Computational Biology and Bioinformatics Services and Consultations

  • Analysis of next generation sequencing data including whole exome-sequencing, RNA-sequencing, smRNA-sequencing, ChIP-sequencing, ATAC-sequencing and whole genome re-sequencing.
  • Analysis of long read sequencing (such as PacBio and Oxford Nanopore Sequencing) including QC and error correction of long reads, gene/gene isoform expression, novel gene discovery and full length isoform identification, de novo fusion gene detection and corresponding fusion isoform expression profiles, allele-specific expression and haplotyping, de novo genome assembly, de novo transcriptome assembly, methylation calling, nucleosome positioning and chromatin accessibility.
  • Single-cell RNA-seq data analysis services:
    • Basic scRNA-seq data analyses, including quality control, alignment, trimming, assembly, differentiation expression, and clustering, using developed pipelines
    • Advanced scRNA-seq data analyses, including but not limited to cell trajectory discovery, cell type prediction, co-regulated gene module identification
    • Selective scRNA-seq analyses in aim to solving specific issues such as drop-out issue, immense expression data (i.e., 10X scRNA-seq data)
    • Result interpretation and interpretation
    • An all-in-one user-friendly web server for scRNA-seq analysis
    • Integrative analysis of single-cell multi-omics data to enhance the effectiveness and efficiency
  • Metagenomic data analysis services:
    • Metagenomic data analysis including species/strain composition profiling, taxonomic analysis, abundance analysis, phylogenetic analysis, whole-genome shotgun analysis
    • Metatranscriptomic data analysis including functional profiling, expression activity analysis,16S ribosomal RNA analysis, whole-transcriptome shotgun analysis
    • Advanced joint metagenomic and metatranscriptomics data analysis for more accurate gene-level, species-level, and strain-level analysis
    • Network studies in microbiome and host–microbiota interactions based on high-throughput multi-omics data
    • Causality study between human microbiota and diseases
    • Existing tools/pipelines recommendation, analysist training and guidance
  • Analysis of microarray datasets, including mRNA (Affymetrix), SNP, and micro-RNA.
  • Analysis of nCounter NanoString data.
  • Proteomics data analysis:
    • Protein/peptide identification and quantification from label-free and label-based tandem mass spectrometry data
    • Post-translational modification analysis (PTM), such as phosphorylation
    • Downstream bioinformatics analysis, such as: differential expression analysis, pathway analysis and functional enrichment, analysis, network analysis, involving finding pivotal proteins in the networks
  • Metabolomics data analysis:
    • LC-MS data preprocessing (including quality control assessment of raw chromatograms, peak calling, retention time alignment, and preliminary identification using MS2 data if available)
    • Interpretation of liquid-chromatography untargeted metabolomics datasets, which include relative abundances of a broad spectrum of polar and non-polar small molecules (< 1500 Daltons)
    • Statistical analysis to identify biologically-relevant metabolites
    • Pathway enrichment analysis of relevant metabolites
  • Integrative analysis of publicly available datasets (dbGaP, GEO, TCGA) using search parameters defined by the OSUCCC researchers.
  • Pathway analysis of results from sequencing and microarray data.
  • Custom bio-molecular data management, application development, deployment and support.
  • CRISPR Screening:
    • Experimental Design
    • Cancer-specific essential genes
    • Synthetic lethal partners
    • Drug resistance mechanism
  • Precision cancer medicine services:
    • Integrating gene expression profiles, mutations and phenotype features to predict target, drug and biomarker in precision cancer medicine
    • Identification of potential druggable targets
    • Assessment of efficacy drugs and associated biomarkers

Training and Workshops: BISR faculty and staff offer short 1-2 day workshops and seminars addressing bioinformatics questions and needs of OSU researches. The workshops contain hands-on activities, to help OSU researchers to understand the process of data analysis and the interpretation of the results.

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