Simulation-based comprehensive benchmarking of RNA-seq aligners von Baruzzo, Giacomo, Hayer, Katharina E, Kim, Eun Ji, Di Camillo, Barbara, FitzGerald, Garret A, Grant, Gregory R

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Direct RNA sequencing reveals m6A modifications on adenovirus RNA are necessary for efficient splicing von Price, Alexander M., Hayer, Katharina E., McIntyre, Alexa B. R., Gokhale, Nandan S., Abebe, Jonathan S., Della Fera, Ashley N., Mason, Christopher E., Horner, Stacy M., Wilson, Angus C., Depledge, Daniel P., Weitzman, Matthew D.

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A Genome-wide Screen Identifies PAPP-AA-Mediated IGFR Signaling as a Novel Regulator of Habituation Learning von Wolman, Marc A., Jain, Roshan A., Marsden, Kurt C., Bell, Hannah, Skinner, Julianne, Hayer, Katharina E., Hogenesch, John B., Granato, Michael

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DNA double-strand breaks induce H2Ax phosphorylation domains in a contact-dependent manner von Collins, Patrick L., Purman, Caitlin, Porter, Sofia I., Nganga, Vincent, Saini, Ankita, Hayer, Katharina E., Gurewitz, Greer L., Sleckman, Barry P., Bednarski, Jeffrey J., Bassing, Craig H., Oltz, Eugene M.

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Promotion of growth factor signaling as a critical function of β-catenin during HCC progression von Kim, Eunsun, Lisby, Amanda, Ma, Connie, Lo, Nathanael, Ehmer, Ursula, Hayer, Katharina E., Furth, Emma E., Viatour, Patrick

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CircaDB: a database of mammalian circadian gene expression profiles von Pizarro, Angel, Hayer, Katharina, Lahens, Nicholas F, Hogenesch, John B

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Adenovirus prevents dsRNA formation by promoting efficient splicing of viral RNA von Price, Alexander M, Steinbock, Robert T, Di, Chao, Hayer, Katharina E, Li, Yize, Herrmann, Christin, Parenti, Nicholas A, Whelan, Jillian N, Weiss, Susan R, Weitzman, Matthew D

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DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing von Abebe, Jonathan S, Price, Alexander M, Hayer, Katharina E, Mohr, Ian, Weitzman, Matthew D, Wilson, Angus C, Depledge, Daniel P

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ATM-dependent Phosphorylation of Nemo SQ Motifs Is Dispensable for Nemo-mediated Gene Expression Changes in Response to DNA Double-Strand Breaks von Glynn, Rebecca A, Hayer, Katharina E, Bassing, Craig H

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Antigen glycosylation regulates efficacy of CAR T cells targeting CD19 von Heard, Amanda, Landmann, Jack H., Hansen, Ava R., Papadopolou, Alkmini, Hsu, Yu-Sung, Selli, Mehmet Emrah, Warrington, John M., Lattin, John, Chang, Jufang, Ha, Helen, Haug-Kroeper, Martina, Doray, Balraj, Gill, Saar, Ruella, Marco, Hayer, Katharina E., Weitzman, Matthew D., Green, Abby M., Fluhrer, Regina, Singh, Nathan

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Impaired Death Receptor Signaling in Leukemia Causes Antigen-Independent Resistance by Inducing CAR T-cell Dysfunction von Singh, Nathan, Lee, Yong Gu, Shestova, Olga, Ravikumar, Pranali, Hayer, Katharina E, Hong, Seok Jae, Lu, Xueqing Maggie, Pajarillo, Raymone, Agarwal, Sangya, Kuramitsu, Shunichiro, Orlando, Elena J, Mueller, Karen Thudium, Good, Charly R, Berger, Shelley L, Shalem, Ophir, Weitzman, Matthew D, Frey, Noelle V, Maude, Shannon L, Grupp, Stephan A, June, Carl H, Gill, Saar, Ruella, Marco

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Novel viral splicing events and open reading frames revealed by long-read direct RNA sequencing of adenovirus transcripts von Price, Alexander M, Steinbock, Robert T, Lauman, Richard, Charman, Matthew, Hayer, Katharina E, Kumar, Namrata, Halko, Edwin, Lum, Krystal K, Wei, Monica, Wilson, Angus C, Garcia, Benjamin A, Depledge, Daniel P, Weitzman, Matthew D

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Cytosine Deaminase APOBEC3A Sensitizes Leukemia Cells to Inhibition of the DNA Replication Checkpoint von Green, Abby M, Budagyan, Konstantin, Hayer, Katharina E, Reed, Morgann A, Savani, Milan R, Wertheim, Gerald B, Weitzman, Matthew D

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Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data von Hayer, Katharina E, Pizarro, Angel, Lahens, Nicholas F, Hogenesch, John B, Grant, Gregory R

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Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts von Schulz, Laura, Torres-Diz, Manuel, Cortés-López, Mariela, Hayer, Katharina E, Asnani, Mukta, Tasian, Sarah K, Barash, Yoseph, Sotillo, Elena, Zarnack, Kathi, König, Julian, Thomas-Tikhonenko, Andrei

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A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression von Lahens, Nicholas F, Ricciotti, Emanuela, Smirnova, Olga, Toorens, Erik, Kim, Eun Ji, Baruzzo, Giacomo, Hayer, Katharina E, Ganguly, Tapan, Schug, Jonathan, Grant, Gregory R

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Retention of CD19 intron 2 contributes to CART-19 resistance in leukemias with subclonal frameshift mutations in CD19 von Asnani, Mukta, Hayer, Katharina E., Naqvi, Ammar S., Zheng, Sisi, Yang, Scarlett Y., Oldridge, Derek, Ibrahim, Fadia, Maragkakis, Manolis, Gazzara, Matthew R., Black, Kathryn L., Bagashev, Asen, Taylor, Deanne, Mourelatos, Zissimos, Grupp, Stephan A., Barrett, David, Maris, John M., Sotillo, Elena, Barash, Yoseph, Thomas-Tikhonenko, Andrei

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Aberrant splicing in B-cell acute lymphoblastic leukemia von Black, Kathryn L, Naqvi, Ammar S, Asnani, Mukta, Hayer, Katharina E, Yang, Scarlett Y, Gillespie, Elisabeth, Bagashev, Asen, Pillai, Vinodh, Tasian, Sarah K, Gazzara, Matthew R, Carroll, Martin, Taylor, Deanne, Lynch, Kristen W, Barash, Yoseph, Thomas-Tikhonenko, Andrei

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STAT3–BDNF–TrkB signalling promotes alveolar epithelial regeneration after lung injury von Paris, Andrew J., Hayer, Katharina E., Oved, Joseph H., Avgousti, Daphne C., Toulmin, Sushila A., Zepp, Jarod A., Zacharias, William J., Katzen, Jeremy B., Basil, Maria C., Kremp, Madison M., Slamowitz, April R., Jayachandran, Sowmya, Sivakumar, Aravind, Dai, Ning, Wang, Ping, Frank, David B., Eisenlohr, Laurence C., Cantu, Edward, Beers, Michael F., Weitzman, Matthew D., Morrisey, Edward E., Worthen, G. Scott

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Locus folding mechanisms determine modes of antigen receptor gene assembly von Allyn, Brittney M, Hayer, Katharina E, Oyeniran, Clement, Nganga, Vincent, Lee, Kyutae, Mishra, Bikash, Sacan, Ahmet, Oltz, Eugene M, Bassing, Craig H

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