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Research Output

2020

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 journalArticle

Open Access
2019

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 journalArticle

Open Access
4 Scopus citations

The relationship between breastfeeding and reported respiratory and gastrointestinal infection rates in young children

TEDDY study group, Sep 18 2019, In : BMC pediatrics. 19, 1, 339.

Research output: Contribution to journalArticle

Open Access
2018

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 journalArticle

14 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 journalArticle

12 Scopus citations

The Environmental Determinants of Diabetes in the Young (TEDDY) Study: 2018 Update

The TEDDY study group, Dec 1 2018, In : Current diabetes reports. 18, 12, 136.

Research output: Contribution to journalReview article

10 Scopus citations
2017

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 journalArticle

7 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 others, Hyöty, 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 journalArticle

30 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 journalArticle

10 Scopus citations

Psychological manifestations of celiac disease autoimmunity in young children

The TEDDY study group, Mar 2017, In : Pediatrics. 139, 3, e20162848.

Research output: Contribution to journalArticle

17 Scopus citations
2016
6 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 others, Proteomics Laboratory & Repository, Jan 2016, In : JAMA Pediatrics. 170, 1, p. 20-28 9 p.

Research output: Contribution to journalArticle

103 Scopus citations

The Geropathology research network: An interdisciplinary approach for integrating pathology into research on aging

Ladiges, W., Ikeno, Y., Niedernhofer, L., Mcindoe, R. A., Ciol, M. A., Ritchey, J. & Liggitt, D., Apr 1 2016, In : Journals of Gerontology - Series A Biological Sciences and Medical Sciences. 71, 4, p. 431-434 4 p.

Research output: Contribution to journalReview article

4 Scopus citations
2015

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. & 419 others, Cooper, 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. G., Guja, C., Gutiérrez, P., Hamou, A., Hatziagelaki, E., Heath, S., Heilman, K., Helmberg, W., Hermon, O., Hernandez, M., Holzheu, I., Hosszufalusi, N., Ilonen, J., Ionescu-Tirgoviste, C., Johannesen, J., Julier, C., Kahles, H., Kinalska, I., Knip, M., Kockum, I., Kojo, E., Kordonouri, O., Kretowski, A., Krikovszky, D., Kurkhaus, A., Kuzmicki, M., Lavant, E., Long, A., Ludvigsson, J., Madacsy, L., Maliszewska, K., Marga, M., Martinez, M. P., Mauricio, D., Mazurkievicz, G., Nerup, J., Norkus, A., Mogollon, F. J. N., Okruszko, A., Pettinari, C., Phillip, M., Pirags, V., Pociot, F., Pozzilli, P., Racasan, R., Raile, K., Rappner, R., Troyano, M. J. R., Roep, B. O., 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., Sumnik, Z., Tilmann, V., Undlien, D., Urbanavicius, V., der Auwera, B. V., San Miguel, F. V., Vazeo-Gerasimidi, A., Velickiene, D., Wägner, A., Walter, M., Williams, A., Ziegler, A., Agleham, M., Aldrich, A., Alemzadeh, R., Alper, C., Aly, T., Anastassiou, D., Arora, S., Austin, A., Becker, D., Benoist, C., Berka, N., Bhatia, S., Bonella, P., Bottini, N., Boyle, S., Braden, J., Brady, B., Brickman, W., Christensen, R., Couch, R., Counts, D., Crandall, J., Daniels, M., Dolan, L., Donaldson, D., Doria, A., Eisenbarth, G., Elder, J., El-Hajj, R., Erlich, H., Fain, P., Fear, A. L., Ferry, R., Fiallo-Scharer, R., Geraghty, D., 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., Merkle, L., Metzger, D., Miao, D., Mickelson, E., Moonsamy, P., Moore, W., Moran, A., Noble, J., Olsem, G., Orban, T., Orlowski, C., Paterson, A., Pietropaolo, M., Pihoker, C., Polychronakos, C., Post, J., Postellon, D., Pugliese, A., Qu, H. Q., Quattrin, T., Rappaport, M., Raskin, P., Risbeck, H., Rodriguez, H., Rodriguez, L., Rogers, M., Rubalcava, L., Russell, B., Schatz, D., Scott, C., She, J. X., Shilling, H., 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., Zhao, L. P., Zimmerman, D., Adlem, E., Allen, J., Brown, J., Clarke, P., Clayton, D., Coleman, G., Cucca, F., Davison, L., Downes, K., Duley, S., Dunger, D., Esposito, L., Everett, V., Field, S., Hafler, J., Hardy, M., Harrison, D., Harrison, I., Hawkins, S., Healy, B., Hood, S., Howell, S., Howson, J., Maisuria, M., Meadows, W., Mistry, T., Nezhenstsev, S., Nutland, S., Ovington, N., Plagnol, V., Rainbow, D., Rainbow, K., Raj, S., Schuilenburg, H., Simpson, A., Smink, L., Smyth, D., Taylor, N., Tuomilehto, J., Wicker, L., Widmer, B., Wilson, M., Withers, H., Yang, J., Brown, M., Crews, A., Griffin, J., Hall, M., Harnish, T., Hepler, J., Hilner, J., King, N., Lohman, K., Lu, L., Nail, J., Perdue, L., Pierce, J., Reboussin, D., Rushing, S., Sale, M., Sides, E., Snively, B., Teuschler, H., Theil, G., Wagenknecht, L., 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., de Bakker, 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., Apr 28 2015, In : Nature Genetics. 47, 4, p. 381-386 6 p.

