UNIVERSITY OF PENNSYLVANIA - PERELMAN SCHOOL OF MEDICINE

Curriculum Vitae

Date: 12/28/2012

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

Address:				1415 Blockley Hall 423 Guardian Drive
				Philadelphia, PA 19104 USA
If you are not a U.S. citizen or holder of a permanent visa, please indicate the type of visa you have:
				none (U.S. citizen)
Education:
			1975		B.S.		Penn State University (Biophysics)
			1982		Ph.D.		Johns Hopkins University (Biophysics)
Postgraduate Training and Fellowship Appointments:
			1982-1986				Post-doctoral fellow, Human Genetics, Yale University
Faculty Appointments:
			1986-1993				Assistant Professor of Anatomy, University of Pennsylvania School of Medicine
			1993-2000				Associate Member, Joseph Stokes Research Institute, Children's Hospital of Philadelphia
			2000				Research Investigator, Sr., Center for Bioinformatics, University of Pennsylvania
			2000-2006				Research Associate Professor of Genetics, University of Pennsylvania School of Medicine
			2006-present				Research Professor of Genetics, University of Pennsylvania School of Medicine
Hospital and/or Administrative Appointments:
			2000-present				Director, Computational Biology & Informatics Lab (CBIL), University of Pennsylvania
Other Appointments:
			2001-present				Member, Penn Genome Frontiers Institute (PGFI)
			2002-present				Member, Genomics and Computational Biology Graduate Group (GCB)
Awards, Honors and Membership in Honorary Societies:
			1986-1988				Cooley's Anemia Foundation Fellowship
			1987-1989				March of Dimes Basil O'Connor Starter Scholarship
			2000				Best Presentation, Critical Assessment of Microarray Data Analysis, Duke U.
Memberships in Professional and Scientific Societies and Other Professional Activities:
International:
1999-Present			Functional Genomics Data Society (formerly MGED) (President 2007-2011, Board of Directors, leader Ontologies Working Group.)
2000-Present			International Society for Computational Biology (ISCB)
2005-2010			ArrayExpress (Advisory Board)
National:
1987-Present			American Association for the Advancement of Science
2002-2005			Working Group of the NIGMS Human Genetic Cell Repository
2004			NIDDK Bioinformatics Advisory Committee
2004-2005			NIH Genome Study Section
2005-2007			NIH GCAT Study Section
Local:
2010-Present			Penn High Throughput Sequence Analysis group (Organizer)
Editorial Positions:
			2005-2007			Associate Editor, Bioinformatics
			2008-2010			Editorial Board, Bioinformatics
			2012-Present			Academic Editor, PeerJ journal.
Academic and Institutional Committees:
			2002			Penn Medicine Strategic Plan - Genetics Team
			2009-2012			Chair, Admissions committe, Genomics & Computational Biology graduate group
			2010-Present			Research Computing Advisory Board
			2010-2011			Chair, Genetics Department Bioinformatics Faculty Search
Major Academic and Clinical Teaching Responsibilities:
			1987-1993			Anatomy 100: Gross Human Anatomy (lecture and dissection)
			1992			Invited lecture: Cell and Molecular Biology 600
			2000			Cell Biology 520: Selected Topics in Cell Biology
			2002			Two lectures and discussion in Bioengineering 567: Modeling Biological Systems
			2003			Lecture and discussion for Genetics 550 - Genetic Principles
			2006			Lecture in "Advances in Technology", Center for Molecular Studies in Digestive and Liver Diseases, U. Penn.
			2010			Lecture in GCB 537 Advanced computational biology seminar
Lectures by Invitation:
			Feb, 1997			"Muscling immune tolerance toward islet grafts into mice," Thomas Jefferson University, Philadelphia PA
			Jun, 1998			"EpoDB: A bioinformatics system for the analysis of gene expression during erythropoiesis," CHI Bioinformatics and Genome Research, Boston MA
			Jun, 1998			"Beyond browsing: Insights into gene regulation through complex queries of databases," Cornell University, Ithaca NY
			Nov, 1998			"Exploring erythropoiesis with gene arrays and computers," A.I.duPont Institute, Wilmington DE
			Feb, 1999			"Identifying trends and lead targets in highly parallel gene expression data," DNA Analysis 1999 Conference, Florence, Italy
			Sep, 1999			"Extending gene annotation with gene expression patterns," Bridging the Gap Between Sequence and Function, Cold Spring Harbor, NY
			Nov, 1999			"RNA abundance database," Microarray Gene Expression Databases, Wellcome Trust Genome Campus, U.K.
			Apr, 2000			"An informatics framework for transcriptome annotation," Stem Cells and Pancreatic Development, NIH, Bethesda, MD
			May, 2000			"Status report on RAD, RNA Abundance Database," The Second International Meeting on Microarray Data Standards, Annotations, Ontologies, and Databases, Heidelberg, Germany
			Sep, 2000			"Microarray database tools for identifying cancer-related genes," 2nd Joint International Workshop - Histologic and cytologic characterization of human tumors: Borderline neoplasia, Capri, Italy
			Dec, 2000			"An informatics framework for gene annotation and analysis," Coriell Institute for Medical Research
			Dec, 2000			"Using non-parametric methods in the context of multiple testing to determine differentially expressed genes," CAMDA'00, Duke U.
			Apr, 2001			"An informatics framework for gene annotation and analysis," Carnegie Institute of Washington, Stanford CA
			Jun, 2001			"An Informatics Infrastructure for the analysis of gene regulation and pathways," Information and Simulation Systems for the Analysis of Gene Regulation and Metabolic Pathways, Dagstuhl, Germany
			Jun, 2001			"The future of PlasmoDB: Beyond genomic sequence," Wellcome Trust Genome Campus, U.K.
			Jul, 2001			"Microarray Gene Expression Database (MGED) Ontology Working Group," 4th Annual Bio-Ontologies Meeting, Copenhagen, Denmark
			Nov, 2001			"From MIAME to MAML: Standards documents from the Microarray Gene Expression Database (MGED) group," CHI's Microarray Data Analysis, Alexandria, VA
			Dec, 2001			"MGED Ontology: An Ontology of Biomaterial Descriptions for Microarrays," Microarray Data Analysis and Management:Bio-ontologies for Microarrays, Hinxton, Cambridge, UK
			Feb, 2002			"PlasmoDB: a case study in making a genome accessible," Dept. of Immunology, MCP-Hahnemann, Philadelphia
			Apr, 2002			"Development and usage of Microarray Gene Expression Data (MGED) standards," Johns Hopkins University, Baltimore
			May, 2002			"EPConDB: an integrated data system for pancreatic studies," Vanderbilt University, Nashville
			May, 2002			"Integrating gene expression information," Oncogenomics 2002, Dublin, Ireland
			Jul, 2002			"Microarrays and Bioinformatics: Think globally, act locally, " House Ear Institute, Los Angeles
			Aug, 2002			"The MGED ontology is an experimental ontology," 5th Annual Bio-Ontologies Meeting, Edmonton, Canada
			Oct, 2002			"Sharing microarray experiment knowledge," Chips to Hits. Philadelphia, PA.
