Generating colorblind-friendly scatter plots for single-cell data by Tejas Guha, Elana J Fertig, Atul Deshpande

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Learning Dysregulated Pathways in Cancers from Differential Variability Analysis by Bahman Afsari, Donald German, Elana J. Fertig

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OutSplice: A Novel Tool for the Identification of Tumor-Specific Alternative Splicing Events by Joseph Bendik, Sandhya Kalavacherla, Nicholas Webster, Joseph Califano, Elana J. Fertig, Michael F. Ochs, Hannah Carter, Theresa Guo

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Integrating single cell sequencing with a spatial quantitative systems pharmacology model spQSP for personalized prediction of triple-negative breast cancer immunotherapy response by Shuming Zhang, Chang Gong, Alvaro Ruiz-Martinez, Hanwen Wang, Emily Davis-Marcisak, Atul Deshpande, Aleksander S. Popel, Elana J. Fertig

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Hybrid modeling of cell signaling and transcriptional reprogramming and its application in C. elegans development by Elana J Fertig, Ludmila V Danilova, Alexander V Favorov, Alexander V Favorov, Alexander V Favorov, Michael F Ochs, Michael F Ochs

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Viral status, immune microenvironment and immunological response to checkpoint inhibitors in hepatocellular carcinoma by Hao Wang, Elizabeth Jaffee, Ludmila Danilova, James M Leatherman, Won Jin Ho, Mark Yarchoan, Su Jin Lim, Rohan Verma, Stephanie Xavier, Marcelo B Sztein, Elana J Fertig

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A Random Forest Genomic Classifier for Tumor Agnostic Prediction of Response to Anti-PD1 Immunotherapy by Emma Bigelow, Suchi Saria, Brian Piening, Brendan Curti, Alexa Dowdell, Roshanthi Weerasinghe, Carlo Bifulco, Walter Urba, Noam Finkelstein, Elana J Fertig, Alex Baras, Neeha Zaidi, Elizabeth Jaffee, Mark Yarchoan

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Integrated immunological analysis of a successful conversion of locally advanced hepatocellular carcinoma to resectability with neoadjuvant therapy by Ihab Kamel, Elizabeth Jaffee, Qingfeng Zhu, Robert Anders, Won Jin Ho, Mark Yarchoan, Matthew Weiss, Elana J Fertig, Gaurav Sharma, Aleksandra Popovic, Jennifer Durham, Genevieve Stein-O'Brien, Guanglan Mo

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Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence by Shuming Zhang, Long Yuan, Ludmila Danilova, Guanglan Mo, Qingfeng Zhu, Atul Deshpande, Alexander T. F. Bell, Jennifer Elisseeff, Aleksander S. Popel, Robert A. Anders, Elizabeth M. Jaffee, Mark Yarchoan, Elana J. Fertig, Luciane T. Kagohara

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Integrated T cell cytometry metrics for immune-monitoring applications in immunotherapy clinical trials by Dimitrios N. Sidiropoulos, Genevieve L. Stein-O’Brien, Ludmila Danilova, Nicole E. Gross, Soren Charmsaz, Stephanie Xavier, James Leatherman, Hao Wang, Mark Yarchoan, Elizabeth M. Jaffee, Elana J. Fertig, Won Jin Ho

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Expression microarray analysis reveals alternative splicing of LAMA3 and DST genes in head and neck squamous cell carcinoma. by Ryan Li, Michael F Ochs, Sun Mi Ahn, Patrick Hennessey, Marietta Tan, Ethan Soudry, Daria A Gaykalova, Mamoru Uemura, Mariana Brait, Chunbo Shao, William Westra, Justin Bishop, Elana J Fertig, Joseph A Califano

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Barcoding intracellular reverse transcription enables high-throughput phenotype-coupled T cell receptor analyses by Sahana Jayaraman, Janelle M. Montagne, Thomas R. Nirschl, Emily Marcisak, Jeanette Johnson, Amanda Huff, Meng-Hsuan Hsiao, Julie Nauroth, Thatcher Heumann, Jelani C. Zarif, Elizabeth M. Jaffee, Nilo Azad, Elana J. Fertig, Neeha Zaidi, H. Benjamin Larman

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Chromatin structure regulates cancer-specific alternative splicing events in primary HPV-related oropharyngeal squamous cell carcinoma by Theresa Guo, Kristina Diana A. Zambo, Fernando T. Zamuner, Tingting Ou, Christopher Hopkins, Dylan Z. Kelley, Hildegard A. Wulf, Eli Winkler, Rossin Erbe, Ludmila Danilova, Michael Considine, David Sidransky, Alexander Favorov, Liliana Florea, Elana J. Fertig, Daria A. Gaykalova

