Genomics and Systems Biology Core

 

  

Directors: Jianhua Luo, MD, PhD and Takis Benos, PhD; Associate Directors:  Yanping Yu, MD, PhD and Maria Chikina, PhD; Core Manager: Silvia (Shuchang) Liu, PhD

Based on your needs, please contact Dr. Luo or Dr. Benos for services.


Expertise of Dr. Jianhua Luo's group:

We have extensive experience in human and mouse genomics. Since 1999, we have established the first genome center in Western Pennsylvania, and have provided numerous collaborations and services across the academic community in Pittsburgh area. Our center offers a wide array of collaborations in the study of human and mouse genomics utilizing Illumina, Affymetrix and Oxford nanopore platforms. Some of the strongest areas in our expertise include whole-genome methylation sequencing, transcriptome sequencing, whole-genome sequencing, single-cell transcriptome sequencing, CNV analysis and sequencing validation. 
 
In addition, we offer bio-informatic and biostatistical collaboration on the data generated from our center or outside sources. For machine learning and statistics, we offer expertise in 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. For Next-Generation Sequencing (NGS) and Long-read Sequencing data analysis, we offer bioinformatics expertise in analyzing 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. 
 
We also offer consultation and expertise of validating biomarker in genomics, epigenomics and protein levels for the discovery of drug targets. 
 
 

Expertise of Dr. Takis Benos's group:

Dr. Takis Benos is a Professor and Vice Chair in the Department of Computational and Systems Biology.  He has >20 years experience in genomics and systems biology and has developed many widely used algorithms for analysis of various types of genomic data.  Since 2012 his group has focused on the development of machine learning methods for high level, integrated analysis of data at different scales.  His causal learning algorithms have been used to analyze clinical, radiographic, microbiome, SNP and omics data on research applications in cancer, COPD, pulmonary fibrosis and pulmonary ICU patients.  Dr. Benos works closely with Dr. Maria Chikina, Assistant Professor, Department of Computational and Systems Biology, who is an expert in RNA-seq, scRNA-seq and genotype data analysis.
 
Services offered by the systems biology group: We offer support to PLRC researchers for analysis of multiple omics data (including differential gene expression and pathway analysis on RNA-seq; cell population changes, gene expression changes and pathways on scRNA-seq data), analysis of microbiome data, biomarker identification for clinical or biomedical outcomes, disease subclassification, modeling of disease progression, and integrative causal modeling of data from different scales (e.g., RNA-seq, lab tests and clinical variables). Our methods can identify the factors that are causally linked to an outcome or to disease progression. For more information and examples of our research and expertise please visit our lab sites below:

Available Services

 
Genomics services
  • U133 2.0 array 
  • R230 2.0 array 
  • R430 2.0 array 
  • CLARIOM array 
  • SNP 6.0 array 
  • CytoscanHD 
  • OncoScan array 
  • Human exon 1.0 ST array 
  • Expression arrays for porcine, bovine, drosophila, etc. 

Illumina sequencing

  • Library ready sequencing
  • Library prep from raw sample or RNA
  • Library prep for whole genome from raw sample or DNA
  • Library prep for exome from raw sample or DNA
  • Library prep for methylation from raw sample or DNA
  • Library prep for single cell sequencing with individual molecule barcoded
Oxford Nanopore long-read sequencing
  • Whole genome sequencing for de novo assembly, structural variation, single nucleotide variation and resequencing analyses
  • Transcriptome sequencing for RNA isofrom and fusion transcript analyses using direct RNA sequencing and ligation sequencing
  • Targeted sequencing include amplicons, sequence capture and exome
  • Epigenetic sequencing including methylation, histone modification and non-coding RNA activity
  • Microbiome sequencing
10X Genomics single cell sequencing
  • Our center is equipped with ControllerTM from 10x Genomics, Inc. We provide collaboration on the analysis of 3’ barcoded and 5’ barcoded single-cell transcriptome sequencing to classify cell type on individual cell level. We also provide exome, copy number and ATAC sequencing for the chromosome structure analysis, all on the single-cell level. Single-cell classification provides high-resolution analysis on cell population. It is a new tool that enables us to understand organ development, cancer evolution and immune cell activation in individual cell level.  
Data analysis - GBSC provides expertise for standard omics analysis and advanced multi-scale modeling.  

Basic analysis services include:

  • RNA-seq and microarray gene expression
  • Single cell RNA-seq
  • microRNA expression
  • Pathway enrichment analysis
  • Methylation
  • Microbiome
Advanced modeling includes:
  • Multi-scale causal modeling (omics and clinical data)
  • Predictive modeling / machine learning
  • Biomarker identification