no code implementations • 17 Dec 2024 • Ziv Yaniv, Ifeanyichukwu U. Anidi, Leanne Arakkal, Armando J. Arroyo-Mejías, Rebecca T. Beuschel, Katy Börner, Colin J. Chu, Beatrice Clark, Menna R. Clatworthy, Jake Colautti, Fabian Coscia, Joshua Croteau, Saven Denha, Rose Dever, Walderez O. Dutra, Sonja Fritzsche, Spencer Fullam, Michael Y. Gerner, Anita Gola, Kenneth J. Gollob, Jonathan M. Hernandez, Jyh Liang Hor, Hiroshi Ichise, Zhixin Jing, Danny Jonigk, Evelyn Kandov, Wolfgang Kastenmüller, Joshua F. E. Koenig, Aanandita Kothurkar, Rosa K. Kortekaas, Alexandra Y. Kreins, Ian T. Lamborn, Yuri Lin, Katia Luciano Pereira Morais, Aleksandra Lunich, Jean C. S. Luz, Ryan B. MacDonald, Chen Makranz, Vivien I. Maltez, John E. McDonough, Ryan V. Moriarty, Juan M. Ocampo-Godinez, Vitoria M. Olyntho, Annette Oxenius, Kartika Padhan, Kirsten Remmert, Nathan Richoz, Edward C. Schrom, Wanjing Shang, Lihong Shi, Rochelle M. Shih, Emily Speranza, Salome Stierli, Sarah A. Teichmann, Tibor Z. Veres, Megan Vierhout, Brianna T. Wachter, Margaret Williams, Nathan Zangger, Ronald N. Germain, Andrea J. Radtke
The iterative bleaching extends multiplexity (IBEX) Knowledge-Base is a central portal for researchers adopting IBEX and related 2D and 3D immunofluorescence imaging methods.
1 code implementation • 9 Sep 2024 • Stathis Megas, Daniel G. Chen, Krzysztof Polanski, Moshe Eliasof, Carola-Bibiane Schonlieb, Sarah A. Teichmann
Celcomen leverages a mathematical causality framework to disentangle intra- and inter- cellular gene regulation programs in spatial transcriptomics and single-cell data through a generative graph neural network.
no code implementations • 26 Jul 2024 • Andrea J. Radtke, Ifeanyichukwu Anidi, Leanne Arakkal, Armando Arroyo-Mejias, Rebecca T. Beuschel, Katy Borner, Colin J. Chu, Beatrice Clark, Menna R. Clatworthy, Jake Colautti, Joshua Croteau, Saven Denha, Rose Dever, Walderez O. Dutra, Sonja Fritzsche, Spencer Fullam, Michael Y. Gerner, Anita Gola, Kenneth J. Gollob, Jonathan M. Hernandez, Jyh Liang Hor, Hiroshi Ichise, Zhixin Jing, Danny Jonigk, Evelyn Kandov, Wolfgang Kastenmueller, Joshua F. E. Koenig, Aanandita Kothurkar, Alexandra Y. Kreins, Ian Lamborn, Yuri Lin, Katia Luciano Pereira Morais, Aleksandra Lunich, Jean C. S. Luz, Ryan B. MacDonald, Chen Makranz, Vivien I. Maltez, Ryan V. Moriaty, Juan M. Ocampo-Godinez, Vitoria M. Olyntho, Kartika Padhan, Kirsten Remmert, Nathan Richoz, Edward C. Schrom, Wanjing Shang, Lihong Shi, Rochelle M. Shih, Emily Speranza, Salome Stierli, Sarah A. Teichmann, Tibor Z. Veres, Megan Vierhout, Brianna T. Wachter, Adam K. Wade-Vallance, Margaret Williams, Nathan Zangger, Ronald N. Germain, Ziv Yaniv
Iterative Bleaching Extends multipleXity (IBEX) is a versatile method for highly multiplexed imaging of diverse tissues.
1 code implementation • 14 Sep 2022 • Vidhi Lalchand, Aditya Ravuri, Emma Dann, Natsuhiko Kumasaka, Dinithi Sumanaweera, Rik G. H. Lindeboom, Shaista Madad, Sarah A. Teichmann, Neil D. Lawrence
Single-cell RNA-seq datasets are growing in size and complexity, enabling the study of cellular composition changes in various biological/clinical contexts.
no code implementations • 28 Jun 2021 • David Osumi-Sutherland, Chuan Xu, Maria Keays, Peter V. Kharchenko, Aviv Regev, Ed Lein, Sarah A. Teichmann
Massive single-cell profiling efforts have accelerated our discovery of the cellular composition of the human body, while at the same time raising the need to formalise this new knowledge.