FULL PUBLICATIONS

2020 - present

Duffy EE, Finander B, Choi G, Carter AC, Pritisanac I, Alam A, Luria V, Karger A, Phu W, Sherman MA, Assad EG, Pajarillo N, Khitun A, Crouch EE, Ganesh S, Chen J, Berger B, Sestan N, O'Donnell-Luria A, Huang EJ, Griffith EC, Forman-Kay JD, Moses AM, Kalish BT, Greenberg ME. Developmental dynamics of RNA translation in the human brain. Nature Neuroscience (2022).

Mudge JM, Ruiz-Orera J, Prensner JR, Brunet MA, Calvet F, Jungreis I, Gonzalez JM, Magrane M, Martinez TF, Schulz JF, Yang YT, Albà MM, Aspden JL, Baranov PV, Bazzini AA, Bruford E, Martin MJ, Calviello L, Carvunis AR, Chen J, Couso JP, Deutsch EW, Flicek P, Frankish A, Gerstein M, Hubner N, Ingolia NT, Kellis M, Menschaert G, Moritz RL, Ohler U, Roucou X, Saghatelian A, Weissman JS, van Heesch S. Standardized annotation of translated open reading frames. Nature Biotechnology (2022).

Gleason AC, Ghadge G, Chen J, Sonobe Y, Roos RP. Machine learning predicts translation initiation sites in neurologic diseases with nucleotide repeat expansions. PloS One (2022).

Wright BW, Yi Z, Weissman JS, Chen J. The dark proteome: translation from noncanonical open reading frames. Trends in Cell Biology (2021).

2016 - 2020 (Postdoc with Jonathan Weissman at UCSF)

Wu D, Poddar A, Ninou E, Hwang E, Cole MA, Liu SJ, Horlbeck MA, Chen J, Replogle JM, Carosso GA, Eng NWL, Chang J, Shen Y, Weissman JS, Lim DA. Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells. Cell Genomics (2022).

Chen CK, Cheng R, Demeter J, Chen J, Weingarten-Gabbay S, Jiang L, Snyder MP, Weissman JS, Segal E, Jackson PK, Chang HY. Structured elements drive extensive circular RNA translation. Molecular Cell (2021).

Lo YH, Kolahi KS, Du Y, Chang CY, Krokhotin A, Nair A, Sobba WD, Karlsson K, Jones SJ, Longacre TA, Mah AT, Tercan B, Sockell A, Xu H, Seoane JA, Chen J, Shmulevich I, Weissman JS, Curtis C, Califano A, Fu H, Crabtree GR, Kuo CJ. A CRISPR/Cas9-Engineered ARID1A-Deficient Human Gastric Cancer Organoid Model Reveals Essential and Nonessential Modes of Oncogenic Transformation. Cancer Discovery (2021).

Nuñez JK, Chen J, Pommier GC, Cogan JZ, Replogle JM, Adriaens C, Ramadoss GN, Shi Q, Hung KL, Samelson AJ, Pogson AN, Kim JYS, Chung A, Leonetti MD, Chang HY, Kampmann M, Bernstein BE, Hovestadt V, Gilbert LA, Weissman JS. Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing. Cell (2021).

Chen J, Brunner A-D, Cogan JZ, Nuñez JK, Fields AP, Adamson B, Itzhak DN, Li JY, Mann M, Leonetti MD, Weissman JS. Pervasive functional translation of noncanonical open reading frames. Science 367: 1140-1146 (2020).

Replogle JM, Norman TM, Xu A, Hussmann J, Chen J, Cogan JZ, Meer EJ, Terry JM, Riordan D, Srinivas N, Fiddes IT, Arthur JG, Alvarado LJ, Pfeiffer KA, Mikkelsen TS, Weissman JS, Adamson B. Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing. Nature Biotechnology 38: 954–961 (2020).

Pai EL, Chen J*, Darbandi SF*, FS Cho, Chen J, Lindtner S, Chu JS, Paz JT, Vogt D, Paredes MF, Rubenstein JL. Maf and Mafb control mouse pallial interneuron fate and maturation through neuropsychiatric disease gene regulation. eLife 9 (2020). *co-second authors

2010 - 2015 (Graduate Student with Jody Puglisi at Stanford University)

Navon SP*, Kornberg G*, Chen J*, Schwartzman T, Tsai A, Puglisi EV, Puglisi JD, Adir N. The amino acid sequence repertoire of the bacterial proteome and the occurrence of untranslatable sequences. Proceedings of the National Academy of Sciences 113: 7166-7170 (2016). *co-first authors

Petrov A, Grosely R, Chen J, O'Leary SE, Puglisi JD. Multiple parallel pathways of translation initiation on CrPV IRES. Molecular Cell 62: 92-103 (2016).