			Oct, 2002			"Integrated Data Systems for Genomic Analysis," Genomics and Bioinformatics for the Advancement of Clinical Sciences, Thomas Jefferson University, Philadelphia, PA.
			Nov, 2002			"The MGED Ontology: A framework for describing functional genomics experiments," Standards and Ontologies for Functional Genomics. Hinxton, Cambridge, UK
			Jan, 2003			Microarray Standards, Advanced Topics in Microarray Analysis, NIH
			Feb, 2003			Generating useful information in toxicogenomics: Focused efforts: Microarray Standards, The National Academies
			Dec, 2003			RADical microarray data: standards, databases, and analysis. Yale Microarray Workshop
			Feb, 2004			Annotating Microarray Data with the MGED Ontology using the RAD Study-Annotator, GSK
			Apr, 2004			Annotating Microarray Data with the MGED Ontology, NCI Center for Bioinformatics
			May, 2004			Computational Approaches to Understanding the Genetics of Tissue Specificity, CBAT lecture, Thomas Jefferrson University
			Jun, 2004			Exploring and Understanding the Transcriptome with ESTs, Genome Sequence Analysis Course, The Jackson Laboratories
			Oct, 2004			The MGED Ontology, SOFG2, Philadelphia, PA
			Oct, 2004			GUS: A Functional Genomics Data Management System, ASM Conference on Functional Genomics and Bioinformatics Approaches to Infectious Disease Research, Portland, OR
			Nov, 2004			Computational Analysis of Tissue Specificity: Decoding Promoters. University of Kentucky
			Oct, 2005			Deconstructing transcriptional regulatory regions, GlaxoSmithKline, King of Prussia, PA
			Nov, 2005			Cracking the promoter code: Identifying regulatory modules for tissue-specific transcripts. University of Nebraska Medical Center, Lincoln, Nebraska
			Nov, 2005			Cracking the promoter code: Identifying regulatory modules for tissue-specific transcripts. Fox Chase Cancer Center, Philadelphia, PA
			Dec, 2005			PlasmoDB 5.0 provides a new look at Plasmodium vivax_ TIGR P. vivax workshop, Rockville, MD
			Dec, 2005			PlasmoDB 5.0 provides a new look at Plasmodium vivax. Vivax Malaria Research: 2005 and beyond. TIGR, Rockville, MD
			Mar, 2006			Annotating Experiments: The MGED Ontology & the Functional Genomics Investigation Ontology NIAID Ontology workshop: focus on immunology, Gaithersburg, MD
			Mar, 2006			Standards and the GUS database system for funtional genomics ITC-irst Distinguished Lecture, Trento, Italy
			Oct, 2006			Computational modeling of malarial parasite protein interactions reveals function on a genome-wide scale. Princeton University.
			Apr, 2007			Biomedical Data Integration:Putting the pieces together to fight parasites, Greater Philadelphia Bioinformatics Alliance Retreat
			Dec, 2007			Predicting protein functions in Plasmodium and other Apicomplexa. Graduate Seminar Series in Parasitology, Penn Veterinary Medicine
			Feb, 2008			Annotation-based meta-analysis of microarray experiments, Yale Biostatistics Seminar Series
			Dec, 2008			Comparative genomics, expression profiles, and study annotations:_Data integration approaches to fighting malaria and diabetes. Computational Biology seminar series at SRI International
			Mar, 2009			"Network models for understanding pancreatic islets," Vanderbilt University, Nashville, TN
			Mar, 2010			"The MGED Society: Facilitating Data Sharing and Integration with Standards," Webinar for the CTSA Omics Data Standards Working group.
			Sep, 2010			"Making the most of functional genomics data", NIH/NIDDK Center for Molecular Studies in Digestive and Liver Diseases, Penn
			Dec, 2010			Bioinformatics: Making sense of genomic data", 2010 Golden Helix Symposium® on Genetic Analysis in Translational Medicine, Athens, Greece
			Feb, 2011			"Annotating and Interpreting Functional Genomics Datasets". Scalable IT & Informatics to Support Data Intensive Life Science, San Francisco, CA.
			Apr, 2011			"Modeling processes in parasite research using the Ontoloy for Biomedical Investigations (OBI)", CaBIG Nanotechnology Working Group Webinar
			Apr, 2011			"Integrative Tools for Protozoan Parasite Research," NCBO webinar.
			Jun, 2011			"Reproducible HTS research: MINSEQE and more," CHOP/Penn NGS Symposium
			Feb, 2012			"Strategies for data mining biomedical networks," Center for Bioinformatics and Computational Biology, University of Maryland
			Oct, 2012			"Issues in Infectious Disease Genomics", FGED, Toronto
Organizing Roles in Scientific Meetings:
			Feb, 2002			MGED4 meeting Boston, MA
			Nov, 2002			Standards and Ontologies for Functional Genomics conference Hinxton, UK
			Sep, 2003			MGED 6 meeting Aix-en-Provence
			Sep, 2004			MGED 7 meeting Toronto, Canada
			Oct, 2004			Standards and Ontologies for Functional Genomics 2 (Host and Organizer) University of Pennsylvania, Phildelphia, PA
			Sep, 2005			MGED 8 Meeting Bergen, Norway
			Sep, 2007			Co-Chair of the Program Committee for DILS 2007 (4th annual workshop on Data Integration in the Life Sciences) Philadelphia, PA
			Sep, 2008			MGED 11 Meeting Riva del Garda, Italy
			Jul, 2009			Organizing and Scientific Committee, International Conference on Biomedical Ontology Buffalo, NY
			Jul, 2010			Organizing committee, MGED13 Boston, MA
			Jul, 2011			Organizing and scientific committee, International Conference on Biomedical Ontology Buffalo, NY
Bibliography:
	Research Publications, peer reviewed (print or other media):
		1. Resch J., Tunkel D., Stoeckert C., Beer M.: Osmium-labeled polysaccharides for atomic microscopy. Journal of Molecular Biology 138(4): 673-83, Apr 25 1980.
		2. Fukumaki Y., Collins F., Kole R., Stoeckert CJ Jr., Jagadeeswaran P., Duncan CH., Weissman SM., Jagadeeswaran P., Pan J., Forget BG., Weissman SM., Biro PA., Pan J., Sood AK., Kole R., Reddy VB., Weissman SM.: Sequences of human repetitive DNA, non-alpha-globin genes, and major histocompatibility locus genes. Cold Spring Harbor Symposia on Quantitative Biology 47 Pt 2: 1079-86, 1983.
		3. Stoeckert CJ Jr., Collins FS., Weissman SM.: Human fetal globin DNA sequences suggest novel conversion event. Nucleic Acids Research 12(11): 4469-79, Jun 11 1984.
