Bond AN, Orzechowski M, Zhang S, Ben-Zion I, Lemmer A, Garry N, Lee K, Chen M, Delano K, Gath E, Golas AL, Nietupski R, Fitzgerald M, Ehrt S, Rubin EJ, Sassetti CM, Schnappinger D, Shoresh N, Hunt DK, Gomez JE, Hung DT. Reference-based chemical-genetic interaction profiling to elucidate small molecule mechanism of action in Mycobacterium tuberculosis. Nat Commun. 2025 Nov 3;16(1):9673.

Neo DM, Ben-Zion I, Bagnall J, Solomon MY, Bond AN, Gath E, Zhang S, Shoresh N, Gomez J, Hung DT. A Multiplexed, Target-Based Phenotypic Screening Platform Using CRISPR Interference in Mycobacterium abscessus. ACS Infect Dis. 2025 Nov 14;11(11):3263-3275.

Goering ER, Clatworthy AE, Parada-Kusz M, Bagnall J, Hung DT. Kmo restricts Salmonella in a whole organism infection model by promoting macrophage lysosomal acidification through kainate receptor antagonism. PLoS Pathog. 2025 Oct;21(10):e1013273. doi: 10.1371/journal.ppat.1013273. eCollection 2025 Oct. PubMed

Sullivan JR, Ferrara K, Barrick R, Romano KP, Warrier T, Hung DT. An Inducible CRISPRi system for phenotypic analysis of essential genes in Pseudomonas aeruginosa. bioRxiv. 2025 Sep 11

Ma P, Chen PD, Jadhav S, He LL, Laibinis HH, Hung DT, Moffitt KL. Longitudinal Antibody Responses to SARS-CoV-2 Infection in Children: Impact of Age, Vaccines and Symptoms. Pediatr Infect Dis J. 2025 Dec 1;44(12):1181-1184.

Khandelwal NK, Gupta M, Gomez JE, Barkho S, Guan Z, Eng AY, Kawate T, Balasubramani SG, Sali A, Hung DT, Stroud RM. Structure and inhibition mechanisms of Mycobacterium tuberculosis essential transporter efflux protein A. Nat Commun. 2025 Apr 1;16(1):3139.

Tse MW, Zhu M, Peters B, Hamami E, Chen J, Davis KP, Nitz S, Weller J, Warrier T, Hunt DK, Morales Y, Kawate T, Gaulin JL, Come JH, Hernandez-Bird J, Huo W, Neisewander I, Yu X, Aceves-Salvador JA, Kiessling LL, Hung DT, Mecsas J, Aldridge BB, Isberg RR, Blainey PC. Large-scale combination screens reveal small-molecule sensitization of antibiotic-resistant gram-negative ESKAPE pathogens. Proc Natl Acad Sci U S A. 2025 Apr;122(13):e2402017122.

Poulsen BE, Warrier T, Barkho S, Bagnall J, Romano KP, White T, Yu X, Kawate T, Nguyen PH, Raines K, Ferrara K, Golas AL, FitzGerald M, Boeszoermenyi A, Kaushik V, Serrano-Wu M, Shoresh N, Hung DT. Discovery of a Pseudomonas aeruginosa-specific small molecule targeting outer membrane protein OprH-LPS interaction by a multiplexed screen. Cell Chem Biol. 2025 Feb 20;32(2):307-324.e15.

Romano KP, Bagnall J, Warrier T, Sullivan J, Ferrara K, Orzechowski M, Nguyen PH, Raines K, Livny J, Shoresh N, Hung DT. Perturbation-specific transcriptional mapping for unbiased target elucidation of antibiotics. Proc Natl Acad Sci U S A. 2024 Nov 5;121(45):e2409747121.

Fihn CA, Lembke HK, Gaulin J, Bouchard P, Villarreal AR, Penningroth MR, Crone KK, Vogt GA, Gilbertsen AJ, Ayotte Y, Coutinho de Oliveira L, Serrano-Wu MH, Drouin N, Hung DT, Hunter RC, Carlson EE. Evaluation of expanded 2-aminobenzothiazole library as inhibitors of a model histidine kinase and virulence suppressors in Pseudomonas aeruginosa. Bioorg Chem. 2024 Dec;153:107840.

Parada-Kusz M, Clatworthy AE, Goering ER, Blackwood SM, Shigeta JY, Mashin E, Salm EJ, Choi C, Combs S, Lee JSW, Rodriguez-Osorio C, Clish C, Tomita S, Hung DT. 3-Hydroxykynurenine targets kainate receptors to promote defense against infection. Nat Chem Biol. 2024 Dec;20(12):1586-1596.

Neo DM, Clatworthy AE, Hung DT. A dual-plasmid CRISPR/Cas9-based method for rapid and efficient genetic disruption in Mycobacterium abscessus. J Bacteriol. 2024 Mar 21;206(3):e0033523.

Sturm A, Sun P, Avila-Pacheco J, Clatworthy AE, Bloom-Ackermann Z, Wuo MG, Gomez JE, Jin S, Clish CB, Kiessling LL, Hung DT. Genetic factors affecting storage and utilization of lipids during dormancy in Mycobacterium tuberculosis. mBio. 2024 Feb 14;15(2):e0320823.

