Richard A McIndoe

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Richard A McIndoe

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1985 …2024

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  • Article

    A big-data approach to understanding metabolic rate and response to obesity in laboratory mice

    Mouse Metabolic Phenotyping Center Energy Balance Working Group, May 2020, In: eLife. 9, p. 1-34 34 p., e53560.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    44 Scopus citations

  • A combined risk score enhances prediction of type 1 diabetes among susceptible children

    Committees, Aug 1 2020, In: Nature Medicine. 26, 8, p. 1247-1255 9 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    74 Scopus citations

  • A Comparison of Rule-based Analysis with Regression Methods in Understanding the Risk Factors for Study Withdrawal in a Pediatric Study

    TEDDY study group, Aug 26 2016, In: Scientific reports. 6, 30828.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    13 Scopus citations

  • A high-throughput population screening system for the estimation of genetic risk for type 1 diabetes: An application for the TEDDY (The Environmental Determinants of Diabetes in the Young) study

    Kiviniemi, M., Hermann, R., Nurmi, J., Ziegler, A. G., Knip, M., Simell, O., Veijola, R., Lövgren, T., Ilonen, J., Rewers, M., Barriga, K., Baxter, J., Deas, A., Eisenbarth, G., Emery, L., Gesualdo, P., Hoffman, M., Norris, J., Waugh, K., Weber, S., & 88 othersShe, J-X., Muir, A., Schatz, D., Hopkins, D., Steed, L., Choate, A., Silvis, K., Shankar, M., Huang, Y. H., Yang, P., Zheng, W. P., Wang, H. J., English, K., McIndoe, R. A., Bonifacio, E., Baumgarten, A., Hummel, S., Kersting, M., Koenig, S., Knopff, A., Locher, A., Roth, R., Schoen, S., Schwaiger, P., Sichert-Hellert, W., Winkler, C., Zimmermann, D., Nanto-Salonen, K., Simell, T., Uusitalo, U., Hyöty, H., Virtanen, S. M., Kronberg-Kippilä, C., Torma, M., Ruohonen, E., Romo, M., Mantymaki, E., Niininen, T., Nyblom, M., Stenius, A., Lernmark, Å., Almgren, P., Andrén-Aronsson, C., Andersson, E., Bianconi-Svensson, S., Carlsson, U. M., Cilio, C., Gerardsson, J., Gustavsson, B., Hansson, A., Hansson, G., Hansson, I., Ivarsson, S., Larsson, H., Karlsson, E., Katsarou, A., Lernmark, B., Massadakis, T., Nilsson, A., Järvirova, M. S., Sjöberg, B., Wallin, A., Wimar, Å., Hagopian, W. A., Brantley, M., Cowen, C., Hui, P., Hay, K. M., Jackson, M., Stepikova, V., Ugale, J., Krischer, J. P., Bray, C., Cuthbertson, D., Gowda, V., Hunt, K., Liu, S., Malloy, J., McCarthy, C., McLeod, W., Moyers, S., Nallamshetty, L., Smith, S., Akolkar, B., Briese, T., Erlich, H., Johnson, S. B. & Oberste, S., Oct 1 2007, In: Diabetes Technology and Therapeutics. 9, 5, p. 460-472 13 p.

    Research output: Contribution to journal › Article › peer-review

    53 Scopus citations

  • Alterations of renal phenotype and gene expression profiles due to protein overload in NOD-related mouse strains

    Wilson, K. H. S., McIndoe, R. A., Eckenrode, S., Morel, L., Agarwal, A., Croker, B. P. & She, J. X., Dec 21 2005, In: BMC Nephrology. 6, 17.

    Research output: Contribution to journal › Article › peer-review

    7 Scopus citations

  • A modified hyperplane clustering algorithm allows for efficient and accurate clustering of extremely large datasets

    Sharma, A., Podolsky, R., Zhao, J. & Mcindoe, R. A., 2009, In: Bioinformatics. 25, 9, p. 1152-1157 6 p.

    Research output: Contribution to journal › Article › peer-review

    16 Scopus citations

  • Analgesic antipyretic use among young children in the TEDDY study: No association with islet autoimmunity

    for the TEDDY Study Group, May 16 2017, In: BMC pediatrics. 17, 1, 127.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    17 Scopus citations

  • An analysis of the dynamic range and linearity of an infrared DNA sequencer

    McIndoe, R. A., Hood, L. & Bumgarner, R. E., Apr 1996, In: ELECTROPHORESIS. 17, 4, p. 652-658 7 p.

    Research output: Contribution to journal › Article › peer-review

    11 Scopus citations

  • Ancestral polymorphisms of MHC class II genes: Divergent allele advantage

    Wakeland, E. K., Boehme, S., She, J. X., Lu, C. C., McIndoe, R. A., Cheng, I., Ye, Y. & Potts, W. K., Jun 1990, In: Immunologic Research. 9, 2, p. 115-122 8 p.