		4. Collins FS., Stoeckert CJ Jr., Serjeant GR., Forget BG., Weissman SM.: G gamma beta+ hereditary persistence of fetal hemoglobin: cosmid cloning and identification of a specific mutation 5' to the G gamma gene. Proceedings of the National Academy of Sciences of the United States of America 81(15): 4894-8, Aug 1984.
		5. Stoeckert CJ Jr., Beer M., Wiggins JW., Wierman JC.: Histone positions within the nucleosome using platinum labeling and the scanning transmission electron microscope. Journal of Molecular Biology 177(3): 483-505, Aug 15 1984.
		6. Collins FS., Boehm CD., Waber PG., Stoeckert CJ Jr., Weissman SM., Forget BG., Kazazian HH Jr.: Concordance of a point mutation 5' to the G gamma globin gene with G gamma beta +. Hereditary persistence of fetal hemoglobin in the black population. Blood 64(6): 1292-6, Dec 1984.
		7. Feingold EA., Collins FS., Metherall JE., Stoeckert CJ Jr., Weissman SM., Forget BG.: Analysis of mutations associated with deletion and nondeletion hereditary persistence of fetal hemoglobin. Progress in Clinical & Biological Research 191: 107-24, 1985.
		8. Stoeckert CJ Jr., Metherall JE., Yamakawa M., Eisenstadt JM., Weissman SM., Forget BG.: Expression of the affected A gamma globin gene associated with Greek nondeletion hereditary persistence of fetal hemoglobin. [erratum appears in Mol Cell Biol 1987 Oct;7(10):3862] Molecular & Cellular Biology 7(8): 2999-3003, Aug 1987.
		9. Metherall JE., Stoeckert CJ Jr., Gillespie FP., Weissman SM., Forget BG.: Support for the causal relationship between gamma globin gene promoter mutations and nondeletion forms of hereditary persistence of fetal hemoglobin. Progress in Clinical & Biological Research 251: 347-61, 1987.
		10. Stoeckert CJ Jr., Nicolaides NC., Haines KM.: Cytosine arabinoside plus hemin treatment of a human erythroid cell line, KMOE, strongly induces embryonic, fetal, and adult beta-like globin genes. Hemoglobin 13(6): 605-17, 1989.
		11. Nicolaides NC., Stoeckert CJ Jr.: A simple, efficient method for the separate isolation of RNA and DNA from the same cells. Biotechniques 8(2): 154-6, Feb 1990.
		12. Stoeckert CJ Jr., Nicolaides NC., Haines KM., Surrey S., Bayever E.: Retroviral transfer of genes into erythroid progenitors derived from human peripheral blood. Experimental Hematology 18(11): 1164-70, Dec 1990.
		13. Schultheiss T., Lin ZX., Ishikawa H., Zamir I., Stoeckert CJ., Holtzer H.: Desmin/vimentin intermediate filaments are dispensable for many aspects of myogenesis. Journal of Cell Biology 114(5): 953-66, Sep 1991.
		14. Stoeckert CJ Jr.: Retroviral transfer of a human fetal globin gene carrying the -202 G gamma beta (+)-HPFH mutation into the human erythroleukemia line, KMOE. Hemoglobin 15(4): 257-68, 1991.
		15. Stoeckert CJ Jr., Green MB.: Erythropoietin and hydroxyurea can act on early erythroid progenitors from adult human peripheral blood to modulate fetal globin mRNA levels. Experimental Hematology 22(3): 278-82, Mar 1994.
		16. West TB., Ohene-Frempong K., Stoeckert CJ Jr., Surrey S.: Erythroid progenitors in the peripheral blood of children with sickle cell disease. American Journal of Pediatric Hematology-Oncology 16(2): 116-9, May 1994.
		17. Chahine AA., Yu M., McKernan MM., Stoeckert C., Lau HT.: Immunomodulation of pancreatic islet allografts in mice with CTLA4Ig secreting muscle cells. Transplantation 59(9): 1313-8, May 15 1995.
		18. Stoeckert CJ Jr., Cheng H.: Partial repression of human gamma-globin genes by LCR element HS3 when linked to beta-globin genes and LCR element HS2 in MEL cells. American Journal of Hematology 51(3): 220-8, Mar 1996.
		19. Lau HT., Yu M., Fontana A., Stoeckert CJ Jr.: Prevention of islet allograft rejection with engineered myoblasts expressing FasL in mice. [see comments] Science 273(5271): 109-12, Jul 5 1996.
		20. Chowrashi PK., Pemrick SM., Li S., Yi P., Clarke T., Maguire B., Ader G., Saintigny P., Mittal B., Tewari M., Stoeckert C., Stedman HH., Sylvester JE., Pepe FA.: The myosin filament XV assembly: contributions of 195 residue segments of the myosin rod and the eight C-terminal residues. Journal of Muscle Research & Cell Motility 17(5): 555-73, Oct 1996.
		21. Salas F., Haas J., Brunk B., Stoeckert CJ Jr., Overton GC.: EpoDB: a database of genes expressed during vertebrate erythropoiesis. Nucleic Acids Research 26(1): 288-9, Jan 1 1998.
		22. Ni H., Yang XD., Stoeckert CJ Jr.: Maturation and developmental stage-related changes in fetal globin gene expression are reproduced in transiently transfected primary adult human erythroblasts. Experimental Hematology 27(1): 46-53, Jan 1999.
		23. Stoeckert CJ Jr., Salas F., Brunk B., Overton GC.: EpoDB: a prototype database for the analysis of genes expressed during vertebrate erythropoiesis. Nucleic Acids Research 27(1): 200-3, Jan 1 1999.
		24. Manduchi E., Grant GR., McKenzie SE., Overton GC., Surrey S., Stoeckert CJ Jr.: Generation of patterns from gene expression data by assigning confidence to differentially expressed genes. Bioinformatics 16(8): 685-98, Aug 2000.
		25. Stoeckert C., Pizarro A., Manduchi E., Gibson M., Brunk B., Crabtree J., Schug J., Shen-Orr S., Overton GC.: A relational schema for both array-based and SAGE gene expression experiments. Bioinformatics (Oxford) 17(4): 300-8, Apr 2001.
		26. Crabtree J., Wiltshire T., Brunk B., Zhao S., Schug J., Stoeckert CJ Jr., Bucan M.: High-resolution BAC-based map of the central portion of mouse chromosome 5. Genome Research 11(10): 1746-57, Oct 2001.
		27. Brazma A., Hingamp P., Quackenbush J., Sherlock G., Spellman P., Stoeckert C., Aach J., Ansorge W., Ball CA., Causton HC., Gaasterland T., Glenisson P., Holstege FC., Kim IF., Markowitz V., Matese JC., Parkinson H., Robinson A., Sarkans U., Schulze-Kremer S., Stewart J., Taylor R., Vilo J., Vingron M.: Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.[comment] Nature Genetics 29(4): 365-71, Dec 2001.
