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

High throughput genomic data analysis by machine learning and statistical methods:

Multi-omics integration, clustering, classification, bi-clustering, meta-analysis, linear models, regression, probability theory, gene regulation, data preprocessing, feature selection, dimension reduction, biomarker detection, pathway analysis, differential expression analysis, microarray (mRNA, SNP, etc) data analysis, clinical/survival data analysis

Next Generation Sequencing (NGS) and Long-read Sequencing data analysis:

Transcriptome sequencing (RNA-Seq), single-cell RNA sequencing (scRNA-seq), whole genome sequencing (WGS), whole exome sequencing (WES), whole genome bisulfite sequencing (WGBS), Chip-Seq, ATAC-seq, Cut&Run seq, long-read sequencing, single-cell RNA-seq (scRNA-seq), spatial transcriptomics (ST), quality control (QC), trimming, alignment, fusion gene detection, gene expression, structural variation (SV) detection, copy number variation (CNV) analysis, SNP calling, peak calling, long-read sequencing (third-generation) analysis


Education

  • B.S. – Shanghai Jiao Tong University, 2008-2012
  • Ph.D. – University of Pittsburgh, 2012-2017
  • Postdoc – The Jackson Laboratory, 2017-2018

Selected Grant Support

  • NIH NIGMS R35GM159862; Role: PI; Advanced computational approaches for single-cell multi-omics integration; 8/2025 - 7/2030
  • Fund for Innovation in Cancer Informatics (ICI); Role: MPI; Discovery and validation of cancer therapeutic targets through the single-cell long-read RNA-seq analysis; 1/1/2024-12/31/2025
  • NIH NIDDK P30DK120531; Role: Co-I (PI: Paul Monga); Pittsburgh Liver Research Center: Genomics and Systems Biology Core; 05/01/2024 -03/31/2029
  • Competitive Medical Research Fund- University of Pittsburgh; Role: PI; Identifying isoform-specific cancer therapeutic targets through the long-read RNA-seq analysis; 7/1/2024-6/30/2026
  • NIH NCI R01CA300059; Role: Co-I (PI: Sungjin Ko); Deciphering the Molecular Mechanisms Underlying Cholangiocarcinoma Development; 04/2025 - 03/2030
  • NIH R01AR082386; Role: Co-I (PI: Hang Lin); Defining the unique capacity of the miniature joint model for investigating the role of adipose tissue and its impacts on osteoarthritis; 05/2024-04/2029

Selected Publications

Advanced computational approaches

  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 P, Pan Y, Chang HC, ..., Tseng GC*, Konnikova L*, Liu S*. Comprehensive evaluation and practical guideline of gating methods for high-dimensional cytometry data: manual gating, unsupervised clustering, and auto-gating. bioRxiv. 2024:2024-08. Brifings in Bioinformatics. 2024 Nov 22;26(1):bbae633. (PMID: 39656848.)

  3. 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)

  4. 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)

  5. Liu S, Nalesnik MA, Singhi A, Wood-Trageser MA, Randhawa P, Ren BG, Humar A, Liu P, Yu YP, Tseng GC, Michalopoulos G, Luo JH. Transcriptome and Exome Analyses of Hepatocellular Carcinoma Reveal Patterns to Predict Cancer Recurrence in Liver Transplant Patients. Hepatol Commun. 2022 Apr;6(4):710-727. (PMID: 33907296)

  6. Liu S, Tsai WH, Ding Y, Chen R, Fang Z, Huo Z, Kim S, Ma T, Chang TY, Priedigkeit NM, Lee AV, Luo J, Wang HW, Chung IF, Tseng GC. Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in pairedend RNA-seq data. Nucleic Acids Res. 2016 Mar 18;44(5):e47. doi: 10.1093/nar/gkv1234. Epub 2015 Nov 17. (PMID: 26582927)

Collaborative projects

  1. Sugimoto A, ..., Liu S, ..., Schwabe RF*. Hepatic stellate cells control liver zonation, size and functions via R-spondin 3. Nature. 2025 Mar 12. (PMID: 40074890)

  2. Lehrich BM, ..., Liu S, ..., Monga SP*. Precision targeting of β-catenin induces tumor reprogramming and immunity in hepatocellular cancers. Nat Commun. 2025 May 30;16(1):5009. (PMID: 40442146)

  3. Dion W, ..., Liu S, ..., Zhu B*. SON-dependent nuclear speckle rehabilitation alleviates proteinopathies. Nat Commun. 2025 Aug 5;16(1):7065. (PMID: 40764481)

  4. 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)

  5. Tao J, Krutsenko Y, Moghe A, Singh S, Poddar M, Bell A, Oertel M, Singhi AD, Geller D, Chen X, Lujambio A, Liu S*, Monga SP*. Nuclear factor erythroid 2-related factor 2 and β-Catenin Coactivation in Hepatocellular Cancer: Biological and Therapeutic Implications. Hepatology. 2021 Aug;74(2):741-759. (PMID: 33529367)

  6. 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)

  7. Chen ZH, Yu YP, Zuo ZH, Nelson JB, Michalopoulos GK, Monga S, Liu S, Tseng G, Luo JH. Targeting genomic rearrangements in tumor cells through Cas9-mediated insertion of a suicide gene. Nat Biotechnol. 2017 Jun;35(6):543-550. (PMID: 28459452)

Last Modified: 10/2025