Welch NL, Zhu M, Hua C, Weller J, Mirhashemi ME, Nguyen TG, Mantena S, Bauer MR, Shaw BM, Ackerman CM, Thakku SG, Tse MW, Kehe J, Uwera MM, Eversley JS, Bielwaski DA, McGrath G, Braidt J, Johnson J, Cerrato F, Moreno GK, Krasilnikova LA, Petros BA, Gionet GL, King E, Huard RC, Jalbert SK, Cleary ML, Fitzgerald NA, Gabriel SB, Gallagher GR, Smole SC, Madoff LC, Brown CM, Keller MW, Wilson MM, Kirby MK, Barnes JR, Park DJ, Siddle KJ, Happi CT, Hung DT, Springer M, MacInnis BL, Lemieux JE, Rosenberg E, Branda JA, Blainey PC, Sabeti PC, Myhrvold C. Author Correction: Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants. Nat Med. 2024 Jan;30(1):307

Ahmed S, Chowdhury S, Gomez J, Hung DT, Parish T. Benzene Amide Ether Scaffold is Active against Non-replicating and Intracellular Mycobacterium tuberculosis. ACS Infect Dis. 2023 Oct 13;9(10):1981-1992.

Kalam H, Chou CH, Kadoki M, Graham DB, Deguine J, Hung DT, Xavier RJ. Identification of host regulators of Mycobacterium tuberculosis phenotypes uncovers a role for the MMGT1-GPR156 lipid droplet axis in persistence. Cell Host Microbe. 2023 Jun 14;31(6):978-992.e5.

Thakku SG, Lirette J, Murugesan K, Chen J, Theron G, Banaei N, Blainey PC, Gomez J, Wong SY, Hung DT. Genome-wide tiled detection of circulating Mycobacterium tuberculosis cell-free DNA using Cas13. Nat Commun. 2023 Mar 31;14(1):1803.

Saebi A, Brown JS, Marando VM, Hartrampf N, Chumbler NM, Hanna S, Poskus M, Loas A, Kiessling LL, Hung DT, Pentelute BL. Rapid Single-Shot Synthesis of the 214 Amino Acid-Long N-Terminal Domain of Pyocin S2. ACS Chem Biol. 2023 Mar 17;18(3):518-527.

Zhang S, Ma P, Orzechowski M, Lemmer A, Rzasa K, Bagnall J, Barkho S, Chen M, He L, Neitupski R, Tran V, Ackerman R, Gath E, Bond A, Frongillo G, Cleland T, Golas A, Gaca A, Fitzgerald M, Kelly K, Hazegh K, Dumont L, Hoffman C, Homer M, Marks P, Woolley A, Wong S, Gomez J, Livny J, Hung D. High-Throughput Neutralization and Serology Assays Reveal Correlated but Highly Variable Humoral Immune Responses in a Large Population of Individuals Infected with SARS-CoV-2 in the US between March and August 2020. mBio. 2023 Apr 25;14(2):e0352322.

Ma P, Amemiya HM, He LL, Gandhi SJ, Nicol R, Bhattacharyya RP, Smillie CS, Hung DT. Bacterial droplet-based single-cell RNA-seq reveals antibiotic-associated heterogeneous cellular states. Cell. 2023 Feb 16;186(4):877-891.e14.

Poulsen BE, Clatworthy AE, Hung DT. The Use of Tn-Seq and the FiTnEss Analysis to Define the Core Essential Genome of Pseudomonas aeruginosa. Methods Mol Biol. 2022;2377:179-197.

Romano KP, Hung DT. Targeting LPS biosynthesis and transport in gram-negative bacteria in the era of multi-drug resistance. Biochim Biophys Acta Mol Cell Res. 2023 Mar;1870(3):119407.

Suliman S, Matias WR, Fulcher IR, Molano FJ, Collins S, Uceta E, Zhu J, Paxton RM, Gonsalves SF, Harden MV, Fisher M, Meldrim J, Gabriel S, Franke MF, Hung DT, Smole SC, Madoff LC, Ivers LC. Evaluation of the Access Bio CareStart rapid SARS-CoV-2 antigen test in asymptomatic individuals tested at a community mass-testing program in Western Massachusetts. Sci Rep. 2022 Dec 9;12(1):21338.

Parker EN, Cain BN, Hajian B, Ulrich RJ, Geddes EJ, Barkho S, Lee HY, Williams JD, Raynor M, Caridha D, Zaino A, Rohde JM, Zak M, Shekhar M, Muñoz KA, Rzasa KM, Temple ER, Hunt D, Jin X, Vuong C, Pannone K, Kelly AM, Mulligan MP, Lee KK, Lau GW, Hung DT, Hergenrother PJ. Correction to "An Iterative Approach Guides Discovery of the FabI Inhibitor Fabimycin, a Late-Stage Antibiotic Candidate with In Vivo Efficacy against Drug-Resistant Gram-Negative Infections". ACS Cent Sci. 2022 Sep 28;8(9):1362.

Parker EN, Cain BN, Hajian B, Ulrich RJ, Geddes EJ, Barkho S, Lee HY, Williams JD, Raynor M, Caridha D, Zaino A, Shekhar M, Muñoz KA, Rzasa KM, Temple ER, Hunt D, Jin X, Vuong C, Pannone K, Kelly AM, Mulligan MP, Lee KK, Lau GW, Hung DT, Hergenrother PJ. An Iterative Approach Guides Discovery of the FabI Inhibitor Fabimycin, a Late-Stage Antibiotic Candidate with In Vivo Efficacy against Drug-Resistant Gram-Negative Infections. ACS Cent Sci. 2022 Aug 24;8(8):1145-1158.

Naz-McLean S, Kim A, Zimmer A, Laibinis H, Lapan J, Tyman P, Hung J, Kelly C, Nagireddy H, Narayanan-Pandit S, McCarthy M, Ratnaparkhi S, Rutherford H, Patel R, Dryden-Peterson S, Hung DT, Woolley AE, Cosimi LA. Feasibility and lessons learned on remote trial implementation from TestBoston, a fully remote, longitudinal, large-scale COVID-19 surveillance study. PLoS One. 2022;17(6):e0269127.

