Office of the Vice Chancellor for Research
UNMC_Acronym_Vert_sm_4c
University of Nebraska Medical Center

Instruments and Services

Instruments


The Bioinformatics and System Biology Core offers services broadly, which fall into six categories: 1) next generation sequencing data analyses, 2) systems biology data services, 3) web applications and databases, 4) machine learning and research computing, 5) grant and publication support and consultation, and 6) other bioinformatics related support. We have equipped with powerful servers, large data storage spaces, and the state-of-the-art analysis tools to support our services.  

Description of primary instruments 

Our servers and storage infrastructure are illustrated as follows. We also have powerful state-of-the-art analysis software tools: Ingenuity Pathway Analysis, CLC Genomics Workbench, Schrödinger, GROMACS, BioCyc, CASSAVA, Partek, MATLAB, GraphPad Prism, SnapGene, R packages, next generation sequencing analysis tools: Tuxedo Suite, bcbio-nextgen, Nextflow, etc.

Services

NGS (Next-Generation Sequencing) Data Analyses 

  • RNAseq and miRNAseq 
  • Exome and whole genome seq; chip-seq; proteomics 
  • Single-cell seq and single-cell ATAC-seq 
  • DNA methylation sequencing
  • Metagenomics sequencing
  • De novo assembly and annotation 
  • Genome Wide Association Studies and PLINK analysis 
  • Alternative splicing analysis for RNAseq 
  • Cell free DNA analysis to identify tumor purity 
  • Nucleotide percentages in open reading frames; genomic ribosome binding sites identification 

System Biology Data Services 

  • Ingenuity Pathway Analysis and gene pathway and network analyses 
  • Functional analysis of gene sets using GSEA, DAVID, ClueGO, KEGG, etc. 
  • Copy-number variation analysis for CGH arrays; DNA methylation arrays 
  • Survival analysis and plotting, volcano, heatmap, and Venn diagram plotting 
  • TCGA ‘Omics’ data analyses and NCBI/GEO array data analysis 
  • Oncomine and cBioPortal data analyses 
  • Single-nucleotide polymorphisms association analysis for single-nucleotide polymorphisms array 
  • Metabolomic pathway and integrated pathway analysis 
  • miRNAseq target gene pathway; lncRNAs targeting gene promoters and mRNA 

Web Applications and Databases

  • Development of web sites and web applications to publish research data 
  • Development of searchable relational databases for complex research data 

Machine Learning and Research Computing 

  • Clustering and modeling experimental data using machine learning 
  • Development of custom programs to analyze complex data 
  • Motifs/pattern discovery from large datasets 

Grant and Publication Support and Consultation 

  • Pre-grant consultation, support letters, collaborations 
  • Consultation on the next generation sequencing/bioinformatics experimental design and budget quotes 
  • Generate figures to represent high-dimensional data 
  • Consultation on Data Management and Sharing Plans 

 

Other Bioinformatic Related Support 

  • Sharing data via file transfer protocol, depositing data into SRA/GEO/NCBI resources, setting custom packages like local BLAST, Galaxy or other servers.