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James Chen

Photo of James Chen
Title(s)Assistant Professor, Microbiology and Immunology
SchoolSchool of Medicine
Phone415-353-4738
Emailjames.chen5@ucsf.edu
PronounsHe/Him/His
ORCID ORCID Icon0000-0002-2311-003X Additional info
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    Collapse Biography 
    Collapse education and training
    New York University, New York, NYPostdoctoral Fellow10/2025Microbiology
    The Rockefeller University, New York, NYPh.D.06/2020Molecular Biophysics
    University of Pennsylvania, Philadelphia, PAB.A.05/2013Biophysics
    Collapse awards and honors
    University of California, San Francisco2025NIAID New Innovators Award
    New York University2022Jane Coffin Childs Fellow
    The Rockefeller University2020Schmidt Science Fellow
    University of Pennsylvania2012Phi Sigma Biological Science Honor Society

    Collapse Overview 

    Collapse Research 
    Collapse research activities and funding
    Structural characterization of the elongasome and divisome in mycobacteria
    NIH DP2AI184740Aug 1, 2025 - Jul 31, 2030
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Structural basis for loading of Transcription Repair-Coupling factor Mfd onto stalled elongation complexes. bioRxiv. 2025 Sep 06. Brewer J, Llewellyn E, Chen J, Campbell EA, Darst SA. PMID: 40949946; PMCID: PMC12424862.
      View in: PubMed   Mentions:
    2. Identification of a depupylation regulator for an essential enzyme in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A. 2024 Dec 03; 121(49):e2407239121. Kahne SC, Yoo JH, Chen J, Nakedi K, Iyer LM, Putzel G, Samhadaneh NM, Pironti A, Aravind L, Ekiert DC, Bhabha G, Rhee KY, Darwin KH. PMID: 39585979; PMCID: PMC11626117.
      View in: PubMed   Mentions:
    3. Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy. Nat Struct Mol Biol. 2024 Nov; 31(11):1778-1788. Saecker RM, Mueller AU, Malone B, Chen J, Budell WC, Dandey VP, Maruthi K, Mendez JH, Molina N, Eng ET, Yen LY, Potter CS, Carragher B, Darst SA. PMID: 38951624; PMCID: PMC11821292.
      View in: PubMed   Mentions:
    4. Protein target highlights in CASP15: Analysis of models by structure providers. Proteins. 2023 12; 91(12):1571-1599. Alexander LT, Durairaj J, Kryshtafovych A, Abriata LA, Bayo Y, Bhabha G, Breyton C, Caulton SG, Chen J, Degroux S, Ekiert DC, Erlandsen BS, Freddolino L, Gilzer D, Greening C, Grimes JM, Grinter R, Gurusaran M, Hartmann MD, Hitchman CJ, Keown JR, Kropp A, Kursula P, Lovering AL, Lemaitre B, Lia A, Liu S, Logotheti M, Lu S, Markússon S, Miller MD, Minasov G, Niemann HH, Opazo F, Phillips GN, Davies OR, Rommelaere S, Rosas-Lemus M, Roversi P, Satchell K, Smith N, Wilson MA, Wu KL, Xia X, Xiao H, Zhang W, Zhou ZH, Fidelis K, Topf M, Moult J, Schwede T. PMID: 37493353; PMCID: PMC10792529.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    5. Structure of an endogenous mycobacterial MCE lipid transporter. Nature. 2023 Aug; 620(7973):445-452. Chen J, Fruhauf A, Fan C, Ponce J, Ueberheide B, Bhabha G, Ekiert DC. PMID: 37495693.
      View in: PubMed   Mentions:
    6. A tale of two inhibitors: diarylquinolines and squaramides. EMBO J. 2023 Aug 01; 42(15):e114912. Chen J, Ekiert DC. PMID: 37435707; PMCID: PMC10390866.
      View in: PubMed   Mentions:
    7. A general mechanism for transcription bubble nucleation in bacteria. Proc Natl Acad Sci U S A. 2023 Apr 04; 120(14):e2220874120. Mueller AU, Chen J, Wu M, Chiu C, Nixon BT, Campbell EA, Darst SA. PMID: 36972428; PMCID: PMC10083551.
