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Publications

2016

  • McCormick ME, Manduchi E, Witschey WR, Gorman RC, Gorman JH 3rd, Jiang YZ, Stoeckert CJ Jr, Barker AJ, Markl M, Davies PF. Integrated Regional Cardiac Hemodynamic Imaging and RNA Sequencing Reveal Corresponding Heterogeneity of Ventricular Wall Shear Stress and Endocardial Transcriptome. J Am Heart Assoc. 2016 Apr 18;5(4). pii: e003170.
    PMID: 27091183

  • Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert CJ Jr, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J. The Ontology for Biomedical Investigations. PLoS One. 2016 Apr 29;11(4):e0154556.
    PMID: 27128319 PMCID: PMC4851331

  • Brochhausen M, Zheng J, Birtwell D, Williams H, Masci AM, Ellis HJ, Stoeckert CJ Jr. OBIB-a novel ontology for biobanking. J Biomed Semantics. 2016 May 2;7:23.
    PMID: 27148435 PMCID: PMC4855778

  • Lin Y, Zheng J, He Y. VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms. J Biomed Semantics. 2016 Apr 19;7:20.
    PMID: 27099700 PMCID: PMC4837519

  • Clayton HW, Osipovich AB, Stancill JS, Schneider JD, Vianna PG, Shanks CM, Yuan W, Gu G, Manduchi E, Stoeckert CJ Jr, Magnuson MA. Pancreatic Inflammation Redirects Acinar to β Cell Reprogramming. Cell Rep. 2016 Nov 15;17(8):2028-2041.
    PMID:27851966 PMCID: PMC5131369

  • 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. 2016 Nov 29.
    PMID:27903906

  • Zheng J, Harris MR, Masci AM, Lin Y, Hero A, Smith B, He Y. The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis. J Biomed Semantics. 2016 Sep 14;7(1):53.
    PMID:27627881 PMCID:PMC5024438

2015

  • Jiang YZ, Manduchi E, Stoeckert CJ Jr, Davies PF. Arterial endothelial methylome: differential DNA methylation in athero-susceptible disturbed flow regions in vivo. BMC Genomics. 2015 Jul 7;16:506.
    PMID: 26148682 PMCID: PMC4492093

  • Gutierrez JB, Harb OS, Zheng J, Tisch DJ, Charlebois ED, Stoeckert CJ Jr, Sullivan SA. A Framework for Global Collaborative Data Management for Malaria Research. Am J Trop Med Hyg. 2015 Aug 10. pii: 15-0003.
    PMID: 26259944

  • Xiang Z, Zheng J, Lin Y, He Y. Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns. J Biomed Semantics. 2015 Jan 9;6:4.
    PMID: 25785185 PMCID: PMC4362828

  • Rocca-Serra P, Walls R, Parnell J, Gallery R, Zheng J, Sansone SA, Gonzalez-Beltran A. Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach. Database (Oxford). 2015 Jan 28;2015. pii: bau132.
    PMID: 25632945 PMCID: PMC4309925

2014

  • Zheng J, Xiang Z, Stoeckert CJ Jr, He Y. Ontodog: A web-based ontology community view generation tool. Bioinformatics. 2014 Jan 9. [Epub ahead of print]
    PMID: 24413522

  • Davies PF, Manduchi E, Stoeckert CJ, Jiménez JM, Jiang YZ. Emerging topic: Flow-related epigenetic regulation of endothelial phenotype through DNA methylation. Vascul Pharmacol. 2014 May 27. pii: S1537-1891(14)00094-9.
    PMID: 24874278

  • Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ Jr, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH. Standardized metadata for human pathogen/vector genomic sequences. PLoS One. 2014 Jun 17;9(6):e99979.
    PMID: 24936976 PMCID: PMC4061050