		28. Davidson SB., Crabtree J., Brunk B., Schug J., Tannen V., Overton GC., Stoeckert CJ Jr.: K2/Kleisli and GUS: Experiments in integrated access to genomic data sources. IBM Systems Journal 40: 512-531, 2001.
		29. The Plasmodium Genome Database Collaborative: PlasmoDB: An integrative atabase of the Plasmodium falciparum genome. Nucleic Acids Research 29: 66-69, 2001.
		30. Bahl A., Brunk B., Coppel RL., Crabtree J., Diskin SJ., Fraunholz MJ., Grant GR., Gupta D., Huestis RL., Kissinger JC., Labo P., Li L., McWeeney SK., Milgram AJ., Roos DS., Schug J., Stoeckert CJ Jr.: PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished). Nucleic Acids Research 30(1): 87-90, Jan 1 2002.
		31. Schug J., Diskin S., Mazzarelli J., Brunk BP., Stoeckert CJ Jr.: Predicting gene ontology functions from ProDom and CDD protein domains. Genome Research 12(4): 648-55, Apr 2002.
		32. Scearce LM., Brestelli JE., McWeeney SK., Lee CS., Mazzarelli J., Pinney DF., Pizarro A., Stoeckert CJ Jr., Clifton SW., Permutt MA., Brown J., Melton DA., Kaestner KH.: Functional genomics of the endocrine pancreas: the pancreas clone set and PancChip, new resources for diabetes research. Diabetes 51(7): 1997-2004, Jul 2002.
		33. Spellman PT., Miller M., Stewart J., Troup C., Sarkans U., Chervitz S., Bernhart D., Sherlock G., Ball C., Lepage M., Swiatek M., Marks WL., Goncalves J., Markel S., Iordan D., Shojatalab M., Pizarro A., White J., Hubley R., Deutsch E., Senger M., Aronow BJ., Robinson A., Bassett D., Stoeckert CJ Jr., Brazma A.: Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biology 3(9): RESEARCH0046, Aug 23 2002.
		34. Manduchi E., Scearce LM., Brestelli JE., Grant GR., Kaestner KH., Stoeckert CJ Jr.: Comparison of different labeling methods for two-channel high-density microarray experiments. Physiological Genomics 10(3): 169-79, Sep 3 2002.
		35. Hackney JA., Charbord P., Brunk BP., Stoeckert CJ., Lemischka IR., Moore KA.: A molecular profile of a hematopoietic stem cell niche. Proceedings of the National Academy of Sciences of the United States of America 99(20): 13061-6, Oct 1 2002.
		36. Kissinger JC., Brunk BP., Crabtree J., Fraunholz MJ., Gajria B., Milgram AJ., Pearson DS., Schug J., Bahl A., Diskin SJ., Ginsburg H., Grant GR., Gupta D., Labo P., Li L., Mailman MD., McWeeney SK., Whetzel P., Stoeckert CJ., Roos DS.: The Plasmodium genome database.[comment] Nature 419(6906): 490-2, Oct 3 2002.
		37. Li, L., Stoeckert, C.J. Jr., Roos, D.S. : OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Res. 13(9): 2178-89, Sept 2003.
		38. Bahl, A., Brunk, B., Crabtree, J., Fraunholz, M. J., Gajria, B., Grant, G. R., Ginsburg, H., Gupta, D., Kissinger, J. C., Labo, P., Li, L., Mailman, M., Milgram, A. J., Pearson, D.S., Roos, D. S., Schug, J., Stoeckert, C. J. Jr., Whetzel, P. : PlasmoDB: The Plasmodium Genome Resource. A database integrating experimental and computational data. Nucleic Acids Res. 31(1): 212-5, 2003.
		39. Grant,G.R., Manduchi,E., Pizarro,A. and Stoeckert,C.J. Jr. : Maintaining data integrity in microarray data management. Biotechnology and Bioengineering 84(7): 795-800, 2003.
		40. Kaestner, K.H., Lee, C.S., Scearce, L.M., Brestelli, J.E., Arsenlis, A., Le, P.P., Lantz, K.A., Crabtree, J., Pizarro, A., Mazzarelli, J., Pinney, D., Fischer, S., Manduchi, E., Stoeckert, C.J. Jr., Gradwohl, G., Clifton, S.W., Brown, J.R., Inoue, H., Cras-Méneur, C., and Permutt M.A.: The transcriptional program of the endocrine pancreas in mouse and human. Diabetes 52: 1604-1610, 2003.
		41. Li, L., Brunk, B.P., Kissinger, J., Pape, D., Tang, K., Cole, R., Martin, J., Wylie, T., Dante, M., Fogarty, S.J., Howe, D.K., Liberator, P., Diaz, C., Anderson, J., White, M., Jerome, M.E.,Johnson, E.A., Radke, J.A., Stoeckert, C.J. Jr, Waterston, R.H., Clifton, S.W., Roos, D.S., Sibley, L.D. : Gene Discovery in the Apicomplexa as Revealed by EST Sequencing and Assembly of a Comparative Gene Database. Genome Res. 13: 443-454, 2003.
		42. Polacek, D.C., Passerini, A.G., Shi, C., Francesco, N.M. Manduchi, E., Grant, G.R., Powell, S., Bischof, H., Winkler, H., Stoeckert, C.J.Jr., Davies, P.F. : Fidelity and enhanced sensitivity of differential transcription profiles following linear amplification of nanogram amounts of endothelial mRNA. Physiological Genomics 13: 147-156, 2003.
		43. Zhu, Y., King, B.L., Parvizi, B., Brunk, B.P., Stoeckert, C.J. Jr, Quackenbush, J., Richardson, J., Bult, C.J. : Integrating Computationally Assembled Mouse Transcript Sequences with the Mouse Genome Informatics (MGI) Database. Genome Biology 4: R16, 2003.
		44. Li,L., Crabtree, J., Fischer, S., Pinney, D., Stoeckert, C.J. Jr., Sibley, L.D., Roos, D.S. : ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites. Nucl. Acids. Res. 32(1): D326-8. Jan 2004.
		45. Passerini, A.G., Polacek, D.C., Shi, C., Francesco, N.M., Manduchi, E., Grant, G.R., Pritchard, W.F., Powell, S., Chang, G.Y., Stoeckert, C.J.Jr., Davies, P.F. : Coexisting pro-inflammatory and anti-oxidative endothelial transcription profiles in a disturbed flow region of the adult porcine aorta. PNAS 101(8): 2482-2487, Feb 2004.
		46. Manduchi E., Grant G.R., He H., Liu J., Mailman M.D., Pizarro A.D., Whetzel P.L., Stoeckert C.J. Jr.: RAD and the RAD Study-Annotator: an approach to collection, organization, and exchange of all relevant information for high-throughput gene expression studies. Bioinformatics 20(4): 452-459, March 2004.
