All Publications

A complete list of publications can be found at MyNCBI.

First-author, co-first-author research papers

  1. Joseph M. Chan, Samir Zaidi, Jillian R. Love, Manu Setty, Kristine M. Wadosky, Anuradha Gopalan, Zi-ning Choo, Sitara Persad, Jungmin Choi, Justin LaClair, Kayla E Lawrence, Ojasvi Chaudhary, Tianhao Xu, Ignas Masilionis, Irina Linkov, Shangqian Wang, Cindy Lee, Afsar Barlas, Michael J. Morris, Linas Mazutis, Ronan Chaligne, Yu Chen, David W. Goodrich, Wouter R. Karthaus, Dana Pe’er, Charles L Sawyers. Lineage plasticity in prostate cancer depends on JAK/STAT inflammatory signaling. Science, 2022.

  2. Joseph M Chan, Alvaro Quintanal-Villalonga, Vianne Ran Gao, Yubin Xie, Viola Allaj, Ojasvi Chaudhary, Ignas Masilionis, Jacklynn Egger, Andrew Chow, Thomas Walle, Marissa Mattar, Dig V K Yarlagadda, James L Wang, Fathema Uddin, Michael Offin, Metamia Ciampricotti, Besnik Qeriqi, Amber Bahr, Elisa de Stanchina, Umesh K Bhanot, W Victoria Lai, Matthew J Bott, David R Jones, Arvin Ruiz, Marina K Baine, Yanyun Li, Natasha Rekhtman, John T Poirier, Tal Nawy, Triparna Sen, Linas Mazutis, Travis J Hollmann, Dana Pe’er, Charles M Rudin. 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. doi: 10.1016/j.ccell.2021.09.008. https://pubmed.ncbi.nlm.nih.gov/34653364/

  3. Samir Zaidi, Jimmy L. Zhao, Joseph Chan, Martine P. Roudier, Kristine M. Wadosky, Anuradha Gopalan, Wouter R. Karthaus, Jungmin Choi, Kayla Lawrence, Ojasvi Chaudhary, Tianhao Xu, Ignas Masilionis, Linas Mazutis, Ronan Chaligne, Irina Linkov, Afsar Barlas, Achim Jungbluth, Natasha Rekhtman, Joachim Silber, Katia Manova–Todorova, Philip A. Watson, Lawrence D. True, Peter S. Nelson, Howard I. Scher, Dana E. Rathkopf, Michael J. Morris, Michael C. Haffner, David W. Goodrich, Dana Pe’er, Charles L. Sawyers. Multilineage plasticity in prostate cancer through expansion of stem–like luminal epithelial cells with elevated inflammatory signaling. bioRxiv, 2021 Nov 3. https://www.biorxiv.org/content/10.1101/2021.11.01.466599v1

  4. Alvaro Quintanal-Villalonga, Joseph M. Chan, Helena A. Yu, Dana Pe’er, Charles L. Sawyers, Triparna Sen, Charles M. Rudin. Lineage plasticity in cancer: a shared pathway of therapeutic resistance. Nature Reviews: Clinical Oncology, 03/2020: DOI: 10.1038/s41571-020-0340-z. https://www.ncbi.nlm.nih.gov/pubmed/32152485/

  5. Adam J Schoenfeld, Joseph M Chan, Daisuke Kubota, Hiroki Sato, Hira Rizvi, Yahya Daneshbod, Jason C. Chang, Paul K. Paik, Michael Offin, Maria E. Arcila, Monika Ashok Davare, Ujwal Shinde, Dana Pe’er, Natasha Rekhtman, Mark G. Kris, Romel Somwar, Gregory J. Riely, Marc Ladanyi, Helena A Yu. Tumor analyses reveal squamous transformation and off-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. https://www.ncbi.nlm.nih.gov/pubmed/31911548/

  6. Michael Offin, Joseph M Chan, Megan Tenet, Hira A. Rizvi, Ronglai Shen, Gregory J. Riely, Natasha Rekhtman, Yahya Daneshbod, Alvaro Quintanal-Villalonga, Alexander Penson, Matthew D. Hellmann, Maria E. Arcila, Marc Ladanyi, Dana Pe’er, Mark G. Kris, Charles M. Rudin, Helena A. Yu. 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 https://www.ncbi.nlm.nih.gov/pubmed/31228622/

  7. Joseph M Chan, Gunnar Carlsson, Raul Rabadan. Topology of viral evolution. PNAS, 2013: 110(46), 18566-18571. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3831954/

  8. Veronique Frattini, Vladimir Trifonov, Joseph Minhow Chan, Angelica Castano, Marie Lia,. . . , Anna Lasorella, Raul Rabadan, Antonio Iavarone. The integrated landscape of driver genomic alterations in glioblastoma. Nature Genetics, 2013: 45(1141-1149). http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799953/

