Bioinformatics and Statistics

bioinformatics and statistics

We love data

The Bioinformatics and Statistics Core provides data management and analysis services for The Wertheim UF Scripps Institute community as well as for external collaborators. We offer scientific support to assist in the collection, analysis, integration and dissemination of biomedical data and knowledge. Projects will often vary in time and cost depending on the scientific goals of the work, and the desired level of detail. Our goal is to use existing software and tools developed by the group, along with open source software, to support your science in a cost-effective manner.

Genomic Analysis

The Genomics and Biostatistics focus area centers primarily around Next-Generation Sequencing (NGS) and RNA Microarrays. Additionally, statistical data analysis on primary data and downstream functional analyses are available.

NGS and microarray data analysis services:

• RNA-Seq and microRNA-Seq data analyses including differential expression and gene co-expression analysis
• Analysis of targeted sequencing (ChIPseq, ATACseq, Exon Capture, etc.)
• Gene expression analysis of in-house and published microarray datasets (Affymetrix, Illumina, etc.)
• Custom Bioinformatics workflows for NGS applications (RNA-Seq, ChIP-Seq, microRNA-Seq)
• De novo genome/transcriptome assembly (in the absence of a reference genome)
• Integration and application of published and popular algorithms and tools
• Multiple genome browser support for visualization of NGS results
• Development and integration of data analysis and visualization tools, including leveraging of R and Python
• Establishing and maintaining customized genomic databases
• Statistical support and consultation including providing advice on various aspects of statistical design and analysis
• Support grant applications with experimental design recommendations and power/sample analysis

Downstream analysis services:

• Pathway and gene ontology analysis
• Classification/clustering analysis
• Gene annotation
• Data visualization
• Promoter analysis
• Preparation of figures for publications

Personnel:

Proteomic analysis

The Proteomics Focus Area provides expertise in analyzing and interpreting data generated by mass spectrometry experiments.

Services provided:

• Experimental design for quantitative proteomics experiments such as TMT based
• Data analysis of quantitative proteomics experiments such as SILAC, TMT, etc.
• Label-free differential expression analysis
• Discovery of unexpected amino acid point mutations
• Interrogation of protein-protein or protein ligand interactions via hydrogen deuterium exchange
• PTM detection and analysis
• Protein sequencing
• Peptide mass fingerprinting
• Detection of labile PTMS and low abundance peptides

We have experience and publications in:

• Integration of proteomics and genomics data
• Mass spectrometry calibration software
• MS1 data analysis
• Proteomics pipeline development and integration
• Development of proteomic algorithms and protocols
• Automated analysis of HD exchange MS data

Personnel:

Gogce Ceren Crynen, PhD, Scientific Director, Publications

Biostatistics

The biostatistics focus area centers primarily around developing and applying statistical methods to a wide range of topics in biological research, and downstream analysis of genomics and proteomics data. Biostatistical services have become increasingly important in the biosciences, one example of which is the updated  standards of Rigor and Reproducibility from the NIH.

We encourage all investigators to consider working with our biostatistics group members on experimental design, letters of support and grant submissions.

Biostatistics analysis services include:

• Pathway and gene ontology analysis
• Classification/clustering analysis
• Gene annotation
• Generalized and/or linear mixed models
• Statistical graphics and programming
• Multivariate analysis
• Population genetics
• Quantitative genetics
• Data visualization
• Promoter analysis
• Preparation of figures for publications
• Statistical support and consultation including providing advice on various aspects of statistical design and analysis
• Support grant applications with experimental design recommendations and power/sample analysis

Personnel:

Gogce Ceren Crynen, PhD, Scientific Director, Publications

Custom software development

The Bioinformatics Core has experience developing software for custom applications, including machine learning, data mining in python and interactive data exploration using RShiny. We are happy to discuss the needs of your project to collaboratively generate solutions. Many problems can become more tractable by utilizing simple software tools.

Personnel:

Alexander Trouern-Trend, MSc, Bioinformatics Analyst, Publications