Genetics and epigenetics of rheumatoid arthritis
Viatte, Sebastien, Darren Plant, and Soumya Raychaudhuri. 2013. “Genetics and Epigenetics of Rheumatoid Arthritis”. Nat Rev Rheumatol 9 (3): 141-53.
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Crowdsourcing genetic prediction of clinical utility in the Rheumatoid Arthritis Responder Challenge
Plenge, Robert, Jeffrey Greenberg, Lara Mangravite, Jonathan Derry, Eli Stahl, Marieke Jh Coenen, Anne Barton, et al. 2013. “Crowdsourcing Genetic Prediction of Clinical Utility in the Rheumatoid Arthritis Responder Challenge”. Nat Genet 45 (5): 468-9.
Applying active learning to high-throughput phenotyping algorithms for electronic health records data
Chen, Yukun, Robert Carroll, Eugenia McPeek Hinz, Anushi Shah, Anne Eyler, Joshua Denny, and Hua Xu. 2013. “Applying Active Learning to High-Throughput Phenotyping Algorithms for Electronic Health Records Data”. J Am Med Inform Assoc 20 (e2): e253-9.
Association of valine and leucine at HLA-DRB1 position 11 with radiographic progression in rheumatoid arthritis, independent of the shared epitope alleles but not independent of anti-citrullinated protein antibodies
Steenbergen, Raychaudhuri, Rodríguez-Rodríguez, Rantapää-Dahlqvist, Berglin, Toes, Huizinga, Fernández-Gutiérrez, Gregersen, and Helm-van Mil. 2015. “Association of Valine and Leucine at HLA-DRB1 Position 11 With Radiographic Progression in Rheumatoid Arthritis, Independent of the Shared Epitope Alleles But Not Independent of Anti-Citrullinated Protein Antibodies”. Arthritis Rheumatol 67 (4): 877-86.
Backbone makes a significant contribution to the electrostatics of alpha/beta-barrel proteins
Raychaudhuri, Younas, Karplus, Faerman, and Ripoll. 1997. “Backbone Makes a Significant Contribution to the Electrostatics of Alpha/Beta-Barrel Proteins”. Protein Sci 6 (9): 1849-57.
Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature
Raychaudhuri, Soumya, Jeffrey Chang, Patrick Sutphin, and Russ Altman. 2002. “Associating Genes With Gene Ontology Codes Using a Maximum Entropy Analysis of Biomedical Literature”. Genome Res 12 (1): 203-14.
Parental origin of sequence variants associated with complex diseases
Kong, Augustine, Valgerdur Steinthorsdottir, Gisli Masson, Gudmar Thorleifsson, Patrick Sulem, Soren Besenbacher, Aslaug Jonasdottir, et al. 2009. “Parental Origin of Sequence Variants Associated With Complex Diseases”. Nature 462 (7275): 868-74.
Cumulative association of 22 genetic variants with seropositive rheumatoid arthritis risk
Karlson, Elizabeth, Lori Chibnik, Peter Kraft, Jing Cui, Brendan Keenan, Bo Ding, Souyma Raychaudhuri, Lars Klareskog, Lars Alfredsson, and Robert Plenge. 2010. “Cumulative Association of 22 Genetic Variants With Seropositive Rheumatoid Arthritis Risk”. Ann Rheum Dis 69 (6): 1077-85.
Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types
Finucane, Hilary, Yakir Reshef, Verneri Anttila, Kamil Slowikowski, Alexander Gusev, Andrea Byrnes, Steven Gazal, et al. 2018. “Heritability Enrichment of Specifically Expressed Genes Identifies Disease-Relevant Tissues and Cell Types”. Nature Genetics 50 (4): 621-29.
High-throughput identification of noncoding functional SNPs via type IIS enzyme restriction
Li, Gang, Marta Martínez-Bonet, Di Wu, Yu Yang, Jing Cui, Hung N. Nguyen, Pierre Cunin, et al. 2018. “High-Throughput Identification of Noncoding Functional SNPs via Type IIS Enzyme Restriction”. Nature Genetics 50 (8): 1180-88.