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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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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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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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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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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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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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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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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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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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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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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A Cyfip2-Dependent Excitatory Interneuron Pathway Establishes the Innate Startle Threshold von Marsden, Kurt C., Jain, Roshan A., Wolman, Marc A., Echeverry, Fabio A., Nelson, Jessica C., Hayer, Katharina E., Miltenberg, Ben, Pereda, Alberto E., Granato, Michael

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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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Modulation of CD22 Protein Expression in Childhood Leukemia by Pervasive Splicing Aberrations: Implications for CD22-Directed Immunotherapies von Zheng, Sisi, Gillespie, Elisabeth, Naqvi, Ammar S, Hayer, Katharina E, Ang, Zhiwei, Torres-Diz, Manuel, Quesnel-Vallières, Mathieu, Hottman, David A, Bagashev, Asen, Chukinas, John, Schmidt, Carolin, Asnani, Mukta, Shraim, Rawan, Taylor, Deanne M, Rheingold, Susan R, O'Brien, Maureen M, Singh, Nathan, Lynch, Kristen W, Ruella, Marco, Barash, Yoseph, Tasian, Sarah K, Thomas-Tikhonenko, Andrei

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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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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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A convergent malignant phenotype in B-cell acute lymphoblastic leukemia involving the splicing factor SRRM1 von Closa, Adria, Reixachs-Solé, Marina, Fuentes-Fayos, Antonio C, Hayer, Katharina E, Melero, Juan L, Adriaanse, Fabienne R S, Bos, Romy S, Torres-Diz, Manuel, Hunger, Stephen P, Roberts, Kathryn G, Mullighan, Charles G, Stam, Ronald W, Thomas-Tikhonenko, Andrei, Castaño, Justo P, Luque, Raúl M, Eyras, Eduardo

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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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