Christian J. Stoeckert, Jr., Ph.D.
Adjunct Professor of Genetics
Senior Fellow, Institute for Biomedical Informatics (IBI)
Penn State University, 1975.
Johns Hopkins University, 1982.
Penn State University, 1975.
Johns Hopkins University, 1982.
Description of Research ExpertiseThe goal of Dr. Stoeckert's work has been to help make sense of the enormous amount of biomedical data. To that end, he has been involved in projects that developed 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 was the development of data warehouses that collect and store information in a useable fashion. In one such project, he worked 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 worked 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 was involved in knowledge representation and developing ontologies, which standardizes data through the use of controlled vocabularies and relationships. Our goal was 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 PublicationsVita R, Zheng J, Jackson R, Dooley D, Overton JA, Miller MA, Berrios DC, Scheuermann RH, He Y, McGinty HK, Brochhausen M, Lin AY, Jain SB, Chibucos MC, Judkins J, Giglio MG, Feng IY, Burns G, Brush MH, Peters B, Stoeckert CJ Jr.: Standardization of assay representation in the Ontology for Biomedical Investigations. Database (Oxford) 2021, July 2021.
Amos B, Aurrecoechea C, Barba M, Barreto A, Basenko EY, Bażant W, Belnap R, Blevins AS, Böhme U, Brestelli J, Brunk BP, Caddick M, Callan D, Campbell L, Christensen MB, Christophides GK, Crouch K, Davis K, DeBarry J, Doherty R, Duan Y, Dunn M, Falke D, Fisher S, Flicek P, Fox B, Gajria B, Giraldo-Calderón GI, Harb OS, Harper E, Hertz-Fowler C, Hickman MJ, Howington C, Hu S, Humphrey J, Iodice J, Jones A, Judkins J, Kelly SA, Kissinger JC, Kwon DK, Lamoureux K, Lawson D, Li W, Lies K, Lodha D, Long J, MacCallum RM, Maslen G, McDowell MA, Nabrzyski J, Roos DS, Rund SSC, Schulman SW, Shanmugasundram A, Sitnik V, Spruill D, Starns D, Stoeckert CJ, Tomko SS, Wang H, Warrenfeltz S, Wieck R, Wilkinson PA, Xu L, Zheng J.: VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. Nucleic Acids Res. Page: gkab929, October 2021.
Osipovich AB, Dudek KD, Greenfest-Allen E, Cartailler JP, Manduchi E, Potter Case L, Choi E, Chapman AG, Clayton HW, Gu G, Stoeckert CJ Jr, Magnuson MA.: A developmental lineage-based gene co-expression network for mouse pancreatic β-cells reveals a role for Zfp800 in pancreas development. Development 148(6): dev196964, March 2021.
Jackson R, Matentzoglu N, Overton JA, Vita R, Balhoff JP, Buttigieg PL, Carbon S, Courtot M, Diehl AD, Dooley DM, Duncan WD, Harris NL, Haendel MA, Lewis SE, Natale DA, Osumi-Sutherland D, Ruttenberg A, Schriml LM, Smith B, Stoeckert CJ Jr, Vasilevsky NA, Walls RL, Zheng J, Mungall CJ, Peters B.: OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies. Database (Oxford). Oxford, 2021: baab069, October 2021.
Sanavia T, Huang C, Manduchi E, Xu Y, Dadi PK, Potter LA, Jacobson DA, Di Camillo B, Magnuson MA, Stoeckert CJ Jr, Gu G.: Temporal Transcriptome Analysis Reveals Dynamic Gene Expression Patterns Driving β-Cell Maturation. Front Cell Dev Biol. 9: 648791, May 2021.
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.