Identifying common transcriptome signatures of cancer by interpreting deep learning models

por Jha, Anupama, Quesnel-Vallières, Mathieu, Wang, David, Thomas-Tikhonenko, Andrei, Lynch, Kristen W, Barash, Yoseph
Publicado 2022

A Bayesian model for unsupervised detection of RNA splicing based subtypes in cancers

por Wang, David, Quesnel-Vallieres, Mathieu, Jewell, San, Elzubeir, Moein, Lynch, Kristen, Thomas-Tikhonenko, Andrei, Barash, Yoseph
Publicado 2023

MOCCASIN: a method for correcting for known and unknown confounders in RNA splicing analysis

por Slaff, Barry, Radens, Caleb M., Jewell, Paul, Jha, Anupama, Lahens, Nicholas F., Grant, Gregory R., Thomas-Tikhonenko, Andrei, Lynch, Kristen W., Barash, Yoseph
Publicado 2021

Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts

por 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
Publicado 2021

FBXW7β isoform drives transcriptional activation of the proinflammatory TNF cluster in human pro-B cells

por Yang, Scarlett Y., Hayer, Katharina E., Fazelinia, Hossein, Spruce, Lynn A., Asnani, Mukta, Black, Kathryn L., Naqvi, Ammar S., Pillai, Vinodh, Barash, Yoseph, Elenitoba-Johnson, Kojo S. J., Thomas-Tikhonenko, Andrei
Publicado 2022

CD19 Alterations Emerging after CD19-Directed Immunotherapy Cause Retention of the Misfolded Protein in the Endoplasmic Reticulum

por Bagashev, Asen, Sotillo, Elena, Tang, Chih-Hang Anthony, Black, Kathryn L., Perazzelli, Jessica, Seeholzer, Steven H., Argon, Yair, Barrett, David M., Grupp, Stephan A., Hu, Chih-Chi Andrew, Thomas-Tikhonenko, Andrei
Publicado 2018

Loss of AID exacerbates the malignant progression of CLL

por Lee, Avery C., Pingali, Sai Ravi, Pinilla-Ibarz, Javier A., Atchison, Michael L., Koumenis, Constantinos, Argon, Yair, Thomas-Tikhonenko, Andrei, De Trez, Carl, Hu, Chih-Chi Andrew, Tang, Chih-Hang Anthony
Publicado 2022

Aberrant splicing in B-cell acute lymphoblastic leukemia

por 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
Publicado 2018

Aberrant splicing in B-cell acute lymphoblastic leukemia

por 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
Publicado 2019

HGG-21. ABERRANT SPLICING OF CLK1 IN PEDIATRIC HIGH-GRADE GLIOMAS DISRUPTS KEY ONCOGENIC TRANSCRIPTIONAL PROGRAMS

por Naqvi, Ammar, Ennis, Brian, Corbett, Ryan, Lahiri, Aditya, Geng, Zhuangzhuang, Kin, Run, Gaonkar, Krutika, Rathi, Komal, Conkrite, Karina, Seghal, Priyanka, Hayer, Katharina, Kraya, Adam, Foster, Jessica, Madsen, Peter, Thomas-Tikhonenko, Andrei, Storm, Phillip, Resnick, Adam, Rokita, Jo Lynne
Publicado 2023

Retention of CD19 intron 2 contributes to CART-19 resistance in leukemias with subclonal frameshift mutations in CD19

por 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
Publicado 2019

High-throughput mutagenesis identifies mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance

por Cortés-López, Mariela, Schulz, Laura, Enculescu, Mihaela, Paret, Claudia, Spiekermann, Bea, Quesnel-Vallières, Mathieu, Torres-Diz, Manuel, Unic, Sebastian, Busch, Anke, Orekhova, Anna, Kuban, Monika, Mesitov, Mikhail, Mulorz, Miriam M., Shraim, Rawan, Kielisch, Fridolin, Faber, Jörg, Barash, Yoseph, Thomas-Tikhonenko, Andrei, Zarnack, Kathi, Legewie, Stefan, König, Julian
Publicado 2022