  • Osipovich AB, Long Q, Manduchi E, Gangula R, Hipkens SB, Schneider J, Okubo T, Stoeckert CJ Jr, Takada S, Magnuson MA. Insm1 promotes endocrine cell differentiation by modulating the expression of a network of genes that includes Neurog3 and Ripply3. Development. 2014 Aug;141(15):2939-49.
    PMID: 25053427

  • Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schürer SC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall CJ, Carey TE, States DJ, Athey BD, He Y. CLO: The cell line ontology. J Biomed Semantics. 2014 Aug 13;5:37.
    PMID: 25852852 PMCID: PMC4387853

2013

  • 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. 2013 Jan 1;41(D1):D684-91.
    PMID: 23175615

  • Greenfest-Allen E, Malik J, Palis J, Stoeckert CJ Jr. Stat and interferon genes identified by network analysis differentially regulate primitive and definitive erythropoiesis. BMC Syst Biol. 2013 May 15;7:38.
    PMID: 23675896

  • Kingsley PD, Greenfest-Allen E, Frame JM, Bushnell TP, Malik J, McGrath KE, Stoeckert CJ, Palis J. Ontogeny of erythroid gene expression. Blood. 2013 Feb 7;121(6):e5-e13.
    PMID: 23243273

2012

  • 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. 2012 May 23;3(1):5. [Epub ahead of print] PubMed PMID: 22621763.

  • 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. 2012 Jan;55(1):154-65. Epub 2011 Sep 23. PubMed PMID: 21947380.

  • 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. 2012 Jan;40(Database issue):D675-81. Epub 2011 Nov 7. PubMed PMID: 22064857; PubMed Central PMCID: PMC3245123.

  • Choi E, Kraus MR-C, Lemaire L, 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. 2012 Aug 3. doi: 10.1002/stem.1192 PMID: 22865702

2011

  • Zheng J, Stoyanovich J, Manduchi E, Liu J, Stoeckert CJ Jr. (2011) AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments. Database (Oxford). 2011 Dec 21;2011:bar045. PMID: 22190598

  • Dorrell C, Schug J, Lin CF, Canaday PS, Fox AJ, Smirnova O, Bonnah R, Streeter PR, Stoeckert CJ Jr, Kaestner KH, Grompe M. (2011) Transcriptomes of the major human pancreatic cell types. Diabetologia. 2011 Nov;54(11):2832-44. Epub 2011 Sep 1. PMID: 21882062

  • Grant GR, Farkas MH, Pizarro AD, Lahens NF, Schug J, Brunk BP, Stoeckert CJ, Hogenesch JB, Pierce EA. (2011) Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinformatics. 2011 Sep 15;27(18):2518-28. Epub 2011 Jul 19. PMID: 21775302

  • Fischer S, Brunk BP, Chen F, Gao X, Harb OS, Iodice JB, Shanmugam D, Roos DS, Stoeckert CJ Jr. (2011) Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups. Curr Protoc Bioinformatics. 2011 Sep;Chapter 6:Unit 6.12.1-19. PMID: 21901743

  • Fischer S, Aurrecoechea C, Brunk BP, Gao X, Harb OS, Kraemer ET, Pennington C, Treatman C, Kissinger JC, Roos DS, Stoeckert CJ. (2011) The strategies WDK: a graphical search interface and web development kit for functional genomics databases. Database (Oxford). 2011 Jun 23;2011:bar027. PMID: 21705364

  • Civelek M, Manduchi E, Riley RJ, Stoeckert CJ Jr, Davies PF (2011) Coronary artery endothelial transcriptome in vivo: identification of endoplasmic reticulum stress and enhanced reactive oxygen species by gene connectivity network analysis. Circ Cardiovasc Genet. 2011 Jun 1;4(3):243-52. PMID: 21493819

  • Chervitz SA, Deutsch EW, Field D, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Stoeckert CJ Jr, Taylor CF, Taylor R, Ball CA. (2011) Data standards for Omics data: the basis of data sharing and reuse. Methods Mol Biol. 2011;719:31-69. PMID: 21370078

