1. Alarcon-Riquelme ME, Ziegler JT, Molineros J, Howard TD, Moreno-Estrada A, Sanchez-Rodriguez E, Ainsworth HC, Ortiz-Tello P, Comeau ME, Rasmussen A, Kelly JA, Adler A, Acevedo-Vazquez EM, Cucho-Venegas JM, Garcia-De la Torre I, Cardiel MH, Miranda P, Catoggio LJ, Maradiaga-Cecena M, Gaffney PM, et al. Genome-Wide Association Study in an Amerindian Ancestry Population Reveals Novel Systemic Lupus Erythematosus Risk Loci and the Role of European Admixture. Arthritis Rheumatol. 2016; 68:932-43.
  2. Alipanahi B, Delong A, Weirauch MT, Frey BJ. Predicting the Sequence Specificities of DNA- and Rna-Binding Proteins by Deep Learning. Nat Biotechnol. 2015; 33:831-8.
  3. Angeles-Han ST, McCracken C, Yeh S, Jang SR, Jenkins K, Cope S, Bohnsack J, Hersh A, Thompson SD, Prahalad S. Hla Associations in a Cohort of Children with Juvenile Idiopathic Arthritis with and without Uveitis. Investigative Ophthalmology & Visual Science. 2015; 56:6043-48.
  4. Baker FN, Porollo A. Coeviz: A Web-Based Tool for Coevolution Analysis of Protein Residues. BMC Bioinformatics. 2016; 17:119.
  5. Benoit JB, Adelman ZN, Reinhardt K, Dolan A, Poelchau M, Jennings EC, Szuter EM, Hagan RW, Gujar H, Shukla JN, Zhu F, Mohan M, Nelson DR, Rosendale AJ, Derst C, Resnik V, Wernig S, Menegazzi P, Wegener C, Peschel N, et al. Unique Features of a Global Human Ectoparasite Identified through Sequencing of the Bed Bug Genome. Nat Commun. 2016; 7:10165.
  6. Bouffi C, Kartashov AV, Schollaert KL, Chen X, Bacon WC, Weirauch MT, Barski A, Fulkerson PC. Transcription Factor Repertoire of Homeostatic Eosinophilopoiesis. J Immunol. 2015; 195:2683-95.
  7. Brothers KB, Holm IA, Childerhose JE, Antommaria AH, Bernhardt BA, Clayton EW, Gelb BD, Joffe S, Lynch JA, McCormick JB, McCullough LB, Parsons DW, Sundaresan AS, Wolf WA, Yu JH, Wilfond BS, Pediatrics Workgroup of the Clinical Sequencing Exploratory Research Consortium, Pediatrics Workgroup of the Clinical Sequencing Exploratory Research CSER Consortium. When Participants in Genomic Research Grow Up: Contact and Consent at the Age of Majority. J Pediatr. 2016; 168:226-31 e1.
  8. Caster DJ, Korte EA, Merchant ML, Klein JB, Wilkey DW, Rovin BH, Birmingham DJ, Harley JB, Cobb BL, Namjou B, McLeish KR, Powell DW. Autoantibodies Targeting Glomerular Annexin A2 Identify Patients with Proliferative Lupus Nephritis. Proteomics Clin Appl. 2015; 9:1012-20.
  9. Chen X, Ernst K, Soman F, Borowczak M, Weirauch MT. Cressint: A User-Friendly Web Resource for Genome-Scale Exploration of Gene Regulation in Arabidopsis Thaliana. Curr Plant Biol. 2015; 3-4:48-55.
  10. Chiaroni-Clarke RC, Li YR, Munro JE, Chavez RA, Scurrah KJ, Pezic A, Akikusa JD, Allen RC, Piper SE, Becker ML, Thompson SD, Lie BA, Flato B, Forre O, Punaro M, Wise C, Saffery R, Finkel TH, Hakonarson H, Ponsonby AL, et al. The Association of Ptpn22 Rs2476601 with Juvenile Idiopathic Arthritis Is Specific to Females. Genes Immun. 2015; 16:495-8.
