Mapping and modeling human colorectal carcinoma interactions with the tumor microenvironment

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

Source: Nature Communications, Vol 14, Iss 1, Pp 1-17 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/27a70ad4c8a74c5881020e751a7a5388

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

Authors: David Wang, Mathieu Quesnel-Vallieres, San Jewell, Moein Elzubeir, Kristen Lynch, Andrei Thomas-Tikhonenko, Yoseph Barash

Source: Nature Communications, Vol 14, Iss 1, Pp 1-15 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/d9bf9b7fdf26407aa5c24b0f3bae250d

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

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

Source: Nature Communications, Vol 13, Iss 1, Pp 1-17 (2022)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/c08d347a8dc943b8ab905da6ad76b36d

Identifying common transcriptome signatures of cancer by interpreting deep learning models

Authors: Anupama Jha, Mathieu Quesnel-Vallières, David Wang, Andrei Thomas-Tikhonenko, Kristen W Lynch, Yoseph Barash

Source: Genome Biology, Vol 23, Iss 1, Pp 1-23 (2022)

Subject Terms: Cancer genomics, Transcriptomics, Deep learning, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/4449558d4ff542678422511f8b71af41

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

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

Source: Nature Communications, Vol 13, Iss 1, Pp 1-11 (2022)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/28ec66e39af349c1b7a1e856e77e57a0

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

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

Source: Nature Communications, Vol 12, Iss 1, Pp 1-9 (2021)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/b8ed04d2aafd4e4a8c327a67fed001a0

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

Authors: Laura Schulz, Manuel Torres-Diz, Mariela Cortés-López, Katharina E. Hayer, Mukta Asnani, Sarah K. Tasian, Yoseph Barash, Elena Sotillo, Kathi Zarnack, Julian König, Andrei Thomas-Tikhonenko

Source: Genome Biology, Vol 22, Iss 1, Pp 1-12 (2021)

Subject Terms: Long-read sequencing, Oxford Nanopore Technologies, Alternative splicing, mRNA isoforms, Exitrons, Reverse transcription, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/7a025226aeea4eeeb954f32ea7752bb3

CAR T-cell therapy is effective for CD19-dim B-lymphoblastic leukemia but is impacted by prior blinatumomab therapy

Authors: Vinodh Pillai, Kavitha Muralidharan, Wenzhao Meng, Asen Bagashev, Derek A. Oldridge, Jaclyn Rosenthal, John Van Arnam, Jos J. Melenhorst, Diwakar Mohan, Amanda M. DiNofia, Minjie Luo, Sindhu Cherian, Jonathan R. Fromm, Gerald Wertheim, Andrei Thomas-Tikhonenko, Michele Paessler, Carl H. June, Eline T. Luning Prak, Vijay G. Bhoj, Stephan A. Grupp, Shannon L. Maude, Susan R. Rheingold

Source: Blood Advances, Vol 3, Iss 22, Pp 3539-3549 (2019)

Subject Terms: Specialties of internal medicine, RC581-951

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2473952920317535; https://doaj.org/toc/2473-9529

Access URL: https://doaj.org/article/e70ab1bdc076485da3ba01a3a1e59b84