    Research output: Contribution to journal › Article › peer-review

    112 Scopus citations

  • A novel network based linear model for prioritization of synergistic drug combinations

    Li, J., Xu, H. & McIndoe, R. A., Apr 2022, In: PloS one. 17, 4 April, e0266382.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    5 Scopus citations

  • Association between early-life antibiotic use and the risk of islet or celiac disease autoimmunity

    Kemppainen, K. M., Vehik, K., Lynch, K. F., Larsson, H. E., Canepa, R. J., Simell, V., Koletzko, S., Liu, E., Simell, O. G., Toppari, J., Ziegler, A. G., Rewers, M. J., Lernmark, Å., Hagopian, W. A., She, J-X., Akolkar, B., Schatz, D. A., Atkinson, M. A., Blaser, M. J., Krischer, J. P., & 185 othersHyöty, H., Agardh, D., Triplett, E. W., Bautista, K., Baxter, J., Bedoy, R., Felipe-Morales, D., Driscoll, K., Frohnert, B. I., Gesualdo, P., Hoffman, M., Karban, R., Norris, J., Samper-Imaz, A., Steck, A., Waugh, K., Wright, H., Adamsson, A., Ahonen, S., Ilonen, J., Jokipuu, S., Kallio, T., Karlsson, L., Kähönen, M., Knip, M., Kovanen, L., Koreasalo, M., Kurppa, K., Latva-Aho, T., Lönnrot, M., Mäntymäki, E., Multasuo, K., Mykkänen, J., Niininen, T., Niinistö, S., Nyblom, M., Rajala, P., Rautanen, J., Riikonen, A., Riikonen, M., Rouhiainen, J., Romo, M., Simell, T., Sjöberg, M., Stenius, A., Leppänen, M., Vainionpää, S., Varjonen, E., Veijola, R., Virtanen, S. M., Vähä-Mäkilä, M., Åkerlund, M., Lindfors, K., Schatz, D., Hopkins, D., Steed, L., Thomas, J., Adams, J., Silvis, K., Haller, M., Gardiner, M., McIndoe, R. A., Sharma, A. K., William, J., Young, G., Anderson, S. W., Jacobsen, L., Beyerlein, A., Bonifacio, E., Hummel, M., Hummel, S., Foterek, K., Janz, N., Kersting, M., Knopff, A., Peplow, C., Roth, R., Scholz, M., Stock, J., Warncke, K., Wendel, L., Winkler, C., Aronsson, C. A., Ask, M., Bremer, J., Carlsson, U. M., Cilio, C., Ericson-Hallström, E., Fransson, L., Gard, T., Gerardsson, J., Bennet, R., Hansen, M., Hansson, G., Hyberg, S., Johansen, F., Jonsdottir, B., Lindström, M., Lundgren, M., Månsson-Martinez, M., Markan, M., Melin, J., Mestan, Z., Ottosson, K., Rahmati, K., Ramelius, A., Salami, F., Sibthorpe, S., Sjöberg, B., Swartling, U., Amboh, E. T., Törn, C., Wallin, A., Wimar, Å., Åberg, S., Killian, M., Crouch, C. C., Skidmore, J., Carson, J., Dalzell, M., Dunson, K., Hervey, R., Johnson, C., Lyons, R., Meyer, A., Mulenga, D., Tarr, A., Uland, M., Willis, J., Becker, D., Franciscus, M., Smith, M. E. D. E., Daftary, A., Klein, M. B., Yates, C., Abbondondolo, M., Austin-Gonzalez, S., Avendano, M., Baethke, S., Brown, R., Burkhardt, B., Butterworth, M., Clasen, J., Cuthbertson, D., Eberhard, C., Fiske, S., Garcia, D., Garmeson, J., Gowda, V., Heyman, K., Laras, F. P., Lee, H. S., Liu, S., Liu, X., Lynch, K., Malloy, J., McCarthy, C., Meulemans, S., Parikh, H., Shaffer, C., Smith, L., Smith, S., Sulman, N., Tamura, R., Uusitalo, U., Vijayakandipan, P., Wood, K., Yang, J., Ballard, L., Hadley, D., McLeod, W., Bourcier, K., Briese, T., Johnson, S. B., Yu, L., Miao, D., Bingley, P., William's, A., Chandler, K., Rokni, S., Willia, C., Wyatt, R., George, G., Grace, S. & Mulholland, N., Dec 2017, In: JAMA Pediatrics. 171, 12, p. 1217-1225 9 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    77 Scopus citations

  • Association of Early Exposure of Probiotics and Islet Autoimmunity in the TEDDY Study

    Dietary Biomarkers Laboratory, Project Scientist, Other contributors, Autoantibody Reference Laboratories, Cortisol Laboratory, Data Coordinating Center, Pennsylvania Satellite Center, Washington Clinical Center, Sweden Clinical Center, Finland Clinical Center, Germany Clinical Center, Georgia/Florida Clinical Center, for the TEDDY Study Group, SNP Laboratory, RNA Laboratory and Gene Expression Laboratory, Microbiome and Viral Metagenomics Laboratory, Metabolomics Laboratory, HbA1c Laboratory, HLA Reference Laboratory, OGTT Laboratory, & 2 othersProteomics Laboratory & Repository, Jan 2016, In: JAMA Pediatrics. 170, 1, p. 20-28 9 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    215 Scopus citations

  • A statistical method for flagging weak spots improves normalization and ratio estimates in microarrays.

    Yang, M. C., Ruan, Q. G., Yang, J. J., Eckenrode, S., Wu, S., McIndoe, R. A. & She, J. X., Oct 10 2001, In: Physiological Genomics. 7, 1, p. 45-53 9 p.