  11. Chimote AA, Hajdu P, Kottyan LC, Harley JB, Yun Y, Conforti L. Nanovesicle-Targeted Kv1.3 Knockdown in Memory T Cells Suppresses Cd40l Expression and Memory Phenotype. J Autoimmun. 2016; 69:86-93.
  12. Clement CC, Moncrieffe H, Lele A, Janow G, Becerra A, Bauli F, Saad FA, Perino G, Montagna C, Cobelli N, Hardin J, Stern LJ, Ilowite N, Porcelli SA, Santambrogio L. Autoimmune Response to Transthyretin in Juvenile Idiopathic Arthritis. JCI Insight. 2016; 1:e85633.
  13. Cokelaer T, Bansal M, Bare C, Bilal E, Bot B, Chaibub N, E, Eduati F, de l, Fuente, A, Gönen M, Hill S. Dreamtools: A Python Package for Scoring Collaborative Challenges. F1000Research. 2016; 4.
  14. Davis B, Stucke E, Khorki M, Litosh V, Rymer J, Rochman M, Travers J, Kottyan L, Rothenberg M. Eosinophilic Esophagitis-Linked Calpain 14 Is an Il-13-Induced Protease That Mediates Esophageal Epithelial Barrier Impairment. pmc/PMC4855700. JCI Insight. 2016; 1:e86355.
  15. Davis BP, Epstein T, Kottyan L, Amin P, Martin LJ, Maddox A, Collins MH, Sherrill JD, Abonia JP, Rothenberg ME. Association of Eosinophilic Esophagitis and Hypertrophic Cardiomyopathy. J Allergy Clin Immunol. 2016; 137:934-6 e5.
  16. Deng Y, Zhao J, Sakurai D, Sestak AL, Osadchiy V, Langefeld CD, Kaufman KM, Kelly JA, James JA, Petri MA, Bae SC, Alarcon-Riquelme ME, Alarcon GS, Anaya JM, Criswell LA, Freedman BI, Kamen DL, Gilkeson GS, Jacob CO, Merrill JT, et al. Decreased Smg7 Expression Associates with Lupus-Risk Variants and Elevated Antinuclear Antibody Production. Ann Rheum Dis. 2016.
  17. Finkel TH, Li J, Wei Z, Wang W, Zhang H, Behrens EM, Reuschel EL, Limou S, Wise C, Punaro M, Becker ML, Munro JE, Flato B, Forre O, Thompson SD, Langefeld CD, Glass DN, Glessner JT, Kim CE, Frackelton E, et al. Variants in Cxcr4 Associate with Juvenile Idiopathic Arthritis Susceptibility. BMC Med Genet. 2016; 17:24.
  18. Hall MA, Verma SS, Wallace J, Lucas A, Berg RL, Connolly J, Crawford DC, Crosslin DR, de Andrade M, Doheny KF, Haines JL, Harley JB, Jarvik GP, Kitchner T, Kuivaniemi H, Larson EB, Carrell DS, Tromp G, Vrabec TR, Pendergrass SA, et al. Biology-Driven Gene-Gene Interaction Analysis of Age-Related Cataract in the Emerge Network. Genet Epidemiol. 2015; 39:376-84.
  19. Hass MR, Liow HH, Chen X, Sharma A, Inoue YU, Inoue T, Reeb A, Martens A, Fulbright M, Raju S, Stevens M, Boyle S, Park JS, Weirauch MT, Brent MR, Kopan R. Spdamid: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers. Mol Cell. 2015; 59:685-97.
  20. He XM, Syed KS, Tillo D, Mann I, Weirauch MT, Vinson C. Gabp Alpha Binding to Overlapping Ets and Cre DNA Motifs Is Enhanced by Creb1: Custom DNA Microarrays. G3-Genes Genomes Genetics. 2015; 5:1909-18.
  21. Li YR, Li J, Zhao SD, Bradfield JP, Mentch FD, Maggadottir SM, Hou C, Abrams DJ, Chang D, Gao F, Guo Y, Wei Z, Connolly JJ, Cardinale CJ, Bakay M, Glessner JT, Li D, Kao C, Thomas KA, Qiu H, et al. Meta-Analysis of Shared Genetic Architecture across Ten Pediatric Autoimmune Diseases. Nat Med. 2015; 21:1018-27.
