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

BI Tongjun New Pub BI Tongjun New Pub
BI Tongjun New Pub
Bioinformatics assistant scientist Tongjun Gu Ph.D. has developed a two-step logistic regression model for association studies where known factors can serve as controls. The model is helpful for studies seeking to identify novel regulators in the RNA editing process where the dominant enzyme was found in the first step and served as a control in the second step. Advantages of the model: It considered the sequencing depth in the analysis. It can be validated in the first step by the association ...
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BI Tongjun New Pub
BI associate scientist contributes to two publications BI associate scientist contributes to two publications
BI associate scientist contributes to two publications
Bioinformatics associate scientist Fahong Yu, Ph.D. provided research assistance in two recent publications (2019). Oral epithelial cells (OEC) that line the oral cavity are the first line of defense against pathogenic organisms including viruses that infect the body through the oral route. The role of the OEC in triggering the immune response to viral infection is poorly understood. ICBR Bioinformatics expert Dr. Fahong Yu performed data analysis and was a key collaborator in a study performed ...
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BI associate scientist contributes to two publications
BI assistant scientist develops a tool for stratifying cancer patients BI assistant scientist develops a tool for stratifying cancer patients
BI assistant scientist develops a tool for stratifying cancer patients
Bioinformatics assistant scientist Tongjun Gu Ph.D. has developed an advanced deep learning method to stratify cancer patients into clinically relevant subgroups and further identify the potential biomarkers between the subgroups. This will help with the development of personalized treatments and prognosis. The method can integrate multi-platform datasets like gene expression, miRNA expression, methylation, copy number alteration, and protein expression. It can also do transfer learning between ...
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BI assistant scientist develops a tool for stratifying cancer patients
Dr. Tongjun Gu, from ICBR Bioinformatics, Improves Discovery Pipeline Dr. Tongjun Gu, from ICBR Bioinformatics, Improves Discovery Pipeline
Dr. Tongjun Gu, from ICBR Bioinformatics, Improves Discovery Pipeline
Bioinformatics assistant scientist Tongjun Gu Ph.D. has improved the pipeline for discovering ncRNA editing sites from four human cancers. Published in JCO Clinical Cancer Informatics, Clinical Relevance of Noncoding Adenosine-to-Inosine RNA Editing in Multiple Human Cancers, Dr. Gu’s research also presents multiple advanced statistical methods for differential and survival analysis. More information: Bioinformatics Services Contact Bioinformatics ...
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Dr. Tongjun Gu, from ICBR Bioinformatics, Improves Discovery Pipeline
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

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