

  3. 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.

  4. 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.


  1. 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.


  1. 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.

  2. 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.



  1. 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.

  2. 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.



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

  2. 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.



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



  1. 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. 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.