IICD Newsletter April 2024

April 01, 2024
April 1st, 2024

IICD Researchers Introduce Starfysh, a Breakthrough Tool Transforming Spatial Gene Expression Analysis

IICD researcher Elham Azizi and her team introduce an innovative computational tool named Starfysh, designed to revolutionize the study of gene expression within tissues. The story was recently published in Nature Biotechnology.

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Connect with IICD on LinkedIn

Have you connected with us on social media? We're thrilled to launch our official LinkedIn page. Join us as we expand our online presence and share valuable insights, news, and opportunities within the IICD community. Follow us on LinkedIn, X, Instagram, and YouTube to stay in the loop with all things IICD!

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IICD Seminar Series: April Seminar


The IICD continues its monthly seminar series on the topic of mathematical sciences underpinning cancer research. Join us for an enlightening session with Cameron Po-Hsuan Chen, Head of AI and Data Science at Need. Seminar hosted by Bianca Dumitrascu.

Date: April 10th, 2024
Time: 2:00 PM (ET)
Location: Fairchild 700 and Online

Register Here

IICD Highlights

     Headshots of the Alliance interns     

The IIICD collaborates once again with the Alliance Program to welcome five new interns from April to July 2024. These interns, hailing from École Polytechnique, will have the opportunity to work in the labs of Drs. Elham Azizi, Khanh Dinh, and Simon Tavaré. Read more.

    Headshot of Thomas Cong

Thomas Cong, a senior high school student working with David Tourigny, was awarded second place at the 2024 Regeneron Science Talent Search, America’s oldest and most prestigious science and math competition for high school seniorsRead more.


IICD affiliate member Scott Fraser, Provost Professor of Biology and Bioengineering at the University of Southern California, was recently named the vice president of science grant programs at the Chan Zuckerberg Initiative. Read more.

    Cameron accepting her award 

Congratulations to biomedical engineering PhD student, Cameron Park, who was awarded second place in the poster presentation at the Columbia University 8th Annual Engineering in Medicine Symposium. See IG photos here.

     Headshot of Apoorva Singh

IICD welcomes Apoorva Singh, a Postdoctoral Research Scientist who joins the lab of Dr. Sanket Rane. Her current research interests lie at the interface of applied mathematics, statistics, and immunology. Read more.


     Headshot of Brent Stockwell 

Brent Stockwell garnered double recognition as he received two awards for his contributions to cellular and metabolic research. His achievements are acknowledged through the 2024 CDD Award by ECDO and as the inaugural recipient of the MetNet Pioneer in Metabolism Award.

Recent Publications from IICD Researchers

A Guideline on the Molecular Ecosystem Regulating Ferroptosis. Dai, E.; Chen, X.; Linkermann, A.; Jiang, X.; Kang, R.; Kagan, V. E.; Bayir, H.;Yang, W. S.;  Garcia-Saez, A. J.; Ioannou, M. S.; Janowitz, T.; Ran, Q.; Gu, W.; Gan, B.; Krysko, D. V.; Zhu, X.; Wang, J.; Krautwald, S.; Toyokuni, S.; Xie, Y.; Greten, F. R.; Yi, Q.; Schick, J.; Liu, J.; Gabrilovich, D. I.; Liu, J.; Zeh, H. J.; Zhang, D. D.; Yang, M.; Iovanna, J.; Kopf, M.; Adolph, T. E.; Chi, J.-T.; Li, C.; Ichijo, H.; Karin, M.; Sankaran, V. G.; Zou, W.;  Galluzzi, L.; Bush, A. I.; Li, B.; Melino, G.; Baehrecke, E. H.; Lotze, M. T.;  Klionsky, D. J.; Stockwell, B. R.; Kroemer, G.; Tang, D. Nature Cell Biology 2024, in press. 