  22. Li YR, Zhao SD, Li J, Bradfield JP, Mohebnasab M, Steel L, Kobie J, Abrams DJ, Mentch FD, Glessner JT, Guo Y, Wei Z, Connolly JJ, Cardinale CJ, Bakay M, Li D, Maggadottir SM, Thomas KA, Qui H, Chiavacci RM, et al. Genetic Sharing and Heritability of Paediatric Age of Onset Autoimmune Diseases. Nat Commun. 2015; 6:8442.
  23. Liu K, Kurien BT, Zimmerman SL, Kaufman KM, Taft DH, Kottyan LC, Lazaro S, Weaver CA, Ice JA, Adler AJ, Chodosh J, Radfar L, Rasmussen A, Stone DU, Lewis DM, Li S, Koelsch KA, Igoe A, Talsania M, Kumar J, et al. X Chromosome Dose and Sex Bias in Autoimmune Diseases: Increased Prevalence of 47,Xxx in Systemic Lupus Erythematosus and Sjogren's Syndrome. Arthritis Rheumatol. 2016; 68:1290-300.
  24. Munroe ME, Lu R, Zhao YD, Fife DA, Robertson JM, Guthridge JM, Niewold TB, Tsokos GC, Keith MP, Harley JB, James JA. Altered Type Ii Interferon Precedes Autoantibody Accrual and Elevated Type I Interferon Activity Prior to Systemic Lupus Erythematosus Classification. Ann Rheum Dis. 2016.
  25. Namjou B, Marsolo K, Lingren T, Ritchie MD, Verma SS, Cobb BL, Perry C, Kitchner TE, Brilliant MH, Peissig PL, Borthwick KM, Williams MS, Grafton J, Jarvik GP, Holm IA, Harley JB. A Gwas Study on Liver Function Test Using Emerge Network Participants. Plos One. 2015; 10:e0138677.
  26. Ombrello MJ, Remmers EF, Tachmazidou I, Grom A, Foell D, Haas JP, Martini A, Gattorno M, Ozen S, Prahalad S, Zeft AS, Bohnsack JFea. Hla-Drb1*11 and Variants of the Mhc Class Ii Locus Are Strong Risk Factors for Systemic Juvenile Idiopathic Arthritis. Proc Natl Acad Sci U S A. 2015; 112:15970-5.
  27. Pelossof R, Singh I, Yang JL, Weirauch MT, Hughes TR, Leslie CS. Affinity Regression Predicts the Recognition Code of Nucleic Acid-Binding Proteins. Nat Biotechnol. 2015; 33:1242-49.
  28. Prahalad S, McCracken CE, Ponder LA, Angeles-Han ST, Rouster Stevens KA, Vogler LB, Langefeld CD, Thompson SD, Childhood A, Rheumatology Research Alliance Registry Investigators. Familial Autoimmunity in the Childhood Arthritis and Rheumatology Research Alliance Registry. Pediatr Rheumatol Online J. 2016; 14:14.
  29. Raj P, Rai E, Song R, Khan S, Wakeland BE, Viswanathan K, Arana C, Liang C, Zhang B, Dozmorov I, Carr-Johnson F, Mitrovic M, Wiley GB, Kelly JA, Lauwerys BR, Olsen NJ, Cotsapas C, Garcia CK, Wise CA, Harley JB, et al. Regulatory Polymorphisms Modulate the Expression of Hla Class Ii Molecules and Promote Autoimmunity. Elife. 2016; 5: e12089.
  30. Rialdi A, Campisi L, Zhao N, Lagda AC, Pietzsch C, Ho JS, Martinez-Gil L, Fenouil R, Chen X, Edwards M, Metreveli G, Jordan S, Peralta Z, Munoz-Fontela C, Bouvier N, Merad M, Jin J, Weirauch M, Heinz S, Benner C, et al. Topoisomerase 1 Inhibition Suppresses Inflammatory Genes and Protects from Death by Inflammation. Science. 2016; 352:aad7993.
