Bioinformatics

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Overview

The Bioinformatics core offers bioinformatics consulting and data analysis services to help researchers analyze and understand the large data sets acquired from next generation sequencing and array-based technologies. We coordinate closely with other ICBR cores (Next-Gen Sequencing, Gene Expression, Cytometry, and Proteomics) on shared projects. 

We collaborate with researchers in designing experiments and analyzing complex datasets by applying various data-analytical and theoretical methods, mathematical modeling and computational techniques.  We develop and operate comprehensive pipelines enabling large-scale data processing, including NGS data analysis (e.g., RNA-Seq, DNA-Seq, methyl-Seq and ChIP-Seq,) single-cell analysistranscriptome and genome annotation (project-based EST/genomic sequence assembly, annotation and gene prediction,) microarray-based data analysis (statistical and functional data analysis from major microarray platforms,) variant detection and metagenomics (characterization of microbial communities.)

Bioinformatics staff members have extensive experience in bioinformatics, genomics, transcriptomics and translational informatics in plant, animal and microbial systems. Our expertise includes big data analysis, statistical analysis, software development and high-performance computing. We strive to be scientific collaborators – rather than just service providers – using our expertise and skills to ensure the success of your projects.

Our services are offered at a standard hourly rate, and can be accessed on a fee-for-service basis or as long-term collaborations.

Core News

The Beast is Here!  ICBR Launches the NovaSeq 6000 DNA Sequencer The Beast is Here! ICBR Launches the NovaSeq 6000 DNA Sequencer
The Beast is Here! ICBR Launches the NovaSeq 6000 DNA Sequencer
Dr. Steven Madore, ICBR Associate Director for Science and UFHCC Associate Director for Shared Resources, next to the new NovaSeq6000 (“the Beast“) with ICBR NGS Core Scientific Director Dr. David Moraga. The ICBR NextGen DNA Sequencing Core provides cutting edge instrumentation and technical expertise required to support campus-wide research activites. Established in 1987, the NGS Core has contributed to significant scientific discoveries on campus. For example, did you know that the first...
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The Beast is Here!  ICBR Launches the NovaSeq 6000 DNA Sequencer
Introducing Core Directors’ Open Consultation Meetings Introducing Core Directors’ Open Consultation Meetings
Introducing Core Directors' Open Consultation Meetings
In a continued effort to provide accessible and specialized expertise to our users, UF ICBR is proud to announce our Core Directors’ Open Consultation Meetings. Each month we will be available for a two hour walk-in session to discuss the best approaches and strategies for using ICBR technologies and expertise to drive your research forward. Our first meeting will be on Monday, October 7th from 11:00am to 1:00pm in CGRC 189. No appointment is require nor do you have to be a current ICBR user t...
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Introducing Core Directors’ Open Consultation Meetings
ICBR Bioinformatics Contributes to Landmark UFHCC Publication ICBR Bioinformatics Contributes to Landmark UFHCC Publication
ICBR Bioinformatics Contributes to Landmark UFHCC Publication
The ICBR Bioinformatics Core contributed to a high-profile paper from the cancer research laboratory of UFHCC Director Dr. Jonathan Licht, recently published in Cancer Discovery. The paper, entitled “A Mutation in Histone H2B Represents a New Class of Oncogenic Driver”, describes how mutations in core histones disrupt nucleosome stability, leading to disregulation of gene expression and acting as a novel oncogenic mechanism. As part of this study the investigators used a technique ca...
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ICBR Bioinformatics Contributes to Landmark UFHCC Publication
ICBR Bioinformatics contributed to a study on Gestational Hypoxia-Induced Cardiac Anomalies ICBR Bioinformatics contributed to a study on Gestational Hypoxia-Induced Cardiac Anomalies
ICBR Bioinformatics contributed to a study on Gestational Hypoxia-Induced Cardiac Anomalies
ICBR Bioinformatics contributed to a study on “Mechanism Sharing Between Genetic and Gestational Hypoxia-Induced Cardiac Anomalies” Gestational hypoxia, such as seen in high-altitude pregnancy, has been known to affect cardiac development, yet the incidence and underlying mechanisms are largely unknown.The results of the study provide insights into a common molecular mechanism underlying non-genetic and genetic cardiac anomalies. Read the study for more details. ...
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ICBR Bioinformatics contributed to a study on Gestational Hypoxia-Induced Cardiac Anomalies
ICBR’s Alberto Riva and MBI look to thwart the effects of time and aging on the brain ICBR’s Alberto Riva and MBI look to thwart the effects of time and aging on the brain
ICBR’s Alberto Riva and MBI look to thwart the effects of time and aging on the brain
Alberto Riva assisted the McKnight Brain Institute in a big methylation study over the past year. The study was published in the Frontiers in Aging Neuroscience journal. The purpose was to determine whether there is a relationship between the decline of cognitive function with aging and epigenetic changes in neurons. The study was performed on rats using a combination of whole-genome bisulfite sequencing (WGBS) to analyze methylation changes, and RNA-seq to investigate downstream effects o...
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ICBR’s Alberto Riva and MBI look to thwart the effects of time and aging on the brain
ICBR’s Bill Farmerie and Alberto Riva contribute to the most cited paper in ISME Journal history ICBR’s Bill Farmerie and Alberto Riva contribute to the most cited paper in ISME Journal history
ICBR’s Bill Farmerie and Alberto Riva contribute to the most cited paper in ISME Journal history
Alberto Riva and Bill Farmerie were co-authors (Eric Triplett was the senior author) on a paper, Pyrosequencing enumerates and contrasts soil microbial diversity (2007). Tripplett’s lab conceived and executed the work. ICBR did the sequencing, and Alberto was responsible for much of the data analysis. This past April, the International Society for Microbial Ecology Journal (ISME) recognized their work as the most cited paper in their 10-year history. ISME published a video (here) celebr...
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ICBR’s Bill Farmerie and Alberto Riva contribute to the most cited paper in ISME Journal history

Staff

NameTitleTelephoneE-mailRoom
W. Brad BarbazukBioinformatics Faculty Director(352) 273-8624bbarbazuk@ufl.edu407 CGRC
Alberto RivaBioinformatics Scientific Director(352) 294-5475ariva@ufl.edu191 CGRC
Fahong YuBioinformatics Associate Scientist(352) 273-8064fyu@ufl.edu191 CGRC
Tongjun GuBioinformatics Assistant Scientist(352) 273-8058tgu@ufl.edu191 CGRC