Xiao Q, Mears J, Nathan A, Ishigaki K, Baglaenko Y, Lim N, Cooney LA, Harris KM, Anderson MS, Fox DA, Smilek DE, Krueger JG, Raychaudhuri S. Immunosuppression causes dynamic changes in expression QTLs in psoriatic skin. Nat Commun. 2023 Oct 7;14(1):6268. doi: 10.1038/s41467-023-41984-2. PMID:37805522; PMCID: PMC10560299.

 Ferri DM, Nassar C, Manion KP, Kim M, Baglaenko Y, Muñoz-Grajales C, Wither JE. Elevated Levels of Interferon-α Act Directly on B Cells to Breach Multiple Tolerance Mechanisms Promoting Autoantibody Production. Arthritis Rheumatol. 2023 Sep;75(9):1542-1555. doi: 10.1002/art.42482. Epub 2023 Jun 30. PMID: 36807718.  

Nathan A, Asgari S, Ishigaki K, Valencia C, Amariuta T, Luo Y, Beynor JI, Baglaenko Y, Suliman S, Price AL, Lecca L, Murray MB, Moody DB, Raychaudhuri S. Single-cell eQTL models reveal dynamic T cell state dependence of disease loci. Nature. 2022 Jun;606(7912):120-128. doi: 10.1038/s41586-022-04713-1. Epub 2022 May 11. PMID: 35545678; PMCID: PMC9842455.

Baglaenko Y, Macfarlane D, Marson A, Nigrovic PA, Raychaudhuri S. Genome editing to define the function of risk loci and variants in rheumatic disease. Nat Rev Rheumatol. 2021 Aug;17(8):462-474. doi: 10.1038/s41584-021-00637-8. Epub 2021 Jun 29. PMID: 34188205.

Nathan A, Beynor JI, Baglaenko Y, Suliman S, Ishigaki K, Asgari S, Huang CC, Luo Y, Zhang Z, Lopez K, Lindestam Arlehamn CS, Ernst JD, Jimenez J, Calderón RI, Lecca L, Van Rhijn I, Moody DB, Murray MB, Raychaudhuri S. Multimodally profiling memory T cells from a tuberculosis cohort identifies cell state Associations with demographics, environment and disease. Nat Immunol. 2021 Jun;22(6):781-793. doi: 10.1038/s41590-021-00933-1. Epub 2021 May 24. PMID: 34031617; PMCID: PMC8162307.

Manion KP, Baglaenko Y, Chang NH, Talaei N, Wither JE. Impaired B cell anergy is not sufficient to breach tolerance to nuclear antigen in Vκ8/3H9 lupus-prone mice. PLoS One. 2020 Jul 28;15(7):e0236664. doi: 10.1371/journal.pone.0236664. PMID: 32722684; PMCID: PMC7386585.

 Gracey E, Hromadová D, Lim M, Qaiyum Z, Zeng M, Yao Y, Srinath A, Baglaenko Y, Yeremenko N, Westlin W, Masse C, Müller M, Strobl B, Miao W, Inman RD. TYK2 inhibition reduces type 3 immunity and modifies disease progression in murine spondyloarthritis. J Clin Invest. 2020 Apr 1;130(4):1863-1878. doi: 10.1172/JCI126567. PMID: 32149730; PMCID: PMC7108927.

 Gutierrez-Arcelus M*, Baglaenko Y*, Arora J, Hannes S, Luo Y, Amariuta T, Teslovich N, Rao DA, Ermann J, Jonsson AH; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; Navarrete C, Rich SS, Taylor KD, Rotter JI, Gregersen PK, Esko T, Brenner MB, Raychaudhuri S. Allele-specific expression changes dynamically during T cell activation in HLA and other autoimmune loci. Nat Genet. 2020 Mar;52(3):247-253. doi: 10.1038/s41588-020-0579-4. Epub 2020 Feb 17. PMID: 32066938; PMCID: PMC7135372.

 Korsunsky I, Millard N, Fan J, Slowikowski K, Zhang F, Wei K, Baglaenko Y, Brenner M, Loh PR, Raychaudhuri S. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat Methods. 2019 Dec;16(12):1289-1296. doi: 10.1038/s41592-019-0619-0. Epub 2019 Nov 18. PMID: 31740819; PMCID: PMC6884693.  

Luo Y, Suliman S, Asgari S, Amariuta T, Baglaenko Y, Martínez-Bonet M, Ishigaki K, Gutierrez-Arcelus M, Calderon R, Lecca L, León SR, Jimenez J, Yataco R, Contreras C, Galea JT, Becerra M, Nejentsev S, Nigrovic PA, Moody DB, Murray MB, Raychaudhuri S. Early progression to active tuberculosis is a highly heritable trait driven by 3q23 in Peruvians. Nat Commun. 2019 Aug 21;10(1):3765. doi: 10.1038/s41467-019-11664-1. PMID: 31434886; PMCID: PMC6704092.

Nathan A, Baglaenko Y, Fonseka CY, Beynor JI, Raychaudhuri S. Multimodal single-cell approaches shed light on T cell heterogeneity. Curr Opin Immunol. 2019 Dec;61:17-25. doi: 10.1016/j.coi.2019.07.002. Epub 2019 Aug 17. PMID: 31430664; PMCID: PMC6901721.