		47. Marciano P.G.,Brettschneider J., Manduchi E.,Davies J.E., Eastman S.,Raghupathi R.,Saatman K.E.,Speed T.P.,Stoeckert C.J.Jr., Eberwine J.H.,McIntosh T.K.: Neuron-specific mRNA complexity responses during hippocampal apoptosis following traumatic brain injury. The Journal of Neuroscience 24(12): 2866-2876, March 2004.
		48. Jones,A.,Hunt,E.,Wastling,J.,Pizarro,A.,Stoeckert,C.J.Jr.: An object model and database for functional genomics. Bioinformatics 20(10): 1583-1590, July 2004.
		49. Schug , J., Schuller, W-P., Kappen, C., Salbaum, J.M., Bucan, M., Stoeckert, C.J. Jr.: Promoter Features Related to Tissue Specificity as Measured by Shannon Entropy. Genome Biology. Genome Biology 6(4): R33, March 2005.
		50. Grant, G.R. , Liu, J., Stoeckert, C.J. Jr: A practical false discovery rate approach to identifying patterns of differential expression in microarray data Bioinformatics 21(11): 2684-90, June 2005.
		51. Passerini AG, Shi C, Francesco NM, Chuan P, Manduchi E, Grant GR, Stoeckert CJ Jr, Karanian JW, Wray-Cahen D, Pritchard WF, Davies PF.: Regional determinants of arterial endothelial phenotype dominate the impact of gender or short-term exposure to a high-fat diet. Biochem Biophys Res Commun 332(1): 142-8, June 2005.
		52. Stoeckert CJ Jr.: Functional genomics databases on the web. Cell Microbiol. 7(8): 1053-9, August 2005.
		53. Chen, F., Mackey, A.J., Stoeckert, C.J. Jr., Roos, D.S. : OrthoMCL-DB: Querying A Comprehensive Collection of Ortholog Groups. Nucleic Acids Research 34: D363-8, Jan 2006.
		54. Sun, Q., Chen, G., Streb, J.W., Long, X., Yang, Stoeckert, C.J.Jr., Miano, J.M. : Defining the mammalian CArGome. Genome Research 16(2): 197-207, Feb 2006.
		55. Date SV, Stoeckert CJ Jr.: Computational modeling of the Plasmodium falciparum interactome reveals protein functionon a genome-wide scale. Genome Research 16(4): 542-9, April 2006.
		56. Whetzel PL, Parkinson H, Causton HC, Fan L, Fostel J, Fragoso G, Game L, Heiskanen M, Morrison N, Rocca-Serra P, Sansone SA, Taylor C, White J, Stoeckert CJ Jr.: The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics 22(7): 866-73, April 2006.
		57. Sharon J. Diskin, Thomas Eck, Joel Greshock, Yael P. Mosse, Tara Naylor,Christian J. Stoeckert, Jr., Barbara L. Weber, John M. Maris, and Gregory R. Grant: STAC: A method for testing the significance of DNA copy- numberaberrations across multiple array-CGH experiments. Genome Research 16(9): 1149-58, Sept. 2006.
		58. Mazzarelli JM, Brestelli J, Gorski RK, Liu J, Manduchi E, Pinney DF, Schug J, White P, Kaestner KH, Stoeckert CJ Jr.: EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes. Nucleic Acids Res Nov. 2006 Notes: Epub ahead of print.
		59. Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ Jr, White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma A.: A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics. 7(1): 489, Nov 2006 Notes: Epub ahead of print.
		60. Deutsch EW, Ball CA, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen J, Davidson D, Eichner LJ, Goo YA, Grimmond S, Henrich T, Johnson MH, Korb M, Mills JC, Oudes A, Parkinson HE, Pascal LE, Quackenbush J, Ramialison M, Ringwald M, Sansone SA, Sherlock G, Stoeckert CJ Jr, Swedlow J, Taylor RC, Walashek L, Zhou Y, Liu AY, True LD.: Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE). OMICS 10(2): 205-8. 2006.
		61. Mazzarelli JM, White P, Gorski R, Brestelli J, Pinney DF, Arsenlis A, Katokhin A, Belova O, Bogdanova V, Elisafenko E, Gubina M, Nizolenko L, Perelman P, Puzakov M, Shilov A, Trifonoff V, Vorobjeva N, Kolchanov N, Kaestner KH, Stoeckert CJ Jr.: Novel genes identified by manual annotation and microarray expression analysis in the pancreas. Genomics. 88(6): 752-61, Dec. 2006.
		62. Stoeckert CJ Jr, Fischer S, Kissinger JC, Heiges M, Aurrecoechea C, Gajria B, Roos DS.: PlasmoDB v5: new looks, new genomes. Trends Parasitol. 22(12): 543-546, Dec. 2006.
		63. Whetzel PL, Brinkman RR, Causton HC, Fan L, Field D, Fostel J, Fragoso G, Gray T, Heiskanen M, Hernandez-Boussard T, Morrison N, Parkinson H, Rocca-Serra P, Sansone SA, Schober D, Smith B, Stevens R, Stoeckert CJ Jr, Taylor C, White J, Wood A; FuGO Working Group.: Development of FuGO: an ontology for functional genomics investigations. OMICS 10(2): 199-204. 2006.
		64. Aurrecoechea C, Heiges M, Wang H, Wang Z, Fischer S, Rhodes P, Miller J, Kraemer E, Stoeckert CJ Jr, Roos DS, Kissinger JC.: ApiDB: integrated resources for the apicomplexan bioinformatics resource center. Nucleic Acids Res. 35: D427-30. Jan 2007 Notes: Database issue.
		65. Hardy OT, Hohmeier HE, Becker TC, Manduchi E, Doliba NM, Gupta RK, White P, Stoeckert CJ Jr, Matschinsky FM, Newgard CB, Kaestner KH.: Functional genomics of the beta-cell: short-chain 3-hydroxyacyl-coenzyme A dehydrogenase regulates insulin secretion independent of K+ currents. Mol Endocrinol. 21(3): 765-73, March 2007.
		66. Gupta RK, Gao N, Gorski RK, White P, Hardy OT, Rafiq K, Brestelli JE, Chen G, Stoeckert CJ Jr, Kaestner KH.: Expansion of adult beta-cell mass in response to increased metabolic demand is dependent on HNF-4alpha. Genes Dev. 21(7 ): 756-69, April 2007.
		67. Guttman M, Mies C, Dudycz-Sulicz K, Diskin SJ, Baldwin DA, Stoeckert CJ Jr, Grant GR.: Assessing the significance of conserved genomic aberrations using high resolution genomic microarrays. PLoS Genet 3(8): e143, Aug 2007.
		68. Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, Degreef J, Hardy N, Hermjakob H, Hubbard SJ, Hussey P, Igra M, Jenkins H, Julian RK Jr, Laursen K, Oliver SG, Paton NW, Sansone SA, Sarkans U, Stoeckert CJ Jr, Taylor CF, Whetzel PL, White JA, Spellman P, Pizarro A.: The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat Biotechnol. 2007 Oct;25(10):1127-33. 25(10): 1127-33. Oct. 2007.