Warrier T, Romano KP, Clatworthy AE, Hung DT. Integrated genomics and chemical biology herald an era of sophisticated antibacterial discovery, from defining essential genes to target elucidation. Cell Chem Biol. 2022 May 19;29(5):716-729.

Koh EI, Oluoch PO, Ruecker N, Proulx MK, Soni V, Murphy KC, Papavinasasundaram K, Reames CJ, Trujillo C, Zaveri A, Zimmerman MD, Aslebagh R, Baker RE, Shaffer SA, Guinn KM, Fitzgerald M, Dartois V, Ehrt S, Hung DT, Ioerger TR, Rubin EJ, Rhee KY, Schnappinger D, Sassetti CM. Chemical-genetic interaction mapping links carbon metabolism and cell wall structure to tuberculosis drug efficacy. Proc Natl Acad Sci U S A. 2022 Apr 12;119(15):e2201632119.

Belov A, Huang Y, Villa CH, Whitaker BI, Forshee R, Anderson SA, Eder A, Verdun N, Joyner MJ, Wright SR, Carter RE, Hung DT, Homer M, Hoffman C, Lauer M, Marks P. Early administration of COVID-19 convalescent plasma with high titer antibody content by live viral neutralization assay is associated with modest clinical efficacy. Am J Hematol. 2022 Jun 1;97(6):770-779.

MacNair CR, Farha MA, Serrano-Wu MH, Lee KK, Hubbard B, Côté JP, Carfrae LA, Tu MM, Gaulin JL, Hunt DK, Hung DT, Brown ED. Preclinical Development of Pentamidine Analogs Identifies a Potent and Nontoxic Antibiotic Adjuvant. ACS Infect Dis. 2022 Apr 8;8(4):768-777.

Thakku SG, Ackerman CM, Myhrvold C, Bhattacharyya RP, Livny J, Ma P, Gomez GI, Sabeti PC, Blainey PC, Hung DT. Multiplexed detection of bacterial nucleic acids using Cas13 in droplet microarrays. PNAS Nexus. 2022 Mar;1(1):pgac021.

Welch NL, Zhu M, Hua C, Weller J, Mirhashemi ME, Nguyen TG, Mantena S, Bauer MR, Shaw BM, Ackerman CM, Thakku SG, Tse MW, Kehe J, Uwera MM, Eversley JS, Bielwaski DA, McGrath G, Braidt J, Johnson J, Cerrato F, Moreno GK, Krasilnikova LA, Petros BA, Gionet GL, King E, Huard RC, Jalbert SK, Cleary ML, Fitzgerald NA, Gabriel SB, Gallagher GR, Smole SC, Madoff LC, Brown CM, Keller MW, Wilson MM, Kirby MK, Barnes JR, Park DJ, Siddle KJ, Happi CT, Hung DT, Springer M, MacInnis BL, Lemieux JE, Rosenberg E, Branda JA, Blainey PC, Sabeti PC, Myhrvold C. Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants. Nat Med. 2022 May;28(5):1083-1094.

Woolley AE, Dryden-Peterson S, Kim A, Naz-McLean S, Kelly C, Laibinis HH, Bagnall J, Livny J, Ma P, Orzechowski M, Shoresh N, Gabriel S, Hung DT, Cosimi LA. At-home Testing and Risk Factors for Acquisition of SARS-CoV-2 Infection in a Major US Metropolitan Area. medRxiv. 2022 Feb 3

Johnson EO, Hung DT. Using Proteolytic Hypomorphs to Detect Small Molecule Mechanism of Action. Methods Mol Biol. 2021;2314:323-342.

Lennon NJ, Bhattacharyya RP, Mina MJ, Rehm HL, Hung DT, Smole S, Woolley A, Lander ES, Gabriel SB. Cross-Sectional Assessment of SARS-CoV-2 Viral Load by Symptom Status in Massachusetts Congregate Living Facilities. J Infect Dis. 2021 Nov 22;224(10):1658-1663.

Davis K, Greenstein T, Viau Colindres R, Aldridge BB. Leveraging laboratory and clinical studies to design effective antibiotic combination therapy. Curr Opin Microbiol. 2021 Dec;64:68-75.

Zhu M, Tse MW, Weller J, Chen J, Blainey PC. The future of antibiotics begins with discovering new combinations. Ann N Y Acad Sci. 2021 Jul;1496(1):82-96. Di Germanio C, Simmons G, Kelly K, Martinelli R, Darst O, Azimpouran M, Stone M, Hazegh K, Grebe E, Zhang S, Ma P, Orzechowski M, Gomez JE, Livny J, Hung DT, Vassallo R, Busch MP, Dumont LJ. SARS-CoV-2 antibody persistence in COVID-19 convalescent plasma donors: Dependency on assay format and applicability to serosurveillance. Transfusion. 2021 Sep;61(9):2677-2687.

Michalska K, Wellington S, Maltseva N, Jedrzejczak R, Selem-Mojica N, Rosas-Becerra LR, Barona-Gómez F, Hung DT, Joachimiak A. Catalytically impaired TrpA subunit of tryptophan synthase from Chlamydia trachomatis is an allosteric regulator of TrpB. Protein Sci. 2021 Sep;30(9):1904-1918.

Reyes M, Filbin MR, Bhattacharyya RP, Sonny A, Mehta A, Billman K, Kays KR, Pinilla-Vera M, Benson ME, Cosimi LA, Hung DT, Levy BD, Villani AC, Sade-Feldman M, Baron RM, Goldberg MB, Blainey PC, Hacohen N. Plasma from patients with bacterial sepsis or severe COVID-19 induces suppressive myeloid cell production from hematopoietic progenitors in vitro. Sci Transl Med. 2021 Jun 16;13(598).