  • Civelek M, Manduchi E, Grant GR, Stoeckert CJ Jr, Davies PF (2011) Discovery approaches to UPR in athero-susceptible endothelium in vivo. Methods Enzymol. 2011;489:109-26.PMID: 21266227

  • 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. (2011) AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species. Nucleic Acids Res. 2011 Jan;39(Database issue):D612-9. PMID: 20974635

2010

  • 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. (2010) Annotare - a tool for annotating high-throughput biomedical investigations and resulting data Bioinformatics. 2010 Aug 23 PMID: 20733062

  • Fang Y, Shi C, Manduchi E, Civelek M, Davies PF. (2010) MicroRNA-10a regulation of proinflammatory phenotype in athero-susceptible endothelium in vivo and in vitro. Proc Natl Acad Sci U S A. 2010 Jul 27;107(30):13450-5 PMID: 20624982

  • 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. (2010) Modeling biomedical experimental processes with OBI. J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S7.PMID: 20626927

  • Steger DJ, Grant GR, Schupp M, Tomaru T, Lefterova MI, Schug J, Manduchi E, Stoeckert CJ Jr, Lazar MA. (2010) Propagation of adipogenic signals through an epigenomic transition state. Genes Dev. 2010 May 15;24(10):1035-44.PMID: 20478996

  • Lefterova M.I., Steger D.J., Zhuo D., Qatanani M., Mullican S.E., Tuteja G., Manduchi E., Grant G.R., Lazar M.A. (2010) Cell-specific determinants of PPARgamma function in adipocytes and macrophages. Mol Cell Biol. 2010 May;30(9):2078-89. PMID: 20176806.

  • Essien K, Stoeckert CJ Jr. (2010) Conservation and divergence of known apicomplexan transcriptional regulons. BMC Genomics. 2010 Mar 3;11:147.PMID: 20199665

  • Civelek M, Grant GR, Irolla CR, Shi C, Riley RJ, Chiesa OA, Stoeckert CJ Jr, Karanian JW, Pritchard WF, Davies PF. (2010) Prelesional arterial endothelial phenotypes in hypercholesterolemia: universal ABCA1 upregulation contrasts with region-specific gene expression in vivo. Am J Physiol Heart Circ Physiol. 2010 Jan;298(1):H163-70.

  • Guerraty MA, Grant GR, Karanian JW, Chiesa OA, Pritchard WF, Davies PF. (2010) Hypercholesterolemia induces side-specific phenotypic changes and peroxisome proliferator-activated receptor-gamma pathway activation in swine aortic valve endothelium. Arterioscler Thromb Vasc Biol. 2010 Feb;30(2):225-31.PMID: 19926833

  • Aurrecoechea C, Brestelli J, Brunk BP, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer ET, Li W, Miller JA, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Srinivasamoorthy G, Stoeckert CJ Jr, Thibodeau R, Treatman C, Wang H. (2010) EuPathDB: a portal to eukaryotic pathogen databases. Nucleic Acids Res.

  • Aslett M, Aurrecoechea C, Berriman M, Brestelli J, Brunk BP, Carrington M, Depledge DP, Fischer S, Gajria B, Gao X, Gardner MJ, Gingle A, Grant G, Harb OS, Heiges M, Hertz-Fowler C, Houston R, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Logan FJ, Miller JA, Mitra S, Myler PJ, Nayak V, Pennington C, Phan I, Pinney DF, Ramasamy G, Rogers MB, Roos DS, Ross C, Sivam D, Smith DF, Srinivasamoorthy G, Stoeckert CJ Jr, Subramanian S, Thibodeau R, Tivey A, Treatman C, Velarde G, Wang H. (2010) TriTrypDB: a functional genomic resource for the Trypanosomatidae Nucleic Acids Res.

2009

  • Bidaut G, Stoeckert CJ Jr. (2009) Large scale transcriptome data integration across multiple tissues to decipher stem cell signatures. Methods Enzymol. 2009;467:229-45.

