Publications

Publications

2020 – present

UT Southwestern Medical Center · Altos Labs (Bay Area Institute of Science) — independent lab
  1. 2026
    Harnessing viral strategies to reverse cognitive dysfunction through the integrated stress response.
    Reineke LC, Zhu PJ, … Chen J, Frost A, Costa-Mattioli M Science 392(6793):eaea8782
  2. ★ 2026
    Functional landscape of non-canonical open reading frames in coordinating cell fate.
    Zhu K, Li WC, Liu J, … Chen J Molecular Cell 86(6):1081–1098.e14
  3. ★ 2025
    Large-scale CRISPR screening in primary human 3D gastric organoids enables comprehensive dissection of gene-drug interactions.
    Lo YH, … Chen J*, Kuo CJ* Nature Communications 16(1):7566
    * co-corresponding authors
  4. 2025
    RACK1 MARylation regulates translation and stress granules in ovarian cancer cells.
    Challa S, … Chen J, Kraus WL Journal of Cell Biology 224(2):e202401101
  5. 2024
    The Fanconi anemia pathway induces chromothripsis and ecDNA-driven cancer drug resistance.
    Engel JL, … Chen J, Cortés-Ciriano I, Lo RS, Ly P Cell 187(21):6055–6070.e22
  6. 2024
    IRE1α mediates hypertrophic growth of cardiomyocytes through initiation-complex formation on TOP-motif transcripts.
    Li C, … Chen J, Wang ZV Circulation 150(13):1010–1029
  7. ★ 2022
    The dark proteome: translation from noncanonical open reading frames.
    Wright BW, Yi Z, Weissman JS, Chen J Trends in Cell Biology 32(3):243–258
  8. 2022
    Developmental dynamics of RNA translation in the human brain.
    Duffy EE, et al. Nature Neuroscience 25(10):1353–1365
  9. 2022
    Standardized annotation of translated open reading frames.
    Mudge JM, et al. Nature Biotechnology 40(7):994–999
  10. 2022
    Machine learning predicts translation initiation sites in neurologic diseases with nucleotide repeat expansions.
    Gleason AC, Ghadge G, Chen J, Sonobe Y, Roos RP PLoS One 17(6):e0256411

2016 – 2020

UCSF · Weissman lab (postdoc, plus ongoing collaborations)
  1. 2024
    Neuronal activity rapidly reprograms dendritic translation via eIF4G2:uORF binding.
    Hacisuleyman E, … Chen J, Weissman JS, Darnell RB Nature Neuroscience 27(5):822–835
  2. 2022
    Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells.
    Wu D, … Chen J, … Weissman JS, Lim DA Cell Genomics 2(11):100177
  3. ★ 2021
    Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing.
    Nuñez JK, Chen J, … Weissman JS Cell 184(9):2503–2519
  4. 2021
    Structured elements drive extensive circular RNA translation.
    Chen CK, … Chen J, … Weissman JS, … Chang HY Molecular Cell 81(20):4300–4318.e13
  5. 2021
    A CRISPR/Cas9-engineered ARID1A-deficient human gastric cancer organoid model reveals essential and non-essential modes of oncogenic transformation.
    Lo YH, … Chen J, … Weissman JS, … Kuo CJ Cancer Discovery 11(6):1562–1581
  6. ★ 2020
    Pervasive functional translation of noncanonical open reading frames.
    Chen J, Brunner A-D, … Weissman JS Science 367:1140–1146
    Highlighted in Science; Nature Reviews Molecular Cell Biology; F1000 "exceptional"
  7. 2020
    Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing.
    Replogle JM, … Chen J, … Weissman JS, Adamson B Nature Biotechnology 38:954–961
  8. 2020
    Maf and Mafb control mouse pallial interneuron fate and maturation through neuropsychiatric disease gene regulation.
    Pai EL, Chen J*, Darbandi SF*, … Rubenstein JL eLife 9
    * co-second authors

