Kottyan Lab

Publications

Shook, MS; Lu, X; Chen, X; Edsall, LE; Granitto, M; Virolainen, SJ; Forney, C; Donmez, OA; Parameswaran, S; Fadden, C; Martin, LJ; Satish, L; Weirauch, MT; Kottyan, LC. Massively parallel analysis of genotype-dependent enhancer activity among atopic dermatitis genetic risk variants. Journal of Allergy and Clinical Immunology. 2025; 156(6):1600-1613.

Martin, LJ; He, H; Spagna, D; Jenkins, S; Grashel, B; Chang, WC; Williams, L; Hammonds, M; Johansson, E; Sherenian, MG; Biagini, JM; Satish, L; Kottyan, L; Khurana Hershey, GK. Genome-wide cross-trait analysis of heterogeneous outcomes in early life atopic dermatitis. Pediatric Allergy and Immunology. 2025; 36(12):e70253.

Granitto, M; Parks, L; Shook, MS; Forney, C; Chen, X; Edsall, LE; Donmez, OA; Parameswaran, S; Fisher, KS; Zabeti, A; Lawson, LP; Weirauch, MT; Kottyan, LC. Genome-wide discovery of multiple sclerosis genetic risk variant allelic regulatory activity. G3: Genes, Genomes, Genetics. 2025; 15(11).

Gill, KK; Moore, C; Nwogu, O; Kroner, JW; Chang, W-C; Burkle, J; Virolainen, SJ; Stevens, ML; Baatyrbek, A; Miraldi, ER; Martin, LJ; Andorf, S; Khurana Hershey, GK; Roskin, KM. B-Cell Repertoire of Children With Atopic Dermatitis Exhibits Altered IgE Maturation Associated With Allergic Food Sensitization. Allergy. European Journal of Allergy and Clinical Immunology. 2025.

Rochman, Y; Kotliar, M; Klingler, AM; Rochman, M; Alameh, M-G; Melamed, JR; Osswald, GA; Caldwell, JM; Felton, JM; Mack, LE; Hargis, J; Lewkowich, IP; Barski, A; Weissman, D; Rothenberg, ME. Allergen-specific mRNA-lipid nanoparticle therapy for prevention and treatment of experimental allergy in mice. Journal of Clinical Investigation. 2025; 135(21).

Azucenas, C; Voulgaridou, A; Elgammal, Y; Ntoumaziou, A; Risinger, M; Seu, K; Sen, S; Kottyan, L; Salomonis, N; Kalfa, T. Erythroid-specific, inducible CDAN1∆/∆ mouse model phenocopies congenital dyserythropoietic anemia type-la. Blood. 2025; 146(Supplement 1):186-186.

Peters, AL; Depasquale, EAK; Begum, G; Roskin, KM; Kotliar, M; Barski, A; Salomonis, N; Shi, T; Ranganathan, S; Woodle, ES; Hildeman, DA. Single-cell transcriptional landscape of liver transplant rejection reveals tissue persistence of clonally expanded, treatment-resistant T cells. American Journal of Transplantation. 2025; 25(11):2345-2360.

Liu, C; Crew, KD; Morse, J; Linder, JE; Antoniou, AC; Carver, T; Cortopassi, J; Peterson, JF; Ta, CN; Hoell, C; Hakonarson, H; Weng, C; Chung, WK; Wiesner, GL. Implementing integrated genomic risk assessments for breast cancer: lessons learned from the Electronic Medical Records and Genomics study. JAMIA Open. 2025; 8(5):ooaf113.

Sayeed, K; Parameswaran, S; Beucler, MJ; Edsall, LE; Vonhandorf, A; Crowther, A; Donmez, OA; Hass, MR; Richards, S; Forney, CR; Zhao, B; Miller, WE; Kottyan, LC; Weirauch, MT. Human cytomegalovirus infection coopts chromatin organization to diminish TEAD1 transcription factor activity. eLife. 2025; 13.

Sayeed, K; Parameswaran, S; Beucler, MJ; Edsall, LE; Vonhandorf, A; Crowther, A; Donmez, OA; Hass, MR; Richards, S; Forney, CR; Zhao, B; Miller, WE; Kottyan, LC; Weirauch, MT. Human cytomegalovirus infection coopts chromatin organization to diminish TEAD1 transcription factor activity. eLife. 2025; 13.

Rouby, NE; Owusu-Obeng, A; Preuss, M; Lee, S; Shi, M; Lape, M; Martin, LJ; Namjou-Khales, B; Kottyan, LC; Van Driest, SL; Mosley, JD; Delbello, MP. Genome-wide associations with metabolic syndrome among UK Biobank participants reporting use of second-generation antipsychotics. Pharmacotherapy. 2025; 45(8):476-485.

Rosenthal, EA; Wei, W-Q; Luo, Y; Namjou-Khales, B; Schaid, DJ; Esplin, ED; Lape, M; Kottyan, L; Pacheco, JA; Weng, C; Grady, WM; Hsu, L; Peters, U; Jarvik, GP. Phenome-wide association study identifies multiple traits associated with a polygenic risk score for colorectal cancer. Human Genomics. 2025; 19(1):77.