		69. Chen G, Jensen ST, Stoeckert CJ Jr.: Clustering of genes into regulons using integrated modeling-COGRIM. Genome Biol. 8(1): R4, 2007.
		70. Shane T. Jensen, Guang Chen, Christian J. Stoeckert, Jr.: Bayesian variable selection and data integration for biological regulatory networks. The Annals of Applied Statistics 1(2): 612-633, 2007.
		71. Gajria B, Bahl A, Brestelli J, Dommer J, Fischer S, Gao X, Heiges M, Iodice J, Kissinger JC, Mackey AJ, Pinney DF, Roos DS, Stoeckert CJ Jr, Wang H, Brunk BP.: ToxoDB: an integrated Toxoplasma gondii database resource. Nucleic Acids Res. 36: D553-6. Jan 2008 Notes: Nov 14; [Epub ahead of print
		72. Deutsch EW, Ball CA, Berman JJ, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen JH, Daian F, Dauga D, Davidson DR, Gimenez G, Goo YA, Grimmond S, Henrich T, Herrmann BG, Johnson MH, Korb M, Mills JC, Oudes AJ, Parkinson HE, Pascal LE, Pollet N, Quackenbush J, Ramialison M, Ringwald M, Salgado D, Sansone SA, Sherlock G, Stoeckert CJ Jr, Swedlow J, Taylor RC, Walashek L, Warford A, Wilkinson DG, Zhou Y, Zon LI, Liu AY, True LD.: Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Nat Biotechnol. 26(3): 305-12, March 2008.
		73. Yan B, Chen G, Saigal K, Yang X, Jensen ST, Van Waes C, Stoeckert CJ, Chen Z.: Systems biology-defined NF-kappaB regulons, interacting signal pathways and networks are implicated in the malignant phenotype of head and neck cancer cell lines differing in p53 status. Genome Biol. 9(3): R53, March 2008.
		74. Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK Jr, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novère N, Leebens-Mack J, Lewis SE, Lord P, Mallon AM, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ Jr, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann S.: Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol 26(8): 889-96. August 2008.
		75. Essien K, Hannenhalli S, Stoeckert CJ Jr.: Computational analysis of constraints on noncoding regions, coding regions and gene expression in relation to Plasmodium phenotypic diversity. PLoS ONE 3(9): e3122. Sept. 2008.
		76. Carlton JM, Adams JH, Silva JC, Bidwell SL, Lorenzi H, Caler E, Crabtree J, Angiuoli SV, Merino EF, Amedeo P, Cheng Q, Coulson RM, Crabb BS, Del Portillo HA, Essien K, Feldblyum TV, Fernandez-Becerra C, Gilson PR, Gueye AH, Guo X, Kang'a S, Kooij TW, Korsinczky M, Meyer EV, Nene V, Paulsen I, White O, Ralph SA, Ren Q, Sargeant TJ, Salzberg SL, Stoeckert CJ, Sullivan SA, Yamamoto MM, Hoffman SL, Wortman JR, Gardner MJ, Galinski MR, Barnwell JW, Fraser-Liggett CM: Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature 455(7214): 757-63. Oct. 2008.
		77. Lefterova MI, Zhang Y, Steger DJ, Schupp M, Schug J, Cristancho A, Feng D, Zhuo D, Stoeckert CJ Jr, Liu XS, Lazar MA.: PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. Genes Dev 22(21): 2941-52. Nov. 2008.
		78. Ochsner SA, Steffen DL, Stoeckert CJ Jr, McKenna NJ.: Much room for improvement in deposition rates of expression microarray datasets. Nat Methods. 5(12): 991, Dec. 2008.
		79. Aurrecoechea C, Brestelli J, Brunk BP, Carlton JM, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Miller JA, Morrison HG, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Stoeckert CJ Jr, Sullivan S, Treatman C, Wang H.: GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis. Nucleic Acids Res. 37: D526-30. January 2009 Notes: Database issue.
		80. Aurrecoechea C, Brestelli J, Brunk BP, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Miller JA, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Stoeckert CJ Jr, Treatman C, Wang H.: PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res. 37: D539-43, January 2009 Notes: Database issue.
		81. Ju W, Eichinger F, Bitzer M, Oh J, McWeeney S, Berthier CC, Shedden K, Cohen CD, Henger A, Krick S, Kopp JB, Stoeckert CJ Jr, Dikman S, Schröppel B, Thomas DB, Schlondorff D, Kretzler M, Böttinger EP: Renal gene and protein expression signatures for prediction of kidney disease progression. Am J Pathol. 174(6): 2073-85. June 2009. PMCID: 19465643
		82. Civelek Mete, Manduchi Elisabetta, Riley Rebecca J, Stoeckert Christian J, Davies Peter F: Chronic endoplasmic reticulum stress activates unfolded protein response in arterial endothelium in regions of susceptibility to atherosclerosis. Circulation research 105(5): 453-61, Aug 2009. PMCID: PMC2746924
		83. Aslett Martin, Aurrecoechea Cristina, Berriman Matthew, Brestelli John, Brunk Brian P, Carrington Mark, Depledge Daniel P, Fischer Steve, Gajria Bindu, Gao Xin, Gardner Malcolm J, Gingle Alan, Grant Greg, Harb Omar S, Heiges Mark, Hertz-Fowler Christiane, Houston Robin, Innamorato Frank, Iodice John, Kissinger Jessica C, Kraemer Eileen, Li Wei, Logan Flora J, Miller John A, Mitra Siddhartha, Myler Peter J, Nayak Vishal, Pennington Cary, Phan Isabelle, Pinney Deborah F, Ramasamy Gowthaman, Rogers Matthew B, Roos David S, Ross Chris, Sivam Dhileep, Smith Deborah F, Srinivasamoorthy Ganesh, Stoeckert Christian J, Subramanian Sandhya, Thibodeau Ryan, Tivey Adrian, Treatman Charles, Velarde Giles, Wang Haiming: TriTrypDB: a functional genomic resource for the Trypanosomatidae. Nucleic acids research Oct 2009.
		84. Granot Zvi, Swisa Avital, Magenheim Judith, Stolovich-Rain Miri, Fujimoto Wakako, Manduchi Elisabetta, Miki Takashi, Lennerz Jochen K, Stoeckert Christian J, Meyuhas Oded, Seino Susumu, Permutt M Alan, Piwnica-Worms Helen, Bardeesy Nabeel, Dor Yuval: LKB1 regulates pancreatic beta cell size, polarity, and function. Cell metabolism 10(4): 296-308, Oct 2009. PMCID: PMC2790403
		85. Bidaut G, Stoeckert CJ Jr.: Characterization of unknown adult stem cell samples by large scale data integration and artificial neural networks. Pac Symp Biocomput. 2009: 356-67. 2009.
