Bioinformatics Core
virtual dna strand

Bioinformatics analysis to support research activities.

The Bioinformatics Core helps researchers identify and interpret patterns in RNA and DNA by placing sequencing data into a biologically meaningful context. This encompasses assisting with experimental design, developing reproducible workflows, analyzing next-generation sequencing data, and supporting manuscript development/publication.

“We are thrilled with the services provided to our team by the BRCF Bioinformatics Core, the services provide enabled us to publish top tier papers and be awarded multiple NIH funded grants. We are very grateful to have this Core available to us on campus!”

Dr. Maria Castro and Dr. Pedro Lowenstein
How we can help you
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Consultations

We offer an initial, free pre-analysis consultation to discuss the types of analysis and support bioinformatics can provide, in addition to assisting with experimental design to best answer the biological question(s) of interest.

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Data Analysis

Offering a variety of analyses

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Workshops & Training

Hosting regular virtual, hands-on workshops

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“I’ve greatly enjoyed my experience working with the Bioinformatics Core. Chris and his team were instrumental in establishing a workflow for the measurement of allele-specific expression using data from targeted RNA-seq and DNA-seq. Their services were timely and helped us to publish and secure continued funding.”

Prof. Beverly Strassmann
Meet the Team
Chris Gates Chris Gates, M.S.
Managing Director

Chris Gates became the Managing Director of the Bioinformatics Core in January 2019. Prior to that, he served as the lead software engineer for the Core. He enjoys building quality software systems and exceptional software delivery teams. Since 1993, he has assumed many different roles in software development and has experience across many business domains including high-throughput genomics, pharmaceutical drug-discovery, publishing, electronic medical record systems, and social-science research. Prior to joining the core, he was the Director of Product Informatics at Compendia Bioscience (part of Life Technologies) where he managed the teams that created and maintained the Oncomine suite of bioinformatic data mining tools.

portrait of MARCI BRANDENBURG Marci Brandenburg, M.S., M.S.I.
Bioinformationist

Marci Brandenburg has her Masters in Biology (Ohio University) and Information (University of Michigan) and is currently Bioinformationist for the Bioinformatics Core, Department of Computational Medicine & Bioinformatics, and the Taubman Health Sciences Library. She is also the Project Manager for the Bioinformatics Core. She specializes in instruction on visualization tools and other information/informatics resources and was the project manager on a grant-funded project related to tranSMART, an open-source framework for knowledge management of translational research data including both molecular and clinical information. Prior to working at the University of Michigan, she was the Biosciences Informationist at the National Cancer Institute – Frederick in Maryland.

Nick Carruthers Nick Carruthers, M.S., Ph.D.
Bioinformatics Analyst

Dr. Nick Carruthers specializes in statistical and functional analysis of RNASeq and Proteomics data. He is interested in data sharing and reproducible analysis pipelines. Prior to working at the University of Michigan, he was a bioinformatician at the Wayne State University Proteomics Facility. He received his Ph.D. in Toxicology and M.S. in Data Science from Wayne State University and B.Sc. in Biology from the University of Waterloo. His free time is spent with his family or on the golf course.

portrait of RAYMOND CAVALCANTE Raymond Cavalcante, Ph.D.
Bioinformatics Analyst

Dr. Cavalcante consults with clients to understand their bioinformatics needs and develop suitable analysis plans. He develops modular, scalable, and reproducible analysis pipelines for epigenomics assays (ChIP-seq, WGBS, ERRBS, ATAC-seq, and the EPIC methylation array). Dr. Cavalcante received his Ph.D. in Bioinformatics at the University of Michigan in August 2017, where he focused on building computational tools to help interpret and give context to epigenomics and metabolomics data. He completed his undergraduate work in Mathematics from Cal Poly, San Luis Obispo and an M.A. in Mathematics from San Francisco State University. When not working, he likes to escape to the Upper Peninsula as much as possible to ski and cook in the winter, or hike and pick berries in the summer.

portrait of DANA KING Dana King, Ph.D.
Bioinformatics Analyst

Dana King received a Bachelors’s in Biology at The College of New Jersey before working as a research assistant at Cold Spring Harbor Laboratories. She went on to receive her Ph.D. in Molecular Genetics & Genomics at Washington University in St. Louis, working with Dr. Barak Cohen to understand the impact of regulatory sequence changes in mouse and human models using Massively Parallel Reporter Assays (MPRAs) and machine learning. Dana’s current focus areas are RNA-seq and functional analysis with additional interest in machine learning and custom analyses.
portrait of TRAVIS SAARI Travis Saari
Bioinformatics Analyst

Travis Saari received his bachelor’s degree in Molecular Biology and Biotechnology from Michigan State University. He then went on to work at Pfizer and the U.S. Environmental Protection Agency. At the EPA, he led the annotation efforts on a draft genome of a minnow species widely used in aquatic toxicology and created a web portal for these data, providing access to these resources to the wider research community. Most recently, he has been focused on fostering scientific reproducibility and best practices by incorporating workflow and environment management tools into bioinformatics analysis pipelines.