    Research output: Contribution to journal › Article › peer-review

    98 Scopus citations

  • Biomarker discovery study design for type 1 diabetes in The Environmental Determinants of Diabetes in the Young (TEDDY) study

    Lee, H. S., Burkhardt, B. R., Mcleod, W., Smith, S., Eberhard, C., Lynch, K., Hadley, D., Rewers, M., Simell, O., She, J. X., Hagopian, B., Lernmark, A., Akolkar, B., Ziegler, A. G., Krischer, J. P., Barriga, K., Bautista, K., Baxter, J., Eisenbarth, G., Frank, N., & 208 othersGesualdo, P., Hoffman, M., Ide, L., Karban, R., Liu, E., Norris, J., Waugh, K., Samper-Imaz, A., Steck, A., Schatz, D., Hopkins, D., Steed, L., Thomas, J., Silvis, K., Haller, M., Shankar, M., Sheehan, E., Gardiner, M., McIndoe, R., Liu, H., Nechtman, J., Sharma, A., Williams, J., Foghis, G., Anderson W., S. W., Beyerlein, A., Bonifacio, E., Hummel, M., Hummel, S., Foterek, K., Kersting, M., Knopff, A., Koletzko, S., Peplow, C., Roth, R., Schenke, J., Stock, J., Strauss, E., Warncke, K., Winkler, C., Simell G., O. G., Hyoty, H., Ilonen, J., Knip, M., Koivu, A., Koreasalo, M., Kahonen, M., Lonnrot, M., Multasuo, K., Mantymaki, E., Mykkanen, J., Nanto-Salonen, K., Niininen, T., Nyblom, M., Rautanen, J., Riikonen, A., Romo, M., Simell, A., Simell, B., Simell, T., Simell, V., Sjoberg, M., Stenius, A., Toppari, J., Varjonen, E., Veijola, R., Virtanen M., S. M., Akerlund, M., Agardh, D., Andrén-Aronsson, C., Ask, M., Bremer, J., Carlsson, U. M., Cilio, C., Ericson-Hallstrom, E., Fransson, L., Gard, T., Gerardsson, J., Hakansson, R., Hansen, M., Hansson, G., Hyberg, S., Johansen, F., Jonasdottir, B., Jonsson, L., Larsson, H., Lernmark, B., Mansson-Martinez, M., Markan, M., Massadakis, T., Melin, J., Mestan, Z., Nilsson, A., Nilsson, E., Rahmati, K., Rosenquist, A., Salami, F., Jarvirova, M. S., Sibthorpe, S., Sjoberg, B., Swartling, U., Trulsson, E., Torn, C., Wallin, A., Wimar, A., Aberg, S., Hagopian A., W. A., Yan, X., Killian, M., Crouch, C. C., Hay M., K. M., Ayres, S., Adams, C., Bratrude, B., Coughlin, D., Fowler, G., Franco, C., Hammar, C., Heaney, D., Marcus, P., Meyer, A., Mulenga, D., Scott, E., Skidmore, J., Stabbert, J., Stepitova, V., Williams, N., Becker, D., Franciscus, M., Dalmagro-Elias, M. E., Daftary, A., Klein, M. B., Abbondondolo, M., Austin-Gonzalez, S., Brown, R., Burkhardt, B., Butterworth, M., Cuthbertson, D., Eberhard, C., Fiske, S., Gowda, V., Lane, P., Liu, S., Liu, X., Malloy, J., McCarthy, C., McLeod, W., Smith, L., Tamura, R., Uusitalo, U., Vehik, K., Washington, E., Yang, J., Bourcier, K., Briese, T., Johnson, S. B., Oberste, S., Triplett, E., Yu, L., Miao, D., Bingley, P., Williams, A., Chandler, K., Rokni, S., Long, A., Boldison, J., Butterly, J., Broadhurst, J., Carreno, G., Curnock, R., Easton, P., Geoghan, I., Goode, J., Pearson, J., Reed, C., Ridewood, S., Wyatt, R., Eriksson, E. A., Karlsson, E. L., Erlund, I., Salminen, I., Sundvall, J., Leiviska, J., Lehtonen, M., Little R., R. R., Tennill L., A. L., Erlich, H., Bugawan, T., Alejandrino, M., Fiehn, O., Wikoff, B., Kind, T., Palazoglu, M., Wong, J., Wohlgemuth, G., Petrosino F., J. F., Marcovina M., S. M., Higgins, H., Ke, S., Zhao, Y., Jiang, N., Rich S., S. S., Chen, W. M., Onengut-Gumuscu, S., Farber, E., Pickin, R. R., Davis, J. & Gallo, D., Jul 2014, In: Diabetes/Metabolism Research and Reviews. 30, 5, p. 424-434 11 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    37 Scopus citations

  • caBIONet - A .NET wrapper to access and process genomic data stored at the National Cancer Institute's Center for Bioinformatics databases

    Kraj, P. & McIndoe, R. A., Aug 15 2005, In: Bioinformatics. 21, 16, p. 3456-3458 3 p.

    Research output: Contribution to journal › Article › peer-review

    5 Scopus citations

  • Cesarean Section on the Risk of Celiac Disease in the Offspring: The Teddy Study

    for the TEDDY Study Group, Mar 1 2018, In: Journal of Pediatric Gastroenterology and Nutrition. 66, 3, p. 417-424 8 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    38 Scopus citations

  • Children’s erythrocyte fatty acids are associated with the risk of islet autoimmunity

    Repository, Other contributors, The TEDDY study group, Colorado Clinical Center, Finland Clinical Center, Georgia/Florida Clinical Center, Germany Clinical Center, Sweden Clinical Center, Washington Clinical Center, Pennsylvania Satellite Center, Data Coordinating Center, Past staff, Autoantibody Reference Laboratories, Dietary Biomarkers Laboratory, HLA Reference Laboratory & SNP Laboratory, Dec 2021, In: Scientific reports. 11, 1, 3627.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    9 Scopus citations

  • Data-adaptive algorithms for calling alleles in repeat polymorphisms

    Stoughton, R., Bumgarner, R., Frederick, W. J. & McIndoe, R. A., Jan 1997, In: ELECTROPHORESIS. 18, 1, p. 1-5 5 p.