  • Granot Z, Swisa A, Magenheim J, Stolovich-Rain M, Fujimoto W, Manduchi E, Miki T, Lennerz JK, Stoeckert CJ Jr, Meyuhas O, Seino S, Permutt MA, Piwnica-Worms H, Bardeesy N, Dor Y. (2009) LKB1 regulates pancreatic beta cell size, polarity, and function. Cell Metab. 2009 Oct;10(4):296-308.

  • Civelek M, Manduchi E, Riley RJ, Stoeckert CJ Jr, Davies PF. (2009) Chronic endoplasmic reticulum stress activates unfolded protein response in arterial endothelium in regions of susceptibility to atherosclerosis. Circ Res. 2009 Aug 28;105(5):453-61.

  • 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, Schroeppel B, Thomas DB, Schlondorff D, Kretzler M, Boettinger EP (2009) Renal gene and protein expression signatures for prediction of kidney disease progression. Am J Pathol. 174(6): 2073-85.

  • Bidaut G, Stoeckert CJ Jr. (2009) Characterization of unknown adult stem cell samples by large scale data integration and artificial neural networks. Pac Symp Biocomput. 2009:356-67. PMID: 19209714

  • Heller R, Manduchi E, Grant GR, Ewens WJ (2009) A flexible two-stage procedure for identifying gene sets that are differentially expressed. Bioinformatics, 25(8): 1019-1025

  • Heller R, Manduchi E, Small D (2009) Matching methods for observational microarray studies. Bioinformatics 25(7): 904-909.

  • 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. (2009) PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res. 2009 Jan;37(Database issue):D539-43

  • 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. (2009) GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis. Nucleic Acids Res. 2009 Jan;37(Database issue):D526-30.

2008

  • Ochsner SA, Steffen DL, Stoeckert CJ Jr, McKenna NJ. (2008) Much room for improvement in deposition rates of expression microarray datasets. Nat Methods. 5(12): 991, Dec. 2008.

  • Lefterova MI, Zhang Y, Steger DJ, Schupp M, Schug J, Cristancho A, Feng D, Zhuo D, Stoeckert CJ Jr, Liu XS, Lazar MA. (2008) PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale Genes Dev 22(21): 2941-52. Nov. 2008.

  • 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 (2008) Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature 455(7214): 757-63. Oct. 2008.

  • Essien K, Hannenhalli S, Stoeckert CJ Jr. (2008) Computational analysis of constraints on noncoding regions, coding regions and gene expression in relation to Plasmodium phenotypic diversity. PLoS ONE. 2008 Sep 1;3(9):e3122.

  • Yan B, Chen G, Saigal K, Yang X, Jensen ST, Van Waes C, Stoeckert CJ, Chen Z. (2008) 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. 2008;9(3):R53. Epub 2008 Mar 11.

  • 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. (2008) ToxoDB: an integrated Toxoplasma gondii database resource. Nucleic Acids Res. 2008 Jan;36(Database issue):D553-6.

  • 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. (2008) Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Nat Biotechnol. 2008 Mar;26(3):305-12.

  • 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, Novère NL, 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. (2008) Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol. 2008 Aug;26(8):889-96.

2007

  • Shane T. Jensen, Guang Chen, Christian J. Stoeckert, Jr. (2007) Bayesian variable selection and data integration for biological regulatory networks. The Annals of Applied Statistics 1(2): 612-633.

  • 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. (2007) 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.

  • Guttman M, Mies C, Dudycz-Sulicz K, Diskin SJ, Baldwin DA, Stoeckert CJ Jr, Grant GR (2007) Assessing the significance of conserved genomic aberrations using high resolution genomic microarrays. PLoS Genet 3(8): e143, Aug 2007

  • Gregory R. Grant, Elisabetta Manduchi, Christian J. Stoeckert, Jr. (2007) Common steps and applications for analysis and management of microarray gene expression data. Current Protocols in Molecular Biology. Unit 19.6

  • Chen G, Jensen ST, Stoeckert CJ Jr. (2007) Clustering of genes into regulons using integrated modeling-COGRIM Genome Biol. 8(1): R4, 2007

  • Gupta RK, Gao N, Gorski RK, White P, Hardy OT, Rafiq K, Brestelli JE, Chen G, Stoeckert CJ Jr, Kaestner KH. (2007) 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.

