SC2Spa: a deep learning based approach to map transcriptome to spatial origins at cellular resolution.

Journal: BMC bioinformatics
Published Date: Jun 2, 2025

Abstract

BACKGROUND: Understanding cellular heterogeneity within tissues hinges on knowledge of their spatial context. However, it is still challenging to accurately map cells to their spatial coordinates.

Authors

  • Linbu Liao
    Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong Province 518055, PR China; College of Software Technology, Zhejiang University, Zhejiang Province 315048, PR China.
  • Esha Madan
    Department of Surgery, School of Medicine, Virginia Commonwealth University, 1200 E Broad St., P.O. Box 980011, Richmond, VA, 23298, USA.
  • António M Palma
    Massey Comprehensive Cancer Center, Virginia Commonwealth University, Richmond, VA, United States; VCU Institute of Molecular Medicine, Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States. Electronic address: antonio.palma@vcuhealth.org.
  • Hyobin Kim
    Department of Bioinformatics, Soongsil University, 369 Sangdo-Ro, Dongjak-Gu, Seoul, 06978, Republic of Korea.
  • Amit Kumar
    Department of Radiology, New York-Presbyterian Hospital and Weill Cornell Medicine, New York, NY, USA.
  • Praveen Bhoopathi
    Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23298, USA.
  • Robert Winn
    Department of Surgery, School of Medicine, Virginia Commonwealth University, 1200 E Broad St., P.O. Box 980011, Richmond, VA, 23298, USA.
  • Jose Trevino
    Department of Surgery, School of Medicine, Virginia Commonwealth University, 1200 E Broad St., P.O. Box 980011, Richmond, VA, 23298, USA.
  • Paul Fisher
    Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany.
  • Cord Herbert Brakebusch
    Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark.
  • Gahyun Kim
    Department of Bioinformatics, Soongsil University, 369 Sangdo-Ro, Dongjak-Gu, Seoul, 06978, Republic of Korea.
  • Junil Kim
    Department of Bioinformatics, Soongsil University, 369 Sangdo-Ro, Dongjak-Gu, Seoul, 06978, Republic of Korea.
  • Rajan Gogna
    Department of Surgery, School of Medicine, Virginia Commonwealth University, 1200 E Broad St., P.O. Box 980011, Richmond, VA, 23298, USA. rajangogna@gmail.com.
  • Kyoung Jae Won
    Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA. kyoungjae.won@cshs.org.

Keywords

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