    Research output: Contribution to journal › Article › peer-review

    4 Scopus citations

  • Designing and implementing sample and data collection for an international genetics study: The Type 1 Diabetes Genetics Consortium (T1DGC)

    the T1DGC, Aug 1 2010, In: Clinical Trials. 7, 1_suppl, p. S5-S32

    Research output: Contribution to journal › Article › peer-review

    Open Access
    15 Scopus citations

  • Detection of a large RIII-derived chromosomal segment on chromosome 10 in the H-2 congenic strain B10.RIII(71NS)/Sn

    Dong, P., Hood, L. & McIndoe, R. A., Jan 15 1996, In: Genomics. 31, 2, p. 266-269 4 p.

    Research output: Contribution to journal › Article › peer-review

    7 Scopus citations

  • Dietary Intake and Body Mass Index Influence the Risk of Islet Autoimmunity in Genetically At-Risk Children: A Mediation Analysis Using the TEDDY Cohort

    Andrén Aronsson, C., Tamura, R., Vehik, K., Uusitalo, U., Yang, J., Haller, M. J., Toppari, J., Hagopian, W., McIndoe, R. A., Rewers, M. J., Ziegler, A. G., Akolkar, B., Krischer, J. P., Norris, J. M., Virtanen, S. M. & Elding Larsson, H., 2023, In: Pediatric Diabetes. 2023, 3945064.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    2 Scopus citations

  • Differences in recruitment and early retention among ethnic minority participants in a large pediatric cohort: The TEDDY Study

    Baxter, J., Vehik, K., Johnson, S. B., Lernmark, B., Roth, R., Simell, T., Rewers, M., Barriga, K., Bautista, K., Baxter, J., Eisenbarth, G., Frank, N., Gesualdo, P., Hoffman, M., Ide, L., Karban, R., Liu, E., Norris, J., Waugh, K., Samper-Imaz, A., & 149 othersSteck, A., She, J-X., Schatz, D., Hopkins, D., Steed, L., Thomas, J., Silvis, K., Haller, M., Shankar, M., English, K., McIndoe, R. A., Liu, H., Nechtman, J., Williams, J., Foghis, G., Stephen, W., Anderson, M. D., Ziegler, A. G., Achenbach, A., Boerschmann, H., Bonifacio, E., Bunk, M., Försch, J., Henneberger, L., Hummel, M., Hummel, S., Joslowski, G., Kersting, M., Knopff, A., Kocher, N., Koletzko, S., Krause, S., Mann, A., Matzke, C., Mittermeier, A., Peplow, C., Pflüger, M., Ramminger, C., Strauss, E., Rash-Sur, S., Roth, R., Schenkel, J., Stock, J., Voit, K., Winkler, C., Wosch, A., Zwilling, M., Simell, O. G., Nanto-Salonen, K., Ilonen, J., Knip, M., Tuula Simell, V., Hyöty, H., Virtanen, S. M., Kronberg-Kippilä, C., Sjöberg, M., Simell, B., Ruohonen, E., Romo, M., Mantymaki, E., Schroderus, H., Nyblom, M., Stenius, A., Lernmark, Å., Agardh, D., Almgren, P., Andersson, E., Andrén-Aronsson, C., Ask, M., Karlsson, U. M., Cilio, C., Bremer, J., Ericson-Hallström, E., Gard, T., Gerardsson, J., Hansson, G., Hansen, M., Hyberg, S., Håkansson, R., Johansen, F., Jonsson, L., Larsson, H., Lernmark, B., Markan, M., Massadakis, T., Melin, J., Månsson-Martinez, M., Nilsson, A., Rahmati, K., Järvirova, M. S., Sibthorpe, S., Sjöberg, B., Skogberg, A., Törn, C., Wallin, A., Wimar, Å., Åberg, S., Hagopian, W. A., Yan, X., Killian, M., Cowen Crouch, C., Hay, K. M., Ayres, S., Adams, C., Bratrude, B., Coughlin, D., Fowler, G., Franco, C., Hammar, C., Heaney, D., Marcus, P., Meyer, A., Mulenga, D., Scott, E., Skidmore, J., Stabbert, J., Stepitova, V., Williams, N., Becker, D., Franciscus, M., Dalmagro-Elias, M. E., Daftary, A., Krischer, J. P., Abbondondolo, M., Ballard, L., Brown, R., Burkhardt, B., Cuthbertson, D., Eberhard, C., Fiske, S., Gowda, V., Hadley, D., Lee, H. S., Liu, S., Lynch, K., Malloy, J., McCarthy, C., McLeod, W., Smith, L., Smith, S., Uusitalo, U., Vehik, K., Washington, E., Yang, J., Akolkar, B., Briese, T., Erlich, H., Johnson, S. B. & Oberste, S., Jul 2012, In: Contemporary Clinical Trials. 33, 4, p. 633-640 8 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    34 Scopus citations

  • Differential gene expression in the salivary gland during development and onset of xerostomia in Sjögren's syndrome-like disease of the C57BL/6.NOD-Aec1Aec2 mouse

    Nguyen, C. Q., Sharma, A., Lee, B. H., She, J. X., McIndoe, R. A. & Peck, A. B., Apr 20 2009, In: Arthritis Research and Therapy. 11, 2, R56.