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Aberrant expression of CPSF1 promotes head and neck squamous cell carcinoma via regulating alternative splicing. by Akihiro Sakai, Mizuo Ando, Takahito Fukusumi, Shuling Ren, Chao Liu, Jesse Qualliotine, Sunny Haft, Sayed Sadat, Yuki Saito, Theresa W Guo, Guorong Xu, Roman Sasik, Kathleen M Fisch, J Silvio Gutkind, Elana J Fertig, Alfredo A Molinolo, Joseph A Califano

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Hypoxia induces ROS-resistant memory upon reoxygenation in vivo promoting metastasis in part via MUC1-C by Inês Godet, Harsh H. Oza, Yi Shi, Natalie S. Joe, Alyssa G. Weinstein, Jeanette Johnson, Michael Considine, Swathi Talluri, Jingyuan Zhang, Reid Xu, Steven Doctorman, Delma Mbulaiteye, Genevieve Stein-O’Brien, Luciane T. Kagohara, Cesar A. Santa-Maria, Elana J. Fertig, Daniele M. Gilkes

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Morphology-guided transcriptomic analysis of human pancreatic cancer organoids reveals microenvironmental signals that enhance invasion by Yea Ji Jeong, Hildur Knutsdottir, Fatemeh Shojaeian, Michael G. Lerner, Maria F. Wissler, Elodie Henriet, Tammy Ng, Shalini Datta, Bernat Navarro-Serer, Peter Chianchiano, Benedict Kinny-Köster, Jacquelyn W. Zimmerman, Genevieve Stein-O’Brien, Matthias M. Gaida, James R. Eshleman, Ming-Tseh Lin, Elana J. Fertig, Andrew J. Ewald, Joel S. Bader, Laura D. Wood

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Entinostat in combination with nivolumab in metastatic pancreatic ductal adenocarcinoma: a phase 2 clinical trial by Marina Baretti, Ludmila Danilova, Jennifer N. Durham, Courtney B. Betts, Leslie Cope, Dimitrios N. Sidiropoulos, Joseph A. Tandurella, Soren Charmsaz, Nicole Gross, Alexei Hernandez, Won Jin Ho, Chris Thoburn, Rosalind Walker, James Leatherman, Sarah Mitchell, Brian Christmas, Ali Saeed, Daria A. Gaykalova, Srinivasan Yegnasubramanian, Elana J. Fertig, Lisa M. Coussens, Mark Yarchoan, Elizabeth Jaffee, Nilofer S. Azad

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Ten challenges and opportunities in computational immuno-oncology by Hong Zhang, Riyue Bao, Song Liu, Mark Long, Sacha Gnjatic, Yi Xing, Elana J Fertig, Alan Hutson, Martin Morgan, Eytan Ruppin, Anant Madabhushi, Natalie Vokes, Daoud Meerzaman, Edgar Gonzalez-Kozlova, Vanessa D Jonsson, Eliezer M Van Allen, Spencer R Rosario, Jennifer Altreuter, Himangi Marathe, Jill S Barnholtz-Sloan, Lyndsay Harris, Qingrong Chen, James Dignam, Andrew J Gentles, Erika Kim, David Van Valen

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CD137 agonism enhances anti-PD1 induced activation of expanded CD8+ T cell clones in a neoadjuvant pancreatic cancer clinical trial by Janelle M. Montagne, Jacob T. Mitchell, Joseph A. Tandurella, Eric S. Christenson, Ludmila V. Danilova, Atul Deshpande, Melanie Loth, Dimitrios N. Sidiropoulos, Emily Davis-Marcisak, Daniel R. Bergman, Qingfeng Zhu, Hao Wang, Luciane T. Kagohara, Logan L. Engle, Benjamin F. Green, Alexander V. Favorov, Won Jin Ho, Su Jin Lim, Rui Zhang, Pan Li, Jessica Gai, Guanglan Mo, Sarah Mitchell, Rulin Wang, Ajay Vaghasia, Wenpin Hou, Yao Xu, Jacquelyn W. Zimmerman, Jennifer H. Elisseeff, Srinivasan Yegnasubramanian, Robert A. Anders, Elizabeth M. Jaffee, Lei Zheng, Elana J. Fertig

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