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

Alex Barrera 4x4.jpeg

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.

 

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Graham Johnson – Postdoctoral Fellow

graham DOT johnson AT duke DOT edu

I am postdoctoral research fellow in the Reddy lab. I am interested in understanding how our genomes are regulated and how non-coding variation contributes to that regulation. In my research, I use and develop high-throughput sequencing technologies to dissect gene regulatory mechanisms. These approaches allow me to identify how the genome responds to environmental stimuli, such as glucocorticoids, and how that response is altered by non-coding genetic variation. Identifying causal non-coding variants underpinning the perturbed gene regulatory responses associated with heritable human diseases, such as diabetes, is a central component of my research. My work is funded by a Ruth L. Kirschstein National Research Service Award through the NIDDK. View my publications

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Dewran Kocak –  Graduate Student

daniel DOT kocak AT duke DOT edu

I am a Ph.D. student in the department of Biomedical Engineering, co-advised by Charlie Gersbach. My research focuses on characterizing molecular mechanisms of the glucocorticoid response. Specifically, I am excited to discover and characterize co-factors of the glucocorticoid response through a variety of genome-engineering and genomic methods.

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Jungkyun Seo – Graduate Student

jungkyun DOT seo AT duke DOT edu

I explore how the interaction of glucocorticoid receptor with various co-regulators, transcription factors, histone modifications and genome determines transcription regulation in diverse cell types. In general, those regulatory mechanisms are governed by different combinations of specific signaling inputs that reflect physiological, gene and cell context. To model this, I utilize statistical modeling and machine learning methods on a variety of high-throughput sequencing data including ChIP-seq, ATAC-seq and RNA-seq. 

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Courtney Williams – Research Tech

courtney DOT a DOT williams AT duke DOT edu

I am a Research Technician who contributes primarily to the Genomics of Gene Regulation and ENCODE projects. I obtained my B.S. in Biology and a B.A. in Chemistry from East Carolina University. I am fascinated by the way our genome regulates our response to environmental stimuli and how variations to the genome can result in disease. This fascination led me to join the Reddy Lab, where I have learned how to perform high-throughput biological assays that allow us to answer interesting biological questions

 

 

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Sarah Cunningham – Graduate Student

sarah DOT cunningham AT duke DOT edu

I am a Ph.D. Candidate in the Genetics and Genomics program at Duke. My research focuses on gene regulation in pregnancy. I use genomic technologies to understand how noncoding variation can contribute to preterm birth risk. I also study the genomic effects of progesterone in pregnancy relevant cells to understand the role of progesterone in maintaining pregnancy.

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Young-Sook Kim – Graduate Student

young DOT sook DOT kim AT duke DOT edu

I am a Ph.D. student in the Computational Biology and Bioinformatics program. As a member of Reddy lab, I am working on developing a statistical model to remove experimental biases from sequencing data. Biases from various experimental steps distort sequencing results, and this can often obscure the true biological signals. My research focuses on developing a statistical model that can resolve the true biological signals by modeling the biases. The model will help elucidate regulatory regions with high sensitivity and specificity. 

 

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Laavanya Sankaranarayanan – Graduate Student

laavanya DOT s AT duke DOT edu

I am from Chennai, India, and I am in the Gentics and Genomics Ph.D. program. I am interested in exploring genome regulation in relation to human health as well as in understanding educational approaches in the context of different communities, gender and language biases that play roles in science education. In the Reddy lab, I hope to work on my interests in the context of PCOS. Outside of research, I enjoy board games, hikes and exploring places and communities through food. 

 

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Ana Berglind – Research Technician

ana DOT berglind AT duke DOT edu

I am interested in understanding how the genome is regulated and how changes in regulatory networks lead to disease states. I perform high-throughput sequencing based assays to decipher transcription regulation. I am fascinated with understanding how enhancers mediate transcription activation.

Darryl Yan - Undergraduate Researcher

darryl DOT yan AT duke DOT edu

Being in the Reddy Lab has allowed me to combine my interests in both computing and medicine. As an undergraduate student studying Computer Science, I support the Reddy Lab in computational aspects of research such as developing data pipelines and web applications for ChIP-seq visualization and quality control. For my work, I regularly interface with open-source bioinformatics software and web development technologies. Through my work, I hope to contribute to the Reddy Lab's goal of understanding the regulation of the human genome.

 

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Keith Siklenka – Postdoctoral Associate

keith DOT siklenka AT duke DOT edu

Alumni

Dr. Karl Guo – Graduate Student

Current position: Investigator at GlaxoSmithKline

Dr. Chris Vockley

Current position: Postdoc at the Broad Institute

Dr. Ian McDowell – Graduate Student

Current position: Scientist at Element Genomics

Dr. Tony D'Ippolito - Graduate Student

Current position: Scientist at Syros Pharmaceuticals

Rotation students:

Erez Cohen
Jacob Hoj
Katie Ritz
Kyle Moran

Dr. Bill Majoros – Graduate Student

Current position: Postdoc in the Allen lab at Duke

Luke Bartelt - Lab Analyst

Current Position: Grad Student at Duke