Klobucar K, Côté JP, French S, Borrillo L, Guo ABY, Serrano-Wu MH, Lee KK, Hubbard B, Johnson JW, Gaulin JL, Magolan J, Hung DT, Brown ED. Chemical Screen for Vancomycin Antagonism Uncovers Probes of the Gram-Negative Outer Membrane. ACS Chem Biol. 2021 May 21;16(5):929-942.

Scheid JF, Barnes CO, Eraslan B, Hudak A, Keeffe JR, Cosimi LA, Brown EM, Muecksch F, Weisblum Y, Zhang S, Delorey T, Woolley AE, Ghantous F, Park SM, Phillips D, Tusi B, Huey-Tubman KE, Cohen AA, Gnanapragasam PNP, Rzasa K, Hatziioanno T, Durney MA, Gu X, Tada T, Landau NR, West AP Jr, Rozenblatt-Rosen O, Seaman MS, Baden LR, Graham DB, Deguine J, Bieniasz PD, Regev A, Hung D, Bjorkman PJ, Xavier RJ. B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV. Cell. 2021 Jun 10;184(12):3205-3221.e24.

Ma P, He LL, Pironti A, Laibinis HH, Ernst CM, Manson AL, Bhattacharyya RP, Earl AM, Livny J, Hung DT. Genetic determinants facilitating the evolution of resistance to carbapenem antibiotics. Elife. 2021 Apr 19;10.

Penaranda C, Chumbler NM, Hung DT. Dual transcriptional analysis reveals adaptation of host and pathogen to intracellular survival of Pseudomonas aeruginosa associated with urinary tract infection. PLoS Pathog. 2021 Apr;17(4):e1009534.

Zhang Y, Guo R, Kim SH, Shah H, Zhang S, Liang JH, Fang Y, Gentili M, Leary CNO, Elledge SJ, Hung DT, Mootha VK, Gewurz BE. SARS-CoV-2 hijacks folate and one-carbon metabolism for viral replication. Nat Commun. 2021 Mar 15;12(1):1676.

Chan LW, Hern KE, Ngambenjawong C, Lee K, Kwon EJ, Hung DT, Bhatia SN. Selective Permeabilization of Gram-Negative Bacterial Membranes Using Multivalent Peptide Constructs for Antibiotic Sensitization. ACS Infect Dis. 2021 Apr 9;7(4):721-732.

Bogart JW, Cabezas MD, Vögeli B, Wong DA, Karim AS, Jewett MC. Cell-Free Exploration of the Natural Product Chemical Space. Chembiochem. 2021 Jan 5;22(1):84-91.

Joung J, Ladha A, Saito M, Kim NG, Woolley AE, Segel M, Barretto RPJ, Ranu A, Macrae RK, Faure G, Ioannidi EI, Krajeski RN, Bruneau R, Huang MW, Yu XG, Li JZ, Walker BD, Hung DT, Greninger AL, Jerome KR, Gootenberg JS, Abudayyeh OO, Zhang F. Detection of SARS-CoV-2 with SHERLOCK One-Pot Testing. N Engl J Med. 2020 Oct 8;383(15):1492-1494.

Ernst CM, Braxton JR, Rodriguez-Osorio CA, Zagieboylo AP, Li L, Pironti A, Manson AL, Nair AV, Benson M, Cummins K, Clatworthy AE, Earl AM, Cosimi LA, Hung DT. Author Correction: Adaptive evolution of virulence and persistence in carbapenem-resistant Klebsiella pneumoniae. Nat Med. 2020 Aug;26(8):1307. Ouyang W, Han J. One-Step Nucleic Acid Purification and Noise-Resistant Polymerase Chain Reaction by Electrokinetic Concentration for Ultralow-Abundance Nucleic Acid Detection. Angew Chem Int Ed Engl. 2020 Jun 26;59(27):10981-10988.

Ackerman CM, Myhrvold C, Thakku SG, Freije CA, Metsky HC, Yang DK, Ye SH, Boehm CK, Kosoko-Thoroddsen TF, Kehe J, Nguyen TG, Carter A, Kulesa A, Barnes JR, Dugan VG, Hung DT, Blainey PC, Sabeti PC. Massively multiplexed nucleic acid detection with Cas13. Nature. 2020 Jun;582(7811):277-282.

Ernst CM, Braxton JR, Rodriguez-Osorio CA, Zagieboylo AP, Li L, Pironti A, Manson AL, Nair AV, Benson M, Cummins K, Clatworthy AE, Earl AM, Cosimi LA, Hung DT. Adaptive evolution of virulence and persistence in carbapenem-resistant Klebsiella pneumoniae. Nat Med. 2020 May;26(5):705-711.

Albin JS, Pentelute BL. Efficient flow synthesis of human antimicrobial peptides. Aust J Chem. 2020 Apr;73(4):380-388.

Zhuang L, Huang S, Liu WQ, Karim AS, Jewett MC, Li J. Total in vitro biosynthesis of the nonribosomal macrolactone peptide valinomycin. Metab Eng. 2020 Jul;60:37-44.

Reyes M, Filbin MR, Bhattacharyya RP, Billman K, Eisenhaure T, Hung DT, Levy BD, Baron RM, Blainey PC, Goldberg MB, Hacohen N. An immune-cell signature of bacterial sepsis. Nat Med. 2020 Mar;26(3):333-340.

Betin V, Penaranda C, Bandyopadhyay N, Yang R, Abitua A, Bhattacharyya RP, Fan A, Avraham R, Livny J, Shoresh N, Hung DT. Hybridization-based capture of pathogen mRNA enables paired host-pathogen transcriptional analysis. Sci Rep. 2019 Dec 17;9(1):19244.

Johnson EO, Office E, Kawate T, Orzechowski M, Hung DT. Large-Scale Chemical-Genetic Strategy Enables the Design of Antimicrobial Combination Chemotherapy in Mycobacteria. ACS Infect Dis. 2020 Jan 10;6(1):56-63.

