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Research Output 1985 2018

  • 3462 Citations
  • 24 h-Index
  • 53 Article
  • 5 Review article
  • 1 Conference contribution
  • 1 Comment/debate
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Article
1985

Patterns of genetic diversity among class II histocompatibility genes in wild mice

McConnell, T. J., McIndoe, R. A. & Wakeland, E. K., Jan 1 1985, In : Federation Proceedings. 44, 3

Research output: Contribution to journalArticle

MHC Class II Genes
Histocompatibility
1986
3 Citations (Scopus)

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., Jan 1 1986, In : Current Topics in Microbiology and Immunology. 127, p. 255-260 6 p.

Research output: Contribution to journalArticle

Muridae
H-2 Antigens
MHC Class II Genes
Histocompatibility Antigens
Chromosome Mapping
1988
85 Citations (Scopus)

The origin of MHC class II gene polymorphism within the genus Mus

McConnell, T. J., Talbot, W. S., McIndoe, R. A. & Wakeland, E. K., Jan 1 1988, In : Nature. 332, 6165, p. 651-654 4 p.

Research output: Contribution to journalArticle

MHC Class II Genes
Major Histocompatibility Complex
Alleles
Short Interspersed Nucleotide Elements
Exons
1990
71 Citations (Scopus)

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 1 1990, In : Immunologic Research. 9, 2, p. 115-122 8 p.

Research output: Contribution to journalArticle

Molecular Sequence Data
MHC Class II Genes
Histocompatibility Antigens Class II
Innate Immunity
Amino Acid Sequence
1995
8 Citations (Scopus)

Single-tube genomic DNA isolation from whole blood without pre-isolating white blood cells

McIndoe, R. A., Linhardt, M. S. & Hood, L., Jan 1 1995, In : BioTechniques. 19, 1

Research output: Contribution to journalArticle

Cell Separation
Leukocytes
Blood
Cells
DNA
1996
11 Citations (Scopus)

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

McIndoe, R. A., Hood, L. & Bumgarner, R. E., Apr 1 1996, In : ELECTROPHORESIS. 17, 4, p. 652-658 7 p.

Research output: Contribution to journalArticle

Noise
Infrared radiation
Fluorescence
DNA
Software
7 Citations (Scopus)

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 journalArticle

Chromosomes, Human, Pair 10
1997
4 Citations (Scopus)

Data-adaptive algorithms for calling alleles in repeat polymorphisms

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

Research output: Contribution to journalArticle

Adaptive algorithms
Polymorphism
Alleles
Electrophoresis
Microsatellite Repeats
104 Citations (Scopus)

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., Jan 1 1997, In : American Journal of Human Genetics. 61, 2, p. 347-353 7 p.

Research output: Contribution to journalArticle

Neoplasm Genes
Prostatic Neoplasms
Genetic Recombination
Chromosomes
Familial Prostate cancer
1999
272 Citations (Scopus)

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., Jan 1 1999, In : American Journal of Human Genetics. 64, 3, p. 776-787 12 p.

Research output: Contribution to journalArticle

Prostatic Neoplasms
Chromosomes
Brain Neoplasms
Loss of Heterozygosity
Genetic Recombination
68 Citations (Scopus)

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 journalArticle

Inbred DBA Mouse
Experimental Arthritis
Chromosomes, Human, Pair 2
Rheumatoid Arthritis
Animal Disease Models
2000
41 Citations (Scopus)

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 1 2000, In : Genetic Epidemiology. 18, 3, p. 251-275 25 p.

Research output: Contribution to journalArticle

Prostatic Neoplasms
Lod Score
Information Storage and Retrieval
Neoplasm Genes
Datasets
29 Citations (Scopus)

WECHE: A novel hematopoietic regulatory factor

Ohneda, O., Ohneda, K., Nomiyama, H., Zheng, Z., Gold, S. A., Arai, F., Miyamoto, T., Taillon, B. E., McIndoe, R. A., Shimkets, R. A., Lewin, D. A., Suda, T. & Lasky, L. A., Feb 1 2000, In : Immunity. 12, 2, p. 141-150 10 p.

Research output: Contribution to journalArticle

Erythroid Cells
Chemokines
Bone Marrow Cells
B-Lymphocytes
Stem Cells
2001
95 Citations (Scopus)

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

Oligonucleotide Array Sequence Analysis
Noise
Gene Expression
Sensitivity and Specificity
4 Citations (Scopus)

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

Mitochondria
RNA
Genes
Carrier Proteins
Proteins
2003
94 Citations (Scopus)

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

Replicon
Interferon-alpha
Antiviral Agents
Gene Expression
Cell Line
26 Citations (Scopus)

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., Jan 1 2003, In : Journal of Molecular Diagnostics. 5, 4, p. 212-221 10 p.

