Silvia (Shuchang) Liu, Ph.D.

Assistant Professor

Department of Pathology

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

Github

Research Interests

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

Clustering, classification, bi-clustering, meta-analysis, omics data 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), whole genome sequencing (WGS), whole exome sequencing (WES), Chip-Seq, Oxford Nanopore sequencing, 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

Collaborations

I'm actively looking for Collaborations!

• Dr. Jianhua Luo, Department of Pathology, University of Pittsburgh
• Dr. George Machalopoulos, Department of Pathology, University of Pittsburgh
• Dr. Satdarshan (Paul) Monga, Department of Pathology, University of Pittsburgh
• Dr. George Tseng, Department of Biostatistics, University of Pittsburgh

Selected Publications

1. Silvia Liu^, Wei-Hsiang Tsai^, Ying Ding^, Rui Chen, Zhou Fang, SungHwan Kim, Tianzhou Ma, Ting-Yu Chang, Jianhua Luo, Hsei-Wei Wang*, I-Fang Chung* and George C. Tseng*. Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data. Nucleic Acids Research. 2016. (Link) (FusionMetaCaller: an R package to combine results of multiple top-performing fusion transcript detection algorithms from paired-end RNA-seq data) (PubMed ID: 26582927)


2. Yan P. Yu^, Silvia Liu^, Zhigang Huo, Amantha Martin, Joel B. Nelson, George C. Tseng and Jian-Hua Luo. Genomic copy number variations in the genomes of leukocytes predict prostate cancer clinical outcomes. PLoS ONE 2015 Aug 21; 10(8): e0135982. (Link) (PubMed ID: 26295840)


3. Jian-Hua Luo*, Silvia Liu, Ze-Hua Zuo, Rui Chen, George C. Tseng*, Yan P. Yu*. Discovery and Classification of Fusion Transcripts in Prostate Cancer and Normal Prostate Tissue. The American Journal of Pathology. Available online 9 May 2015, ISSN 0002-9440, http://dx.doi.org/10.1016/j.ajpath.2015.03.008.(Link) (PubMed ID: 25963990)


4. Lin Wang^, Silvia Liu^, Ying Ding, Shin-sheng Yuan , Yen-Yi Ho*, and George C. Tseng*. Meta-analytic framework for liquid association. Bioinformatics. (2017). (Link) (PubMed ID: 28334340)


5. Zhang-Hui Chen, …, Silvia Liu, …, Jian-Hua Luo*. Targeting genomic rearrangements in tumor cells using Cas9-mediated insertion of a suicide gene. Nature biotechnology, 35.6 (2017) 543-550. (Link) (PubMed ID: 28459452)