Christian J. Stoeckert, Jr., Ph.D.

faculty photo
Research Professor of Genetics
Department: Genetics

Contact information
D105 Richards
3700 Hamilton Walk
Philadelphia, PA 19104
Office: 215-573-4409
Fax: 215-573-3111
Education:
B.S. (Biophysics)
Penn State University, 1975.
Ph.D. (Biophysics)
Johns Hopkins University, 1982.
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Description of Research Expertise

The goal of Dr. Stoeckert's work is to help make sense of the enormous amount of biomedical data. To that end, he is involved in projects that are developing tools that enable researchers to mine and integrate data from a variety of different sources and types of experiments.

The first step in that process is the development of data warehouses that collect and store information in a useable fashion. In one such project, he has been working with David S. Roos, Ph.D., E. Otis Kendall Professor of Biology at Penn, Jessica Kissinger, Ph.D., at University of Georgia, and others to develop a bioinformatics resource center for eukaryotic pathogens, funded by the National Institute of Allergy and Infectious Diseases. Within the resource center, we have built databases that serve research communities interested in specific pathogens. For example, PlasmoDB, houses information on the parasites that cause malaria. He also works with Li-San Wang at Penn on the National Institute on Aging Genetics of Alzheimer's Disease Data Storage Site (NIAGADS).

We also have been involved in the analysis of genomics datasets particularly in the areas of red blood cell development, pancreatic islet cells, and Plasmodium genomes.

To maximize the utility of data warehouses, we must have ways to represent and store data that enables researchers to make connections between experiments and between data from different types of experiments. Therefore, part of my group is involved in knowledge representation and developing ontologies, which standardizes data through the use of controlled vocabularies and relationships. Our goal is to provide the standards, including ontologies, to allow people to annotate their experiments or mark up their papers in a way that another researcher could efficiently search for and combine particular kinds of results from a variety of sources. We have been applying these to clinical epidemiological datasets available through ClinEpiDB.

We work with a number of groups on ontology projects, including the Ontology for Biomedical Investigations Consortium which is a member of the Open Biological and Biomedical Ontologies (OBO) Foundry.

The TURBO (Transforming and Unifying Research with Biomedical Ontologies) project uses the expressive power of ontologies in graph databases to represent and integrate clinical data. Powerful searches of individual medications and diagnosis codes are made possible through association to ontology classes of drug roles and diseases.

Selected Publications

Hayden G.Freedman, Heather Williams, Mark A.Miller, David Birtwell, Danielle L.Mowery, Christian J.Stoeckert Jr: A novel tool for standardizing clinical data in a semantically rich model. Journal of Biomedical Informatics: X 8, December 2020.

Ruhamyankaka E, Brunk BP, Dorsey G, Harb OS, Helb DA, Judkins J, Kissinger JC, Lindsay B, Roos DS, San EJ, Stoeckert CJ, Zheng J, Tomko SS.: ClinEpiDB: an open-access clinical epidemiology database resource encouraging online exploration of complex studies. Gates Open Res. 3: 1661, April 2020 Notes: eCollection 2019.

Held MA, Greenfest-Allen E, Su S, Stoeckert CJ, Stokes MP, Wojchowski DM.: Phospho-PTM proteomic discovery of novel EPO- modulated kinases and phosphatases, including PTPN18 as a positive regulator of EPOR/JAK2 Signaling. Cell Signal. 69: 109554, February 2020.

Held MA, Greenfest-Allen E, Jachimowicz E, Stoeckert CJ, Stokes MP, Wood AW, Wojchowski DM.: Phospho-proteomic discovery of novel signal transducers including thioredoxin-interacting protein as mediators of erythropoietin-dependent human erythropoiesis. Exp Hematol. 84: 29-44. April 2020.

Breuza L, Arighi CN, Argoud-Puy G, Casals-Casas C, Estreicher A, Famiglietti ML, Georghiou G, Gos A, Gruaz-Gumowski N, Hinz U, Hyka-Nouspikel N, Kramarz B, Lovering RC, Lussi Y, Magrane M, Masson P, Perfetto L, Poux S, Rodriguez-Lopez M, Stoeckert C, Sundaram S, Wang LS, Wu E, Orchard S; IMEx Consortium, UniProt Consortium.: A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets. J Alzheimers Dis. 77(1): 257-273, 2020.

Ong E, Wang LL, Schaub J, O'Toole JF, Steck B, Rosenberg AZ, Dowd F, Hansen J, Barisoni L, Jain S, de Boer IH, Valerius MT, Waikar SS, Park C, Crawford DC, Alexandrov T, Anderton CR, Stoeckert C, Weng C, Diehl AD, Mungall CJ, Haendel M, Robinson PN, Himmelfarb J, Iyengar R, Kretzler M, Mooney S, He Y; Kidney Precision Medicine Project.: Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project. Nat Rev Nephrol. 16(11): 686-696. November 2020.

Francislon S. Oliveira, John Brestelli, Shon Cade, Jie Zheng, John Iodice, Steve Fischer, Cristina Aurrecoechea, Jessica C. Kissinger, Brian P. Brunk, Christian J. Stoeckert Jr, Gabriel R. Fernandes, David S. Roos, Daniel P. Beiting: MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments. Nucleic Acids Research 46: D684-D691, Jan 2018.

Basenko EY, Pulman JA, Shanmugasundram A, Harb OS, Crouch K, Starns D, Warrenfeltz S, Aurrecoechea C, Stoeckert CJ Jr, Kissinger JC, Roos DS, Hertz-Fowler C.: FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes. J Fungi 4(1): E39, March 2018.

Huang C, Walker EM, Dadi PK, Hu R, Xu Y, Zhang W, Sanavia T, Mun J, Liu J, Nair GG, Tan HYA, Wang S, Magnuson MA, Stoeckert CJ Jr, Hebrok M, Gannon M, Han W, Stein R, Jacobson DA, Gu G.: Synaptotagmin 4 Regulates Pancreatic β Cell Maturation by Modulating the Ca2+ Sensitivity of Insulin Secretion Vesicles. Dev Cell. 45(3): 347-361, May 2018.

Aurrecoechea C, Barreto A, Basenko EY, Brestelli J, Brunk BP, Cade S, Crouch K, Doherty R, Falke D, Fischer S, Gajria B, Harb OS, Heiges M, Hertz-Fowler C, Hu S, Iodice J, Kissinger JC, Lawrence C, Li W, Pinney DF, Pulman JA, Roos DS, Shanmugasundram A, Silva-Franco F, Steinbiss S, Stoeckert CJ Jr, Spruill D, Wang H, Warrenfeltz S, Zheng J.: EuPathDB: the eukaryotic pathogen genomics database resource. Nucleic Acids Res. 45: D581-D591, January 2017 Notes:

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Last updated: 01/04/2021
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