Cellstich: A Flexible Pipeline for 3D Segmentation Leveraging Optimal Transport
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Spatial profiling of transcriptional states in 3D provides valuable insights into cellular interactions in the context of tissue microenvironment. The Azizi and Blumberg groups collaborated to design Cellstitch, a flexible and lightweight pipeline for 3D segmentation leveraging optimal transport. The study was published last month in BMC Bioinformatics.
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Faces of IICD: Henry Kotkin, SRP Alumnus
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Henry Kotkin is a senior at Kenyon College, double majoring in chemistry and economics with a minor in French. He participated in the 2023 IICD Summer Research Program (SRP). In the latest "Faces of IICD" blog series, Henry shares his experience in the SRP and how it contributed to his career goal.
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February is #CancerPrevention Month
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Throughout the month, we'll be shining a spotlight on YOU – our dedicated members who contribute to the field of cancer prevention. Whether you're involved in groundbreaking research, community initiatives, or advocacy, we want to hear and celebrate your efforts. Let's make February a month of unity, awareness, and celebration of our collective impact in the fight against cancer.
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IICD Seminar Series: Genomic, Host and Microenvironment Determinants of Cancer Progression
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Join us for an enlightening session with Dr. Christina Curtis, PhD: Professor of Medicine, Genetics, and Biomedical Data Science, and the esteemed Director of AI and Cancer Genomics at Stanford University. Hosted by Simon Tavaré, this seminar touches insights into the intersection of artificial intelligence and cancer genomics.
Date: February 14, 2024
Time: 2:00 PM (ET)
Location: Fairchild 700 and Online
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Congratulations to Lingting Shi was awarded a T32 grant from the Genome and Epigenome Integrity in Cancer Training Program leadership. The GEIC prepares predoctoral students and postdoctoral fellows for productive careers in basic and translational cancer research on the roles of genomic and epigenomic instability in cancer. Read more.
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The IICD Welcomes Three New Members
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Maria Topel is the new Manager of Finance and Administration. Maria will oversee all financial matters. Previously, she served as the Assistant Director for Budget & Operations at Columbia Business School and as the Program Manager for the Higher and Postsecondary Education program at Teachers College.
Brittani Wright recently joined the team as the Communications Specialist. She previously served as Marketing Manager and Editor at University of St. Thomas and as a Publication Writer at Texas A&M University. Her skill set is finely tuned in storytelling and strategic marketing.
Ozgur Beker is our visiting student from Sabanci University. Oz joins Bianca Dumitrascu's group for a year. With a BS in Computer Science & Engineering, Ozgur brings expertise from previous work on machine learning approaches (with Prof. Ogun Adebali), drug target identification for the blood-brain barrier (with Prof. Nur Mustafaoglu), and deconvolution pipelines (with Dr. Irene Papatheodorou, EMBL-EBI).
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Gordon Research Conference (GRC) and Gordon Research Seminar (GRS) on Single-Cell Cancer Biology
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The Gordon Research Conference on Single-Cell Cancer Biology (June 9-14, 2024) will bring together leading researchers with different backgrounds that use single cell and spatial technologies to address a range of problems in basic cancer biology, translational, and clinical oncology. GRC will be preceded by the inaugural Gordon Research Seminar (June 8-9, 2024), a unique forum for young doctoral and post-doctoral researchers in the field to present their work, discuss new methods, cutting edge ideas, and pre-published data, as well as to build collaborative relationships with their peers.
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Recent Publications from IICD Researchers
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Cellstitch: 3D Cellular Anisotropic Image Segmentation via Optimal Transport. Liu, Y.; Jin, Y.; Azizi, E.; Blumberg, A. J. BMC Bioinformatics 2023, 24 (1), 480.
Circulating Tumour Mutation Detection in Triple-Negative Breast Cancer as an Adjunct to Tissue Response Assessment. Zaikova, E.; Cheng, B. Y. C.; Cerda, V.; Kong, E.; Lai, D.; Lum, A.; Bates, C.; den Brok, W.; Kono, T.; Bourque, S.; Chan, A.; Feng, X.; Fenton, D.; Gurjal, A.; Levasseur, N.; Lohrisch, C.; Roberts, S.; Shenkier, T.; Simmons, C.; Taylor, S.; Villa, D.; Miller, R.; Aguirre-Hernandez, R.; Aparicio, S.; Gelmon, K. NPJ Breast Cancer 2024, 10 (1), 3.
CRISPRmap: Sequencing-Free Optical Pooled Screens Mapping Multi-Omic Phenotypes in Cells and Tissue. Gu, J.; Iyer, A.; Wesley, B.; Taglialatela, A.; Leuzzi, G.; Hangai, S.; Decker, A.; Gu, R.; Klickstein, N.; Shuai, Y.; Jankovic, K.; Parker-Burns, L.; Jin, Y.; Zhang, J. Y.; Hong, J.; Niu, S.; Chou, J.; Landau, D. A.; Azizi, E.; Chan, E. M.; Ciccia, A.; Gaublomme, J. T. bioRxiv 2023.
Enabling Continuous Immune Cell Recirculation on a Microfluidic Array to Study Immunotherapeutic Interactions in a Recapitulated Tumour Microenvironment. Chi, C. W.; Lao, Y. H.; Ahmed, A. H. R.; He, S.; Merghoub, T.; Leong, K. W.; Wang, S. Lab Chip 2024, 24, 396-407.
Glioma-Induced Alterations in Excitatory Neurons are Reversed by mTOR Inhibition. Goldberg, A. R.; Dovas, A.; Torres, D.; Sharma, S. D.; Mela, A.; Merricks, E. M.; Olabarria, M.; Shokoohm, L. A.; Zhao, H. T.; Kotidis, C.; Calvaresi, P.; Viswanathan, A.; Banu, M. A.; Razavilar, A.; Sudhakar, T. D.; Saxena, A.; Chokran, C.; Humala, N.; Mahajan, A.; Xu, W.; Metz, J. B.; Chen, C.; Bushong, E. A.; Boassa, D.; Ellisman, M. H.; Hillman, E. M. C.; McKhann II, G. M.; Gill, B. J. A.; Rosenfeld, S. S.; Schevon, C. A.; Bruce, J. N.; Sims, P. A.; Peterka, D. S.; Canoll, P. bioRxiv 2024.
Kinases Controlling Stability of the Oncogenic MYCN Protein. Smith, N.; Reznik, E.; Bisikirska, B.; Polychronidou, V.; Wang, Q.; Zask, A.; Forouhar, F.; Califano, A.; Stockwell, B. R. ACS Medicinal Chemistry Letters 2023, 14 (12), 1664-1672.
Spatial Pharmacology Using Mass Spectrometry Imaging. Rajbhandari, P.; Neelakantan, T. V.; Hosny, N.; Stockwell, B. R. Trends Pharmacol Sci 2023, in press.
Weakly Supervised Deep Learning Predicts Immunotherapy Response in Solid Tumors Based on PD-L1 Expression. Ligero, M.; Serna, G.; El Nahhas, O. S. M.; Sansano, I.; Mauchanski, S.; Viaplana, C.; Calderaro, J.; Toledo, R. A.; Dienstmann, R.; Vanguri, R. S.; Sauter, J. L.; Sanchez-Vega, F.; Shah, S. P.; Ramon, Y. C. S.; Garralda, E.; Nuciforo, P.; Perez-Lopez, R.; Kather, J. N. Cancer Res Commun 2023, 4 (1), 92-102.
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