Choi J, Ieong KW, Demirci H, Chen J, Petrov A, Prabhakar A, O'Leary SE, Dominissini D, Rechavi G, Soltis SM, Ehrenberg M, Puglisi JD. N-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics. Nature structural & molecular biology 23: 110-115 (2016).

Chen J*, Choi J*, OLeary SE*, Prabhakar A, Petrov A, Grosely R, Puglisi EV, Puglisi JD. The molecular choreography of protein synthesis: translational control, regulation, and pathways. Quarterly Reviews of Biophysics 49 (2016). *co-first authors

Chen J, Coakley A, O'Connor M, Petrov A, O'Leary SE, Atkins JF, Puglisi JD. Coupling of mRNA structure rearrangement to ribosome movement during bypassing of non-coding regions. Cell 163, 1267-1280 (2015).

Fuchs G, Petrov AN, Marceau CD, Popov LM, Chen J, O'Leary SE, Wang R, Carette JE, Sarnow P, Puglisi JD. Kinetic pathway of 40S ribosomal subunit recruitment to hepatitis C virus internal ribosome entry site. Proceedings of the National Academy of Sciences 112: 319-25 (2015).

Chen J, Petrov A, Johansson M, Tsai A, O'Leary SE, Puglisi JD. Dynamic pathways of -1 translational frameshifting. Nature 512: 328-32 (2014).

Noriega TR, Chen J, Walter P, Puglisi JD. Real-time observation of signal recognition particle binding to actively translating ribosomes. eLife 3 (2014).

Noriega TR, Tsai A, Elvekrog MM, Petrov A, Neher SB, Chen J, Bradshaw N, Puglisi JD, Walter P. Signal recognition particle-ribosome binding is sensitive to nascent chain length. The Journal of biological chemistry 289: 19294-305 (2014).

Johansson M, Chen J, Tsai A, Kornberg G, Puglisi JD. Sequence-dependent elongation dynamics on macrolide-bound ribosomes. Cell Reports 7: 1534-46 (2014).

Chen J*, Dalal RV*, Petrov AN, Tsai A, O'Leary SE, Chapin K, Cheng J, Ewan M, Hsiung PL, Lundquist P, Turner SW, Hsu DR, Puglisi JD. High-throughput platform for real-time monitoring of biological processes by multicolor single-molecule fluorescence. Proceedings of the National Academy of Sciences 111: 664-9 (2014). *co-first authors

Tsai A, Kornberg G, Johansson M, Chen J, Puglisi JD. The dynamics of SecM-induced translational stalling. Cell Reports 7: 1521-33 (2014).

O'Leary SE, Petrov A, Chen J, Puglisi JD. Dynamic recognition of the mRNA cap by Saccharomyces cerevisiae eIF4E. Structure 21: 2197-207 (2013).

Chen J, Petrov A, Tsai A, O'Leary SE, Puglisi JD. Coordinated conformational and compositional dynamics drive ribosome translocation. Nature structural & molecular biology 20: 718-27 (2013).

Chen J, Tsai A, Petrov A, Puglisi JD. Nonfluorescent quenchers to correlate single-molecule conformational and compositional dynamics. Journal of the American Chemical Society 134: 5734-7 (2012).

Chen J, Tsai A, OLeary SE, Petrov A, Puglisi JD. Unraveling the dynamics of ribosome translocation. Current opinion in structural biology 22: 804-814 (2012).

Petrov A, Chen J, O’Leary SE, Tsai A, Puglisi JD. Single-Molecule Analysis of Translational Dynamics. Cold Spring Harbor perspectives in biology 4 (2012).

Before 2010

Rajan NK, Routenberg DA, Chen J, Reed MA. Temperature dependence of 1/f noise mechanisms in silicon nanowire biochemical field effect transistors. Applied Physics Letters 97, 243501 (2010).

Rajan NK, Routenberg DA, Chen J, Reed MA. 1/f Noise of Silicon Nanowire BioFETs. IEEE Electron Device Letters 31, 615-617 (2010).