  • Hardy OT, Hohmeier HE, Becker TC, Manduchi E, Doliba NM, Gupta RK, White P, Stoeckert CJ Jr, Matschinsky FM, Newgard CB, Kaestner KH. (2007) Functional genomics of the beta-cell: SCHAD regulates insulin secretion independent of K+ currents. Mol. Endocrinol. 21(3): 765-73, March 2007

  • Aurrecoechea C, Heiges M, Wang H, Wang Z, Fischer S, Rhodes P, Miller J, Kraemer E, Stoeckert CJ Jr, Roos DS, Kissinger JC (2007) ApiDB: integrated resources for the apicomplexan bioinformatics resource center Nucleic Acids Research 35: D427-30. Jan 2007

2006

  • 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. (2006) A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB BMC Bioinformatics 7(1): 489, 2006

  • Mazzarelli JM, Brestelli J, Gorski RK, Liu J, Manduchi E, Pinney DF, Schug J, White P, Kaestner KH, Stoeckert CJ Jr. (2006) EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes. Nucleic Acids Research Nov. Epub ahead of print.

  • Patricia L. Whetzel, Helen Parkinson, and Christian J. Stoeckert, Jr. (2006) Using Ontologies to Annotate Microarray Experiments. Methods in Enzymology. Brian Oliver & Alan Kimmel (eds.). Elsevier, Vol. 411, 2006

  • 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. (2006) 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

  • 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. (2006) Novel genes identified by manual annotation and microarray expression analysis in the pancreas. Genomics. 88(6): 752-61, Dec. 2006.

  • Stoeckert CJ Jr, Fischer S, Kissinger JC, Heiges M, Aurrecoechea C, Gajria B, Roos DS. (2006) PlasmoDB v5: new looks, new genomes. Trends Parasitol. 22(12): 543-546, Dec. 2006

  • 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 (2006) STAC: A method for testing the significance of DNA copy- numberaberrations across multiple array-CGH experiments. Genome Research 16(9): 1149-58, Sept. 2006.

  • 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 (2006) Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE). OMICS 10(2): 205-8. 2006

  • 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 (2006) Development of FuGO: an ontology for functional genomics investigations. OMICS 10(2): 199-204. 2006

  • 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. (2006) The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics 22(7): 866-73, April 2006.

  • Date SV, Stoeckert CJ Jr. (2006) Computational modeling of the Plasmodium falciparum interactome reveals protein functionon a genome-wide scale Genome Res. 2006 Apr;16(4):542-9.

  • Sun, Q., Chen, G., Streb, J.W., Long, X., Yang, Stoeckert, C.J.Jr., Miano, J.M. (2006) Defining the mammalian CArGome. Genome Research 16(2): 197-207, Feb 2006.

  • Chen, F., Mackey, A.J., Stoeckert, C.J. Jr., Roos, D.S. (2006) OrthoMCL-DB: Querying A Comprehensive Collection of Ortholog Groups. Nucleic Acids Research Vol. 34: D363-8, Jan 2006.

  • Duraisingh M, Ferdig MT, Stoeckert CJ, Volkman SK, McGovern VP. (2006) Plasmodium research in the postgenomic era. Trends Parasitol. 22(1), Jan 2006.

2005

  • Stoeckert CJ Jr. (2005) Functional genomics databases on the web Cell Microbiol. 7(8): 1053-9.

  • Passerini AG, Shi C, Francesco NM, Chuan P, Manduchi E, Grant GR, Stoeckert CJ Jr, Karanian JW, Wray-Cahen D, Pritchard WF, Davies PF (2005) Regional determinants of arterial endothelial phenotype dominate the impact of gender or short-term exposure to a high-fat diet. Biochemical and Biophysical Research Communications, 332:142-148.