    Research output: Contribution to journal › Article › peer-review

    46 Scopus citations

  • Differential gene expressions in the lacrimal gland during development and onset of keratoconjunctivitis sicca in Sjögren's syndrome (SJS)-like disease of the C57BL/6.NOD-Aec1Aec2 mouse

    Nguyen, C. Q., Sharma, A., She, J. X., McIndoe, R. A. & Peck, A. B., Mar 2009, In: Experimental eye research. 88, 3, p. 398-409 12 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    34 Scopus citations

  • Dynamic changes in immune gene co-expression networks predict development of type 1 diabetes

    Repository, RNA Laboratory and Gene Expression Laboratory, SNP Laboratory, The TEDDY study group, Colorado Clinical Center, Finland Clinical Center, Georgia/Florida Clinical Center, Germany Clinical Center, Sweden Clinical Center, Washington Clinical Center, Pennsylvania Satellite Center, Data Coordinating Center, Autoantibody Reference Laboratories & HLA Reference Laboratory, Dec 2021, In: Scientific reports. 11, 1, 22651.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    4 Scopus citations

  • Early pathogenic events associated with Sjögren's syndrome (SjS)-like disease of the nod mouse using microarray analysis

    Killedar, S. Y., Eckenrode, S. E., McIndoe, R. A., She, J. X., Nguyen, C. Q., Peck, A. B. & Cha, S. R., Dec 2 2006, In: Laboratory Investigation. 86, 12, p. 1243-1260 18 p.

    Research output: Contribution to journal › Article › peer-review

    70 Scopus citations

  • Evidence for a rare prostate cancer-susceptibility locus at chromosome 1p36

    Gibbs, M., Stanford, J. L., McIndoe, R. A., Jarvik, G. P., Kolb, S., Goode, E. L., Chakrabarti, L., Schuster, E. F., Buckley, V. A., Miller, E. L., Brandzel, S., Li, S., Hood, L. & Ostrander, E. A., 1999, In: American journal of human genetics. 64, 3, p. 776-787 12 p.

    Research output: Contribution to journal › Article › peer-review

    278 Scopus citations

  • Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers

    Onengut-Gumuscu, S., Chen, W. M., Burren, O., Cooper, N. J., Quinlan, A. R., Mychaleckyj, J. C., Farber, E., Bonnie, J. K., Szpak, M., Schofield, E., Achuthan, P., Guo, H., Fortune, M. D., Stevens, H., Walker, N. M., Ward, L. D., Kundaje, A., Kellis, M., Daly, M. J., Barrett, J. C., & 418 othersCooper, J. D., Deloukas, P., Todd, J. A., Wallace, C., Concannon, P., Rich, S. S., Baskerville, T., Bautista, N., Bhatia, E., Bhatia, V., Hasan, K. B., Bonnici, F., Brodnicki, T., Browning, B., Cameron, F., Chaichanwatanakul, K., Cheung, P. T., Colman, P., Cotterill, A., Couper, J., Crock, P., Cutfield, R., Davis, T., Dixon, P., Donaghue, K., Dowling, K., Drury, P., Dye, S., Gellert, S., Ghani, R. A., Greer, R., Han, X., Harrison, L., Homatopoulos, N., Ji, L., Jones, T., Yin, L. K., Kamaruddin, N. A., Kanga, U., Kanungo, A., Kaur, G., Kek, B., Knowles, S., Krebs, J., Kumar, N., Lee, Y. J., Li, X., Liktimaskul, S., Lloyd, M., Loth, A., Louey, A., Mehra, N., Merriman, T., Min, L., Morahan, G., Moses, R., Mraz, G., Murphy, R., Nicholson, I., Panelo, A., Poh, P., Price, G., Ratnam, N., Sanjeevi, C., Sedimbi, S., Shen, S., Ying, G. S., Tait, B., Tandon, N., Thomas, A., Varney, M., Weerakulwattana, P., Willis, J., Akwo, E. A., Albret, L., Ampudia-Blasco, F., Argente, J., Avbelj, M., Babadjanova, G., Badenhoop, K., Battelino, T., Beilhack, G., Bergholdt, R., Bingley, P., Boehm, B., Bolidson, J., Brismar, K., Brorsson, C., Carlson, J., Castano, L., Chandler, K., Cherubini, V., Cinek, O., Cipponeri, E., Collado, R. C., de Leiva, A., Dzivite, I., Fagulha, A., Balcells, M. F., Cuartero, B. G., Lacalle, C. 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C., Field, L., Gabriel, S., Garge, N., Gaudieri, S., Goldstein, B., Gorodezky, C., Hamon, S., He, C., Humphreys, K., James, I., Lathrop, M., Lie, B. A., Li, D., Mack, S., McGinnis, R., McKinnon, E., McLaren, W., Nolan, D., Olsson, M., Ott, J., Owerbach, D., Patterson, C., Podolsky, R., Ramsay, P., Rangantah, V., Risch, N., Ronningen, K. S., Shao, X., Single, R., Steffes, M., Thomson, G., Valdes, A. M., Vandiedonck, C., Whittaker, P. & Zhang, Q., Apr 28 2015, In: Nature Genetics. 47, 4, p. 381-386 6 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    470 Scopus citations

  • Frequent HPV-independent p16/INK4A overexpression in head and neck cancer

    Lechner, M., Chakravarthy, A. R., Walter, V., Masterson, L., Feber, A., Jay, A., Weinberger, P. M., McIndoe, R. A., Forde, C. T., Chester, K., Kalavrezos, N., O'Flynn, P., Forster, M., Jones, T. M., Vaz, F. M., Hayes, D. N. & Fenton, T. R., Aug 2018, In: Oral Oncology. 83, p. 32-37 6 p.