Bhattacharyya RP, Bandyopadhyay N, Ma P, Son SS, Liu J, He LL, Wu L, Khafizov R, Boykin R, Cerqueira GC, Pironti A, Rudy RF, Patel MM, Yang R, Skerry J, Nazarian E, Musser KA, Taylor J, Pierce VM, Earl AM, Cosimi LA, Shoresh N, Beechem J, Livny J, Hung DT. Simultaneous detection of genotype and phenotype enables rapid and accurate antibiotic susceptibility determination. Nat Med. 2019 Dec;25(12):1858-1864.

Johnson EO, Hung DT. A Point of Inflection and Reflection on Systems Chemical Biology. ACS Chem Biol. 2019 Dec 20;14(12):2497-2511.

Romano KP, Warrier T, Poulsen BE, Nguyen PH, Loftis AR, Saebi A, Pentelute BL, Hung DT. Mutations in pmrB Confer Cross-Resistance between the LptD Inhibitor POL7080 and Colistin in Pseudomonas aeruginosa. Antimicrob Agents Chemother. 2019 Sep;63(9).

Balaban NQ, Helaine S, Lewis K, Ackermann M, Aldridge B, Andersson DI, Brynildsen MP, Bumann D, Camilli A, Collins JJ, Dehio C, Fortune S, Ghigo JM, Hardt WD, Harms A, Heinemann M, Hung DT, Jenal U, Levin BR, Michiels J, Storz G, Tan MW, Tenson T, Van Melderen L, Zinkernagel A. Definitions and guidelines for research on antibiotic persistence. Nat Rev Microbiol. 2019 Jul;17(7):441-448.

Balaban NQ, Helaine S, Lewis K, Ackermann M, Aldridge B, Andersson DI, Brynildsen MP, Bumann D, Camilli A, Collins JJ, Dehio C, Fortune S, Ghigo JM, Hardt WD, Harms A, Heinemann M, Hung DT, Jenal U, Levin BR, Michiels J, Storz G, Tan MW, Tenson T, Van Melderen L, Zinkernagel A. Publisher Correction: Definitions and guidelines for research on antibiotic persistence. Nat Rev Microbiol. 2019 Jul;17(7):460.

Johnson EO, LaVerriere E, Office E, Stanley M, Meyer E, Kawate T, Gomez JE, Audette RE, Bandyopadhyay N, Betancourt N, Delano K, Da Silva I, Davis J, Gallo C, Gardner M, Golas AJ, Guinn KM, Kennedy S, Korn R, McConnell JA, Moss CE, Murphy KC, Nietupski RM, Papavinasasundaram KG, Pinkham JT, Pino PA, Proulx MK, Ruecker N, Song N, Thompson M, Trujillo C, Wakabayashi S, Wallach JB, Watson C, Ioerger TR, Lander ES, Hubbard BK, Serrano-Wu MH, Ehrt S, Fitzgerald M, Rubin EJ, Sassetti CM, Schnappinger D, Hung DT. Large-scale chemical-genetics yields new M. tuberculosis inhibitor classes. Nature. 2019 Jul;571(7763):72-78.

Michalska K, Gale J, Joachimiak G, Chang C, Hatzos-Skintges C, Nocek B, Johnston SE, Bigelow L, Bajrami B, Jedrzejczak RP, Wellington S, Hung DT, Nag PP, Fisher SL, Endres M, Joachimiak A. Conservation of the structure and function of bacterial tryptophan synthases. IUCrJ. 2019 Jul 1;6(Pt 4):649-664.

Poulsen BE, Yang R, Clatworthy AE, White T, Osmulski SJ, Li L, Penaranda C, Lander ES, Shoresh N, Hung DT. Defining the core essential genome of Pseudomonas aeruginosa. Proc Natl Acad Sci U S A. 2019 May 14;116(20):10072-10080.

Bhattacharyya RP, Walker M, Boykin R, Son SS, Liu J, Hachey AC, Ma P, Wu L, Choi K, Cummins KC, Benson M, Skerry J, Ryu H, Wong SY, Goldberg MB, Han J, Pierce VM, Cosimi LA, Shoresh N, Livny J, Beechem J, Hung DT. Rapid identification and phylogenetic classification of diverse bacterial pathogens in a multiplexed hybridization assay targeting ribosomal RNA. Sci Rep. 2019 Mar 14;9(1):4516.

Penaranda C, Hung DT. Single-Cell RNA Sequencing to Understand Host-Pathogen Interactions. ACS Infect Dis. 2019 Mar 8;5(3):336-344.

Bhattacharyya RP, Grad YH, Hung DT. Genomics and Infectious Disease. In: Kasper DL, Fauci AS, Hauser SL, Longo DL, Jameson JL, Loscalzo J, editors. Harrison’s Principles of Internal Medicine 20 ed. New York: McGraw-Hill; 2018.

Parada-Kusz M, Penaranda C, Hagedorn EJ, Clatworthy A, Nair AV, Henninger JE, Ernst C, Li B, Riquelme R, Jijon H, Villablanca EJ, Zon LI, Hung D, Allende ML. Generation of mouse-zebrafish hematopoietic tissue chimeric embryos for hematopoiesis and host-pathogen interaction studies. Dis Model Mech. 2018 Nov 5;11(11).

Ma P, Laibinis HH, Ernst CM, Hung DT. Carbapenem Resistance Caused by High-Level Expression of OXA-663 β-Lactamase in an OmpK36-Deficient Klebsiella pneumoniae Clinical Isolate. Antimicrob Agents Chemother. 2018 Nov;62(11).

