Perfecting antigen prediction

por Hoyos, David, Greenbaum, Benjamin D.
Publicado 2022

Using First Passage Statistics to Extract Environmentally Dependent Amino Acid Correlations

por Greenbaum, Benjamin D., Kumar, Pradeep, Libchaber, Albert
Publicado 2014

Patterns of Oligonucleotide Sequences in Viral and Host Cell RNA Identify Mediators of the Host Innate Immune System

por Greenbaum, Benjamin D., Rabadan, Raul, Levine, Arnold J.
Publicado 2009

P53 and the defenses against genome instability caused by transposons and repetitive elements

por Levine, Arnold J., Ting, David T., Greenbaum, Benjamin D.
Publicado 2016

Bird to Human Transmission Biases and Vaccine Escape Mutants in H5N1 Infections

por Wagh, Kshitij, Bhatia, Aatish, Greenbaum, Benjamin D., Bhanot, Gyan
Publicado 2014

Patterns of Evolution and Host Gene Mimicry in Influenza and Other RNA Viruses

por Greenbaum, Benjamin D., Levine, Arnold J., Bhanot, Gyan, Rabadan, Raul
Publicado 2008

The Heterogeneous Landscape and Early Evolution of Pathogen-Associated CpG Dinucleotides in SARS-CoV-2

por Di Gioacchino, Andrea, Šulc, Petr, Komarova, Anastassia V, Greenbaum, Benjamin D, Monasson, Rémi, Cocco, Simona
Publicado 2021

A statistical strategy to identify recombinant viral ribonucleoprotein of avian, human, and swine influenza A viruses with elevated polymerase activity

por Chin, Alex W. H., Greenbaum, Benjamin D., Li, Olive T. W., Webby, Richard J., Poon, Leo L. M.
Publicado 2013

Probing T-cell response by sequence-based probabilistic modeling

por Bravi, Barbara, Balachandran, Vinod P., Greenbaum, Benjamin D., Walczak, Aleksandra M., Mora, Thierry, Monasson, Rémi, Cocco, Simona
Publicado 2021

A tumor-specific endogenous repetitive element is induced by herpesviruses

por Nogalski, Maciej T., Solovyov, Alexander, Kulkarni, Anupriya S., Desai, Niyati, Oberstein, Adam, Levine, Arnold J., Ting, David T., Shenk, Thomas, Greenbaum, Benjamin D.
Publicado 2019

Revelation of Influencing Factors in Overall Codon Usage Bias of Equine Influenza Viruses

por Kumar, Naveen, Bera, Bidhan Chandra, Greenbaum, Benjamin D., Bhatia, Sandeep, Sood, Richa, Selvaraj, Pavulraj, Anand, Taruna, Tripathi, Bhupendra Nath, Virmani, Nitin
Publicado 2016

Global Cancer Transcriptome Quantifies Repeat Element Polarization between Immunotherapy Responsive and T Cell Suppressive Classes

por Solovyov, Alexander, Vabret, Nicolas, Arora, Kshitij S., Snyder, Alexandra, Funt, Samuel A., Bajorin, Dean F., Rosenberg, Jonathan E., Bhardwaj, Nina, Ting, David T., Greenbaum, Benjamin D.
Publicado 2018

sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs

por Di Gioacchino, Andrea, Legendre, Rachel, Rahou, Yannis, Najburg, Valérie, Charneau, Pierre, Greenbaum, Benjamin D., Tangy, Frédéric, van der Werf, Sylvie, Cocco, Simona, Komarova, Anastassia V.
Publicado 2022

Intrahost Dynamics of Antiviral Resistance in Influenza A Virus Reflect Complex Patterns of Segment Linkage, Reassortment, and Natural Selection

por Rogers, Matthew B., Song, Timothy, Sebra, Robert, Greenbaum, Benjamin D., Hamelin, Marie-Eve, Fitch, Adam, Twaddle, Alan, Cui, Lijia, Holmes, Edward C., Boivin, Guy, Ghedin, Elodie
Publicado 2015

Identification of transcriptional programs using dense vector representations defined by mutual information with GeneVector

por Ceglia, Nicholas, Sethna, Zachary, Freeman, Samuel S., Uhlitz, Florian, Bojilova, Viktoria, Rusk, Nicole, Burman, Bharat, Chow, Andrew, Salehi, Sohrab, Kabeer, Farhia, Aparicio, Samuel, Greenbaum, Benjamin D., Shah, Sohrab P., McPherson, Andrew
Publicado 2023