  • Schug J, Schuller WP, Kappen C, Salbaum JM, Bucan M, Stoeckert CJ Jr. (2005) Promoter features related to tissue specificity as measured by Shannon entropy. Genome Biol. 2005;6(4):R33. Epub 2005 Mar 29.

  • Grant GR, Liu J, Stoeckert CJ Jr. (2005) A practical false discovery rate approach to identifying patterns of differential expression in microarray data. Bioinformatics. 2005 Mar 29

  • Simmons C.A., Grant G.R., Manduchi E., Davies P.F. (2005) Spatial heterogeneity of endothelial phenotypes correlates with side-specific vulnerability to calcification in normal porcine aortic valves. Circulation Research, 96(7):792-799

2004

  • Jones,A.,Hunt,E.,Wastling,J.,Pizarro,A.,Stoeckert,C.J.Jr (2004) An object model and database for functional genomics. Bioinformatics 20(10): 1583-1590, July 2004.

  • Friedman JR, Larris B, Le PP, Peiris TH, Arsenlis A, Schug J, Tobias JW, Kaestner KH, Greenbaum LE. (2004) Orthogonal analysis of C/EBPbeta targets in vivo during liver proliferation. Proc Natl Acad Sci U S A. 2004 Aug 31;101(35):12986-91.

  • 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. (2004) Neuron-specific mRNA complexity responses during hippocampal apoptosis following traumatic brain injury. The Journal of Neuroscience, 24(12): 2866-2876

  • Manduchi E., Grant G.R., He H., Liu J., Mailman M.D., Pizarro A.D., Whetzel P.L., Stoeckert C.J. Jr. (2004) 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

  • Li,L., Crabtree, J., Fischer, S., Pinney, D., Stoeckert, C.J. Jr., Sibley, L.D., Roos, D.S. (2004) ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites. Nucl. Acids. Res. 32(1): D326-8. Jan 2004

  • 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. (2004) Coexisting pro-inflammatory and anti-oxidative endothelial transcription profiles in a disturbed flow region of the adult porcine aorta. PNAS, 101(8): 2482-2487

2003

  • Manduchi E. (2003) Gene expression array studies: challenges, standards, and infrastructures. Minerva Biotecnologica, 15(4): 201-206.

  • Stoeckert, C.J. Jr. (2003) Common objects: Think global, act local. Omics Vol. 7: 103-104

  • Grant G.R., Manduchi E., Pizarro A., Stoeckert C.J. Jr. (2003) Maintaining data integrity in microarray data management. Biotechnology and Bioengineering, 84(7):795-800.

  • Li, L., Stoeckert, C.J. Jr., Roos, D.S. (2003) OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Res. 2003 Sep;13(9):2178-89.

  • 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-Meneur C., Permutt M.A. (2003) Transcriptional Program of the Endocrine Pancreas in Mice and Humans. Diabetes 52(7): 1604-1610

  • 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. (2003) Fidelity and enhanced sensitivity of differential transcription profiles following linear amplification of nanogram amounts of endothelial mRNA Physiological Genomics, 13: 147-156

  • Zhu, Y., King, B.L., Parvizi, B., Brunk, B.P., Stoeckert, C.J. Jr., Quackenbush, J., Richardson, J., Bult, C.J. (2003) Integrating computationally assembled mouse transcript sequences with the Mouse Genome Informatics (MGI) database. Genome Biol. 2003;4(2):R16.

  • Li, L., Brunk, B.P., Kissinger, J.C., Pape, D., Tang, K., Cole, R.H., 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. (2003) Gene Discovery in the Apicomplexa as Revealed by EST Sequencing and Assembly of a Comparative Gene Database. Genome Res. 2003 Mar;13(3):443-54.

