Silvia

Silvia (Shuchang) Liu, Ph.D.

Assistant Professor

Organ Pathobiology and Therapeutics Institute

Department of Pharmacology and Chemical Biology

Pittsburgh Liver Research Center

School of Medicine

University of Pittsburgh


Contact Me:

Email: shl96@pitt.edu

Phone: 412-648-4288

Office: S-406 Biomedical Science Tower, 203 Lothrop Street, Pittsburgh, PA 15261


External Link:

My CV

Linkedin

Google Scholar

Research Interests


I. Bulk and single-cell long-read RNA-seq analysis:

LongRead
    We developed computational tool IFDlong, an isoform and fusion detector for accurate annotation and quantification of long-read RNA-seq data. The long-read analysis pipelines were applied to both colon and liver cancer samples.

Publications:

  1. Wang W, Li Y, Ko S, Feng N, Zhang M, Liu JJ, Zheng S, Ren B, Yu YP, Luo JH, Tseng GC, Liu S*. IFDlong: an isoform and fusion detector for accurate annotation and quantification of long-read RNA-seq data. bioRxiv. 2024 May 14:2024.05.11.593690. (PMID: 38798496)

  2. Liu S*, Yu YP, Ren BG, Ben-Yehezkel T, Obert C, Smith M, Wang W, Ostrowska A, Soto-Gutierrez A, Luo JH*. Long-read single-cell sequencing reveals expressions of hypermutation clusters of isoforms in human liver cancer cells. Elife. 2024 Jan 11;12:RP87607. (PMID: 38206124)

  3. Liu S, Wu I, Yu YP, Balamotis M, Ren B, Ben Yehezkel T, Luo JH. Targeted transcriptome analysis using synthetic long read sequencing uncovers isoform reprograming in the progression of colon cancer. Commun Biol. 2021 Apr 27;4(1):506. (PMID: 33907296)

  4. Liu S*, Obert C, Yu YP, Zhao J, Ren BG, Liu JJ, Wiseman K, Krajacich BJ, Wang W, Metcalfe K, Smith M, Ben-Yehezkel T, Luo JH*. Utility analyses of AVITI sequencing chemistry. BMC Genomics. 2024 Aug 10;25(1):778. (PMID: 39127634)



II. Multi-omics integration:

spatial
    We are interesting in the single-cell and spatial transcriptomics data analysis. In addition, we are working on the bulk and single-cell multi-omics integration and communications analysis.

Publications:

  1. Hu S, Liu S, Bian Y, Poddar M, Singh S, Cao C, McGaughey J, Bell A, Blazer LL, Adams JJ, Sidhu SS, Angers S, Monga SP. Single-cell spatial transcriptomics reveals a dynamic control of metabolic zonation and liver regeneration by endothelial cell Wnt2 and Wnt9b. Cell Rep Med. 2022 Oct 18;3(10):100754. (PMID: 36220068)

  2. Mooring M, Yeung GA, Luukkonen P, Liu S, Akbar MW, Zhang GJ, Balogun O, Yu X, Mo R, Nejak-Bowen K, Poyurovsky MV, Booth CJ, Konnikova L, Shulman GI, Yimlamai D. Hepatocyte CYR61 polarizes profibrotic macrophages to orchestrate NASH fibrosis. Sci Transl Med. 2023 Sep 27;15(715):eade3157. (PMID: 37756381)

  3. Wang L^, Liu S^, Ding Y, Yuan SS, Ho YY, Tseng GC. Meta-analytic framework for liquid association. Bioinformatics. 2017 Jul 15;33(14):2140-2147. (PMID: 28334340)

  4. Huo Z, Ding Y, Liu S, Oesterreich S, Tseng G. Meta-analytic framework for sparse K-means to identify disease subtypes in multiple transcriptomic studies. J Am Stat Assoc. 2016;111(513):27-42. PMID: 27330233)



III. Collaborative works:

interaction
    We are currently working on diverse collaborative works, including computational analysis on DNA-seq, RNA-seq, ATAC-seq, single-cell RNA-seq, proteomics, metabolomics, and cytometry data.

    We are actively looking for collaborations!

Publications:

  1. Liu P^, Liu S^, Fang Y, Xue X, Zou J, Tseng G, Konnikova L. Recent Advances in Computer-Assisted Algorithms for Cell Subtype Identification of Cytometry Data. Front Cell Dev Biol. 2020 Apr 28;8:234. (PMID: 32411698)

  2. Liu S, Gui Y, Wang MS, Zhang L, Xu T, Pan Y, Zhang K, Yu Y, Xiao L, Qiao Y, Bonin C, Hargis G, Huan T, Yu Y, Tao J, Zhang R, Kreutzer DL, Zhou Y, Tian XJ, Wang Y, Fu H, An X, Liu S*, Zhou D*. Serum integrative omics reveals the landscape of human diabetic kidney disease. Mol Metab. 2021 Dec;54:101367. (PMID: 34737094)

  3. Velazquez JJ, LeGraw R, Moghadam F, Tan Y, Kilbourne J, Maggiore JC, Hislop J, Liu S, Cats D, Chuva de Sousa Lopes SM, Plaisier C, Cahan P, Kiani S, Ebrahimkhani MR. Gene Regulatory Network Analysis and Engineering Directs Development and Vascularization of Multilineage Human Liver Organoids. Cell Syst. 2021 Jan 20;12(1):41-55.e11. (PMID: 33290741)

  4. Fu H, Liu S, Bastacky SI, Wang X, Tian XJ, Zhou D. Diabetic kidney diseases revisited: A new perspective for a new era. Mol Metab. 2019 Dec;30:250-263. (PMID: 31767176)

  5. Gui Y, Wang Y, Palanza Z, Wang JL, Gupta P, Tao J, Qiao Y, Hargis G, Kreutzer DL, Bastacky SI, Yu Y, Wang Y, Liu S, Fu H, Zhou D. Calponin 2 harnesses metabolic reprogramming to determine kidney fibrosis. Mol Metab. 2023 May;71:101712. (PMID: 36963615)

  6. Liu S, Zahorchak AF, Dobrowolski SF, Metes DM, Thomson AW, Abdelsamed HA. Epigenetic signature of human vitamin D3 and IL-10 conditioned regulatory DCs. Sci Rep. 2024 Nov 20;14(1):28748. (PMID: 39567586)

Last Modified: 02/2025