Y RNAs are conserved endogenous RIG-I ligands across RNA virus infection and are targeted by HIV-1

por Vabret, Nicolas, Najburg, Valérie, Solovyov, Alexander, Gopal, Ramya, McClain, Christopher, Šulc, Petr, Balan, Sreekumar, Rahou, Yannis, Beauclair, Guillaume, Chazal, Maxime, Varet, Hugo, Legendre, Rachel, Sismeiro, Odile, Sanchez David, Raul Y., Chauveau, Lise, Jouvenet, Nolwenn, Markowitz, Martin, van der Werf, Sylvie, Schwartz, Olivier, Tangy, Frédéric, Bhardwaj, Nina, Greenbaum, Benjamin D., Komarova, Anastassia V.
Publicado 2022

HNRNPM controls circRNA biogenesis and splicing fidelity to sustain cancer cell fitness

por Ho, Jessica SY, Di Tullio, Federico, Schwarz, Megan, Low, Diana, Incarnato, Danny, Gay, Florence, Tabaglio, Tommaso, Zhang, JingXian, Wollmann, Heike, Chen, Leilei, An, Omer, Chan, Tim Hon Man, Hall Hickman, Alexander, Zheng, Simin, Roudko, Vladimir, Chen, Sujun, Karz, Alcida, Ahmed, Musaddeque, He, Housheng Hansen, Greenbaum, Benjamin D, Oliviero, Salvatore, Serresi, Michela, Gargiulo, Gaetano, Mann, Karen M, Hernando, Eva, Mulholland, David, Marazzi, Ivan, Wee, Dave Keng Boon, Guccione, Ernesto
Publicado 2021

Satellite repeat RNA expression in epithelial ovarian cancer associates with a tumor-immunosuppressive phenotype

por Porter, Rebecca L., Sun, Siyu, Flores, Micayla N., Berzolla, Emily, You, Eunae, Phillips, Ildiko E., KC, Neelima, Desai, Niyati, Tai, Eric C., Szabolcs, Annamaria, Lang, Evan R., Pankaj, Amaya, Raabe, Michael J., Thapar, Vishal, Xu, Katherine H., Nieman, Linda T., Rabe, Daniel C., Kolin, David L., Stover, Elizabeth H., Pepin, David, Stott, Shannon L., Deshpande, Vikram, Liu, Joyce F., Solovyov, Alexander, Matulonis, Ursula A., Greenbaum, Benjamin D., Ting, David T.
Publicado 2022

Neoantigen quality predicts immunoediting in survivors of pancreatic cancer

por Łuksza, Marta, Sethna, Zachary M., Rojas, Luis A., Lihm, Jayon, Bravi, Barbara, Elhanati, Yuval, Soares, Kevin, Amisaki, Masataka, Dobrin, Anton, Hoyos, David, Guasp, Pablo, Zebboudj, Abderezak, Yu, Rebecca, Chandra, Adrienne Kaya, Waters, Theresa, Odgerel, Zagaa, Leung, Joanne, Kappagantula, Rajya, Makohon-Moore, Alvin, Johns, Amber, Gill, Anthony, Gigoux, Mathieu, Wolchok, Jedd, Merghoub, Taha, Sadelain, Michel, Patterson, Erin, Monasson, Remi, Mora, Thierry, Walczak, Aleksandra M., Cocco, Simona, Iacobuzio-Donahue, Christine, Greenbaum, Benjamin D., Balachandran, Vinod P.
Publicado 2022

Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection

por Desai, Niyati, Neyaz, Azfar, Szabolcs, Annamaria, Shih, Angela R., Chen, Jonathan H., Thapar, Vishal, Nieman, Linda T., Solovyov, Alexander, Mehta, Arnav, Lieb, David J., Kulkarni, Anupriya S., Jaicks, Christopher, Pinto, Christopher J., Juric, Dejan, Chebib, Ivan, Colvin, Robert B., Kim, Arthur Y., Monroe, Robert, Warren, Sarah E, Danaher, Patrick, Reeves, Jason W, Gong, Jingjing, Rueckert, Erroll H, Greenbaum, Benjamin D., Hacohen, Nir, Lagana, Stephen M., Rivera, Miguel N., Sholl, Lynette M., Stone, James R., Ting, David T., Deshpande, Vikram
Publicado 2020