  • 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.D., Milgram, A.J., Pearson, D.S., Roos, D.S., Schug, J., Stoeckert, C.J. Jr., Whetzel, P. (2003) PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data. Nucleic Acids Res. 2003 Jan 1;31(1):212-5.

  • Christian J. Stoeckert Jr, Helen Parkinson (2003) The MGED ontology: A Framework for Describing Functional Genomics Experiments Comparative and Functional Genomics Volume 4, Issue 1, 2003. Pages: 127-132

  • Schug, J. (2003) Using TESS to Predict Transcription Factor Binding Sites in DNA Sequence Appears in Baxevanis, A.D., Davison, D.B., Page, R.D.M., Petsko, G.A., Stein, L.D., and Stormo, G.D. (eds.) 2003. Current Protocols in Bioinformatics. John Wiley & Sons.

2002

2001

  • Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C.A., Causton, H.C., Gaasterland, T., Glenisson, P., Holstege, F.C.P., Kim, I.F., Markowitz, V., Matese, J.C., Parkinson, H., Robinson, A., Sarkans, U., Schulze-Kremer, S., Stewart, J., Taylor, R., Vilo, J., Vingron, M. (2001) Minimum Information About a Microarray Experiment (MIAME): Toward Standards for Microarray Data. Nature Genetics 29:365-371, 2001.

  • The RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium [including CBIL annotator Joan Mazzarelli] (2001) Functional annotation of a full-length mouse cDNA collection Nature 20001 Feb 8; 409 (6821):685-90

  • Crabtree, J., Wiltshire, T., Brunk, B., Zhao, S., Schug, J., Stoeckert, C., Bucan, M. (2001) High-resolution BAC-based Map of the Central Portion of Mouse Chromosome 5. Genome Res. October 2001; 11: 1746-1757.
    Manduchi, E., Pizarro, A., Stoeckert, C. (2001) RAD (RNA Abundance Database): an infrastructure for array data analysis. Proc. SPIE, vol 4266, pp. 68-78.

  • Ewens, W., Grant, G. (2001) Statistical Methods in Bioinformatics: An Introduction. Springer-Verlag

  • Davidson, S.B., Crabtree, J., Brunk, Brian P., Schug, J., Tannen, V., Overton, G.C., Stoeckert, C.J. Jr. (2001) K2/Kleisli and GUS: Experiments in Integrated Access to Genomic Data Sources. IBM Systems Journal: 40(2), p. 512-531.

  • Stoeckert, C., Pizarro, A., Manduchi, E., Gibson, M., Brunk, B., Crabtree, J., Schug, S., Shen-Orr, S., Overton, G.C. (2001) A relational schema for both array-based and SAGE gene expression experiments. Bioinformatics 17(4), 300-308 (2001).

  • The Plasmodium Genome Database Collaborative (2001) PlasmoDB: An integrative database of the Plasmodium falciparum genome. Tools for accessing and analyzing finished and unfinished sequence data. Nucleic Acids Res., 2001, Vol. 29, No. 1 66-69

2000

  • Manduchi, E., Grant, G.R., McKenzie, S.E., Overton, G.C., Surrey, S., Stoeckert, C.J. Jr. (2000) Generation of patterns from gene expression data by assigning confidence to differentially expressed genes. Bioinformatics 16(8), 685-698 (2000).<

  • Phillips, R.L., Ernst, R.E., Brunk B., Ivanova, N., Mahan, M.A., Deanehan, J.K., Moore, K.A., Overton, G.C., Lemischka, I.R. (2000) The genetic program of hematopoietic stem cells. Science 288, 1635-1640.

  • Kolchanov, N.A., Podkolodnaya, O.A., Ananko, E.A., Ignatieva, E.V., Stepanenko, I.L., Kel-Margoulis, O.V., Kel, A.E., Merkulova, T.I., Goryachkovskaya, T.N., Busygina, T.V., Kolpakov, F.A., Podkolodny, N.L., Naumochkin, A.N., Korostishevskaya, I.M., Romashchenko, A.G., Overton, G.C. (2000) Transcription regulatory regions database (TRRD): its status in 2000. Nucleic Acids Res. 2000 Jan 1;28(1):298-301.