    Research output: Contribution to journal › Article › peer-review

    37 Scopus citations

  • Gastrointestinal Infections Modulate the Risk for Insulin Autoantibodies as the First-Appearing Autoantibody in the TEDDY Study

    On behalf of the TEDDY Study Group, Nov 2023, In: Diabetes Care. 46, 11, p. 1908-1915 8 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    1 Scopus citations

  • Gene expression associated with interferon alfa antiviral activity in an HCV replicon cell line

    Zhu, H., Zhao, H., Collins, C. D., Eckenrode, S. E., Run, Q., McIndoe, R. A., Crawford, J. M., Nelson, D. R., She, J. X. & Liu, C., May 1 2003, In: Hepatology. 37, 5, p. 1180-1188 9 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    101 Scopus citations

  • Gene Expression Profiles Define a Key Checkpoint for Type 1 Diabetes in NOD Mice

    Eckenrode, S. E., Ruan, Q., Yang, P., Zheng, W., McIndoe, R. A. & She, J-X., Feb 2004, In: Diabetes. 53, 2, p. 366-375 10 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    30 Scopus citations

  • Gene expression profiling during all-trans retinoic acid-induced cell differentiation of acute promyelocytic leukemia cells

    Yang, L., Zhao, H., Li, S. W., Ahrens, K., Collins, C., Eckenrode, S., Ruan, Q. G., McIndoe, R. A. & She, J-X., Nov 2003, In: Journal of Molecular Diagnostics. 5, 4, p. 212-221 10 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    36 Scopus citations

  • Gene expression profiling of early-phase Sjögren's syndrome in C57BL/6.NOD-Aec1Aec2 mice identifies focal adhesion maturation associated with infiltrating leukocytes

    Peck, A. B., Saylor, B. T., Nguyen, L., Sharma, A. K., She, J-X., Nguyen, C. Q. & McIndoe, R. A., Jul 2011, In: Investigative Ophthalmology and Visual Science. 52, 8, p. 5647-5655 9 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    21 Scopus citations

  • Genetic diversity of class II genes in wild mice: definition of five evolutionary groups by RFLP analysis of A alpha and A beta.

    Wakeland, E. K., McIndoe, R. A. & McConnell, T. J., 1986, In: Current topics in microbiology and immunology. 127, p. 255-260 6 p.