portrait of REBECCA TAGETT Rebecca Tagett, M.S.
Bioinformatics Analyst

Rebecca holds a Bachelor’s in Physics (Emory), a Master’s in Atmospheric Sciences (UCLA), and a Master’s in Molecular Biology (CUNY). Her career in Bioinformatics includes the Human Genome Project in Los Alamos, the INSERM in France, and 10 years at a molecular diagnostics start-up, now part of Qiagen, where she was a founding member. While full time in the Bioinformatics Core, she is also wrapping up a Ph.D. at Wayne State, under Dr. Draghici (CEO of Advaita Bioinformatics), applying systems methods in unconventional contexts. She enjoys the diversity and impact of projects at our Core and is currently taking transcriptomics and custom requests.

portrait of WEISHENG WU Weisheng Wu, Ph.D.
Bioinformatics Analyst

Weisheng Wu received his Ph.D. in Integrative Biosciences and Graduate Minor degree in Statistics from Pennsylvania State University in 2011. His Ph.D. and postdoctoral research in Dr. Ross Hardison’s lab in the Center for Comparative Genomics and Bioinformatics at Penn State has given him versatile experiences of generation and analysis of genome-scale high-throughput sequencing data in a mouse model. Dr. Wu’s research has been focusing on elucidating the dynamics of genome-scale epigenetic landscapes in hematopoiesis through next-generation sequencing technology. He has made interesting discoveries about the roles of histone modifications associated with transcription factor binding and gene regulation during erythroid differentiation. Dr. Wu is also making active contributions to both Human ENCODE and Mouse ENCODE projects.
Questions?
Contact Us
North Campus Research Complex (NCRC), Building 22
2800 Plymouth Road
Ann Arbor, MI 48109-2800
About Us
The Bioinformatics Core is one of the Biomedical Research Core Facilities, and a part of the Medical School Office of Research, where our mission is to foster an environment of innovation and efficiency that serves the Michigan Medicine research community and supports biomedical science from insight to impact.
Upcoming Research Events All Office of Research Events
Amendments and Continuing Reviews
This course is a follow-up to Initial Project Applications and will examine the process for submitting amendments and scheduled continuing reviews to IRBMED using eResearch once a project’s initial application has been approved.
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Data and Safety Monitoring Boards and Data Safety Monitoring Plans
This course will review when studies are required to have a DSMP or DSMB and how to develop an appropriate DSMP. A DSMB is an independent group that advises the study team regarding subject safety, study conduct, and efficacy. The DSMB will also make recommendations concerning the continuation, modification, or termination of the trial. A DSMP outlines how subject safety and data integrity will be maintained to ensure the validity of collected data.
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Microscopy Core: Advanced Biological EM Methods Interest Group
Learn About Advanced Electron Microscopy (EM) Methods.
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Storage and Retention of Data
This course will review the fundamentals of maintaining confidentiality of subject data, including data encryption and protection, using secure environments and external websites, and distinguishing among anonymized, coded, and de- identified datasets.
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Bioinformatics Core Summer Workshop Series
Composed of the two companion workshops (Computational Foundations and RNA-Seq Demystified), this virtual workshop series is for researchers who would like to better understand the analysis of differential gene expression in bulk RNA-Seq data.
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Introduction to sIRBs
This course will identify the Single IRB model for Multi-Site research, show the regulatory requirements of sIRB review and the exceptions to sIRB requirements, and explain sIRB requests of IRBMED as sIRB (accepting oversight), External IRB as sIRB (ceding oversight), and UofM as the Coordinating Center.
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Flow Cytometry Core FlowJo™ Software Training
Learn how to use the FlowJo™ workspace, including how to load files, evaluate sample quality, draw gates, generate tabular and graphical layouts, and perform compensation. Designed for those new to the software or need a refresher.
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Microscopy Core: Advanced Biological EM Methods Interest Group
Learn About Advanced Electron Microscopy (EM) Methods.
A close up of a microscope's eye pieces.
FDA Research Involving Drugs and Devices
This course will review what research is subject to FDA oversight, highlight the differences between OHRP and FDA regulations, learn the responsibilities of sponsors, investigators, and the IRB when conducting and reviewing research involving drugs and devices, and examine the requirements for conducting research with a drug or biologic/medical device.
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Featured Research News All Office of Research News Fun illustration in red, white, and blue, with the words "fourth of July"
Office of Research
Several Cores Closed for the Holiday
In observance of the Independence Day, several cores will have a change in operations.
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Office of Research
New RN Pool Available to Support MCRU Overnight & Extended Hours
The Michigan Clinical Research Unit (MCRU) is excited to announce the development of an overnight RN pool to support overnight/extended hours. If you have current or upcoming studies that require overnight RN services in MCRU, contact [email protected] for more information.
FFMI fastPACE spring 2024
Office of Research
Register Today! FFMI fastPACE Spring Cohort Begins Friday, May 10
Don't miss your chance to participate in this project-based, experiential course designed to help academics launch new innovations, including medical devices/diagnostics, digital solutions, drugs, educational/training interventions, research tools, and many others.