services EQUIPMENT

BIOINFORMATICS

Thank you for using KIDDRC Core Services. Please acknowledge the Smith Intellectual and Developmental Disabilities Research Center (NIH U54 HD 090216 ) at the University of Kansas Medical Center, Kansas City, KS 66160 in future publications.

core staff

Hardware

Linux x86 64 Cluster • 3 nodes with 8-core and 48GB memory eachLinux x86 64 servers • 12-core with 72GB memory • 24-core with 128GB memory • 12-core with 144GB memoryWindows Workstations40TB Data Storage

Software

We use a number of open-source software packages such as R for data pro-cessing and analysis. Licenses of proprietary software are as follows.

Matlab • Bioinformatics Toolbox • Computer Vision System Toolbox • Curve Fitting Toolbox • DSP System Toolbox • Fixed-Point Toolbox • Image Processing Toolbox • Neural Network Toolbox • Optimization Toolbox • Parallel Computing Toolbox • Signal Processing Toolbox • SimBiology • Statistics Toolbox • Wavelet ToolboxPartek Genomics SuiteAcumenta The Literature LabTMIngenuity IPAIBM SPSSCLC Genomics Workbench

We provide a variety of services in bioinformatics and computational biology. Some of these services are listed below. Please feel free to contact the Bioinformatics Core for more information on these services. The Bioinformatics Core will also be happy to discuss with you the feasibility of supporting customer applications speci�c to your research.

High-throughput sequencing:RNA-Seq: provides an unbiased deep coverage and base level resolution of the whole transcriptome. Has a low background signal and does not have an upper limit of quanti�cation.Chip-Seq: combines chromatin immunoprecipitation with high-throughput sequencing to provide an unbiased whole genome mapping of the binding sites of DNA-associated proteins.Whole Genome Sequencing: sequences the whole DNA sequence of an organism's genome.De novo Sequencing: provides the primary genetic sequence of an organism.Metagenomic Sequencing: sequencing and identifying the genomes ofwhole microbial communities.Methyl-Seq: analysis of methylation patterns on a genome wide scale.

Microarray analysis:A�ymetrix 3' Expression Arrays: target the 3' end of genes.A�ymetrix Exon Arrays: provides expression levels for every known exon in the genome.A�ymetrix miRMA Arrays: provides measurements of small non-coding RNA transcripts involved in gene regulation.A�ymetrix Genome-Wide Human SNP Array: copy number analysisA�ymetrix GeneChip Tiling Arrays: gene regulation analysis

Biological Functional and Pathway Analysis: we have software from Ingenuity Systems (IPA) that can analyze your expression data to ascertain the top biological functions and pathways associated with them.

Biological Literature Survey: we have software from Acumenta (Literature Lab) that helps perform data mining tasks on experimentally derived gene lists.

miRNA target prediction: we use in house software and open source software such as TargetScan, miRanda for detecting genomic targets for miRNAs.

Transcription Factor Binding Site Prediction: we use in house software and open source software such as MEME, Homer, PGMotifScan to identify protein DNA interaction sites.

Genomics TGIF

Model Development

Intergrative Imaging GenomicsBio-informaticsBehavioral metabolic phenotyping

Model Characterization

Hema Pappu, M.S.Software Engineer2146 West 39th AvenueHemenway Bldg 64, Room 2062Kansas City, Kansas 66160Phone: (913) 588-5966Fax: (913) 588-5677hpappu@kumc.edu

Sumedha Gunewardena, D.Phil.Bioinformatics SpecialistResearch Assistant Professor, Molecular and Integrative Physiology2146 West 39th AvenueHemenway Bldg 64, Room 2027Kansas City, Kansas 66160Phone: (913) 945-6878Fax: (913) 588-5677sgunewardena@kumc.edu

Jennifer Knapp, Ph.D.Bioinformatics Specialist2146 West 39th AvenueHemenway Bldg 64, Room 2025Kansas City, Kansas 66160Phone: (913) 588-7266Fax: (913) 588-5677jknapp5@kumc.edu

KIDDRC MODEL DEVELOPMENT PIPELiNe