JCVI: About / Bios / Ramana Madupu
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Ramana Madupu, Ph.D.
Assistant Professor

Research Interests and Accomplishments

Dr.Ramana Madupu is an Assistant Professor within the Genomic Medicine group at the J. Craig Venter Institute (JCVI). During her tenure at TIGR/JCVI Dr.Madupu has worked on diverse, large-scale sequencing projects and has extensive experience on microbial genome interpretation, comparative genome analyses, metagenome and genome annotation, process design and development of annotation pipelines. Dr.Madupu's research focuses on several human microbiome projects including omics analysis, survey of bacterial and viral species associated with the gut microbiome in Type 1 Diabetes, role of microbiota in esophageal adenocarcinoma and wound infections.  She has lead efforts for bench marking and evaluation of annotation methods for reference genomes and metagenomic data for the Human Microbiome Project (HMP). Her research interests include genome annotation, interpretation and analysis of viral, microbial and metagenomes, tool development for genome analysis, process design and development of annotation pipelines, and improving gene annotation methods. She has co-authored several genome analysis papers and book chapters.

She has also been involved in education and outreach programs at JCVI to promote educational exchanges between research communities. As part of an award from NSF Dr.Madupu is currently leading an effort to develop genomics workshops, designed to train undergraduate faculty to advance curricular needs in the classroom.

Dr.Madupu is currently PI on a Type 1 Diabetes biomarker discovery study that involves application of OMICS techniques to identify molecular signatures and candidate biomarkers  that are predictive diagnostic markers. Dr.Madupu is currently the Project Leader of two NIAID-funded Genome Sequencing Center projects: 1) Adenovirus genome sequencing project where historical and outbreak samples are being analyzed from a phylogenetic and evolutionary standpoint to understand tissue tropism 2)Norovirus sequencing project for sequencing vaccine and placebo strains in addition to isolates from normal and immunocompromised individuals to understand evolutionary mechanisms in the population and its application to vaccine development. Her current focus through these projects is application of novel strategies for viral genome annotation and analyses as well as identification of molecular mechanisms responsible for genetic diversity and phylodynamic features from different clinical isolates and viral genotypes.

Prior to joining JCVI in 2001, she was a post doctoral fellow at the National Eye Institute, NIH where she studied the genetics of retinal diseases. She received her B.S. degree in Genetics and Ph.D. degree in Microbiology from Osmania University, India.

Select Publications

Karen E.Nelson
Next-Generation Sequencing, Metagenomes and the Human Microbiome

2014 Feb 01;[more]

Madupu R, Szpakowski S, et al.
Microbiome in Human Health and Disease.

Science Progress. 2013 Nov 01; 96: 153-70.[more]

Salzberg, S. L., Sommer, D. D., et al.
Genome Sequence and Rapid Evolution of the Rice Pathogen Xanthomonas oryzae Pv. oryzae PXO99A

BMC Genomics. 2008 May 01; 9(1): 204.[more]

Angiuoli, S. V., Gussman, A., et al.
Toward an Online Repository of Standard Operating Procedures (SOPs) for (Meta)genomic Annotation

Omics. 2008 Apr 16; 12(2): 137-41.[more]

Myers, G. S., Parker, D., et al.
Genome Sequence and Identification of Candidate Vaccine Antigens from the Animal Pathogen Dichelobacter nodosus

Nat Biotechnol. 2007 Apr 29;[more]

Seshadri, R., Joseph, S. W., et al.
Genome Sequence of Aeromonas hydrophila ATCC 7966T: The Jack of All Trades

J Bacteriol. 2006 Sep 15; 188: 8272-8282.[more]

Dunning Hotopp, J. C., Lin, M., et al.
Comparative Genomics of Emerging Human Ehrlichiosis Agents

PLoS Genet. 2006 Feb 17; 2(2): e21.[more]

Wu, M., Ren, Q., et al.
Life In Hot Carbon Monoxide: The Complete Genome Sequence of Carboxydothermus hydrogenoformans Z-2901

PLoS Genet. 2005 Nov 25; 1(5): e65.[more]

Methe, B. A., Nelson, K. E., et al.
The Psychrophilic Lifestyle as Revealed by the Genome Sequence of Colwellia psychrerythraea 34H Through Genomic and Proteomic Analyses

Proc Natl Acad Sci U S A. 2005 Jul 25; 102(31): 10913-8.[more]