Yang D*, Jones MG*, Naranjo S, Rideout W, Min KH, Ho R, Wu W, Qiu X, Replogle JM, Page J, Quinn JJ, Horns F, Chen MZ, Freed-Pastor W, McGinnis CS, Patterson DM, Gartner ZJ, Chow E, Bivona TG, Chan MM, Yosef N, Jacks T and Weissman JS. (2022) Lineage tracing reveals the phylodynamics, plasticity and paths of tumor evolution. Cell, Volume 185(11):1905-1923. *Equal Contribution.
Jones MG*, Yang D*, ^, Weissman JS^. (2022) New tools for lineage tracing in cancer in vivo. Annual Review of Cancer Biology. *Equal Contribution, ^Co-corresponding author.
Qiu X*, Zhang Y*, Martin-Rufino J, Weng C, Hosseinzadeh S, Yang D, Pogson A, Wang L, Shurtleff M, Yuan R, Xu S, Ma Y, Replogle JM, Darmanis S, Bahar I, Xing J, Weissman JS. (2022) Mapping transcriptomic vector fields of single cells. Cell, Volume 185(4):690-711 *Equal Contribution.
Hussmann JA, Ling J, Ravisankar P, Yan J, Cirincione A, Xu A, Simpson D, Yang D, …, Adamson B. (2021) Mapping the genetic landscape of DNA double-strand break repair. Cell, Volume 184(22):5653-5669.
Koblan LW, Hussmann JA, Shen M, Arbab M, Sisley, T, Yang D, Replogle JM, Mok B, Adamson B, Weissman JS, Liu DR (2021). Development of a set of C•G-to-G•C transversion base editors from CRISPRi screens, target-library analysis, and machine learning. Nature Biotechnology, Volume 39(11):1414-1425.
Yang D, Qu F, Cai H, Chuang CH, Lim JS, Jahchan N, Grüner BM, S Kuo C, Kong C, Oudin MJ, Winslow MM, Sage J. (2019) Axon-like protrusions promote small cell lung cancer migration and metastasis. Elife, pii: e50616.
Chan M, Smith ZD, Grosswendt S, Kretzmer H, Norman TM, Adamson B, Jost M, Quinn JJ, Yang D, Jones MG, Khodaverdian A, Yosef N, Meissner A, Weissman JS. (2019) Molecular recording of mammalian embryogenesis. Nature, Volume 570(7759):77-82.
Yang D, Denny SK, Greenside PG, Chaikovsky A, Brady JJ, Ouadah Y, Granja JM, Jahchan NS, Lim JS, Kowk S, Kong CS, Berghoff AS, Schmitt A, Reinhardt HC, Park KS, Preusser M, Kundaje A, Greenleaf WJ, Sage J and Winslow MM. (2018) Intertumoral heterogeneity is influenced by the cell type of origin. Cancer Discovery, Volume 8(10): 1316-1331.
Lim JS, Ibaseta A, Fischer MM, Cancilla B, O’Young G, Cristea S, Luca V, Yang D, Jahchan N, Hamard C, Antoine M, Wislez M, …, Murriel CL and Sage J. (2017) Notch signaling defines a novel level of intratumoral heterogeneity that contributes to tumorigenesis in small cell lung cancer. Nature, Volume 545(7654): 360-364.
Chuang CH, Greenside PG, Rogers ZN, Brady JJ, Yang D, Caswell DR, Ma RK, Winters A, Kopecky KE, Chiou SH, Grüner BM, Ramaswami G, Sweet-Cordero EA, Li JB, Kundaje A, and Winslow MM. (2017) Molecular definition of a metastatic lung cancer state reveals a targetable CD109/Jak/Stat axis. Nature Medicine, Volume 23(3): 291-300.
Denny SK*, Yang D*, Chuang CH, Brady JJ, Lim JS, Grüner BM, Chiou SH, Schep AN, Baral J, Hamard C, Antoine M, Wislez M, Kong CS, Connolly AJ, Park KS, Sage J, Greenleaf WJ, Winslow MM. (2016) Nfib promotes metastasis through a widespread increase in chromatin accessibility. Cell, Volume 166(2), 328-42.*Equal Contribution, Co-first author.
Grüner BM*, Schulze CJ*, Yang D, Ogasawara D, Dix M, Chuang CH, Rogers ZN, Brown JM, Cravatt B, Bogyo M, Winslow MM. (2016) An in vivo multiplexed small-molecule screening platform. Nature Methods, Volume 13(10): 883-9. *Equal Contribution.
Weiskopf K, Jahchan NS, Schnorr PJ, Cristea S, Ring AM, Maute RL, Volkmer AK, Volkmer JP, Liu J, Lim JS, Yang D, …, Weissman IL, Sage J. (2016) Cd47-blocking immunotherapies stimulate macrophage-mediated destruction of small-cell lung cancer. Journal of Clinical Investigation, Volume 126(7), 2610-20.
George J, Lim JS, Jang SJ, Cun Y, Ozretić L, Kong G, Leenders F, Lu X, Fernández-Cuesta L, Bosco G, Müller C, Dahmen I, Jahchan NS, Park KS, Yang D, …, Haas SA, Brambilla E, Peifer M, Sage J, Thomas RK. (2015) Comprehensive genomic profiles of small cell lung cancer. Nature, Volume 524(7563), 47-53.
Chiou SH, Winters IP, Wang J, Naranjo S, Dudgeon C, Tamburini FB, Brady JJ, Yang D, Grüner BM, …, Kim SK, Winslow MM. (2015) Pancreatic cancer modeling using retrograde viral vector delivery and in vivo CRISPR/Cas9-mediated somatic genome editing. Genes and Development, Volume 29(14), 1576-1585.
Caswell DR*, Chuang CH*, Yang D, Chiou SH, Cheemalavagu S, Kim-Kiselak C, Connolly A, Winslow MM. (2014) Obligate progression precedes lung adenocarcinoma dissemination. Cancer Discovery, Volume 4(7), 781-9. *Equal Contribution.
