The Bioinformatics Core addresses the increasing demand for bioinformatics and clinical trial informatics from investigators at the Robert H. Lurie Cancer Center. The Bioinformatics Core works closely with the Genomics Core, the Proteomics Core, and the Biostatistics Core to ensure coordination of experimental and analytics through the different phases of a project.
To improve human health and reduce death and suffering from cancer through excellence in bioinformatics and medical informatics.
- To develop and maintain state of the art computational approaches in key fields such as cancer genomics, proteomics and clinical trials.
- To provide local expertise to the cancer research community and to coordinate broadly enabling technologies at Northwestern
Bioinformatics and Biomedical Informatics Infrastructure Development
- Pipeline for Next Generation Sequencing: high-performance computing on QUEST, including BWA, BLAT, Bowtie, and SAMtools
- Benchmarking and Method Validation: statistical prediction and prognostic tools for genomics data
- Software Development for Translational Cancer Genomics: Lumi (Illumina expression and methylation microarrays), MassSpectWavelet (proteomics) and GeneAnswers (pathways) packages in Bioconductor, and FunDO web service for translational genomics
- Software Development for clinical trial informatics: NOTIS, caBIGÂ®, caBIGÂ® Patient Study Calendar, life science focused web-database development, secure server management, data management and architecture design
- To provide NGS and microarray study design: ChIP-Seq, RNA-Seq, expression and methylation microarrays
- To collaborate on project data analysis and preparing manuscripts/grants: Illumina, 454 and SOLiD sequence analysis; Illumina and Affymetrix microarrays; methylation analysis; gene network and pathway analysis; meta-analysis of large-scale cancer profiles; transcription factor binding site analysis.
- To design and support clinical trial informatics tools: NOTIS, caBIGÂ®, caBIGÂ® Patient Study Calendar, Clinical informatics (Prostate, Ovarian, Breast), Disease Ontology (an NU initiative), Tissue Banking Informatics (caBIGÂ® tools, SAMPLE), Imaging data management, Life science focused web-database development, Secure server management, data management and architecture design services
In addition to general consulting on about 30 ongoing investigations per year, the Core participates in major national efforts in bioinformatics and genomics, such as the NCIâ€™s caBIG, TARGET, Bioconductor, CAMDA, MAQC, and SEQC. The Core coordinates its activities and directions closely with those of caBIG and NCI initiatives in integrative research. Recent five collaborative publications with the Cancer Center members include:
- ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics, 11(1):237, 2010
- The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nature Biotechnol, 28: 827-838, 2010.
- Annotating the human genome with Disease Ontology. BMC Genomics. Jul 7;10 Suppl 1:S6. 2009.
- Expression of cyclophilin B is associated with malignant progression and regulation of genes implicated in the pathogenesis of breast cancer. Am J Pathol. 174(1):297-308, 2009
- An integrated genome screen identifies the Wnt signaling pathway as a major target of WT1. Proc Natl Acad Sci USA. Jul 7;106(27):11154-9, 2009
- 200 Xeon core cluster â€“ configured to allow investigators to transition to the Quest cluster
- More than 40 file, application, and web servers and more than 100 virtual machines
- Manage and administer four domains with more than 200 users (total)
- Two multiprocessor Linux Oracle database servers -1.5 terabytes of disk storage each
- 200 terabytes of online storage
- Quantum LTO-3 16 tape autoloader, 400GB/tape
- BWA, BLAT, Bowtie, and SAMtools
Warren Kibbe, PhD
Simon Lin, MD
750 N Lake Shore Dr, Suite 1100
Chicago, IL 60611.