Laederach A, Chan JM*, Schwartzman A, Willgohs E, Altman RB. Coplanar and Coaxial Orientations of RNA Bases and Helices. RNA, 05/2007: 13(5):643-50. PMCID: 1852812
Chan J*, Holmes A, Rabadan R. Network Analysis of Global Inuenza Spread. PLoS Comput Biol, 2010: 6(11): e1001005. PMCID: PMC2987833.
Singh D, Chan JM*, Zoppoli P, Niola F, Sullivan R, Castano A, Liu EM, Reichel J, Porrati P, Pellegatta S, Qiu K, Gao Z, Ceccarelli M, Riccardi R, Brat DJ, Guha A, Aldape K, Golfinos JG, Zagzag D, Mikkelsen T, Finocchiaro G, Lasorella A, Rabadan R, Iavarone A. Transforming Fusions of FGFR and TACC Genes in Human Glioblastoma. Science, 07/2012: 337(6099), 1231-1235. PMCID: PMC3677224
Chan JM* and Rabadan R. Quantifying Pathogen Surveillance Using Temporal Genomic Data. mBio, 2013: 4(1):e00524-12. PMCID: PMC3560527.
Frattini V, Trifonov V, Chan JM*, Castano A, Lia M, Abate F, Keir ST, Ji AX, Zoppoli P, Niola F, Danussi C, Dolgalev I, Porrati P, Pellegatta S, Heguy A, Gupta G, Pisapia DJ, Canoll P, Bruce JN, McLendon RE, Yan H, Aldape K, Finocchiaro G, Mikkelsen T, Gilbert G. Darell P, Bigner D, Lasorella A, Rabadan R, Iavarone A. The integrated landscape of driver genomic alterations in glioblastoma. Nature Genetics, 2013: 45(1141-1149). PMCID: PMC3799953.
Chan JM*, Carlsson G, Rabadan R. Topology of viral evolution. PNAS, 2013: 110(46), 18566-18571. PMCID: PMC3831954.
Offin M, Chan JM*, Tenet M, Rizvi HA, Shen R, Riely GJ, Rekhtman N, Daneshbod Y, Quintanal-Villalonga A, Penson A, Hellmann MD, Arcila ME, Ladanyi M, Pe’er D, Kris MG, Rudin CM, Yu HA. Concurrent RB1 and TP53 alterations define a subset of EGFR-mutant lung cancers at risk for histologic transformation and inferior clinical outcomes. Journal of Thoracic Oncology, 06/2019: 0(0): 10.1016/j.jtho.2019.06.002. PMCID: PMC6764905.
Schoenfeld AJ, Chan JM*, Kubota D, Sato H, Rizvi H, Daneshbod Y, Chang JC, Paik PK, Offin M, Arcila ME, Ashok Davare M, Shinde U, Pe’er D, Rekhtman N, Kris MG, Somwar R, Riely GJ, Ladanyi M, Yu HA. Tumor analyses reveal squamous transformation and on-target alterations as early resistance mechanisms to first-line osimertinib in EGFR-mutant lung cancer. Clinical Cancer Research, 01/2020: doi: 10.1158/1078-0432.CCR-19-3563. PMCID PMC7448565.
Quintanal-Villalonga A, Chan JM*, Yu HA, Pe’er D, Sawyers CL, Sen T, Rudin CM. Lineage plasticity in cancer: a shared pathway of therapeutic resistance. Nature Reviews: Clinical Oncology, 03/2020. 17(6):360-371. doi: 10.1038/s41571-020-0340-z. PMCID: PMC7397755.
Quintanal-Villalonga A, Taniguchi H, Zhan YA, Hasan MM, Chavan SS, Meng F, Uddin F, Allaj V, Manoj P, Shah NS, Chan JM, Ciampricotti M, Chow A, Offin M, Ray-Kirton J, Egger JD, Bhanot UK, Linkov I, Asher M, Roehrl MH, Ventura K, Qiu J, de Stanchina E, Chang JC, Rekhtman N, Houck-Loomis B, Koche RP, Yu HA, Sen T, Rudin CM. Comprehensive molecular characterization of lung tumors implicates AKT and MYC signaling in adenocarcinoma to squamous cell transdifferentiation. J Hematol Oncol, 2021. 14(1):170. doi: 10.1186/s13045-021-01186-z. PMCID: PMC8520275.
Quintanal-Villalonga A, Taniguchi H, Zhan YA, Hasan MM, Chavan SS, Meng F, Uddin F, Manoj P, Donoghue M, Won HH, Chan JM, Ciampricotti M, Chow A, Offin M, Chang JC, Ray-Kirton J, Tischfield SE, Egger J, Bhanot UK, I Linkov, Asher M, Sinha S, Silber J, Iacobuzio-Donahue CA, Roehrl MH, Hollmann TJ, Yu HA, Qiu J, de Stanchina E, Baine MK, Rekhtman N, Poirier JT, Loomis B, Koche RP, Rudin CM, Sen T. Multi-omic analysis of lung tumors defines pathways activated in neuroendocrine transformation. Cancer Discovery, 2021. 11(12):3028-3047. doi: 10.1158/2159-8290.CD-20-1863. PMCID: PMC9437746.
Chan JM*, Quintanal-Villalonga A, Gao VR, Xie Y, Allaj V, Chaudhary O, Masilionis I, Egger J, Chow A, Walle T, Mattar M, Yarlagadda D, Wang JL, Uddin F, Offin M, Ciampricotti M, Qeriqi M, Bahr A, de Stanchina E, Bhanot UK, Lai WV, Bott MJ, Jones DR, Ruiz A, Baine MK, Li Y, Rekhtman N, Poirier JT, Nawy T, Sen T, Mazutis L, Hollmann TJ, Pe’er D, Rudin CM. Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer. Cancer Cell, 2021 Nov 8;39(11):1479-1496.e18. PMCID: PMC8628860.
Chan JM*, Zaidi S, Love JR, Setty M, Wadosky KM, Gopalan A, Choo Z, Persad S, Choi J, LaClair J, Lawrence K, Chaudhary O, Xu T, Masilionis I, Linkov I, Wang S, Lee C, Barlas A, Morris MJ, Mazutis L, Chaligne R, Chen Y, Goodrich DW, Karthaus WR, Pe’er D, Sawyers CL. Lineage plasticity in prostate cancer depends on JAK/STAT inflammatory signaling. Science, Aug 2022; 377(6611): 1180-1191. PMID: PMC9653178.
Complete List of Published Work: