Suchergebnisse - "Greenbaum, Benjamin D."

Temporal and spatial heterogeneity of host response to SARS-CoV-2 pulmonary infection von 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, Xu, Katherine H., Raabe, Michael J., 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

“… The relationship of SARS-CoV-2 pulmonary infection and severity of disease is not fully understood. Here we show analysis of autopsy specimens from 24 patients …”
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Revelation of Influencing Factors in Overall Codon Usage Bias of Equine Influenza Viruses von Kumar, Naveen, Bera, Bidhan Chandra, Greenbaum, Benjamin D., Bhatia, Sandeep, Sood, Richa, Selvaraj, Pavulraj, Anand, Taruna, Tripathi, Bhupendra Nath, Virmani, Nitin

“… Equine influenza viruses (EIVs) of H3N8 subtype are culprits of severe acute respiratory infections in horses, and are still responsible for significant …”
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Patterns of Evolution and Host Gene Mimicry in Influenza and Other RNA Viruses von Greenbaum, Benjamin D., Levine, Arnold J., Bhanot, Gyan, Rabadan, Raul

“… It is well known that the dinucleotide CpG is under-represented in the genomic DNA of many vertebrates. This is commonly thought to be due to the methylation …”
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Systemic and Oligo-Acquired Resistance to PD-(L)1 Blockade in Lung Cancer von Schoenfeld, Adam J, Rizvi, Hira A, Memon, Danish, Shaverdian, Narek, Bott, Matthew J, Sauter, Jennifer L, Tsai, C Jillian, Lihm, Jayon, Hoyos, David, Plodkowski, Andrew J, Perez-Johnston, Rocio, Sawan, Peter, Egger, Jacklynn V, Greenbaum, Benjamin D, Rimner, Andreas, Riely, Gregory J, Rudin, Charles M, Rusch, Valerie W, Gomez, Daniel R, Hellmann, Matthew D

“… Clinical patterns and the associated optimal management of acquired resistance to PD-(L)1 blockade are poorly understood. All cases of metastatic lung cancer …”
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Stage-Specific Human Induced Pluripotent Stem Cells Map the Progression of Myeloid Transformation to Transplantable Leukemia von Kotini, Andriana G, Chang, Chan-Jung, Chow, Arthur, Yuan, Han, Ho, Tzu-Chieh, Wang, Tiansu, Vora, Shailee, Solovyov, Alexander, Husser, Chrystel, Olszewska, Malgorzata, Teruya-Feldstein, Julie, Perumal, Deepak, Klimek, Virginia M, Spyridonidis, Alexandros, Rampal, Raajit K, Silverman, Lewis, Reddy, E Premkumar, Papaemmanuil, Elli, Parekh, Samir, Greenbaum, Benjamin D, Leslie, Christina S, Kharas, Michael G, Papapetrou, Eirini P

“… Myeloid malignancy is increasingly viewed as a disease spectrum, comprising hematopoietic disorders that extend across a phenotypic continuum ranging from …”
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Global Cancer Transcriptome Quantifies Repeat Element Polarization between Immunotherapy Responsive and T Cell Suppressive Classes von 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.

“… It has been posited that anti-tumoral innate activation is driven by derepression of endogenous repeats. We compared RNA sequencing protocols to assess repeat …”
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Pan-cancer multi-omic model of LINE-1 activity reveals locus heterogeneity of retrotransposition efficiency von Solovyov, Alexander, Behr, Julie M., Hoyos, David, Banks, Eric, Drong, Alexander W., Thornlow, Bryan, Zhong, Jimmy Z., Garcia-Rivera, Enrique, McKerrow, Wilson, Chu, Chong, Arisdakessian, Cedric, Zaller, Dennis M., Kamihara, Junne, Diao, Liyang, Fromer, Menachem, Greenbaum, Benjamin D.