Baglaenko Y*, Chang NH, Johnson SR, Hafiz W, Manion K, Ferri D, Noamani B, Bonilla D, Rusta-Sellehy S, Lisnevskaia L, Silverman E, Bookman A, Landolt-Marticorena C, Wither J. The presence of anti-nuclear antibodies alone is associated with changes in B cell activation and T follicular helper cells similar to those in systemic autoimmune rheumatic disease. Arthritis Res Ther. 2018 Nov 29;20(1):264. doi: 10.1186/s13075-018-1752-3. PMID: 30486869; PMCID: PMC6263058.

Shinde R, Hezaveh K, Halaby MJ, Kloetgen A, Chakravarthy A, da Silva Medina T, Deol R, Manion KP, Baglaenko Y, Eldh M, Lamorte S, Wallace D, Chodisetti SB, Ravishankar B, Liu H, Chaudhary K, Munn DH, Tsirigos A, Madaio M, Gabrielsson S, Touma Z, Wither J, De Carvalho DD, McGaha TL. Apoptotic cell-induced AhR activity is required for immunological tolerance and suppression of systemic lupus erythematosus in mice and humans. Nat Immunol. 2018 Jun;19(6):571-582. doi: 10.1038/s41590-018-0107-1. Epub 2018 May 14. PMID: 29760532; PMCID: PMC5976527.

Wu CM*, Roth TL*, Baglaenko Y*, Ferri DM, Brauer P, Zuniga-Pflucker JC, Rosbe KW, Wither JE, Marson A, Allen CDC. Genetic engineering in primary human B cells with CRISPR-Cas9 ribonucleoproteins. J Immunol Methods. 2018 Jun;457:33-40. doi: 10.1016/j.jim.2018.03.009. Epub 2018 Mar 31. PMID: 29614266; PMCID: PMC6124898.  

Chang NH, Manion KP, Loh C, Pau E, Baglaenko Y, Wither JE. Multiple tolerance defects contribute to the breach of B cell tolerance in New Zealand Black chromosome 1 congenic mice. PLoS One. 2017 Jun 19;12(6):e0179506. doi: 10.1371/journal.pone.0179506. PMID: 28628673; PMCID: PMC5476272.

Baglaenko Y, Cruz Tleugabulova M, Gracey E, Talaei N, Manion KP, Chang NH, Ferri DM, Mallevaey T, Wither JE. Invariant NKT Cell Activation Is Potentiated by Homotypic <i>trans</i>-Ly108 Interactions. J Immunol. 2017 May 15;198(10):3949-3962. doi: 10.4049/jimmunol.1601369. Epub 2017 Apr 3. PMID:28373584.

Gracey E, Qaiyum Z, Almaghlouth I, Lawson D, Karki S, Avvaru N, Zhang Z, Yao Y, Ranganathan V, Baglaenko Y, Inman RD. IL-7 primes IL-17 in mucosal-associated invariant T (MAIT) cells, which contribute to the Th17-axis in ankylosing spondylitis. Ann Rheum Dis. 2016 Dec;75(12):2124-2132. doi: 10.1136/annrheumdis-2015-208902. Epub 2016 May 10. PMID: 27165176.

Baglaenko Y, Manion KP, Chang NH, Gracey E, Loh C, Wither JE. IL-10 Production Is Critical for Sustaining the Expansion of CD5+ B and NKT Cells and Restraining Autoantibody Production in Congenic Lupus-Prone Mice. PLoS One. 2016 Mar 10;11(3):e0150515. doi: 10.1371/journal.pone.0150515. PMID: 26964093; PMCID: PMC4786215.  

Gracey E, Yao Y, Green B, Qaiyum Z, Baglaenko Y, Lin A, Anton A, Ayearst R, Yip P, Inman RD. Sexual Dimorphism in the Th17 Signature of Ankylosing Spondylitis. Arthritis Rheumatol. 2016 Mar;68(3):679-89. doi: 10.1002/art.39464. PMID: 26473967.

Gracey E, Baglaenko Y, Prayitno N, Van Rooijen N, Akram A, Lin A, Chiu B, Inman RD. Pulmonary Chlamydia muridarum challenge activates lung interstitial macrophages which correlate with IFN-γ production and infection control in mice. Eur J Immunol. 2015 Dec;45(12):3417-30. doi: 10.1002/eji.201545874. Epub 2015 Sep 28. PMID: 26344246.

Baglaenko Y, Manion KP, Chang NH, Loh C, Lajoie G, Wither JE. Suppression of autoimmunity by CD5(+) IL-10-producing B cells in lupus-prone mice. Genes Immun. 2015 Jul-Aug;16(5):311-20. doi: 10.1038/gene.2015.17. Epub 2015 May 14. PMID: 25973757.

Loh C, Pau E, Lajoie G, Li TT, Baglaenko Y, Cheung YH, Chang NH, Wither JE. Epistatic suppression of fatal autoimmunity in New Zealand black bicongenic mice. J Immunol. 2011 May 15;186(10):5845-53. doi: 0.4049/jimmunol.1003426. Epub 2011 Apr 4. PMID: 21464090.