  9. Chan JM and Rabadan R. Quantifying Pathogen Surveillance Using Temporal Genomic Data. mBio, 2013: 4(1):e00524-12. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3560527/

  10. Devendra Singh, Joseph Minhow Chan, Pietro Zoppoli, Francesco Niola,. . . , Anna Lasorella, Raul Rabadan, Antonio Iavarone. Transforming Fusions of FGFR and TACC Genes in Human Glioblastoma. Science, 07/2012: 337(6099), 1231-1235. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3677224/

  11. Chan J, Holmes A, Rabadan R. Network Analysis of Global Influenza Spread. PLoS Comput Biol, 2010: 6(11): e1001005. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2987833/

  12. 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. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852812/

Other Original Publications

  1. Pai J, Hellmann M, Sauter J, Mattar M, Rizvi H, Woo H, Shah N, Nguyen E, Uddin F, Quintanal-Villalonga A, Chan J, Manoj P, Allaj V, Baine M, Bhanot U, Jain M, Linkov I, Meng F, Brown D, Chaft J, Plodkowski A, Gigoux M, Won H, Sen T, Wells D, Donoghue M, de Stanchina E, Wolchok J, Loomis B, Merghoub T, Rudin C, Chow A, Satpathy A. Lineage tracing reveals clonal progenitors and long-term persistence of tumor-specific T cells during immune checkpoint blockade. Cancer Cell, 2023. https://doi.org/10.1016/j.ccell.2023.03.009.

  2. Chow A, Uddin F, Liu M, Dobrin A, Nabet B, Mangarin L, Lavin Y, Rizvi H, Tischfield S, Quintanal-Villalonga A, Chan J, Shah N, Allaj V, Manoj P, Mattar M, Meneses M, Landau R, Ward M, Kulick A, Kwong C, Wierzbicki M, Yavner J, Egger J, Chavan S. Farillas A, Holland A, Sridhar H, Ciampricotti M, Hirschhorn D, Guan X, Richards A, Heller G, Mansilla-Soto J, Sadelain M, Klebanoff C, Hellmann M, Sen T, de Stanchina E, Wolchok J, Merghoub T, Rudin C. The ectonucleotidase CD39 identifies tumor-reactive CD8+ T cells predictive of immune checkpoint blockade efficacy in human lung cancer. Immunity, 2023: 56, 93-106.e6. 10.1016/j.immuni.2022.12.001.

  3. Nguyen EM, Taniguchi H, Chan JM, Zhan YA, Chen X, Qiu J, de Stanchina E, Allaj V, Shah NS, Uddin F, Manoj P, Liu M, Cai SF, Levine R, Quintanal-Villalonga ÅLA, Sen T, Chow A, Rudin CM. Targeting Lysine-Specific Demethylase 1 Rescues Major Histocompatibility Complex Class I Antigen Presentation and Overcomes Programmed Death-Ligand 1 Blockade Resistance in SCLC. J Thorac Oncol, 2022.

  4. Taniguchi H, Caeser R, Chavan SS, Zhan YA, Chow A, Manoj P, Uddin F, Kitai H, Qu R, Hayatt O, Shah NS, Quintanal Villalonga A, Allaj V, Nguyen EM, Chan J, Michel AO, Mukae H, de Stanchina E, Rudin CM, Sen T. WEE1 inhibition enhances the antitumor immune response to PD-L1 blockade by the concomitant activation of STING and STAT1 pathways in SCLC. Cell Rep, 2022.

  5. Quintanal-Villalonga A, Taniguchi H, Hao Y, Chow A, Zhan YA, Chavan SS, Uddin F, Allaj V, Manoj P, Shah NS, Chan JM, Offin M, Ciampricotti M, Ray-Kirton J, Egger J, Bhanot U, Linkov I, Asher M, Roehrl MH, Qiu J, de Stanchina E, Hollmann TJ, Koche RP, Sen T, Poirier JT, Rudin CM. Inhibition of XPO1 Sensitizes Small Cell Lung Cancer to First- and Second-Line Chemotherapy. Cancer Res, 2022. 

  6. A Quintanal-Villalonga, H Taniguchi, YA Zhan, MM Hasan, SS Chavan, F Meng, F Uddin, P Manoj, M Donoghue, HH Won, JM Chan, M Ciampricotti, A Chow, M Offin, JC Chang, J Ray-Kirton, SE Tischfield, J Egger, UK Bhanot, I Linkov, M Asher, S Sinha, J Silber, CA Iacobuzio-Donahue, MH Roehrl, TJ Hollmann, HA Yu, J Qiu, E de Stanchina, MK Baine, N Rekhtman, JT Poirier, B Loomis, RP Koche, CM Rudin, T Sen. Multi-omic analysis of lung tumors defines pathways activated in neuroendocrine transformation. Cancer Discovery, 2021.

  7. 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.