1999

  • Grant, G.R., Manduchi, E., Cheung, V.G., Ewens, W.J. (1999) Significance testing for direct identity-by-descent mapping. Ann. Hum. Genet., 63: 441-454.

  • Fischer, S., Crabtree, J., Brunk, B., Gibson, M., Overton, G.C. (1999) bioWidgets: Data Interaction Components for Genomics. Bioinformatics 15(10): 837-846 (1999).

  • Stoeckert, C.J. Jr., Salas, F., Brunkb, B., Overton, G.C. (1999) EpodDB: a prototype database for the analysis of genes expressed during vertebrate erythropoiesis. Nucl. Acids Res. 27:200-203. Reproduced with permission from NAR Online.

1998

  • Ajioka, J.W., Boothroyd, J.C., Brunk, B.P., Hehl, A., Hillier, L., Manger, I.D., Marra, M., Overton, G.C., Roos, D.S., Wan, K.L., Waterston, R., Sibley, L.D. (1998) Gene discovery by EST sequencing in Toxoplasma gondii reveals sequences restricted to the Apicomplexa. Genome Res. 1998 Jan;8(1):18-28.

  • Salas, F., Haas, J., Brunk, B., Stoeckert, C.J. Jr., Overton, G.C. (1998) EpoDB: a database of genes expressed during vertebrate erythropoiesis. Nucl. Acids Res. 26:288-289.

  • Stoeckert, C., Podkolodnaya, O.A., Kel, A.E., Brunk, B., Haas, J., Salas, F., Stepanenko, I.L., Ignatieva, E.V., Kel-Margoulis, O.V., Ananko, E.A., Podkolodny, N.L., Overton, G.C., Kolchanov, N.A. (1998) EpoGERD. Proceedings of the First International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'98), 1, 20-24.

  • Overton, G.C., Bailey, C., Crabtree, J., Gibson, M., Fischer, S., Schug, J. (1998) The GAIA software framework for genome annotation. Pacific Symposium on Biocomputing, 1998: 291-302.

  • Bailey, L.C., Searls, D.B., Overton, G.C. (1998) Analysis of EST-driven gene annotation in human genomic sequence. Genome Res. 8(4): 362-76

1997

  • Schug, J., Overton, G.C. (1997) TESS: Transcription Element Search Software on the WWW Technical Report CBIL-TR-1997-1001-v0.0, of the Computational Biology and Informatics Laboratory, School of Medicine, University of Pennsylvania, 1997

  • Schug, J., Overton, G.C. (1997) Modeling transcription factor binding sites with Gibbs Sampling and Minimum Description Length encoding. ISMB 1997; 5:268-71.

1996

  • Pollak, E.S., Hung, H.L., Godin, W., Overton, G.C., High, K.A. (1996) Functional characterization of the human factor VII 5'-flanking region. J Biol Chem. 1996 Jan 19;271(3):1738-47.

  • Salas, F., Haas, J., Stoeckert, C.J. Jr., Overton, G.C. (1996) EpoDB: an erythropoiesis gene expression database in progress. Proceedings of the German Conference on Bioinformatics, Leipzig, Germany, Sept. 30-Oct.2, 1996.

1994

  • Hart, K.W., Searls, D.B., Overton, G.C. (1994) SORTEZ: a relational translator for NCBI's ASN.1 database. Comput Appl Biosci. 1994 Jul;10(4):369-78.

  • Overton, G.C., Aaronson, J.S., Haas, J., Adams, J. (1994) QGB: a system for querying sequence database fields and features. J Comput Biol. 1994 Spring;1(1):3-14.

1993

  • Aaronson, J.S., Haas, J., Overton, G.C. (1993) Knowledge discovery in GenBank. ISMB 1993;1:3-11.

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