Fang C, Lee KK, Nietupski R, Bates RH, Fernandez-Menendez R, Lopez-Roman EM, Guijarro-Lopez L, Yin Y, Peng Z, Gomez JE, Fisher S, Barros-Aguirre D, Hubbard BK, Serrano-Wu MH, Hung DT. Discovery of heterocyclic replacements for the coumarin core of anti-tubercular FadD32 inhibitors. Bioorg Med Chem Lett. 2018 Dec 1;28(22):3529-3533. Ouyang W, Li Z, Han J. Pressure-Modulated Selective Electrokinetic Trapping for Direct Enrichment, Purification, and Detection of Nucleic Acids in Human Serum. Anal Chem. 2018 Oct 2;90(19):11366-11375.

Bhattacharyya RP, Thakku SG, Hung DT. Harnessing CRISPR Effectors for Infectious Disease Diagnostics. ACS Infect Dis. 2018 Sep 14;4(9):1278-1282.

Choi K, Ryu H, Siddle KJ, Piantadosi A, Freimark L, Park DJ, Sabeti P, Han J. Negative Selection by Spiral Inertial Microfluidics Improves Viral Recovery and Sequencing from Blood. Anal Chem. 2018 Apr 3;90(7):4657-4662.

Clatworthy AE, Romano KP, Hung DT. Whole-organism phenotypic screening for anti-infectives promoting host health. Nat Chem Biol. 2018 Apr;14(4):331-341.

Wellington S, Hung DT. The Expanding Diversity of Mycobacterium tuberculosis Drug Targets. ACS Infect Dis. 2018 May 11;4(5):696-714.

Kim M, Wu L, Kim B, Hung DT, Han J. Continuous and High-Throughput Electromechanical Lysis of Bacterial Pathogens Using Ion Concentration Polarization. Anal Chem. 2018 Jan 2;90(1):872-880.

Avital G, Avraham R, Fan A, Hashimshony T, Hung DT, Yanai I. scDual-Seq: mapping the gene regulatory program of Salmonella infection by host and pathogen single-cell RNA-sequencing. Genome Biol. 2017 Oct 27;18(1):200.

Wellington S, Nag PP, Michalska K, Johnston SE, Jedrzejczak RP, Kaushik VK, Clatworthy AE, Siddiqi N, McCarren P, Bajrami B, Maltseva NI, Combs S, Fisher SL, Joachimiak A, Schreiber SL, Hung DT. A small-molecule allosteric inhibitor of Mycobacterium tuberculosis tryptophan synthase. Nat Chem Biol. 2017 Sep;13(9):943-950.

Piantadosi A, Mukerji SS, Chitneni P, Cho TA, Cosimi LA, Hung DT, Goldberg MB, Sabeti PC, Kuritzkes DR, Grad YH. Metagenomic Sequencing of an Echovirus 30 Genome From Cerebrospinal Fluid of a Patient With Aseptic Meningitis and Orchitis. Open Forum Infect Dis. 2017 Summer;4(3):ofx138.

Barczak AK, Avraham R, Singh S, Luo SS, Zhang WR, Bray MA, Hinman AE, Thompson M, Nietupski RM, Golas A, Montgomery P, Fitzgerald M, Smith RS, White DW, Tischler AD, Carpenter AE, Hung DT. Systematic, multiparametric analysis of Mycobacterium tuberculosis intracellular infection offers insight into coordinated virulence. PLoS Pathog. 2017 May;13(5):e1006363.

Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, Verdine V, Donghia N, Daringer NM, Freije CA, Myhrvold C, Bhattacharyya RP, Livny J, Regev A, Koonin EV, Hung DT, Sabeti PC, Collins JJ, Zhang F. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science. 2017 Apr 28;356(6336):438-442. Gomez JE, Kaufmann-Malaga BB, Wivagg CN, Kim PB, Silvis MR, Renedo N, Ioerger TR, Ahmad R, Livny J, Fishbein S, Sacchettini JC, Carr SA, Hung DT. Ribosomal mutations promote the evolution of antibiotic resistance in a multidrug environment. Elife. 2017 Feb 21;6.

Cerqueira GC, Earl AM, Ernst CM, Grad YH, Dekker JP, Feldgarden M, Chapman SB, Reis-Cunha JL, Shea TP, Young S, Zeng Q, Delaney ML, Kim D, Peterson EM, O'Brien TF, Ferraro MJ, Hooper DC, Huang SS, Kirby JE, Onderdonk AB, Birren BW, Hung DT, Cosimi LA, Wortman JR, Murphy CI, Hanage WP. Multi-institute analysis of carbapenem resistance reveals remarkable diversity, unexplained mechanisms, and limited clonal outbreaks. Proc Natl Acad Sci U S A. 2017 Jan 31;114(5):1135-1140. Zhang D, Gomez JE, Chien JY, Haseley N, Desjardins CA, Earl AM, Hsueh PR, Hung DT. Genomic Analysis of the Evolution of Fluoroquinolone Resistance in Mycobacterium tuberculosis Prior to Tuberculosis Diagnosis. Antimicrob Agents Chemother. 2016 Nov;60(11):6600-6608.

Avraham R, Hung DT. A perspective on single cell behavior during infection. Gut Microbes. 2016 Nov;7(6):518-525.

Outterson K, Rex JH, Jinks T, Jackson P, Hallinan J, Karp S, Hung DT, Franceschi F, Merkeley T, Houchens C, Dixon DM, Kurilla MG, Aurigemma R, Larsen J. Accelerating global innovation to address antibacterial resistance: introducing CARB-X. Nat Rev Drug Discov. 2016 Sep;15(9):589-590.

Avraham R, Haseley N, Fan A, Bloom-Ackermann Z, Livny J, Hung DT. A highly multiplexed and sensitive RNA-seq protocol for simultaneous analysis of host and pathogen transcriptomes. Nat Protoc. 2016 Aug;11(8):1477-91.

