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Bianca Dumitrascu: Understanding How Biological Matter Encodes Computation
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The Irving Institute for Cancer Dynamics and the Department of Statistics welcome a new faculty member, Dr. Bianca Dumitrascu, Assistant Professor of Statistics and Herbert and Florence Irving Assistant Professor of Cancer Data Research (in the Herbert and Florence Institute for Cancer Dynamics). Her group will focus on understanding how biological matter encodes computation and whether we can mimic, predict, and control this computation.
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Multimodal Sequencing Achieves High-Quality Results from Small Volumes of Frozen Tumor Specimens
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A team led by Benjamin Izar and Elham Azizi have invented a new RNA sequencing method that achieves high-quality results from small volumes of frozen tumor specimens. They demonstrated the success of their technique in two clinical studies that profiled dozens of tumor samples, both those archived and those freshly collected, to understand how they respond to anti-tumor therapy. The paper was published in Nature Genetics.
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Mathematical and Computational Methods in Cancer and Biology Symposium
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 IICD Faculty Elham Azizi is giving a presentation titled “Machine Learning for Modeling Dynamic Cell-Cell Communication in the Tumor Microenvironment” at the upcoming ASTCT Transplantation & Cellular Therapy Meeting as part of the “Tumor Microenvironment and Relapse After Immunotherapy” session.
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 Fenisha Shah, a Master's student pursuing biomedical engineering, joins Dr. Tavaré’s lab this spring. Fenisha graduated from the University of Miami in 2022 with a B.S. in electrical and computer engineering. She is interested in leveraging her software tools from her undergraduate experience to study biological data and improve existing machine learning methods.
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 IICD researchers Ignacio Vázquez-García, Sohrab P. Shah, et al published a new study in Nature on the impact of mutational processes on the tumor microenvironment in ovarian cancer. A summary of the findings can be found in Nature News & Views: "Genetics and anatomy sculpt immune-cell partners of ovarian cancer." Read more.
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 Join virtually the Columbia University 7th Annual Engineering in Medicine Symposium on February 23rd. The symposium comprises five sessions showcasing the role of engineering in the fields of Single Cell, Machine Learning, Neuroscience of Decision-Making, Development + Aging, and Tissue Engineering + Instructive Biomaterials. Register here.
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 The virtual reality technology that could revolutionize cancer treatment: The IMAXT team, which includes several IICD researchers, was featured on ITV News for their use of virtual reality to create a 3D tumor visualization tool. Watch here. |
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Recent Publications from IICD Researchers
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ConDoR: Tumor Phylogeny Inference with a Copy-Number Constrained Mutation Loss Model. Sashittal, P.; Zhang, H.; Iacobuzio-Donnahue, C. A.; Raphael, B. J. BioRxiv 2023.
Exploiting Allele-Specific Transcriptional Effects of Subclonal Copy Number Alterations for Genotype-Phenotype Mapping in Cancer Cell Populations. Shi, H.; Williams, M. J.; Satas, G.; Winer, A. C.; McPherson, A.; Shah, S. P. BioRxiv 2023.
Multimodal Single-Cell and Whole-Genome Sequencing of Small, Frozen Clinical Specimens. Wang, Y.; Fan, J. L.; Melms, J. C.; Amin, A. D.; Georgis, Y.; Barrera, I.; Ho, P.; Tagore, S.; Abril-Rodríguez, G.; He, S.; Jin, Y.; Biermann, J.; Hofree, M.; Caprio, L.; Berhe, S.; Khan, S. A.; Henick, B. S.; Ribas, A.; Macosko, E. Z.; Chen, F.; Taylor, A. M.; Schwartz, G. K.; Carvajal, R. D.; Azizi, E.*; Izar, B.* Nature Genetics 2023, 55, 19-25.
NetMix2: A Principled Network Propagation Algorithm for Identifying Altered Subnetworks. Chitra, U.; Park, T. Y.; Raphael, B. J. J. Comput. Biol. 2022, 29 (12), 1305-1323.
Ovarian Cancer Mutational Processes Drive Site-Specific Immune Evasion. Vázquez-García, I.; Uhlitz, F.; Ceglia, N.; Lim, J. L. P.; Wu, M.; Mohibullah, N.; Niyazov, J.; Ruiz, A. E. B.; Boehm, K. M.; Bojilova, V.; Fong, C. J.; Funnell, T.; Grewal, D.; Havasov, E.; Leung, S.; Pasha, A.; Patel, D. M.; Pourmaleki, M.; Rusk, N.; Shi, H.; Vanguri, R.; Williams, M. J.; Zhang, A. W.; Broach, V.; Chi, D. S.; Da Cruz Paula, A.; Gardner, G. J.; Kim, S. H.; Lennon, M.; Long Roche, K.; Sonoda, Y.; Zivanovic, O.; Kundra, R.; Viale, A.; Derakhshan, F. N.; Geneslaw, L.; Issa Bhaloo, S.; Maroldi, A.; Nunez, R.; Pareja, F.; Stylianou, A.; Vahdatinia, M.; Bykov, Y.; Grisham, R. N.; Liu, Y. L.; Lakhman, Y.; Nikolovski, I.; Kelly, D.; Gao, J.; Schietinger, A.; Hollmann, T. J.; Bakhoum, S. F.; Soslow, R. A.; Ellenson, L. H.; Abu-Rustum, N. R.; Aghajanian, C.; Friedman, C. F.; McPherson, A.; Weigelt, B.; Zamarin, D.; Shah, S. P. Nature 2022, 612, 778-786.
PASTE2: Partial Alignment of Multi-slice Spatially Resolved Transcriptomics Data. Liu, X.; Zeira, R.; Raphael, B. J. BioRxiv 2023.
Starfysh Reveals Heterogeneous Spatial Dynamics in the Breast Tumor Microenvironment. He, S.; Jin, Y.; Nazaret, A.; Shi, L.; Chen, X.; Rampersaud, S.; Dhillon, B. S.; Valdez, I.; Friend, L. E.; Fan, J. L.; Park, C. Y.; Mintz, R.; Lao, Y.-H.; Carrera, D.; Fang, K. W.; Mehdi, K.; Rohde, M.; McFaline-Figueroa, J. L.; Blei, D.; Leong, K. W.; Rudensky, A. Y.; Plitas, G.; Azizi, E. BioRxiv 2022. [Code/Highlights]
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