      View in: PubMed   Mentions:
    8. An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options. Proc Natl Acad Sci U S A. 2023 02 21; 120(8):e2215945120. Kang JY, Mishanina TV, Bao Y, Chen J, Llewellyn E, Liu J, Darst SA, Landick R. PMID: 36795753; PMCID: PMC9974457.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    9. Structural basis for substrate selection by the SARS-CoV-2 replicase. Nature. 2023 Feb; 614(7949):781-787. Malone BF, Perry JK, Olinares PDB, Lee HW, Chen J, Appleby TC, Feng JY, Bilello JP, Ng H, Sotiris J, Ebrahim M, Chua EYD, Mendez JH, Eng ET, Landick R, Götte M, Chait BT, Campbell EA, Darst SA. PMID: 36725929; PMCID: PMC9891196.
      View in: PubMed   Mentions:
    10. Basis of narrow-spectrum activity of fidaxomicin on Clostridioides difficile. Nature. 2022 Apr; 604(7906):541-545. Cao X, Boyaci H, Chen J, Bao Y, Landick R, Campbell EA. PMID: 35388215; PMCID: PMC9635844.
      View in: PubMed   Mentions:
    11. Ensemble cryo-EM reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication-transcription complex. Nat Struct Mol Biol. 2022 Mar; 29(3):250-260. Chen J, Wang Q, Malone B, Llewellyn E, Pechersky Y, Maruthi K, Eng ET, Perry JK, Campbell EA, Shaw DE, Darst SA. PMID: 35260847; PMCID: PMC8935131.
      View in: PubMed   Mentions:
    12. Structural origins of Escherichia coli RNA polymerase open promoter complex stability. Proc Natl Acad Sci U S A. 2021 Oct 05; 118(40). Saecker RM, Chen J, Chiu CE, Malone B, Sotiris J, Ebrahim M, Yen LY, Eng ET, Darst SA. PMID: 34599106; PMCID: PMC8501879.
      View in: PubMed   Mentions:
    13. Structural basis for backtracking by the SARS-CoV-2 replication-transcription complex. Proc Natl Acad Sci U S A. 2021 May 11; 118(19). Malone B, Chen J, Wang Q, Llewellyn E, Choi YJ, Olinares PDB, Cao X, Hernandez C, Eng ET, Chait BT, Shaw DE, Landick R, Darst SA, Campbell EA. PMID: 33883267; PMCID: PMC8126829.
      View in: PubMed   Mentions:
    14. Structural basis for transcription complex disruption by the Mfd translocase. Elife. 2021 Jan 22; 10. Kang JY, Llewellyn E, Chen J, Olinares PDB, Brewer J, Chait BT, Campbell EA, Darst SA. PMID: 33480355; PMCID: PMC7864632.
      View in: PubMed   Mentions:
    15. Native Mass Spectrometry-Based Screening for Optimal Sample Preparation in Single-Particle Cryo-EM. Structure. 2021 Feb 04; 29(2):186-195.e6. Olinares PDB, Kang JY, Llewellyn E, Chiu C, Chen J, Malone B, Saecker RM, Campbell EA, Darst SA, Chait BT. PMID: 33217329; PMCID: PMC7867593.
      View in: PubMed   Mentions:
    16. The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase. Proc Natl Acad Sci U S A. 2020 Dec 01; 117(48):30423-30432. Lilic M, Chen J, Boyaci H, Braffman N, Hubin EA, Herrmann J, Müller R, Mooney R, Landick R, Darst SA, Campbell EA. PMID: 33199626; PMCID: PMC7720108.
      View in: PubMed   Mentions:
    17. Diverse and unified mechanisms of transcription initiation in bacteria. Nat Rev Microbiol. 2021 Feb; 19(2):95-109. Chen J, Boyaci H, Campbell EA. PMID: 33122819; PMCID: PMC7855538.
      View in: PubMed   Mentions:
    18. Time-resolved cryo-EM using Spotiton. Nat Methods. 2020 Sep; 17(9):897-900. Dandey VP, Budell WC, Wei H, Bobe D, Maruthi K, Kopylov M, Eng ET, Kahn PA, Hinshaw JE, Kundu N, Nimigean CM, Fan C, Sukomon N, Darst SA, Saecker RM, Chen J, Malone B, Potter CS, Carragher B. PMID: 32778833; PMCID: PMC7799389.
      View in: PubMed   Mentions:
    19. Structural Basis for Helicase-Polymerase Coupling in the SARS-CoV-2 Replication-Transcription Complex. Cell. 2020 Sep 17; 182(6):1560-1573.e13. Chen J, Malone B, Llewellyn E, Grasso M, Shelton PMM, Olinares PDB, Maruthi K, Eng ET, Vatandaslar H, Chait BT, Kapoor TM, Darst SA, Campbell EA. PMID: 32783916; PMCID: PMC7386476.