Research output: Contribution to journalArticle

243 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 journalArticle

11 Scopus citations
2014

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 others, Gesualdo, 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 journalArticle

18 Scopus citations

The same self-peptide selects conventional and regulatory CD4 + T cells with identical antigen receptors

Wojciech, L., Ignatowicz, A., Seweryn, M., Rempala, G., Singh Pabla, S., McIndoe, R. A., Kisielow, P. & Ignatowicz, L., 2014, In : Nature communications. 5, 5061.

Research output: Contribution to journalArticle

14 Scopus citations
2013

Thymus-derived regulatory T cells contribute to tolerance to commensal microbiota

Cebula, A., Seweryn, M., Rempala, G. A., Pabla, S. S., McIndoe, R. A., Denning, T. L., Bry, L., Kraj, P., Kisielow, P. & Ignatowicz, L., Apr 29 2013, In : Nature. 497, 7448, p. 258-262 5 p.

Research output: Contribution to journalArticle

208 Scopus citations
2012

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 others, Steck, 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 journalArticle

25 Scopus citations

Rare and functional SIAE variants are not associated with autoimmune disease risk in up to 66,924 individuals of European ancestry

Type 1 Diabetes Genetics Consortium, UK Inflammatory Bowel Disease (IBD) Genetics Consortium & Wellcome Trust Case Control Consortium, Jan 1 2012, In : Nature Genetics. 44, 1, p. 3-5 3 p.

Research output: Contribution to journalLetter

32 Scopus citations

Research resource: DkCOIN, the National Institute of Diabetes, Digestive and Kidney Diseases (NIDDK) Consortium Interconnectivity Network: A pilot program to aggregate research resources generated by multiple research consortia

McKenna, N. J., Howard, C. L., Aufiero, M., Easton-Marks, J., Steffen, D. L., Becnel, L. B., Magnuson, M. A., McIndoe, R. A. & Cartailler, J. P., Oct 1 2012, In : Molecular Endocrinology. 26, 10, p. 1675-1681 7 p.

Research output: Contribution to journalArticle

2 Scopus citations
2011
9 Scopus citations
2010
13 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 journalArticle

19 Scopus citations

Para SAM: A parallelized version of the significance analysis of microarrays algorithm

Sharma, A. K., Zhao, J., Podolsky, R. & McIndoe, R. A., Apr 15 2010, In : Bioinformatics. 26, 11, p. 1465-1467 3 p., btq161.

Research output: Contribution to journalArticle

1 Scopus citations
2009

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

Sharma, A., Podolsky, R., Zhao, J. & Mcindoe, R. A., May 7 2009, In : Bioinformatics. 25, 9, p. 1152-1157 6 p.

Research output: Contribution to journalArticle

14 Scopus citations
28 Scopus citations
26 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 others, Bhatia, 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. 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Research output: Contribution to journalArticle

1103 Scopus citations

Mouse models of diabetic nephropathy

Brosius, F. C., Alpers, C. E., Bottinger, E. P., Breyer, M. D., Coffman, T. M., Gurley, S. B., Harris, R. C., Kakoki, M., Kretzler, M., Leiter, E. H., Levi, M., McIndoe, R. A., Sharma, K., Smithies, O., Susztak, K., Takahashi, N. & Takahashi, T., Dec 1 2009, In : Journal of the American Society of Nephrology. 20, 12, p. 2503-2512 10 p.