2010 – 2016

Stanford (Ph.D., Puglisi lab) · Yale (undergrad, Reed & Levene labs)
  1. 2016
    The amino acid sequence repertoire of the bacterial proteome and the occurrence of untranslatable sequences.
    Navon SP*, Kornberg G*, Chen J*, … Adir N Proc. Natl. Acad. Sci. 113:7166–7170
    * co-first authors
  2. 2016
    Multiple parallel pathways of translation initiation on CrPV IRES.
    Petrov A, Grosely R, Chen J, O’Leary SE, Puglisi JD Molecular Cell 62:92–103
  3. 2016
    N-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics.
    Choi J, … Chen J, … Puglisi JD Nature Structural & Molecular Biology 23:110–115
  4. 2016
    The molecular choreography of protein synthesis: translational control, regulation, and pathways.
    Chen J*, Choi J*, O’Leary SE*, … Puglisi JD Quarterly Reviews of Biophysics 49
    * co-first authors
  5. ★ 2015
    Coupling of mRNA structure rearrangement to ribosome movement during bypassing of non-coding regions.
    Chen J, Coakley A, O’Connor M, … Puglisi JD Cell 163:1267–1280
  6. 2015
    Kinetic pathway of 40S ribosomal subunit recruitment to hepatitis C virus internal ribosome entry site.
    Fuchs G, … Chen J, … Puglisi JD Proc. Natl. Acad. Sci. 112:319–325
  7. ★ 2014
    Dynamic pathways of -1 translational frameshifting.
    Chen J, Petrov A, Johansson M, … Puglisi JD Nature 512:328–332
  8. 2014
    High-throughput platform for real-time monitoring of biological processes by multicolor single-molecule fluorescence.
    Chen J*, Dalal RV*, … Puglisi JD Proc. Natl. Acad. Sci. 111:664–669
    * co-first authors
  9. 2014
    Real-time observation of signal recognition particle binding to actively translating ribosomes.
    Noriega TR, Chen J, Walter P, Puglisi JD eLife 3
  10. 2014
    Signal recognition particle-ribosome binding is sensitive to nascent chain length.
    Noriega TR, … Chen J, … Walter P J. Biol. Chem. 289:19294–19305
  11. 2014
    Sequence-dependent elongation dynamics on macrolide-bound ribosomes.
    Johansson M, Chen J, … Puglisi JD Cell Reports 7:1534–1546
  12. 2014
    The dynamics of SecM-induced translational stalling.
    Tsai A, … Chen J, Puglisi JD Cell Reports 7:1521–1533
  13. 2013
    Coordinated conformational and compositional dynamics drive ribosome translocation.
    Chen J, Petrov A, Tsai A, O’Leary SE, Puglisi JD Nature Structural & Molecular Biology 20:718–727
  14. 2013
    Dynamic recognition of the mRNA cap by Saccharomyces cerevisiae eIF4E.
    O’Leary SE, Petrov A, Chen J, Puglisi JD Structure 21:2197–2207
  15. 2012
    Nonfluorescent quenchers to correlate single-molecule conformational and compositional dynamics.
    Chen J, Tsai A, Petrov A, Puglisi JD Journal of the American Chemical Society 134:5734–5737
  16. 2012
    Unraveling the dynamics of ribosome translocation.
    Chen J, Tsai A, O’Leary SE, Petrov A, Puglisi JD Current Opinion in Structural Biology 22:804–814
  17. 2012
    Single-molecule analysis of translational dynamics.
    Petrov A, Chen J, O’Leary SE, Tsai A, Puglisi JD Cold Spring Harbor Perspectives in Biology 4
  18. 2010
    Temperature dependence of 1/f noise mechanisms in silicon nanowire biochemical field effect transistors.
    Rajan NK, Routenberg DA, Chen J, Reed MA Applied Physics Letters 97:243501
  19. 2010
    1/f noise of silicon nanowire BioFETs.
    Rajan NK, Routenberg DA, Chen J, Reed MA IEEE Electron Device Letters 31:615–617