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

Contact Alexander Trouern-Trend (aj.trouerntrend@ufl.edu) for Genomics projects.

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

Contact Gogce Ceren Crynen, PhD, Scientific Director, (gogce@ufl.edu) for Proteomics/ MS projects.

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:

Contact Gogce Ceren Crynen, PhD, (gogce@ufl.edu) for Biostatistics projects.

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

How to cite us

Please consider core lab members for authorship for support such as:

Experimental design

Troubleshooting

Data analysis

Method development

Manuscript review and editing

Figure generation

Pipeline development

Alternatively, authors can include the core in methods or in acknowledgement section using the following text:

The analysis was performed at The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Bioinformatics and Statistics Core Facility (RRID:SCR_023048).

Contact

We are available via email and iLab. We are happy to discuss your project/question in person or through Zoom call. We accept projects from internal and external users (both not for profit and for-profit).

Personnel:

Gogce C Crynen

Shared Services Core / Bioinformatics and Statistics Core Director

Department: SR-BIOINFORMATICS

Email: gogce@ufl.edu

Grants:

• Apr 2023 – Apr 2023
  Preclinical Studies for the Therapeutic Development of a Novel Neuroprotectant for ALS
  US ARMY MED RES ACQUISITION · Co-Investigator

• Apr 2023 ACTIVE
  Next-Generation Biomedical Big Data Platform for Cancer Research and Collaboration Across Florida
  UNIV OF MIAMI · Principal Investigator

Education:

• 2006
  PhD, School of Forest Resources and Conservation
  University of Florida
• 2000
  MSc, Biological Sciences
  Middle East Technical University
• 1997
  BSc, Biological Sciences
  Middle East Technical University

Alexander Trouern-Trend

Bioinformatics Analyst III

Department: SR-BIOINFORMATICS

Email: aj.trouerntrend@ufl.edu

Please follow the link above and login to iLab to see the list of all the cores on our campus and the services we provide.