  8. A Chow, S Schad, MD Green, MD Hellmann, V Allaj, N Ceglia, G Zago, NS Shah, SK Sharma, M Mattar, J Chan, H Rizvi, H Zhong, C Liu, Y Bykov, D Zamarin, H Shi, S Budhu, C Wohlhieter, F Uddin, A Gupta, I Khodos, JJ Waninger, A Qin, GJ Markowitz, V Mittal, V Balachandran, JN Durham, DT Le, W Zou, SP Shah, A McPherson, K Panageas, JS Lewis, JS Perry, E de Stanchina, T Sen, JT Poirier, JD Wolchok, CM Rudin, T Merghoub. Tim-4+ cavity-resident macrophages impair anti-tumor CD8+ T cell immunity. Cancer Cell, 2021.

  9. HTAN consortium. The Human Tumor Atlas Network: Charting tumor transitions across space and time at single-cell resolution. Cell. 2020.

  10. B Badal, A Solovyov, S Di Cecilia, J Chan, L Chang, R Iqbal, I Aydin, G Rajan, C Chen, F abbate, K Arora A Tanne, S Gruber, T Johnson, D Fullen, L Raskin R Phelps, N Bhardwaj, E Bernstein, D Ting, G Brunner, E Schadt, B Greenbaum, J Celebi. Transcriptional dissection of melanoma identifies a high-risk subtype underlying TP53 family genes and epigenome deregulation. Journal of Clinical Investigation, 2017.

  11. D Kennedy, JM Chan, D Kaw, A Ravindaran, S Ratnam, D Malhotra, J Shapiro. Use of Surface-Enhanced Laser Desorption/Ionization with Time of Flight (SELDI-TOF) of the Urine in the Assessment of Acute Kidney Injury (AKI). Marshall Journal of Medicine, 2016: Vol. 2: Iss. 2, Article 11.

  12. K Emmett, J Chan, D Rosenbloom, R Rabadan. Applying Topological Principles to Genomic Analysis. Microbe, 2015.

  13. H Khibanian, Z Carpenter, J Kugelman, J Chan, V Trifonov, E Nagle, T Warren, P Iversen, S Bavari, G Palacios, R Rabadan. Viral diversity and clonal evolution from unphased genomic data. BMC Genomics, 2014: 15 (Suppl 6), S17.

  14. D Llobet-Navas, R Rodriguez-Barrueco, V Castro, A Ugalde, P Sumazin, D Jacob-Sendler, B Demircan, M Castillo-Martin, P Putcha, N Marshall, P Villagrasa, J Chan, F Sanchez-Garcia, D Pe’er, R Rabadan, A Iavarone, C Cordon-Cardo, A Califano, C Lopez-Otin, E Ezhkova, J Silva. The miR-424 (322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland. Genes and Development, 2014: 28(7), 765-782. http://genesdev.cshlp.org/content/early/2014/03/13/gad.237404.114.abstract

  15. S J Anthony, J A St Leger, K Pugliares, H S Ip, J M Chan, Z W Carpenter, I Navarrete-Macias, M Sanchez-Leon, JT Saliki, J Pedersen, W Karesh, P Daszak, R Rabadan, T Rowles, W I Lipkin. Emergence of fatal avian influenza in New England harbor seals. mBio, 01/2012: 3(4). http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3419516/

  16. Laura Pasqualucci, Vladimir Trifonov, Giulia Fabbri, Jing Ma, Davide Rossi, Annalisa Chiarenza, Victoria A Wells, Adina Grunn, Monica Messina, Oliver Elliot, Joseph Chan, Govind Bhagat, Amy Chadburn, Gianluca Gaidano, Charles G Mullighan, Raul Rabadan, Riccardo Dalla-Favera. Analysis of the Coding Genome of Diffuse Large B-Cell Lymphoma. Nature Genetics, 2011: 43(9), 830-837. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3297422/

  17. Grossmann V, Tiacci E, Holmes AB, Kohlmann A, Martelli M, Kern W, Spanhol-Rosseto A, Klein H, Dugas M, Schindela S, Trifonov V, Schnittger S, Haferlach C, Bassan R, Wells V, Spinelli O, Chan J, Rossi R, Baldoni S, de Carolis L, Goetze K, Serve H, Peceny R Kreuzer K, Oruzio D, Specchia G, di Raimondo F, Fabbiano F, Sborgia M, Liso A, Farinelli L, Rambaldi A, Pasqualucci L, Rabadan R, Haferlach T, Falini B. Whole-exome sequencing identifies mutations of BCOR in acute myeloid leukemia with normal karyotype. Blood, 2011: 118(23), 6153-6163. http://bloodjournal.hematologylibrary.org/content/118/23/6153.long

  18. Carlos Xavier Hernandez, Joseph Chan, Hossein Khiabanian, Raul Rabadan. Understanding the Origins of a Pandemic Virus. arXiv, 2011: 1104.4568. Columbia University Academic Commons, AC:P:9893. http://arxiv.org/abs/1104.4568