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The Molecular Origins of Two Types of Cancer Are Closer Than We Knew
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A new paper by Karol Nowicki-Osuch, IICD Associate Research Scientist, and Rebecca Fitzgerald, Director of the Early Detection Institute at Cambridge University, paves the way for better detection and prevention of certain precancerous changes in the esophagus and stomach. The study was published in the journal Cancer Discovery.
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The IICD Hosts a Mathematical and Computational Methods in Cancer and Biology Symposium
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The IICD recently hosted its first in-person symposium since March 2020. The three-day event highlighted the importance of mathematical and computational sciences and technological developments in driving fundamental discoveries in cancer biology and many other biological fields. The symposium also celebrated two milestones: Simon Tavaré’s 70th birthday and the 5th anniversary of the Irving Institute for Cancer Dynamics.
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Next Speaker in the IICD Seminar Series
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Computational Challenges in Single-Cells Genomics
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Hosted by Simon Tavaré, FRS
Date: April 19, 2023 at 2 PM (ET)
Location: Schermerhorn Hall 603
and via Zoom
Light refreshments will be served
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The IICD Welcomes Three New Members
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 Maithê Rocha Monteiro de Barros is a new postdoctoral research scientist working under the supervision of Dr. Karol Nowicki-Osuch. During her PhD, she became interested in bioinformatics and she is now transitioning from wet to dry-lab. Her current research focuses on single-cell sequencing-based assessment of gastric and esophageal cancer development.
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 Tu Duyen Nguyen is an intern from the Alliance program who studies applied mathematics as well as biology fundamentals at the Ecole Polytechnique (France). She specializes in statistics and machine learning, and is excited to put her knowledge to good use by using deep learning to uncover new things from biological data in the Azizi lab.
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 Amanda Samuel graduated from the University of Peradeniya (Sri Lanka) in 2021 with a BSc Hons in Statistics. She is currently a MSc student in Statistics. She is looking forward to utilizing her software skills and statistical background from her undergraduate research experience to study biological data and contribute to cancer research in Dr. Dinh’s lab.
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Cancer AI Research:
Computational Approaches Addressing Imperfect Data
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Virtual workshop organized by the National Cancer Institute. The goals of this workshop are to (1) examine the state of the science for AI methods designed to operate on noisy, complex, or low-dimensional data, (2) explore how these methods may be applied to key areas of cancer research, and (3) discuss processes for identifying the biological questions that will motivate further advances in machine learning. This workshop will highlight the importance of leveraging advances across fields to accelerate cancer research and discovery through AI. IICD member Elham Azizi is among the speakers.
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Recent Publications from IICD Researchers
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ALOX5-Mediated Ferroptosis Acts as a Distinct Cell Death Pathway upon Oxidative Stress in Huntington's Disease. Song, S.; Su, Z.; Kon, N.; Chu, B.; Li, H.; Jiang, X.; Luo, J.; Stockwell, B. R.; Gu, W. Genes Dev 2023, in press.
Dietary Restriction of Cysteine and Methionine Sensitizes Gliomas to Ferroptosis and Induces Alterations in Energetic Metabolism. Upadhyayula, P. S.; Higgins, D. M.; Mela, A.; Banu, M.; Dovas, A.; Zandkarimi, F.; Patel, P.; Mahajan, A.; Humala, N.; Nguyen, T. T. T.; Chaudhary, K. R.; Liao, L.; Argenziano, M.; Sudhakar, T.; Sperring, C. P.; Shapiro, B. L.; Ahmed, E. R.; Kinslow, C.; Ye, L. F.; Siegelin, M. D.; Cheng, S.; Soni, R.; Bruce, J. N.; Stockwell, B. R.; Canoll, P. Nat Commun 2023, 14 (1), 1187.
Gene-Level Alignment of Single Cell Trajectories Informs the Progression of in vitro T Cell Differentiation. Sumanaweera, D.; Suo, C.; Muraro, D.; Dann, E.; Polanski, K.; Steemers, A. S.; Park, J.-E.; Dumitrascu, B.; Teichmann, S. A. bioRxiv 2023.
In Silico Tissue Generation and Power Analysis for Spatial Omics. Baker, E. A. G.; Schapiro, D.; Dumitrascu, B.; Vickovic, S.; Regev, A. Nat Methods 2023, in press.
Multiplex Single-Cell Chemical Genomics Reveals the Kinase Dependence of the Response to Targeted Therapy. McFaline-Figueroa, J. L.; Srivatsan, S.; Hill, A. J.; Gasperini, M.; Jackson, D. L.; Saunders, L.; Domcke, S.; Regalado, S. G.; Lazarchuck, P.; Alvarez, S.; Monnat, R. J.; Shendure, J.; Trapnell, C. bioRxiv 2023.
Single-Cell RNA Sequencing Unifies Developmental Programs of Esophageal and Gastric Intestinal Metaplasia. Nowicki-Osuch, K.; Zhuang, L.; Cheung, T. S.; Black, E. L.; Masque-Soler, N.; Devonshire, G.; Redmond, A. M.; Freeman, A.; di Pietro, M.; Pilonis, N.; Januszewicz, W.; O'Donovan, M.; Tavaré, S.; Shields, J. D.; Fitzgerald, R. C. Cancer Discov 2023, in press.
Spatial Epigenome-Transcriptome Co-Profiling of Mammalian Tissues. Zhang, D.; Deng, Y.; Kukanja, P.; Agirre, E.; Bartosovic, M.; Dong, M.; Ma, C.; Ma, S.; Su, G.; Bao, S.; Liu, Y.; Xiao, Y.; Rosoklija, G. B.; Dwork, A. J.; Mann, J. J.; Leong, K. W.; Boldrini, M.; Wang, L.; Haeussler, M.; Raphael, B. J.; Kluger, Y.; Castelo-Branco, G.; Fan, R. Nature 2023, in press.
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