		86. Aurrecoechea Cristina, Brestelli John, Brunk Brian P, Fischer Steve, Gajria Bindu, Gao Xin, Gingle Alan, Grant Greg, Harb Omar S, Heiges Mark, Innamorato Frank, Iodice John, Kissinger Jessica C, Kraemer Eileen T, Li Wei, Miller John A, Nayak Vishal, Pennington Cary, Pinney Deborah F, Roos David S, Ross Chris, Srinivasamoorthy Ganesh, Stoeckert Christian J, Thibodeau Ryan, Treatman Charles, Wang Haiming: EuPathDB: a portal to eukaryotic pathogen databases. Nucleic acids research 38: D415-9, January 2010 Notes: Epub 2009 Nov 13. PMCID: PMC2808945
		87. Civelek Mete, Grant Gregory R, Irolla Chrysta R, Shi Congzhu, Riley Rebecca J, Chiesa Oscar A, Stoeckert Christian J, Karanian John W, Pritchard William F, Davies Peter F: Prelesional arterial endothelial phenotypes in hypercholesterolemia: universal ABCA1 upregulation contrasts with region-specific gene expression in vivo. American journal of physiology. Heart and circulatory physiology 298(1): H163-70, Jan 2010. PMCID: PMC2806137
		88. Essien K, Stoeckert CJ Jr.: Conservation and divergence of known apicomplexan transcriptional regulons. BMC Genomics 11(1): 147, March 2010. PMCID: PMC2841118
		89. Steger DJ, Grant GR, Schupp M, Tomaru T, Lefterova MI, Schug J, Manduchi E, Stoeckert CJ Jr, Lazar MA.: Propagation of adipogenic signals through an epigenomic transition state. Genes Dev. 24(10): 1035-44, May 2010. PMCID: PMC2867208
		90. Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Soldatova LN, Stoeckert CJ Jr, Turner JA, Zheng J; OBI consortium.: Modeling biomedical experimental processes with OBI. J Biomed Semantics 1: Suppl 1:S7, June 2010. PMCID: PMC2903726
		91. Shankar R, Parkinson H, Burdett T, Hastings E, Liu J, Miller M, Srinivasa R, White J, Brazma A, Sherlock G, Stoeckert CJ Jr, Ball CA.: Annotare - a tool for annotating high-throughput biomedical investigations and resulting data. Bioinformatics August 2010. PMCID: PMC2944206
		92. Aurrecoechea C, Barreto A, Brestelli J, Brunk BP, Caler EV, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Iodice J, Kissinger JC, Kraemer ET, Li W, Nayak V, Pennington C, Pinney DF, Pitts B, Roos DS, Srinivasamoorthy G, Stoeckert CJ Jr, Treatman C, Wang H.: AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species. Nucleic Acids Res. 39: D612-9, January 2011. PMCID: PMC3013638
		93. Civelek M, Manduchi E, Riley RJ, Stoeckert CJ Jr, Davies PF: Coronary artery endothelial transcriptome in vivo: identification of endoplasmic reticulum stress and enhanced reactive oxygen species by gene connectivity network analysis. Circ Cardiovasc Genet. 4 (3): 243-52, June 2011.
		94. Fischer S, Aurrecoechea C, Brunk BP, Gao X, Harb OS, Kraemer ET, Pennington C, Treatman C, Kissinger JC, Roos DS, Stoeckert CJ.: The strategies WDK: a graphical search interface and web development kit for functional genomics databases. Database 2011: bar027, June 2011. PMCID: PMC3122067
		95. Grant GR, Farkas MH, Pizarro A, Lahens N, Schug J, Brunk B, Stoeckert CJ Jr, Hogenesch JB, Pierce EA.: Comparative Analysis of RNA-Seq Alignment Algorithms and the RNA-Seq Unified Mapper (RUM). Bioinformatics. July 2011 Notes: Epub ahead of print]
		96. Dorrell C, Schug J, Lin CF, Canaday PS, Fox AJ, Smirnova O, Bonnah R, Streeter PR, Stoeckert CJ Jr, Kaestner KH, Grompe M.: Transcriptomes of the major human pancreatic cell types. Diabetologia 54(11): 2832-44, Nov. 2011.
		97. Zheng J, Stoyanovich J, Manduchi E, Liu J, Stoeckert CJ Jr.: AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments. Database (Oxford) 2011: bar045, Dec. 2011. PMCID: PMC3244265
		98. Hald J, Galbo T, Rescan C, Radzikowski L, Sprinkel AE, Heimberg H, Ahnfelt-Rønne J, Jensen J, Scharfmann R, Gradwohl G, Kaestner KH, Stoeckert C Jr, Jensen JN, Madsen OD.: Pancreatic islet and progenitor cell surface markers with cell sorting potential. Diabetologia 55(1): 154-65, Jan 2012.
		99. Stajich JE, Harris T, Brunk BP, Brestelli J, Fischer S, Harb OS, Kissinger JC, Li W, Nayak V, Pinney DF, Stoeckert CJ Jr, Roos DS.: FungiDB: an integrated functional genomics database for fungi. Nucleic Acids Res. 40(Database issue): D675-81, January 2012. PMCID: PMC3245123
		100. Parikh PP, Zheng J, Logan-Klumper F, Stoeckert CJ Jr, Louis C, Topalis P, Protasio AV, Sheth AP, Carrington M, Berriman M, Sahoo SS.: The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms. J Biomed Semantics 3(1): 5, May 2012.
		101. Choi E, Kraus MR, Lemaire LA, Yoshimoto M, Vemula S, Potter LA, Manduchi E, Stoeckert CJ Jr, Grapin-Botton A, Magnuson MA.: Dual lineage-specific expression of Sox17 during mouse embryogenesis. Stem Cells 30(10): 2297-308, Oct. 2012.
		102. Kingsley PD, Greenfest-Allen E, Frame JM, Bushnell TP, Malik J, McGrath KE, Stoeckert CJ Jr, Palis J.: Ontogeny of erythroid gene expression. Blood Dec. 2012.
		103. Aurrecoechea C, Barreto A, Brestelli J, Brunk BP, Cade S, Doherty R, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Hu S, Iodice J, Kissinger JC, Kraemer ET, Li W, Pinney DF, Pitts B, Roos DS, Srinivasamoorthy G, Stoeckert CJ Jr, Wang H, Warrenfeltz S.: EuPathDB: The Eukaryotic Pathogen database. Nucleic Acids Res. 41(D1): D684-91, January 2013.
	Research Publications, peer-reviewed reviews:
		1. Duraisingh M, Ferdig MT, Stoeckert CJ, Volkman SK, McGovern VP.: Plasmodium research in the postgenomic era. Trends Parasitol. 22(1), Jan 2006.
		2. Ochsner SA, Steffen DL, Stoeckert CJ Jr, McKenna NJ.: Much room for improvement in deposition rates of expression microarray datasets. Nat Methods. 5(12): 991, Dec. 2008.
		3. Chervitz SA, Deutsch EW, Field D, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Stoeckert CJ Jr, Taylor CF, Taylor R, Ball CA.: Data standards for Omics data: the basis of data sharing and reuse. Methods Mol Biol. 719: 31-69, 2011.