Grant SS, Wellington S, Kawate T, Desjardins CA, Silvis MR, Wivagg C, Thompson M, Gordon K, Kazyanskaya E, Nietupski R, Haseley N, Iwase N, Earl AM, Fitzgerald M, Hung DT. Baeyer-Villiger Monooxygenases EthA and MymA Are Required for Activation of Replicating and Non-replicating Mycobacterium tuberculosis Inhibitors. Cell Chem Biol. 2016 Jun 23;23(6):666-77.

Wivagg CN, Wellington S, Gomez JE, Hung DT. Loss of a Class A Penicillin-Binding Protein Alters β-Lactam Susceptibilities in Mycobacterium tuberculosis. ACS Infect Dis. 2016 Feb 12;2(2):104-10.

Avraham R, Haseley N, Brown D, Penaranda C, Jijon HB, Trombetta JJ, Satija R, Shalek AK, Xavier RJ, Regev A, Hung DT. Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses. Cell. 2015 Sep 10;162(6):1309-21.

Hou HW, Bhattacharyya RP, Hung DT, Han J. Direct detection and drug-resistance profiling of bacteremias using inertial microfluidics. Lab Chip. 2015 May 21;15(10):2297-307.

Shishkin AA, Giannoukos G, Kucukural A, Ciulla D, Busby M, Surka C, Chen J, Bhattacharyya RP, Rudy RF, Patel MM, Novod N, Hung DT, Gnirke A, Garber M, Guttman M, Livny J. Simultaneous generation of many RNA-seq libraries in a single reaction. Nat Methods. 2015 Apr;12(4):323-5.

Wivagg CN, Bhattacharyya RP, Hung DT. Mechanisms of β-lactam killing and resistance in the context of Mycobacterium tuberculosis. J Antibiot (Tokyo). 2014 Sep;67(9):645-54.

Stanley SA, Barczak AK, Silvis MR, Luo SS, Sogi K, Vokes M, Bray MA, Carpenter AE, Moore CB, Siddiqi N, Rubin EJ, Hung DT. Identification of host-targeted small molecules that restrict intracellular Mycobacterium tuberculosis growth. PLoS Pathog. 2014 Feb;10(2):e1003946.

Slater LH, Clatworthy AE, Hung DT. Bacterial toxins and small molecules elucidate endosomal trafficking. Trends Microbiol. 2014 Feb;22(2):53-5.

Kawate T, Iwase N, Shimizu M, Stanley SA, Wellington S, Kazyanskaya E, Hung DT. Synthesis and structure-activity relationships of phenyl-substituted coumarins with anti-tubercular activity that target FadD32. Bioorg Med Chem Lett. 2013 Nov 15;23(22):6052-9.

Grant SS, Kawate T, Nag PP, Silvis MR, Gordon K, Stanley SA, Kazyanskaya E, Nietupski R, Golas A, Fitzgerald M, Cho S, Franzblau SG, Hung DT. Identification of novel inhibitors of nonreplicating Mycobacterium tuberculosis using a carbon starvation model. ACS Chem Biol. 2013 Oct 18;8(10):2224-34.

Stanley SA, Kawate T, Iwase N, Shimizu M, Clatworthy AE, Kazyanskaya E, Sacchettini JC, Ioerger TR, Siddiqi NA, Minami S, Aquadro JA, Grant SS, Rubin EJ, Hung DT. Diarylcoumarins inhibit mycolic acid biosynthesis and kill Mycobacterium tuberculosis by targeting FadD32. Proc Natl Acad Sci U S A. 2013 Jul 9;110(28):11565-70.

Slater LH, Hett EC, Clatworthy AE, Mark KG, Hung DT. CCT chaperonin complex is required for efficient delivery of anthrax toxin into the cytosol of host cells. Proc Natl Acad Sci U S A. 2013 Jun 11;110(24):9932-7.

Wright GD, Hung DT, Helmann JD. How antibiotics kill bacteria: new models needed?. Nat Med. 2013 May;19(5):544-5.

Hett EC, Slater LH, Mark KG, Kawate T, Monks BG, Stutz A, Latz E, Hung DT. Chemical genetics reveals a kinase-independent role for protein kinase R in pyroptosis. Nat Chem Biol. 2013 Jun;9(6):398-405.

Grant SS, Hung DT. Persistent bacterial infections, antibiotic tolerance, and the oxidative stress response. Virulence. 2013 May 15;4(4):273-83.

Slater LH, Hett EC, Mark K, Chumbler NM, Patel D, Lacy DB, Collier RJ, Hung DT. Identification of novel host-targeted compounds that protect from anthrax lethal toxin-induced cell death. ACS Chem Biol. 2013 Apr 19;8(4):812-22.

Grad YH, Lipsitch M, Griggs AD, Haas BJ, Shea TP, McCowan C, Montmayeur A, FitzGerald M, Wortman JR, Krogfelt KA, Bingen E, Weill FX, Tietze E, Flieger A, Lander ES, Nusbaum C, Birren BW, Hung DT, Hanage WP. Reply to Guy et al.: Support for a bottleneck in the 2011 Escherichia coli O104:H4 outbreak in Germany. Proc Natl Acad Sci U S A. 2012 Dec 26;109(52):E3629-30.

Chand NS, Clatworthy AE, Hung DT. The two-component sensor KinB acts as a phosphatase to regulate Pseudomonas aeruginosa Virulence. J Bacteriol. 2012 Dec;194(23):6537-47.

McMahon TC, Stanley S, Kazyanskaya E, Hung D, Wood JL. The first synthesis of an epidiselenodiketopiperazine. Org Lett. 2012 Sep 7;14(17):4534-6.