      View in: PubMed   Mentions:
    20. Stepwise Promoter Melting by Bacterial RNA Polymerase. Mol Cell. 2020 04 16; 78(2):275-288.e6. Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA. PMID: 32160514; PMCID: PMC7166197.
      View in: PubMed   Mentions: 66     Fields:    Translation:Cells
    21. E. coli TraR allosterically regulates transcription initiation by altering RNA polymerase conformation. Elife. 2019 12 16; 8. Chen J, Gopalkrishnan S, Chiu C, Chen AY, Campbell EA, Gourse RL, Ross W, Darst SA. PMID: 31841111; PMCID: PMC6970531.
      View in: PubMed   Mentions: 46     Fields:    Translation:Cells
    22. Eliminating effects of particle adsorption to the air/water interface in single-particle cryo-electron microscopy: Bacterial RNA polymerase and CHAPSO. J Struct Biol X. 2019; 1. Chen J, Noble AJ, Kang JY, Darst SA. PMID: 32285040; PMCID: PMC7153306.
      View in: PubMed   Mentions:
    23. Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding. Nature. 2019 Jan; 565(7739):382-385. Boyaci H, Chen J, Jansen R, Darst SA, Campbell EA. PMID: 30626968; PMCID: PMC6399747.
      View in: PubMed   Mentions:
    24. Structural Basis for NusA Stabilized Transcriptional Pausing. Mol Cell. 2018 Mar 01; 69(5):816-827.e4. Guo X, Myasnikov AG, Chen J, Crucifix C, Papai G, Takacs M, Schultz P, Weixlbaumer A. PMID: 29499136; PMCID: PMC5842316.
      View in: PubMed   Mentions:
    25. Fidaxomicin jams Mycobacterium tuberculosis RNA polymerase motions needed for initiation via RbpA contacts. Elife. 2018 Feb 26; 7. Boyaci H, Chen J, Lilic M, Palka M, Mooney RA, Landick R, Darst SA, Campbell EA. PMID: 29480804; PMCID: PMC5837556.
      View in: PubMed   Mentions:
    26. 6S RNA Mimics B-Form DNA to Regulate Escherichia coli RNA Polymerase. Mol Cell. 2017 Oct 19; 68(2):388-397.e6. Chen J, Wassarman KM, Feng S, Leon K, Feklistov A, Winkelman JT, Li Z, Walz T, Campbell EA, Darst SA. PMID: 28988932; PMCID: PMC5683422.
      View in: PubMed   Mentions:
    27. Structural basis of transcription arrest by coliphage HK022 Nun in an Escherichia coli RNA polymerase elongation complex. Elife. 2017 Mar 20; 6. Kang JY, Olinares PD, Chen J, Campbell EA, Mustaev A, Chait BT, Gottesman ME, Darst SA. PMID: 28318486; PMCID: PMC5386594.
      View in: PubMed   Mentions:
    28. Effects of Increasing the Affinity of CarD for RNA Polymerase on Mycobacterium tuberculosis Growth, rRNA Transcription, and Virulence. J Bacteriol. 2017 Feb 15; 199(4). Garner AL, Rammohan J, Huynh JP, Onder LM, Chen J, Bae B, Jensen D, Weiss LA, Manzano AR, Darst SA, Campbell EA, Nickels BE, Galburt EA, Stallings CL. PMID: 27920294; PMCID: PMC5287406.
      View in: PubMed   Mentions:
    29. CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex. Elife. 2015 Sep 08; 4. Bae B, Chen J, Davis E, Leon K, Darst SA, Campbell EA. PMID: 26349034; PMCID: PMC4593161.
      View in: PubMed   Mentions:
    30. Mycobacterial RNA polymerase forms unstable open promoter complexes that are stabilized by CarD. Nucleic Acids Res. 2015 Jan; 43(1):433-45. Davis E, Chen J, Leon K, Darst SA, Campbell EA. PMID: 25510492; PMCID: PMC4288152.
      View in: PubMed   Mentions:
    31. Requirements for catalysis in the Cre recombinase active site. Nucleic Acids Res. 2010 Sep; 38(17):5817-32. Gibb B, Gupta K, Ghosh K, Sharp R, Chen J, Van Duyne GD. PMID: 20462863; PMCID: PMC2943603.
      View in: PubMed   Mentions:
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