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Computational Health Informatics Program Research

Research Overview

Dr. Liang Sun leads the Bioinformatics team within the Research Informatics group at Boston Children’s Hospital. He has over a decade of experience in bioinformatics, with expertise spanning single-cell RNA-seq analysis, spatial transcriptomics, bulk RNA-seq, proteomics, metabolomics, whole-genome sequencing (WGS), whole-exome sequencing (WES), and bioinformatics software development. Dr. Sun is highly skilled in data visualization and integration, enabling the seamless incorporation of diverse data types, including genomics, epigenomics, and other experimental datasets. 

Research Background

Liang earned his bioinformatics PhD from the University of Delaware, where his research focused on RNA-seq analysis, data visualization, and the development of web-based bioinformatics tools. Currently, Liang leads a bioinformatics team at Boston Children’s Hospital, providing critical support to researchers in addressing complex bioinformatics questions.

Selected Publications

  1. Sun, Liang, Qianyi Ma, Chunhui Cai, Maryam Labaf, Ashish Jain, Caroline Dias, Shira Rockowitz, and Piotr Sliz. "scDown: A Pipeline for Single-Cell RNA-Seq Downstream Analysis." International Journal of Molecular Sciences 26, no. 11 (2025): 5297.
  2. Qian, Xuyu, Kyle Coleman, Shunzhou Jiang, Andrea J. Kriz, Jack H. Marciano, Chunyu Luo, Liang Sun, et al. "Spatial transcriptomics reveals human cortical layer and area specification." Nature (2025): 1-11.
  3. Jain, Aakanksha, Benjamin M. Gyori, Sara Hakim, Ashish Jain, Liang Sun, Veselina Petrova, Shamsuddin A. Bhuiyan et al. "Nociceptor-immune interactomes reveal insult-specific immune signatures of pain." Nature Immunology 25, no. 7 (2024): 1296-1305.
  4. Leyva-Castillo, Juan Manuel*, Liang Sun*, Shih-Ying Wu*, Shira Rockowitz, Piotr Sliz, and Raif Geha. "Single cell transcriptome profile of mouse skin undergoing antigen driven allergic inflammation recapitulates findings in atopic dermatitis skin lesions." Journal of Allergy and Clinical Immunology (2022). (Co-first author).
  5. Liang Sun#, Yingbin Ge, Allen Spark, Zach Robinson, and Elison Blancaflor. "TDNAscan: A Software to Identify Complete and Truncated T-DNA Insertions." Frontiers in Genetics: Bioinformatics and Computational Biology Journal 10 (2019):685. ( # Corresponding author)
  6. Liang Sun#, Sufen Dong, Yingbin Ge, Jose Pedro Fonseca, Zach T. Robinson, Kirankumar S. Mysore, Perdeep Mehta. “DiVenn: an integrated web-based visualization tool for comparing gene lists” Frontiers in Genetics: Bioinformatics and Computational Biology Journal 10 (2019). ( # Corresponding author)
  7. Liang Sun, Upinder S. Gill, Raja Sekhar Nandety, Soonil Kwon, Perdeep Mehta, Rebecca Dickstein, Michael K. Udvardi, Kirankumar S. Mysore, Jiangqi Wen (2019). “Tnt1 insertion is positively correlated with gene methylation in Medicago truncatula” The Plant Journal.
  8. Liang Sun#, et al. "FNBtools: A Software to Identify Homozygous Lesions in Deletion Mutant Populations." Frontiers in Plant Science: Bioinformatics and Computational Biology 9 (2018): 976. ( # Corresponding author)
  9. Liang Sun et al. "WebGIVI: a web-based gene enrichment analysis and visualization tool." BMC Bioinformatics 18.1 (2017): 237.
  10. Liang Sun, Susan J. Lamont, Amanda M. Cooksey, Fiona McCarthy, Catalina O. Tudor, K. Vijay-Shanker, Rachael M. DeRita et al. "Transcriptome response to heat stress in a chicken hepatocellular carcinoma cell line." Cell Stress and Chaperones 20, no. 6 (2015): 939-950.

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