“Proteotranscriptomic Dissection of Breast Cancer T Cell States Identifies CD103+ Tfh-Derived Cytotoxic Cells Linked to Immunotherapy Response”. 2026. https://pmc.ncbi.nlm.nih.gov/articles/PMC12803361/ .
Publications
2026
2025
Webber, James T., Daniel A. Bartlett, Ghamdan Al-Eryani, Akanksha Khorgade, Asa Shin, Christophe Georgescu, Houlin Yu, Brian J. Haas, Victoria Popic, and Aziz M Al’Khafaji. 2025. “Multi-Platform Evaluation and Optimization of Single-Cell RNA Isoform Sequencing”. BioRxiv. https://doi.org/10.1101/2025.02.22.639662.
Gaglione, Stephanie A., Jonathan Krog, Frances R. Keer, Emma N. Finburgh, Elif Kulaksizoglu, Connor S Dobson, David Gifford, Aziz M Al’Khafaji, Paul C. Blainey, and Michael E. Birnbaum. 2025. “Deep Mapping of the TCR-Antigen Interface Using PMHC-Pseudotyped Viruses and Yeast Display”. BioRxiv. https://doi.org/10.1101/2025.08.25.671738.
Simmons, Sean K., Xian Adiconis, Nathan Haywood, Jacob Parker, Zechuan Lin, Zhixiang Liao, Idil Tuncali, et al. 2025. “Experimental and Computational Methods for Allelic Imbalance Analysis from Single-Nucleus RNA-Seq Data”. BioRxiv. https://doi.org/10.1101/2024.08.13.607784.
Qin, Qian, Victoria Popic, Kirsty Wienand, Houlin Yu, Emily White, Akanksha Khorgade, Asa Shin, et al. (2025) 2025. “Accurate Fusion Transcript Identification from Long- and Short-Read Isoform Sequencing at Bulk or Single-Cell Resolution.”. Genome Research 35 (4): 967-86. https://doi.org/10.1101/gr.279200.124.
2024
Penter, Livius, Mehdi Borji, Adi Nagler, Haoxiang Lyu, Wesley S Lu, Nicoletta Cieri, Katie Maurer, et al. (2024) 2024. “Integrative Genotyping of Cancer and Immune Phenotypes by Long-Read Sequencing.”. Nature Communications 15 (1): 32. https://doi.org/10.1038/s41467-023-44137-7.
Al’Khafaji, Aziz M, Jonathan T Smith, Kiran Garimella V, Mehrtash Babadi, Victoria Popic, Moshe Sade-Feldman, Michael Gatzen, et al. (2024) 2024. “High-Throughput RNA Isoform Sequencing Using Programmed CDNA Concatenation.”. Nature Biotechnology 42 (4): 582-86. https://doi.org/10.1038/s41587-023-01815-7.
2023
Gentili, Matteo, Bingxu Liu, Malvina Papanastasiou, Deborah Dele-Oni, Marc A Schwartz, Rebecca J Carlson, Aziz M Al’Khafaji, et al. (2023) 2023. “ESCRT-Dependent STING Degradation Inhibits Steady-State and CGAMP-Induced Signalling.”. Nature Communications 14 (1): 611. https://doi.org/10.1038/s41467-023-36132-9.
Martin-Rufino, Jorge D, Nicole Castano, Michael Pang, Emanuelle I Grody, Samantha Joubran, Alexis Caulier, Lara Wahlster, et al. (2023) 2023. “Massively Parallel Base Editing to Map Variant Effects in Human Hematopoiesis.”. Cell 186 (11): 2456-2474.e24. https://doi.org/10.1016/j.cell.2023.03.035.
2022
Gupta, Anika, Jorge D Martin-Rufino, Thouis R Jones, Vidya Subramanian, Xiaojie Qiu, Emanuelle I Grody, Alex Bloemendal, et al. (2022) 2022. “Inferring Gene Regulation from Stochastic Transcriptional Variation across Single Cells at Steady State.”. Proceedings of the National Academy of Sciences of the United States of America 119 (34): e2207392119. https://doi.org/10.1073/pnas.2207392119.