To investigators grappling with next-generation / whole-genome sequencing projects, we offer services spanning from experimental design, consultation, data processing and analysis, including the following services.
We have extensive experience in the analysis of RNA sequences (RNA-seq) and the identification of differentially expressed genes. Our typical RNA-seq workflow will includes quality control and cleaning of input sequence data, alignment to the reference genome and genes of the organism, quantification of transcript abundances, and statistical testing for genes with significant differences in expression between conditions.
De Novo Transcriptome Assembly
Next-generation sequencing, and the rapid production of large volumes of sequence data thereof, has extended the promise of whole-transcriptome reconstruction to investigators of non-model organisms, albeit with significant computational challenges. We aim to meet those challenges and offer de novo transcriptome assembly services which incorporate quality control, error correction, Trinity and additional cutting-edge assembly algorithms, assembly evaluation, filtration, and protein annotation.
Core personnel have developed a resequencing toolkit to study whole genomic and/or targeted sequence-identification of variations in individuals and within populations, to identify novel mutations, single nucleotide polymorphisms (SNPs), indels, and structural variations for applications including Genotyping-by-sequencing and direct forward genetic mapping-by-sequencing. This toolkit includes GATK, FreeBayes, Bcftools, Picard, SHOREmap and MAQGene software. Resequencing data are analyzed via SAMtools and GATK, and tailored to sequencing platform and application to provide robust, reproducible and meaningful identification of sequence variations.
Genome-Wide Association Studies
Services include the design and analysis of genome wide association studies (GWAS). The Core has developed streamlined analytic pipelines for SNP association studies, whose data are analyzed biostatistically, processed bioinformatically, and interpreted respective to phenotypic and clinical metrics. We support clinical and translational research via GWAS in disease association studies.
Microarray Data Services
We employ several proven approaches to analyzing experimental data from microarray experiments, with targeted quality control, robust normalization techniques, and whole-genome data mining. Supported platforms include Affymetrix, Nimblegen, Illumina Bead Arrays, and more.
The Nevada Bioinformatics Core provides biostatistical tools for university investigators to fulfill their clinical, genomic, proteomic and other research including experimental design, data quality control protocols, power studies, standard hypothesis tests to examine differences in cohort measures or gene expression values, regression, clustering, and other standard statistical methods.
Network analysis is used in systems biology to identify putative functional gene groupings. Gene co-expression network analysis has found many uses in the life sciences; for example, the identification of functional gene groupings in plants under stress conditions, or the identification of molecular targets for future targeted gene therapies. The Bioinformatics Core has developed mathematically robust and statistically meaningful network analysis methods to generate and interrogate networks from whole-genome datasets.
The Center makes available services and access to high-end computational servers pre-configured with bioinformatics tools. See the facilities description for technical specifications.
Systems Administration and Support
Have our experienced systems staff help make your projects successful. With expertise ranging from cluster design to software engineering, we can help research, design, develop, provision, manage, secure and service your systems.
Project Consultation & Pre-proposal Support
We gladly provide investigators biostatistical, bioinformatic, and sequencing consultation services to guide researchers towards the effective design, execution, and analysis of their studies and research questions. We further offer support to researchers at the pre-proposal phase to help researchers win competitive grant funding.
Teaching and Training
We perform workshops, seminars, and personal training sessions for our investigators, for students, and for our collaborative undergraduate institutions. Past workshops have covered topics such as: BLAST, sequence assembly, and sequence analysis with functional annotation.