“… Somatic mobilization of LINE-1 (L1) has been implicated in cancer etiology. We analyzed a recent TCGA data release comprised of nearly 5000 pan-cancer paired …”
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Author Correction: Pan-cancer multi-omic model of LINE-1 activity reveals locus heterogeneity of retrotransposition efficiency von Solovyov, Alexander, Behr, Julie M., Hoyos, David, Banks, Eric, Drong, Alexander W., Thornlow, Bryan, Zhong, Jimmy Z., Garcia-Rivera, Enrique, McKerrow, Wilson, Chu, Chong, Arisdakessian, Cedric, Zaller, Dennis M., Kamihara, Junne, Diao, Liyang, Fromer, Menachem, Greenbaum, Benjamin D.

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

“… With the increasing ability to use high-throughput next-generation sequencing to quantify the diversity of the human T cell receptor (TCR) repertoire, the …”
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Identification of transcriptional programs using dense vector representations defined by mutual information with GeneVector von 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

“… Deciphering individual cell phenotypes from cell-specific transcriptional processes requires high dimensional single cell RNA sequencing. However, current …”
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Distinguishing the immunostimulatory properties of noncoding RNAs expressed in cancer cells von Tanne, Antoine, Muniz, Luciana R, Puzio-Kuter, Anna, Leonova, Katerina I, Gudkov, Andrei V, Ting, David T, Monasson, Rémi, Cocco, Simona, Levine, Arnold J, Bhardwaj, Nina, Greenbaum, Benjamin D

“… Recent studies have demonstrated abundant transcription of a set of noncoding RNAs (ncRNAs) preferentially within tumors as opposed to normal tissue. Using an …”
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A tumor-specific endogenous repetitive element is induced by herpesviruses von Nogalski, Maciej T., Solovyov, Alexander, Kulkarni, Anupriya S., Desai, Niyati, Oberstein, Adam, Levine, Arnold J., Ting, David T., Shenk, Thomas, Greenbaum, Benjamin D.

“… Tandem satellite repeats account for 3% of the human genome. One of them, Human Satellite II (HSATII), is highly expressed in several epithelial cancers and …”
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Quantitative theory of entropic forces acting on constrained nucleotide sequences applied to viruses von Greenbaum, Benjamin D, Cocco, Simona, Levine, Arnold J, Monasson, Rémi

“… We outline a theory to quantify the interplay of entropic and selective forces on nucleotide organization and apply it to the genomes of single-stranded RNA …”
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Patterns of Oligonucleotide Sequences in Viral and Host Cell RNA Identify Mediators of the Host Innate Immune System von Greenbaum, Benjamin D., Rabadan, Raul, Levine, Arnold J.

“… The innate immune response provides a first line of defense against pathogens by targeting generic differential features that are present in foreign organisms …”
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Y RNAs are conserved endogenous RIG-I ligands across RNA virus infection and are targeted by HIV-1 von 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.

“… Pattern recognition receptors (PRRs) protect against microbial invasion by detecting specific molecular patterns found in pathogens and initiating an immune …”
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Intrahost Dynamics of Antiviral Resistance in Influenza A Virus Reflect Complex Patterns of Segment Linkage, Reassortment, and Natural Selection von 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

“… Resistance following antiviral therapy is commonly observed in human influenza viruses. Although this evolutionary process is initiated within individual …”
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Viral reassortment as an information exchange between viral segments von Greenbaum, Benjamin D, Li, Olive T W, Poon, Leo L M, Levine, Arnold J, Rabadan, Raul

“… Viruses have an extraordinary ability to diversify and evolve. For segmented viruses, reassortment can introduce drastic genomic and phenotypic changes by …”
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Using First Passage Statistics to Extract Environmentally Dependent Amino Acid Correlations von Greenbaum, Benjamin D., Kumar, Pradeep, Libchaber, Albert

“… In this work, we study the first passage statistics of amino acid primary sequences, that is the probability of observing an amino acid for the first time at a …”
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Trade-offs inside the black box of neoantigen prediction von Yao, Ning, Greenbaum, Benjamin D

“… Success of precision neoantigen-based immunotherapies hinges on the selection of immunogenic neoantigens, yet currently neither large-scale datasets nor …”
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Perfecting antigen prediction von Hoyos, David, Greenbaum, Benjamin D

“… Advances in genomics and precision measurement have continued to demonstrate the importance of the immune system across many disease types. At the heart of …”
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