Tim Reddy, Principal Investigator

Tim Reddy, Principal Investigator

Assistant Professor
Department of Biostatistics & Bioinformatics
Center for Genomic & Computational Biology

Curriculum Vitae 

 

Email: tim DOT reddy AT duke DOT edu

Lab Members

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Alex Barrera – Research Analyst

alejandro DOT barrera AT duke DOT edu

The experimental assays carried out in the lab typically generate huge amounts of sequencing data that need to be systematically processed. As an IT Analyst, I support lab members with the computational aspects of their research by creating reproducible pipelines to process, analyze, and visually represent their results. I’m interested in the impact that working with and visualizing biological data can have on our understanding of the role of genomics and gene regulation in human health.

 

Graham Johnson – Postdoctoral Fellow

graham DOT johnson AT duke DOT edu

I came to the Reddy lab as a postdoctoral scientist after completing my PhD work at the Wayne State University School of Medicine. I am interested in understanding how variation in the genome can contribute to disease and other organismal traits. Specifically, I explore how the interplay of regulatory elements and local differences in transcription factor availability dictate chromatin environments and gene expression thereby driving mammalian phenotypes. Please see google scholar for a list of my published work.

Sarah Leichter –  Lab Analyst

sarah DOT leichter AT duke DOT edu

As a Research Technician, I am responsible for carrying out experiments in the lab, primarily for the Genomics of Gene Regulation project. I have a BS in Biology with a minor is genetics from North Carolina State University where I initially studied ecology and conservation biology. I discovered that I preferred the hard data and the possibility of proving hypotheses of plant genetics to the observation and extrapolation of ecology. I’ve enjoyed learning the difference between plant and animal systems in the Reddy lab as well as new molecular biology tools, different assays, and ways of studying gene regulation and expression. I plan to apply these new skills in advanced study, returning to a focus on plants, specifically on how to ensure a sustainable global food system. 

Jessica Leete – Rotation Student

Dewran Kocak – Graduate Student (co-advised by Charles Gersbach)

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Luke Bartelt – Lab Analyst

luke DOT bartelt AT duke DOT edu

I contribute to the Genomics of Gene Regulation project as a Research Technician. I have a BS in Biochemistry from the University of North Carolina at Chapel Hill, and my past research experience involves protein engineering through bacterial plasmids. I’m interested in both medicine and research, and I appreciate that I can combine these interests here in the Reddy lab, where we strive to better understand the regulation of the human genome in order to better understand disease. This knowledge will lead to better disease treatment, ultimately benefiting individuals and society.

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Anthony D'Ippolito – Graduate Student

anthony DOT d DOT ippolito AT duke DOT edu

am a Phd student in the Duke University Program in Genetics and Genomics. My thesis research focuses on glucocorticoids, drugs that reduce inflammation and immune response but can cause adverse effects, including diabetes. By exploring the molecular mechanisms underlying the glucocorticoid response, I hope to contribute to advances in treatment. More specifically, I am using genomics methodologies to better understand glucocorticoid mediated transcriptional repression. 

 

 

Linda Hong –  Lab Analyst

linda DOT hong AT duke DOT edu

As a Research Analyst in the lab, I am primarily responsible for overseeing data production – planning and overseeing experiments that both use and produce data on a large scale. I enjoy finding ways to maximize efficiency, the challenge of completing sometimes finicky assays, and keeping up with new next-gen sequencing technologies. Before joining the Reddy lab I was the project lead at the former Genomic Analysis Facility within Duke’s Center for Human Genome Variation where I coordinated workflow, developed methods, troubleshot instrumentation, managed budgeting and invoicing, and revised protocols with an eye towards greater efficiency. My Bachelor's degree is from North Carolina State where I double majored in Biology and Plant Biology. My publications are here.

Ian McDowell – Graduate Student

ian DOT mcdowell AT duke DOT edu

Tens of millions of prescriptions for oral glucocorticoids (GCs) are written annually in the United States, primarily for their immunosuppressive effects. Prolonged use of synthetic GCs, however, can lead to harmful metabolic effects like diabetes. Using a variety of high-throughput sequencing techniques – including RNA-seq, DNase-seq, and ChIP-seq – and statistical modeling designed to integrate these diverse data types, I model the genomics of the GC response. These models will serve as a blueprint for modifying the response by means of genetic engineering.

 

Bill Majoros – Graduate Student

bmajoros AT duke DOT edu

I’m interested in how mutations in DNA can lead to human disease. I study how genetic variants affect the way genes are spliced after transcription into RNA, and how those splicing changes can result in disease. More broadly I'm interested in molecular mechanisms behind the regulation of splicing, and how splicing regulation and nonsense-mediated decay can be co-opted by evolution to effectively regulate gene expression levels. As a computational scientist I make heavy use of machine-learning methods, particularly those based on formal grammars and/or graphical models, such as Hidden Markov Models, Conditional Random Fields, and Stochastic Context Free Grammars. More at my website and at google scholar.

 

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Dr. Chris Vockley - Grad Student

christopher DOT vockley AT duke DOT edu

I am a fifth year PhD student in the Developmental and Stem Cell Biology Program and the Center for Genomic and Computational Biology co-advised by Dr. Reddy and Dr. Brigid Hogan. In my research I focus on understanding the basic mechanisms that control how our genes are regulated. I am especially interested in developing new high-throughput technologies that will enable us to study how all genes are regulated all at once. In particular, I have developed massively parallel functional assays to understand how genetic variants influence the regulation of gene expression, and to investigate how individual TF binding sites act together and in combination to regulate gene expression. Most of my work involves using the glucocorticoid receptor, a ligand inducible transcription factor as a well-controlled model system. My work at Duke is funded by a Ruth L. Kirschstein National Research Service Award through the NHLBI. I am a Lung Repair and Regeneration Consortium Young Investigator. Please see Google Scholar for a list of my published work.


Alumni

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Dr. Karl Guo – Graduate Student

Karl completed his PhD in the University Program in Genetics and Genomics. He focused on developing and applying new techniques to study how genetic variation alters gene regulation. As of 2016, Karl is an investigator at GSK in Philadelphia. 

Kyle Moran – Rotation Student

First-year graduate student in the Computational Biology & Bioinformatics Program. Kyle worked on identifying patterns of regulatory elements driving the human response to glucocorticoids.  

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Jacob Hoj – Rotation Student

First-year graduate student in the Molecular Cancer Biology program. Jake worked on defining the role of HKDC1 in breast cancer.

Erez Cohen – Rotation Student

Katie Ritz – Rotation Student