Patterns of oligonucleotide sequences in viral and host cell RNA identify mediators of the host innate immune system. by Benjamin D Greenbaum, Raul Rabadan, Arnold J Levine

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Bird to human transmission biases and vaccine escape mutants in H5N1 infections. by Kshitij Wagh, Aatish Bhatia, Benjamin D Greenbaum, Gyan Bhanot

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Patterns of evolution and host gene mimicry in influenza and other RNA viruses. by Benjamin D Greenbaum, Arnold J Levine, Gyan Bhanot, Raul Rabadan

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Probing T-cell response by sequence-based probabilistic modeling. by Barbara Bravi, Vinod P Balachandran, Benjamin D Greenbaum, Aleksandra M Walczak, Thierry Mora, Rémi Monasson, Simona Cocco

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A tumor-specific endogenous repetitive element is induced by herpesviruses by Maciej T. Nogalski, Alexander Solovyov, Anupriya S. Kulkarni, Niyati Desai, Adam Oberstein, Arnold J. Levine, David T. Ting, Thomas Shenk, Benjamin D. Greenbaum

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Revelation of Influencing Factors in Overall Codon Usage Bias of Equine Influenza Viruses. by Naveen Kumar, Bidhan Chandra Bera, Benjamin D Greenbaum, Sandeep Bhatia, Richa Sood, Pavulraj Selvaraj, Taruna Anand, Bhupendra Nath Tripathi, Nitin Virmani

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Global Cancer Transcriptome Quantifies Repeat Element Polarization between Immunotherapy Responsive and T Cell Suppressive Classes by Alexander Solovyov, Nicolas Vabret, Kshitij S. Arora, Alexandra Snyder, Samuel A. Funt, Dean F. Bajorin, Jonathan E. Rosenberg, Nina Bhardwaj, David T. Ting, Benjamin D. Greenbaum

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Intrahost Dynamics of Antiviral Resistance in Influenza A Virus Reflect Complex Patterns of Segment Linkage, Reassortment, and Natural Selection by Matthew B. Rogers, Timothy Song, Robert Sebra, Benjamin D. Greenbaum, Marie-Eve Hamelin, Adam Fitch, Alan Twaddle, Lijia Cui, Edward C. Holmes, Guy Boivin, Elodie Ghedin

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Identification of transcriptional programs using dense vector representations defined by mutual information with GeneVector by Nicholas Ceglia, Zachary Sethna, Samuel S. Freeman, Florian Uhlitz, Viktoria Bojilova, Nicole Rusk, Bharat Burman, Andrew Chow, Sohrab Salehi, Farhia Kabeer, Samuel Aparicio, Benjamin D. Greenbaum, Sohrab P. Shah, Andrew McPherson

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Pan-cancer multi-omic model of LINE-1 activity reveals locus heterogeneity of retrotransposition efficiency by Alexander Solovyov, Julie M. Behr, David Hoyos, Eric Banks, Alexander W. Drong, Bryan Thornlow, Jimmy Z. Zhong, Enrique Garcia-Rivera, Wilson McKerrow, Chong Chu, Cedric Arisdakessian, Dennis M. Zaller, Junne Kamihara, Liyang Diao, Menachem Fromer, Benjamin D. Greenbaum

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Y RNAs are conserved endogenous RIG-I ligands across RNA virus infection and are targeted by HIV-1 by Nicolas Vabret, Valérie Najburg, Alexander Solovyov, Ramya Gopal, Christopher McClain, Petr Šulc, Sreekumar Balan, Yannis Rahou, Guillaume Beauclair, Maxime Chazal, Hugo Varet, Rachel Legendre, Odile Sismeiro, Raul Y. Sanchez David, Lise Chauveau, Nolwenn Jouvenet, Martin Markowitz, Sylvie van der Werf, Olivier Schwartz, Frédéric Tangy, Nina Bhardwaj, Benjamin D. Greenbaum, Anastassia V. Komarova

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Satellite repeat RNA expression in epithelial ovarian cancer associates with a tumor-immunosuppressive phenotype by Rebecca L. Porter, Siyu Sun, Micayla N. Flores, Emily Berzolla, Eunae You, Ildiko E. Phillips, Neelima KC, Niyati Desai, Eric C. Tai, Annamaria Szabolcs, Evan R. Lang, Amaya Pankaj, Michael J. Raabe, Vishal Thapar, Katherine H. Xu, Linda T. Nieman, Daniel C. Rabe, David L. Kolin, Elizabeth H. Stover, David Pepin, Shannon L. Stott, Vikram Deshpande, Joyce F. Liu, Alexander Solovyov, Ursula A. Matulonis, Benjamin D. Greenbaum, David T. Ting

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HNRNPM controls circRNA biogenesis and splicing fidelity to sustain cancer cell fitness by Jessica SY Ho, Federico Di Tullio, Megan Schwarz, Diana Low, Danny Incarnato, Florence Gay, Tommaso Tabaglio, JingXian Zhang, Heike Wollmann, Leilei Chen, Omer An, Tim Hon Man Chan, Alexander Hall Hickman, Simin Zheng, Vladimir Roudko, Sujun Chen, Alcida Karz, Musaddeque Ahmed, Housheng Hansen He, Benjamin D Greenbaum, Salvatore Oliviero, Michela Serresi, Gaetano Gargiulo, Karen M Mann, Eva Hernando, David Mulholland, Ivan Marazzi, Dave Keng Boon Wee, Ernesto Guccione

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Temporal and spatial heterogeneity of host response to SARS-CoV-2 pulmonary infection by Niyati Desai, Azfar Neyaz, Annamaria Szabolcs, Angela R. Shih, Jonathan H. Chen, Vishal Thapar, Linda T. Nieman, Alexander Solovyov, Arnav Mehta, David J. Lieb, Anupriya S. Kulkarni, Christopher Jaicks, Katherine H. Xu, Michael J. Raabe, Christopher J. Pinto, Dejan Juric, Ivan Chebib, Robert B. Colvin, Arthur Y. Kim, Robert Monroe, Sarah E. Warren, Patrick Danaher, Jason W. Reeves, Jingjing Gong, Erroll H. Rueckert, Benjamin D. Greenbaum, Nir Hacohen, Stephen M. Lagana, Miguel N. Rivera, Lynette M. Sholl, James R. Stone, David T. Ting, Vikram Deshpande

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