	Research Publications, non-peer reviewed:
		1. Helen Parkinson, Stuart Aitken, Richard A. Baldock, Jonathan B. L. Bard, Albert Burger, Terry F. Hayamizu, Alan Rector, Martin Ringwald, Jeremy Rogers, Cornelius Rosse, Christian J. Stoeckert Jr, Duncan Davidson: The SOFG anatomy entry list (SAEL): an annotation tool for functional genomics data. Comparative and Functional Genomics 5(6-7): 521-527, August 2004.
	Abstracts:
		1. Chahine AA., Yu M., McKernan M., Stoeckert C., Linsley PS., Lau HT.: Local CTLA4Ig synergizes with one-dose anti-LFA-1 to achieve long-term acceptance of pancreatic islet allografts. Transplantation Proceedings 26(6): 3296, Dec 1994.
	Editorials, Reviews, Chapters, including participation in committee reports (print or other media):
		1. Beer M., Wiggins JW., Stoeckert CJ., Marenus K., Kuhn E., Erickson M.: Johns Hopkins University, Baltimore, Maryland. [Review] [37 refs] Ultramicroscopy 8(1-2): 207-18, 1982.
		2. Poncz M., Henthorn P., Stoeckert C., Surrey S.: Globin gene expression in hereditary persistence of fetal haemoglobin and (delta beta) (0)-thalassaemia. [Review] [189 refs] Oxford Surveys on Eukaryotic Genes 5: 163-203, 1988.
		3. Chahine AA., Stoeckert C., Lau HT.: Local immunomodulation to promote co-stimulatory blockade. [Review] [31 refs] Clinical Transplantation 9(3 Pt 2): 215-8, Jun 1995.
		4. Lau HT., Stoeckert CJ.: FasL--too much of a good thing? Transplanted grafts of pancreatic islet cells engineered to express Fas ligand are destroyed not protected by the immune system.[comment] Nature Medicine 3(7): 727-8, Jul 1997.
		5. Fortina P., Graves D., Stoeckert, C., Jr., McKenzie S., Surrey S.: Technology options and applications of DNA microarrays. Biochip Technology. Cheng J., Kricka L. (eds.). Harrowed Academic Publisher 2000 Notes: Chapter 10.
		6. Manduchi E., Pizarro A., Stoeckert CJ Jr.: RAD (RNA Abundance Database): an infrastructure for array data analysis. SPIE 2001 Notes: Invited overview paper.
		7. Ball CA., Sherlock G., Parkinson H., Rocca-Sera P., Brooksbank C., Causton HC., Cavalieri D., Gaasterland T., Hingamp P., Holstege F., Ringwald M., Spellman P., Stoeckert CJ Jr., Stewart JE., Taylor R., Brazma A., Quackenbush J., Microarray Gene Expression Data (MGED) Society.: Standards for microarray data. Science 298(5593): 539, Oct. 2002.
		8. Grant G., Manduchi E., Stoeckert CJ Jr.: Using non-parametric methods in the context of multiple testing to determine differentially expressed genes. Methods of microarray data analysis. S.M. Lin and K.F. Johnson (eds.). Kluwer Academic Publishers (Boston), Page: 37-55, 2002 Notes: Proceedings of the Critical Analysis of Microarray Data (CAMDA).
		9. Stoeckert, C.J. Jr., Causton, H.C., Ball, C.A. : Microarray Databases: Standards and ontologies. Nature Genetics 32(Suppl2): 469-73, 2002.
		10. Stoeckert, C.J.,Jr., Pizarro, P., Crabtree, J.C., Manduchi, E., Le, P. McWeeney, S., Grant, G.R., and Liu, J. : RAD - The RNA Abundance Database. Analyzing Gene Expression: A handbook of methods - possibilities and pitfalls. S. Lorkowski and P. Cullen (eds.). Wiley-VCH, Page: 842-843, 2002.
		11. Stoeckert, C.J. Jr., Parkinson, H. : The MGED Ontology: A framework for describing functional genomics experiments. Comparative and Functional Genomics 4: 127-132, 2003.
		12. Stoeckert, C.J.Jr: Common objects: Think global, act local. Omics 7: 103-104, 2003.
		13. Stoeckert, C.J., Jr., Quackenbush, J., Brazma, A., Ball, C. : Minimum Information About a Functional Genomics Experiment: The state of microarray standards and their extension to other technologies. Drug Discovery Today: TARGETS 3(4): 159-164, August 2004.
		14. Stoeckert C, Ball C, Brazma A, Brinkman R, Causton H, Fan L, Fostel J, Fragoso G, Heiskanen M, Holstege F, Morrison N, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Sarkans U, Sherlock G, Stevens R, Taylor C, Taylor R, Whetzel P, White J.: Wrestling with SUMO and bio-ontologies. Nat Biotechnol. 24(1): 21-2. Jan 2006.
		15. Quackenbush J, Stoeckert C, Ball C, Brazma A, Gentleman R, Huber W, Irizarry R, Salit M, Sherlock G, Spellman P, Winegarden N.: Top-down standards will not serve systems biology. Nature 440(7080): 24, March 2006.
		16. Patricia L. Whetzel, Helen Parkinson, and Christian J. Stoeckert, Jr.: Using Ontologies to Annotate Microarray Experiments. Methods in Enzymology. Brian Oliver & Alan Kimmel (eds.). Elsevier, 411, 2006 Notes: In press.
		17. Patricia L. Whetzel, Shailesh V. Date, Kobby Essien, Martin J. Fraunholz, Bindu Gajria, Gregory R. Grant, John Iodice, Jessica C. Kissinger, Philip T. Labo, Arthur J. Milgram, David S. Roos, and Christian J. Stoeckert Jr.: PlasmoDB: The Plasmodium Genomics and Functional Genomics Resource. In silico Genomics and Proteomics: Functional Annotation ofGenomes and Proteins. Nicola Mulder and Rolf Apweiler (eds.). Nova Science Publishers, 2006 Notes: In press.
		18. Gregory R. Grant, Elisabetta Manduchi, Christian J. Stoeckert, Jr.: Unit 19.6. Common steps and applications for analysis and management of microarray gene expression data. Current Protocols in Molecular Biology 2007.
		19. Bidaut Ghislain, Stoeckert Christian J: Large scale transcriptome data integration across multiple tissues to decipher stem cell signatures. Methods in enzymology 467: 229-45, 2009.
		20. Fischer S, Brunk BP, Chen F, Gao X, Harb OS, Iodice JB, Shanmugam D, Roos DS, Stoeckert CJ Jr.: Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups. Curr Protoc Bioinformatics. Chapter 6: Unit 6.12.1-19, Sept. 2011.
		21. Civelek M, Manduchi E, Grant GR, Stoeckert CJ Jr, Davies PF.: Discovery approaches to UPR in athero-susceptible endothelium in vivo. Methods Enzymol. 489: 109-26. 2011.