Current Status of Artificial Intelligence Methods for Skin Cancer Survival Analysis: A Scoping Review. Schreidah, C. M.; Gordon, E. R.; Adeuyan, O.; Chen, C.; Lapolla, B. A.; Kent, J. A.; Reynolds, G. B.; Fahmy, L. M.; Weng, C.; Tatonetti, N. P.; Chase, H. S.; Pe’er, I.; Geskin, L. J. Front. Med. 2024, 11, in press.

DeST-OT: Alignment of Spatiotemporal Transcriptomics Data. Halmos, P.; Liu, X.; Gold, J.; Chen, F.; Ding, L.; Raphael, B. J. bioRxiv 2024.

Homologous Recombination Deficiency and Tumor Suppressor Heterozygosity Mediate Resistance to Front-Line Therapy in Breast Cancer. Safonov, A.; Marra, A.; Bandlamudi, C.; O’Leary, B.; Wubbenhorst, B.; Moiso, E.; Lee, M.; Donoghue, M. T. A.; An, J.;  Will, M.; Pareja, F.; Ahmed, M.; Nizialek, E.; Lukashchuk, N.; Sofianopoulou, E.; Liu, Y.; Huang, X.;  Schultz, N.; Berger, M.; Scaltriti, M.; Reis-Filho, J. S.;  Li, B. T.; Offit, K.; Norton, L.; Solit, D. B.;  Shah, S.; Maxwell, K. N.; Domchek, S. M.; Couch, F.; Nathanson, K. L.; Robson, M. E.; Turner, N. C.; Chandarlapaty, S.; Razavi, P. bioRxiv 2024.

Improving Regulatory T Cell Production through Mechanosensing. Shi, L.; Lim, J. Y.; Kam, L. C. Journal of biomedical materials research. Part A 2024, in press

Maximum Likelihood Inference of Time-scaled Cell Lineage Trees with Mixed-type Missing Data. Mai, U.; Chu, G.; Raphael, B. J. bioRxiv 2024.

Multimodal Histopathologic Models Stratify Hormone Receptor-Positive Early Breast Cancer. Boehm, K. M.; El Nahhas, O. S. M.; Marra, A.; Selenica, P.;Wen, H. Y.; Weigelt, B.;  Paul, E. D.; Cekan, P.; Erber, R.; Loeffler, C. M. L.; Guerini-Rocco, E.; Fusco, N.; Frascarelli, C.; Mane, E.; Munzone, E.; Dellapasqua, S.; Zagami, P.; Curigliano, G.; Razavi, P.; Reis-Filho, J. S.;Pareja, F.;  Chandarlapaty, S.; Shah, S.; Kather, J. N. bioRxiv 2024

Notch2 Controls Developmental Fate Choices between Germinal Center and Marginal Zone B Cells upon Immunization.Babushku, T.; Lechner, M.; Ehrenberg, S.; Rambold, U.; Schmidt-Supprian, M.; Yates, A. J.; Rane, S.; Zimber-Strobl, U.; Strobl, L. J. Nature Communications 2024, 15 (1), 1960.

PHLDA2-Mediated Phosphatidic Acid Peroxidation Triggers a Distinct Ferroptotic Response during Tumor Suppression. Yang, X.; Wang, Z.; Samovich, S. N.; Kapralov, A. A.; Amoscato, A. A.; Tyurin, V. A.; Dar, H. H.;Li, Z.;  Duan, S.; Kon, N.; Chen, D.; Tycko, B.; Zhang, Z.; Jiang, X.; Bayir, H.; Stockwell, B. R.; Kagan, V. E.; Gu, W. Cell Metab 2024, in press.

Standardised Measurements for Monitoring and Comparing Multiphoton Microscope Systems. Lees, R. M.; Bianco, I. H.; Campbell, R. A. A.; Orlova, N.; Peterka, D. S.; Pichler, B.; Smith, S. L.; Yatsenko, D.; Yu, C.-H.; Packer, A. M. bioRxiv 2024.

Starfysh Integrates Spatial Transcriptomic and Histologic Data to Reveal Heterogeneous Tumor-Immune Hubs. 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. L.; 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. Nature Biotechnology 2024in press.

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