Grant SS, Kaufmann BB, Chand NS, Haseley N, Hung DT. Eradication of bacterial persisters with antibiotic-generated hydroxyl radicals. Proc Natl Acad Sci U S A. 2012 Jul 24;109(30):12147-52.

Stanley SA, Grant SS, Kawate T, Iwase N, Shimizu M, Wivagg C, Silvis M, Kazyanskaya E, Aquadro J, Golas A, Fitzgerald M, Dai H, Zhang L, Hung DT. Identification of novel inhibitors of M. tuberculosis growth using whole cell based high-throughput screening. ACS Chem Biol. 2012 Aug 17;7(8):1377-84.

Barczak AK, Gomez JE, Kaufmann BB, Hinson ER, Cosimi L, Borowsky ML, Onderdonk AB, Stanley SA, Kaur D, Bryant KF, Knipe DM, Sloutsky A, Hung DT. RNA signatures allow rapid identification of pathogens and antibiotic susceptibilities. Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):6217-22.

Weiner B, Gomez J, Victor TC, Warren RM, Sloutsky A, Plikaytis BB, Posey JE, van Helden PD, Gey van Pittius NC, Koehrsen M, Sisk P, Stolte C, White J, Gagneux S, Birren B, Hung D, Murray M, Galagan J. Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region. PLoS One. 2012;7(2):e26038.

Grad YH, Lipsitch M, Feldgarden M, Arachchi HM, Cerqueira GC, Fitzgerald M, Godfrey P, Haas BJ, Murphy CI, Russ C, Sykes S, Walker BJ, Wortman JR, Young S, Zeng Q, Abouelleil A, Bochicchio J, Chauvin S, Desmet T, Gujja S, McCowan C, Montmayeur A, Steelman S, Frimodt-Møller J, Petersen AM, Struve C, Krogfelt KA, Bingen E, Weill FX, Lander ES, Nusbaum C, Birren BW, Hung DT, Hanage WP. Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011. Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):3065-70.

Chindelevitch L, Stanley S, Hung D, Regev A, Berger B. MetaMerge: scaling up genome-scale metabolic reconstructions with application to Mycobacterium tuberculosis. Genome Biol. 2012 Jan 31;13(1):r6.

Wivagg CN, Hung DT. Resuscitation-promoting factors are required for β-lactam tolerance and the permeability barrier in Mycobacterium tuberculosis. Antimicrob Agents Chemother. 2012 Mar;56(3):1591-4.

Liu X, Bolla K, Ashforth EJ, Zhuo Y, Gao H, Huang P, Stanley SA, Hung DT, Zhang L. Systematics-guided bioprospecting for bioactive microbial natural products. Antonie Van Leeuwenhoek. 2012 Jan;101(1):55-66.

Chand NS, Hung DT. The two-component sensor kinase KinB acts as a non-canonical switch between acute and chronic infection. Virulence. 2011 Nov-Dec;2(6):553-8.

Tamayo AG, Slater L, Taylor-Parker J, Bharti A, Harrison R, Hung DT, Murphy JR. GRP78(BiP) facilitates the cytosolic delivery of anthrax lethal factor (LF) in vivo and functions as an unfoldase in vitro. Mol Microbiol. 2011 Sep;81(5):1390-401.

McMahon TC, Stanley SA, Kazyanskaya E, Hung DT, Wood JL. A scaleable formal total synthesis of dehydrogliotoxin. Tetrahedron letters. 2011 April; 52(17):2262-2264.

Chand NS, Lee JS, Clatworthy AE, Golas AJ, Smith RS, Hung DT. The sensor kinase KinB regulates virulence in acute Pseudomonas aeruginosa infection. J Bacteriol. 2011 Jun;193(12):2989-99.

Gomez JE, Clatworthy A, Hung DT. Probing bacterial pathogenesis with genetics, genomics, and chemical biology: past, present, and future approaches. Crit Rev Biochem Mol Biol. 2011 Feb;46(1):41-66.

Kaufmann BB, Hung DT. The fast track to multidrug resistance. Mol Cell. 2010 Feb 12;37(3):297-8. doi: 10.1016/j.molcel.2010.01.027. PubMed PMID: 20159549.

Hett EC, Hung DT. Targeting multiple biofilm pathways. Chem Biol. 2009 Dec 24;16(12):1216-8. doi: 10.1016/j.chembiol.2009.12.003. PubMed PMID: 20064430.

Stanley SA, Hung DT. Toward a systems-level analysis of infection biology: a new method for conducting genetic screens in human cells. Sci Transl Med. 2009 Dec 16;1(11):11ps13.

Stanley SA, Hung DT. Chemical tools for dissecting bacterial physiology and virulence. Biochemistry. 2009 Sep 22;48(37):8776-86.

Barczak AK, Hung DT. Productive steps toward an antimicrobial targeting virulence. Curr Opin Microbiol. 2009 Oct;12(5):490-6.

Clatworthy AE, Lee JS, Leibman M, Kostun Z, Davidson AJ, Hung DT. Pseudomonas aeruginosa infection of zebrafish involves both host and pathogen determinants. Infect Immun. 2009 Apr;77(4):1293-303.

Hett EJ, Hung DT. Pathogen-Host Interactions: Chemical Biology Approach. In: T BP, editor. Wiley Encyclopedia of Chemical Biology Hoboken, NJ: John Wiley and Sons; 2008.

Nusbaum C, Ohsumi TK, Gomez J, Aquadro J, Victor TC, Warren RM, Hung DT, Birren BW, Lander ES, Jaffe DB. Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing. Nat Methods. 2009 Jan;6(1):67-9.

Clatworthy AE, Pierson E, Hung DT. Targeting virulence: a new paradigm for antimicrobial therapy. Nat Chem Biol. 2007 Sep;3(9):541-8.