    Research output: Contribution to journal › Article › peer-review

    3 Scopus citations

  • Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes

    Barrett, J. C., Clayton, D. G., Concannon, P., Akolkar, B., Cooper, J. D., Erlich, H. A., Julier, C., Morahan, G., Nerup, J., Nierras, C., Plagnol, V., Pociot, F., Schuilenburg, H., Smyth, D. J., Stevens, H., Todd, J. A., Walker, N. M., Rich, S. S., Baskerville, T., Bautista, N., & 380 othersBhatia, E., Bhatia, V., Bin Hasan, K., Bonnici, F., Brodnicki, T., Cameron, F., Chaichanwatanakul, K., Cheung, P. T., Colman, P., Cotterill, A., Couper, J., Cutfield, R., Davis, T., Dixon, P., Donaghue, K., Dowling, K., Drury, P., Dye, S., Gellert, S., Abdul Ghani, R., Greer, R., Han, X., Harrison, L., Homatopoulos, N., Ji, L., Jones, T., Yin, L. K., Kamaruddin, N. A., Kanga, U., Kanungo, A., Kaur, G., Kek, B., Knowles, S., Krebs, J., Kumar, N., Lee, Y. J., Li, X., Liktimaskul, S., Lloyd, M., Loth, A., Louey, A., Mehra, N., Merriman, T., Min, L., Morahan, G., Moses, R., Mraz, G., Murphy, R., Nicholson, I., Panelo, A., Poh, P., Price, G., Ratnam, N., Sanjeevi, C., Sedimbi, S., Shen, S., Ying, G. S., Tait, B., Tandon, N., Thomas, A., Varney, M., Weerakulwattana, P., Willis, J., Albret, L., Ampudia-Blasco, F., Argente, J., Babadjanova, G., Badenhoop, K., Battelino, T., Beilhack, G., Bergholdt, R., Bingley, P., Boehm, B., Bolidson, J., Brorsson, C., Carlson, J., Castano, L., Chandler, K., Cinek, O., Cipponeri, E., Corripio, R., Garcia Cuartero, B., de Leiva, A., Fagulha, A., Fernandez Balcells, M., Guja, C., Gutierrez, P., Hatziagelaki, E., Heath, S., Helmberg, W., Hernandez, M., Holzheu, I., Hosszufalusi, N., Ionescu-Tirgoviste, C., Johannesen, J., Julier, C., Kahles, H., Knip, M., Kockum, I., Kojo, E., Koprivarova, K., Kordonouri, O., Kretowski, A., Krikovszky, D., Kurkhaus, A., Lalic, N., Lavant, E., Long, A., Ludvigsson, J., Madacsy, L., Marga, M., Mauricio, D., Mazurkievicz, G., Nerup, J., Novoa Mogollon, F. J., Petersen, M. T., Phillip, M., Pirags, V., Pociot, F., Pozzilli, P., Rappner, R., Roep, B., Rokni, S., Rosinger, S., Rubio-Cabezas, O., Ruckgaber, C., Satman, I., Schober, E., Seufert, J., Sing, R., Skrha, J., Sobngwi, E., Somerville, M., Spinas, G., Tilmann, V., Undlien, D., Urbanavicius, V., Van der Auwera, B., Vasquez San Miguel, F., Vazeo-Gerasimidi, A., Velickiene, D., Wagner, A., Williams, A., Wurzburger, M., Ziegler, A., Agleham, M., Aldrich, A., Alemzadeh, R., Aly, T., Arora, S., Austin, A., Becker, D., Benoist, C., Berka, N., Bhatia, S., Bonella, P., Bottini, N., Boyle, S., Brady, B., Brickman, W., Christensen, R., Concannon, P., Couch, R., Counts, D., Crandall, J., Daniels, M., Dolan, L., Donaldson, D., Doria, A., Eisenbarth, G., El-Hajj, R., Erlich, H., Fain, P., Fear, A. L., Ferry, R., Fiallo-Scharer, R., Ghosh, S., Gitelman, S., Godwin, M., Goland, R., Goodman, N., Goodwin, G., Gravely, J., Greenbaum, C., Gudgeon, C., Gunville, F., Hagopian, W., Hakonarson, H., Hansen, J., Harrington, K., Hassing, J., Hilliker, W., Hoffman, R., Hulbert, E., Izquierdo, R., Jospe, N., Kaiserman, K., Kaufman, F., Kim, S., Kloos, E., Kosoy, R., Lane, J., Lane, J., Lawrence, J., Levetan, C., Levin, P., Lipton, R., Lonsdale, J., Magnuson, V., Marks, J., Mayer-Davis, B., McEvoy, R., McIndoe, R. A., Merkle, L., Metzger, D., Miao, D., Mickelson, E., Moonsamy, P., Moore, W., Moran, A., Noble, J., Olsem, G., Onengut-Gumuscu, S., Orban, T., Orlowski, C., Paterson, A., Pietropaolo, M., Pihoker, C., Polychronakos, C., Post, J., Postellon, D., Pugliese, A., Qu, H., Quattrin, T., Rappaport, M., Raskin, P., Risbeck, H., Rodriguez, H., Rodriguez, L., Rogers, M., Russell, B., Schatz, D., Scott, C., She, J-X., Shulman, D., Soyka, L., Speiser, P., Starkman, H., Steck, A., Stender, S., Stratton, L., Sur, D., Taback, S., Thrailkill, K., Toth, E., Trymbiski, P., Tsalikian, E., Vertachnik, K., Wahlen, J., Wang, X., Weber, S., Wherrett, D., Willi, S., Wilson, D., Youkey, J., Young, N., Yu, L., Zimmerman, D., Adlem, E., Allen, J., Brown, J., Burren, O., Clarke, P., Clayton, D., Coleman, G., Cooper, J., Cucca, F., Duley, S., Dunger, D., Everett, V., Hardy, M., Harrison, D., Harrison, I., Hawkins, S., Healy, B., Hood, S., Howell, S., Maisuria, M., Meadows, W., Mistry, T., Nutland, S., Ovington, N., Schuilenburg, H., Simpson, A., Smink, L., Stevens, H., Taylor, N., Todd, J., Tuomilehto, J., Walker, N., Widmer, B., Wilson, M., Withers, H., Brown, M., Chen, W. M., Crews, A., Griffin, J., Hall, M., Harnish, T., Hepler, J., Hilner, J., King, N., Lohman, K., Lu, L., Mychaleckyj, J., Nail, J., Perdue, L., Pierce, J., Reboussin, D., Rich, S., Rushing, S., Sale, M., Sides, E., Snively, B., Teuschler, H., Theil, G., Williams, D., Akolkar, B., McKeon, C., Nierras, C., Thomson, E., Altshuler, D., Au, K., Bain, S., Barcellos, L., Barral, S., Becker, T., Briggs, F., Bronson, P., Daly, M., de Bakker, P., Deloukas, P., Devlin, B., Eike, M. C., Field, L., Gabriel, S., Garge, N., Gaudieri, S., Goldstein, B., Gorodezky, C., Hamon, S., He, C., Howson, J., Humphreys, K., James, I., Lathrop, M., Lie, B. A., Li, D., Mack, S., McGinnis, R., McKinnon, E., McLaren, W., Nolan, D., Olsson, M., Ott, J., Owerbach, D., Patterson, C., Podolsky, R., Ramsay, P., Rangantah, V., Risch, N., Ronningen, K. S., Shao, X., Single, R., Steffes, M., Thomson, G., Valdes, A. M., Vandiedonck, C., Whittaker, P. & Zhang, Q., Jun 1 2009, In: Nature Genetics. 41, 6, p. 703-707 5 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    1388 Scopus citations

  • Hepatic gene expression profiling reveals key pathways involved in leptin-mediated weight loss in ob/ob mice

    Sharma, A., Bartell, S. M., Baile, C. A., Chen, B., Podolsky, R. H., McIndoe, R. A. & She, J. X., 2010, In: PloS one. 5, 8, e12147.