Research output: Contribution to journalArticle

Acute Promyelocytic Leukemia
Gene Expression Profiling
Tretinoin
Cell Differentiation
Genes
2 Citations (Scopus)

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

CDNA Microarray
Microarrays
Data Management
Oligonucleotide Array Sequence Analysis
Information management
52 Citations (Scopus)

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

Inbred NOD Mouse
Microarray Analysis
Kidney
Gene Expression
Genes
2004
27 Citations (Scopus)

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

Inbred NOD Mouse
Type 1 Diabetes Mellitus
Transcriptome
Genes
Gene Expression
39 Citations (Scopus)

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

Sample Size
Research Design
Systems Biology
Software
Technology
4 Citations (Scopus)

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

Immunization
Inbred NOD Mouse
Genes
Insulin
Medical problems
2005
6 Citations (Scopus)

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

Inbred NOD Mouse
Proteinuria
Transcriptome
Phenotype
Kidney
5 Citations (Scopus)
Wrapper
National Cancer Institute (U.S.)
Bioinformatics
Computational Biology
Application programming interfaces (API)
2006
43 Citations (Scopus)

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

Inbred NOD Mouse
Microarray Analysis
Inbred C57BL Mouse
Submandibular Gland
Genes
11 Citations (Scopus)

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

Huntington Disease
Alleles
Mothers
46 Citations (Scopus)

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

Collins, C. D., Purohit, S. B., 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

Precision Medicine
Preventive Medicine
Proteomics
Biomarkers
Technology
2007
43 Citations (Scopus)

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

Type 1 Diabetes Mellitus
Costs and Cost Analysis
Population
Polymerase Chain Reaction
HLA Antigens
175 Citations (Scopus)

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

Type 1 Diabetes Mellitus
Newborn Infant
Environmental Exposure
HLA Antigens
Autoimmunity
2008
20 Citations (Scopus)

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

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

Research output: Contribution to journalArticle

K-means Algorithm
Cluster Analysis
Microarrays
Clustering algorithms
Clustering Algorithm
11 Citations (Scopus)

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

immunosuppressive agents
Natural Killer T-Cells
Immunosuppressive Agents
interleukin-10
Interleukin-10
2009
14 Citations (Scopus)

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

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

Research output: Contribution to journalArticle

Clustering algorithms
Large Data Sets
Hyperplane
Clustering Algorithm
Cluster Analysis
25 Citations (Scopus)
Xerostomia
Inbred NOD Mouse
Salivary Glands
Gene Expression
Genes
25 Citations (Scopus)
Keratoconjunctivitis Sicca
Lacrimal Apparatus
Inbred NOD Mouse
Gene Expression
Genes
1057 Citations (Scopus)

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. 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 journalArticle

Genome-Wide Association Study
Type 1 Diabetes Mellitus
Meta-Analysis
Interleukin-27
Interleukin-10
2010
13 Citations (Scopus)
Type 1 Diabetes Mellitus
National Institute of Diabetes and Digestive and Kidney Diseases (U.S.)
Siblings
HLA Antigens
North America
19 Citations (Scopus)

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., Oct 20 2010, In : PloS one. 5, 8, e12147.

Research output: Contribution to journalArticle

Gene Expression Profiling
Leptin
leptin
Gene expression
Weight Loss
1 Citation (Scopus)

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

Microarray Analysis
Microarrays
Microarray
Large Data Sets
Permutation
2011
8 Citations (Scopus)
Inbred NOD Mouse
Focal Adhesions
Gene Expression Profiling
Lacrimal Apparatus
Leukocytes
2012
22 Citations (Scopus)

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 1 2012, In : Contemporary Clinical Trials. 33, 4, p. 633-640 8 p.

Research output: Contribution to journalArticle

Type 1 Diabetes Mellitus
Pediatrics
Minority Groups
Hispanic Americans
Ethnic Groups
2 Citations (Scopus)

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

National Institute of Diabetes and Digestive and Kidney Diseases (U.S.)
Informatics
Research
Endocrine System Diseases
Atlases
2013
185 Citations (Scopus)

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

Microbiota
Regulatory T-Lymphocytes
Thymus Gland
Antigens
T-Lymphocytes
2014
14 Citations (Scopus)

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

Type 1 Diabetes Mellitus
Biomarkers
Quality Control
Autoantibodies
Metagenomics
12 Citations (Scopus)

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., Jan 1 2014, In : Nature Communications. 5, 5061.

Research output: Contribution to journalArticle

Antigen Receptors
T-cells
antigens
Regulatory T-Lymphocytes
Thymocytes
2015
8 Citations (Scopus)

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

Postpartum Depression
Psychological Stress
Anxiety
Mothers
Type 1 Diabetes Mellitus
2016
6 Citations (Scopus)
Regression Analysis
Pediatrics
Logistic Models
Population
Health
85 Citations (Scopus)

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

Probiotics
Autoimmunity
Type 1 Diabetes Mellitus
Genotype
Autoantibodies
2017
5 Citations (Scopus)

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

Antipyretics
Autoimmunity
Analgesics
Acetaminophen
Anti-Inflammatory Agents
15 Citations (Scopus)

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

Celiac Disease
Autoimmunity
Type 1 Diabetes Mellitus
Anti-Bacterial Agents
Autoantibodies
8 Citations (Scopus)

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

Type 1 Diabetes Mellitus
Autoantibodies
Joints
Bayes Theorem
Statistical Models