A convergent malignant phenotype in B-cell acute lymphoblastic leukemia involving the splicing factor SRRM1

por 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
Publicado 2022

Mapping and modeling human colorectal carcinoma interactions with the tumor microenvironment

por Li, Ning, Zhu, Qin, Tian, Yuhua, Ahn, Kyung Jin, Wang, Xin, Cramer, Zvi, Jou, Justine, Folkert, Ian W., Yu, Pengfei, Adams-Tzivelekidis, Stephanie, Sehgal, Priyanka, Mahmoud, Najia N., Aarons, Cary B., Roses, Robert E., Thomas-Tikhonenko, Andrei, Furth, Emma E., Stanger, Ben Z., Rustgi, Anil, Haldar, Malay, Katona, Bryson W., Tan, Kai, Lengner, Christopher J.
Publicado 2023

Modulation of CD22 Protein Expression in Childhood Leukemia by Pervasive Splicing Aberrations: Implications for CD22-Directed Immunotherapies

por 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
Publicado 2022

Alternative splicing of its 5′-UTR limits CD20 mRNA translation and enables resistance to CD20-directed immunotherapies

por Ang, Zhiwei, Paruzzo, Luca, Hayer, Katharina E., Schmidt, Carolin, Torres Diz, Manuel, Xu, Feng, Zankharia, Urvi, Zhang, Yunlin, Soldan, Samantha, Zheng, Sisi, Falkenstein, Catherine D., Loftus, Joseph P., Yang, Scarlett Y., Asnani, Mukta, King Sainos, Patricia, Pillai, Vinodh, Chong, Emeline, Li, Marilyn M., Tasian, Sarah K., Barash, Yoseph, Lieberman, Paul M., Ruella, Marco, Schuster, Stephen J., Thomas-Tikhonenko, Andrei
Publicado 2023

IFITM3 functions as PIP3-scaffold to amplify PI3K signaling in B-cells

por Lee, Jaewoong, Robinson, Mark E., Ma, Ning, Artadji, Dewan, Ahmed, Mohamed A., Xiao, Gang, Sadras, Teresa, Deb, Gauri, Winchester, Janet, Cosgun, Kadriye Nehir, Geng, Huimin, Chan, Lai N., Kume, Kohei, Miettinen, Teemu P., Zhang, Ye, Nix, Matthew A., Klemm, Lars, Chen, Chun Wei, Chen, Jianjun, Khairnar, Vishal, Wiita, Arun P., Thomas-Tikhonenko, Andrei, Farzan, Michael, Jung, Jae U., Weinstock, David M., Manalis, Scott R., Diamond, Michael S., Vaidehi, Nagarajan, Müschen, Markus
Publicado 2020

Targeting CD123 in blastic plasmacytoid dendritic cell neoplasm using allogeneic anti-CD123 CAR T cells

por Cai, Tianyu, Gouble, Agnès, Black, Kathryn L., Skwarska, Anna, Naqvi, Ammar S., Taylor, Deanne, Zhao, Ming, Yuan, Qi, Sugita, Mayumi, Zhang, Qi, Galetto, Roman, Filipe, Stéphanie, Cavazos, Antonio, Han, Lina, Kuruvilla, Vinitha, Ma, Helen, Weng, Connie, Liu, Chang-Gong, Liu, Xiuping, Konoplev, Sergej, Gu, Jun, Tang, Guilin, Su, Xiaoping, Al-Atrash, Gheath, Ciurea, Stefan, Neelapu, Sattva S., Lane, Andrew A., Kantarjian, Hagop, Guzman, Monica L., Pemmaraju, Naveen, Smith, Julianne, Thomas-Tikhonenko, Andrei, Konopleva, Marina
Publicado 2022