Research output: Contribution to journalReview article

350 Scopus citations
2008

ParaKMeans: Implementation of a parallelized K-means algorithm suitable for general laboratory use

Kraj, P., Sharma, A., Garge, N., Podolsky, R. & McIndoe, R. A., Apr 16 2008, In : BMC Bioinformatics. 9, 200.

Research output: Contribution to journalArticle

21 Scopus citations

The IL-10 and IFN-γ pathways are essential to the potent immunosuppressive activity of cultured CD8+ NKT-like cells

Zhou, L., Wang, H., Zhong, X., Jin, Y., Mi, Q. S., Sharma, A. K., McIndoe, R. A., Garge, N., Podolsky, R. & She, J-X., Jul 29 2008, In : Genome Biology. 9, 7, R119.

Research output: Contribution to journalArticle

11 Scopus citations
2007

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 others, She, 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 journalArticle

44 Scopus citations
1 Scopus citations

Recipes for creating animal models of diabetic cardiovascular disease

Hsueh, W., Abel, E. D., Breslow, J. L., Maeda, N., Davis, R. C., Fisher, E. A., Dansky, H., McClain, D. A., McIndoe, R., Wassef, M. K., Rabadán-Diehl, C. & Goldberg, I. J., May 1 2007, In : Circulation research. 100, 10, p. 1415-1427 13 p.

Research output: Contribution to journalReview article

160 Scopus citations

The Environmental Determinants of Diabetes in the Young (TEDDY) study: Study design

Krischer, J., Rewers, M., Barriga, K., Baxter, J., Deas, A., Eisenbarth, G., Emery, L., Gesualdo, P., Hoffman, M., Norris, J., Waugh, K., Weber, S., She, J-X., Muir, A., Schatz, D., Hopkins, D., Steed, L., Silvis, K., Shankar, M., huang, Y. H. & 84 others, Yang, P., Zheng, W. P., Wang, H. J., English, K., McIndoe, R. A., Ziegler, A. G., 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., Simell, O. G., Nanto-Salonen, K., Ilonen, J., Knip, M., Veijola, R., Simell, T., Uusitalo, U., Hyöty, H., Virtanen, S. M., Kronberg-Kippila̧, 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., Bennett Johnson, S. & Oberste, S., Oct 1 2007, In : Pediatric Diabetes. 8, 5, p. 286-298 13 p.

Research output: Contribution to journalArticle

182 Scopus citations
2006

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 journalArticle

46 Scopus citations

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 journalArticle

11 Scopus citations

The application of genomic and proteomic technologies in predictive, preventive and personalized medicine

Collins, C. D., Purohit, S., Podolsky, R. H., Zhao, H. S., Schatz, D., Eckenrode, S. E., Yang, P., Hopkins, D., Muir, A., Hoffman, M., McIndoe, R. A., Rewers, M. & She, J. X., Nov 1 2006, In : Vascular Pharmacology. 45, 5, p. 258-267 10 p.

Research output: Contribution to journalArticle

47 Scopus citations
2005

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 journalArticle

6 Scopus citations
5 Scopus citations
2004

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 1 2004, In : Diabetes. 53, 2, p. 366-375 10 p.

Research output: Contribution to journalArticle

27 Scopus citations

Microarray experimental design: Power and sample size considerations

Yang, M. C. K., Yang, J. J., McIndoe, R. A. & She, J. X., Apr 1 2004, In : Physiological Genomics. 16, p. 24-28 5 p.

Research output: Contribution to journalArticle

40 Scopus citations

Molecular pathways altered by insulin B9-23 immunization

Eckenrode, S. E., Ruan, Q. G., Collins, C. D., Yang, P., McIndoe, R. A., Muir, A. & She, J-X., Jan 1 2004, In : Annals of the New York Academy of Sciences. 1037, p. 175-185 11 p.

Research output: Contribution to journalArticle

4 Scopus citations
2003

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 journalArticle

95 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 journalArticle

26 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 journalArticle

2 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 journalArticle

52 Scopus citations
2001

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 journalArticle

95 Scopus citations

Rapid decrease of RNA level of a novel mouse mitochondria solute carrier protein (Mscp) gene at 4-5 weeks of age

Li, Q. Z., Eckenrode, S., Ruan, Q. G., Wang, C. Y., Shi, J. D., McIndoe, R. A. & She, J-X., Jan 1 2001, In : Mammalian Genome. 12, 11, p. 830-836 7 p.

Research output: Contribution to journalArticle

4 Scopus citations