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Michelle G. Giglio, PhD

Academic Title:

Associate Professor

Primary Appointment:


Administrative Title:

Associate Director, Analysis

Additional Title:

Academic and Outreach Coordinator, Institute for Genome Sciences; Associate Director for Analysis, Informatics Resource Center, Institute for Genome Sciences


Health Sciences Facility III, 670 West Baltimore St, Baltimore 21201

Phone (Primary):

(410) 706-7694

Education and Training

B.S. University of Maryland College Park, 1990

Ph.D. Johns Hopkings University School of Medicine, 1997

Postdoc The Insititue for Genomic Research, Rockville, MD 1997-1998


Staff Scientist, The Institute for Genomic Research, 1998-2007

Assistant Professor, University of Maryland School of Medicine, Department of Medicine and Institute for Genome Sciences, 2007-2015

Associate Professor, University of Maryland School of Medicine, Department of Medicine and Institute for Genome Sciences, 2015-Present

Research/Clinical Keywords

genomics, transcriptomics, metagenomics, microbiome, annotation, ontology

Highlighted Publications


Chibucos MC, Hu JC, Siegele DA, Giglio M. The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations. In Christophe Dessimoz & Nives Škunca(eds.), The Gene Ontology Handbook, Methods in Molecular Biology, vol. 1446,pp. 245-259. New York City: Humana Press (Springer). ISBN ISBN 978-1-4939-3743-1.  2016

Bastian FB, Chibucos MC, Gaudet P, Giglio M, Holliday GL, Huang H, Lewis SE, Niknejad A, Orchard S, Poux S, Skunca N, Robinson-Rechavi M.The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations. Database (Oxford). 2015 May 9;2015:bav043.

Marcus C. Chibucos, Adrienne E Zweifel, Jonathan C. Herrera, William Meza, Shabnam Eslamfam, Peter Uetz, Deborah A. Siegele, James C. Hu, Michelle G. Giglio. An Ontology for Microbial Phenotypes. BMC Microbiology. 2014 Nov 30;14(1):294

Marcus C. Chibucos, Christopher J. Mungall, Rama Balakrishnan, Karen R. Christie, Rachael P. Huntley, Owen White, Judith A. Blake, Suzanna E. Lewis, Michelle Giglio. Standardized description of scientific evidence using the Evidence Ontology (ECO). Database. 2014, July 22.

Pascale Gaudet, Cecilia Arighi, Frederic Bastian, Alex Bateman, Judith A. Blake, J. Michael Cherry, Peter D’Eustachio, Robert Finn, Michelle Giglio, Lynette Hirschman, Renate Kania, William Klimke, Maria Jesus Martin, Ilene Karsch Mizrachi, Monica Munoz-Torres, Darren Natale, Claire O’Donovan, Francis Ouellette, Kim D. Pruitt, Marc Robinson-Rechavi, Susanna-Assunta Sansone, Paul Schofield, Granger Sutton, Kimberly Van Auken, Sona Vasudevan, Cathy Wu, Jasmine Young, Raja Mazumder. Recent advances in biocuration: Meeting Report from the 5th International Biocuration Conference. Database, 2012 Oct. 29.

The Human Microbiome Project Consortium (Giglio, 5th out of 248 authors). A framework for human microbiome research. Nature, June 2012, 486, 215–221.

Kevin Galens, Joshua Orvis, Sean Daugherty, Heather H. Creasy, Sam Angiuoli, Owen White, Jennifer Wortman, Anup Mahurkar, Michelle Gwinn Giglio. The IGS Standard Operating Procedure for Automated Prokaryotic Annotation. SIGS 2011 Apr:Vol 4, No 2

Giglio MG, Collmer CW, Lomax J, Ireland A.  Applying the Gene Ontology in Microbial Annotation. Trends Microbiol. 2009 Jul;17(7):262-8.

Research Interests

Prokaryotic sequence analysis:  I'm the PI for the Analysis Engine project, funded by the NIGMS to provide free analysis services for prokaryotic sequences. Services include single genome annotation, comparative genomics, and transcriptomics. Analysis tools are made available in a variety of ways to allow users to choose the approach most suited to them. Under this project we continue to develop the pipelines and tools to further meet users needs.

Microbiome analysis: I am part of the Data Coorindation Center for the Intregrative Human Microbiome Project (iHMP), (Owen White PI.) In this capacity I help develop web resources and contribute to analyses of HMP data.

Ontology Development: I am part of the Gene Ontology Consortium and was active in term development for many years. More recently, I have been involved in the Evidence Ontology and the Ontology of Microbial Phenotypes.

Outreach: I organize and run several outreach events to local K-12 schools/programs each year. Most of these are focused at middle school students and help to get them excited about science and in particular biology.

Training: I run a professional development workshop program that includes five different workshops focused on different aspects of bioinformatics including genomics, transcriptomics, metagenomics, comparative genomics, and programming.


Awards and Affiliations

I was named one of Maryland's Top 100 Women by the Daily Record in 2014

Community Service

I am involved in multiple outreach events to local K-12 students including the CURE Scholars program.