  31. Rydyznski CE, Waggoner SN. Boosting Vaccine Efficacy the Natural (Killer) Way. Trends Immunol. 2015; 36:536-46.
  32. Sadhasivam S, Zhang X, Chidambaran V, Mavi J, Pilipenko V, Mersha TB, Meller J, Kaufman KM, Martin LJ, McAuliffe J. Novel Associations between Faah Genetic Variants and Postoperative Central Opioid-Related Adverse Effects. Pharmacogenomics J. 2015; 15:436-42.
  33. Sun C, Molineros JE, Looger LL, Zhou XJ, Kim K, Okada Y, Ma J, Qi YY, Kim-Howard X, Motghare P, Bhattarai K, Adler A, Bang SY, Lee HS, Kim TH, Kang YM, Suh CH, Chung WT, Park YB, Choe JY, et al. High-Density Genotyping of Immune-Related Loci Identifies New Sle Risk Variants in Individuals with Asian Ancestry. Nat Genet. 2016; 48:323-30.
  34. Taylor RL, Cruickshank MN, Karimi M, Ng HL, Quail E, Kaufman KM, Harley JB, Abraham LJ, Tsao BP, Boackle SA, Ulgiati D. Focused Transcription from the Human Cr2/Cd21 Core Promoter Is Regulated by Synergistic Activity of Tata and Initiator Elements in Mature B Cells. Cell Mol Immunol. 2016; 13:119-31.
  35. Valencia CA, Husami A, Holle J, Johnson JA, Qian Y, Mathur A, Wei C, Indugula SR, Zou F, Meng H, Wang L, Li X, Fisher R, Tan T, Hogart Begtrup A, Collins K, Wusik KA, Neilson D, Burrow T, Schorry E, et al. Clinical Impact and Cost-Effectiveness of Whole Exome Sequencing as a Diagnostic Tool: A Pediatric Center's Experience. Front Pediatr. 2015; 3:67.
  36. Waggoner SN, Reighard SD, Gyurova IE, Cranert SA, Mahl SE, Karmele EP, McNally JP, Moran MT, Brooks TR, Yaqoob F, Rydyznski CE. Roles of Natural Killer Cells in Antiviral Immunity. Curr Opin Virol. 2016; 16:15-23.
  37. Young KA, Munroe ME, Guthridge JM, Kamen DL, Niewold TB, Gilkeson GS, Weisman MH, Ishimori ML, Kelly J, Gaffney PM, Sivils KH, Lu R, Wallace DJ, Karp DR, Harley JB, James JA, Norris JM. Combined Role of Vitamin D Status and Cyp24a1 in the Transition to Systemic Lupus Erythematosus. Ann Rheum Dis. 2016.
  38. Yucesoy B, Kaufman KM, Lummus ZL, Weirauch MT, Zhang G, Cartier A, Boulet LP, Sastre J, Quirce S, Tarlo SM, Cruz MJ, Munoz X, Harley JB, Bernstein DI. Genome-Wide Association Study Identifies Novel Loci Associated with Diisocyanate-Induced Occupational Asthma. Toxicol Sci. 2015; 146:192-201.
  39. Zhao J, Giles BM, Taylor RL, Yette GA, Lough KM, Ng HL, Abraham LJ, Wu H, Kelly JA, Glenn SB, Adler AJ, Williams AH, Comeau ME, Ziegler JT, Marion M, Alarcon-Riquelme ME, Biolupus Genles Networks, Alarcon GS, Anaya JM, Bae SC, et al. Preferential Association of a Functional Variant in Complement Receptor 2 with Antibodies to Double-Stranded DNA. Ann Rheum Dis. 2016; 75:242-52.
  40. Zhao J, Wu H, Langefeld CD, Kaufman KM, Kelly JA, Bae SC, Marta EA-RftB, networks G, Alarcon GS, Anaya JM, Criswell LA, Freedman BI, Kamen DL, Gilkeson GS, Jacob CO, James JA, Merrill JT, Gaffney PM, Sivils KM, Niewold TB, et al. Genetic Associations of Leptin-Related Polymorphisms with Systemic Lupus Erythematosus. Clin Immunol. 2015; 161:157-62.