“Accurate Strand-Specific Long-Read Transcript Isoform Discovery and Quantification at Bulk, Single-Cell, and Single-Nucleus Resolution”. 2026. https://pubmed.ncbi.nlm.nih.gov/41726986/.
Publications
2026
“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/ .
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.