    Research output: Contribution to journal › Article › peer-review

    23 Scopus citations

  • High serum levels of inflammatory markers are associated with early recurrence in patients with high-grade serous ovarian cancer after platinum therapy

    Brzezinska, B., Mysona, D. P., Richardson, K. P., Rungruang, B., Hopkins, D., Bearden, G., Higgins, R., Johnson, M., Satter, K. B., McIndoe, R., Ghamande, S. & Purohit, S., Dec 2023, In: Gynecologic Oncology. 179, p. 1-8 8 p.

    Research output: Contribution to journal › Article › peer-review

  • HLA Genotype and Probiotics Modify the Association Between Timing of Solid Food Introduction and Islet Autoimmunity in the TEDDY Study

    TEDDY study group, Oct 2023, In: Diabetes Care. 46, 10, p. 1839-1847 9 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    1 Scopus citations

  • Intake of B vitamins and the risk of developing islet autoimmunity and type 1 diabetes in the TEDDY study

    Hakola, L., Mramba, L. K., Uusitalo, U., Andrén Aronsson, C., Hummel, S., Niinistö, S., Erlund, I., Yang, J., Rewers, M. J., Akolkar, B., McIndoe, R. A., Rich, S. S., Hagopian, W. A., Ziegler, A., Lernmark, Å., Toppari, J., Krischer, J. P., Norris, J. M. & Virtanen, S. M., 2024, (Accepted/In press) In: European Journal of Nutrition.

    Research output: Contribution to journal › Article › peer-review

    Open Access

  • Intergeneration CAG expansion and contraction in a Chinese HD family

    Tang, Y., Wang, Y., Yang, P., Liu, Y., Wang, B., Podolsky, R., McIndoe, R. A. & Wang, C. Y., Apr 5 2006, In: American Journal of Medical Genetics - Neuropsychiatric Genetics. 141 B, 3, p. 242-244 3 p.

    Research output: Contribution to journal › Article › peer-review

    12 Scopus citations

  • Is staff consistency important to parents’ satisfaction in a longitudinal study of children at risk for type 1 diabetes: the TEDDY study

    TEDDY study group, Dec 2022, In: BMC Endocrine Disorders. 22, 1, 19.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    4 Scopus citations

  • Joint modeling of longitudinal autoantibody patterns and progression to type 1 diabetes: results from the TEDDY study

    Ancillary Studies, Diet, Genetics, Human Subjects/Publicity/Publications, Immune Markers, Infectious Agents, Laboratory Implementation, Maternal Studies, Psychosocial, Quality Assurance, Steering, Study Coordinators, Celiac Disease, Clinical Implementation & TEDDY study group, Nov 1 2017, In: Acta Diabetologica. 54, 11, p. 1009-1017 9 p.

    Research output: Contribution to journal › Article › peer-review

    24 Scopus citations

  • Linkage analysis of 150 high-risk prostate cancer families at 1q24-25

    Goode, E. L., Stanford, J. L., Chakrabarti, L., Gibbs, M., Kolb, S., McIndoe, R. A., Buckley, V. A., Schuster, E. F., Neal, C. L., Miller, E. L., Brandzel, S., Hood, L., Ostrander, E. A. & Jarvik, G. P., Mar 2000, In: Genetic Epidemiology. 18, 3, p. 251-275 25 p.

    Research output: Contribution to journal › Article › peer-review

    42 Scopus citations

  • Linkage analysis of 49 high-risk families does not support a common familial prostate cancer-susceptibility gene at 1q24-25

    McIndoe, R. A., Stanford, J. L., Gibbs, M., Jarvik, G. P., Brandzel, S., Neal, C. L., Li, S., Gammack, J. T., Gay, A. A., Goode, E. L., Hood, L. & Ostrander, E. A., Aug 1997, In: American journal of human genetics. 61, 2, p. 347-353 7 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    108 Scopus citations

  • Localization of non-Mhc collagen-induced arthritis susceptibility loci in DBA/1j mice

    Mcindoe, R. A., Bohlman, B., Chi, E., Schuster, E., Lindhardt, M. & Hood, L., Mar 2 1999, In: Proceedings of the National Academy of Sciences of the United States of America. 96, 5, p. 2210-2214 5 p.

    Research output: Contribution to journal › Article › peer-review

    69 Scopus citations

  • MADGE: Scalable distributed data management software for cDNA microarrays

    McIndoe, R. A., Lanzen, A. & Hurtz, K., Jan 1 2003, In: Bioinformatics. 19, 1, p. 87-89 3 p.

    Research output: Contribution to journal › Article › peer-review

    2 Scopus citations

  • Maternal anxiety about a child's diabetes risk in the TEDDY study: The potential role of life stress, postpartum depression, and risk perception

    TEDDY study group, Jun 1 2015, In: Pediatric Diabetes. 16, 4, p. 287-298 12 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    20 Scopus citations

  • Metabolite-related dietary patterns and the development of islet autoimmunity

    The TEDDY study group, Dec 1 2019, In: Scientific reports. 9, 1, 14819.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    28 Scopus citations

  • Microarray analysis of gene expression in the kidneys of new- and post-onset diabetic NOD mice

    Wilson, K. H. S., Eckenrode, S. E., Li, Q. Z., Ruan, Q. G., Yang, P., Shi, J. D., Davoodi-Semiromi, A., McIndoe, R. A., Croker, B. P. & She, J-X., Aug 1 2003, In: Diabetes. 52, 8, p. 2151-2159 9 p.

    Research output: Contribution to journal › Article › peer-review

    55 Scopus citations