Lape, M; Schnell, D; Parameswaran, S; Ernst, K; O'connor, S; Salomonis, N; Martin, LJ; Harnett, BM; Kottyan, LC; Weirauch, MT. A survey of pathogenic involvement in non-communicable human diseases. Communications Medicine. 2025; 5(1):242.

Lawson, LP; Parameswaran, S; Panganiban, RA; Constantine, GM; Weirauch, MT; Kottyan, LC. Update on the genetics of allergic diseases. Journal of Allergy and Clinical Immunology. 2025; 155(6):1738-1752.

Uscategui Calderon, M; Spaeth, ML; Granitto, M; Gonzalez, BA; Weirauch, MT; Kottyan, LC; Yutzey, KE. GDF10 promotes rodent cardiomyocyte maturation during the postnatal period. Journal of Molecular and Cellular Cardiology. 2025; 201:16-31.

Kim, J; Williams, A; Noh, H; Jasper, EA; Jones, SH; Jaworski, JA; Shuey, MM; Ruiz-Narváez, EA; Wise, LA; Palmer, JR; Wei, W-Q; Edwards, TL; Velez Edwards, DR; Hellwege, JN. Genome-wide meta-analysis identifies novel risk loci for uterine fibroids within and across multiple ancestry groups. Nature Communications. 2025; 16(1):2273.

Lin, S; Kotliar, M; Vallabh, S; Ptasinska, A; Assi, SA; Wunderlich, M; Bonifer, C; Barski, A; Mulloy, JC. Fusion-specific chromatin profiles mediate transcriptional heterogeneity in MLL-rearranged acute lymphoblastic leukemia. Blood advances. 2025; 9(4):856-861.

Liu, H; Abedini, A; Ha, E; Ma, Z; Sheng, X; Dumoulin, B; Qiu, C; Aranyi, T; Li, S; Dittrich, N; Edwards, TL; Voight, BF; Hung, AM; Susztak, K. Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants. Science. 2025; 387(6734):eadp4753.

Hui, D; Dudek, S; Kiryluk, K; Walunas, TL; Kullo, IJ; Wei, W-Q; Tiwari, H; Peterson, JF; Chung, WK; Davis, BH; Smith, JL; Karlson, EW; Jarvik, GP; Ritchie, MD. Risk factors affecting polygenic score performance across diverse cohorts. eLife. 2025; 12.

Brown, AP; Parameswaran, S; Cai, L; Elston, S; Pham, C; Barski, A; Weirauch, MT; Ji, H. Silencing TET1 expression alters the epigenomic landscape and amplifies transcriptomic responses to allergen in airway epithelial cells. Environmental Epigenetics. 2025; 11(1):dvaf007.

Koritala, BSC; Parameswaran, S; Donmez, OA; Forney, C; Rowden, H; Moore, CA; Duggins, AL; Sestito, A; Leader, BA; Weirauch, MT; Kottyan, LC; Smith, DF. Genome-wide epigenetic profiling and transcriptome analysis in pediatric Obstructive Sleep Apnea: A focus on Black female children. Heliyon. 2024; 10(23):e40830.

Wright, BL; Abonia, JP; Abud, EM; Aceves, SS; Ackerman, SJ; Braskett, M; Chang, JW; Chehade, M; Constantine, GM; Davis, CM; Spergel, JM; Uchida, AM; Wechsler, JB; Pesek, RD. Advances and ongoing challenges in eosinophilic gastrointestinal disorders presented at the CEGIR/TIGERs Symposium at the 2024 American Academy of Allergy, Asthma & Immunology meeting. Journal of Allergy and Clinical Immunology. 2024; 154(4):882-892.

Correia Marques, M; Rubin, D; Shuldiner, EG; Datta, M; Schmitz, E; Gutierrez Cruz, G; Patt, A; Bennett, E; Grom, A; Foell, D; Woo, P; Ozen, S; Deng, Z; Ombrello, MJ. Enrichment of Rare Variants of Hemophagocytic Lymphohistiocytosis Genes in Systemic Juvenile Idiopathic Arthritis. Arthritis & Rheumatology. 2024; 76(10):1566-1572.

Shook, MS; Lu, X; Chen, X; Edsall, LE; Granitto, M; Virolainen, SJ; Forney, C; Donmez, OA; Parameswaran, S; Fadden, C; Martin, L; Satish, L; Weirauch, MT; Kottyan, LC. Massively Parallel Analysis of Genotype-Dependent Enhancer Activity Among Atopic Dermatitis Genetic Risk Variants. . 2024.

Sun, KY; Bai, X; Chen, S; Bao, S; Zhang, C; Kapoor, M; Backman, J; Joseph, T; Maxwell, E; Mitra, G; Marchini, J; Reid, JG; Salerno, W; Balasubramanian, S. A deep catalogue of protein-coding variation in 983,578 individuals. Nature. 2024; 631(8021):583-592.

Armstrong, ND; Patki, A; Srinivasasainagendra, V; Ge, T; Lange, LA; Kottyan, L; Namjou, B; Shah, AS; Rasmussen-Torvik, LJ; Jarvik, GP; Meigs, JB; Karlson, EW; Limdi, NA; Irvin, MR; Tiwari, HK. Variant level heritability estimates of type 2 diabetes in African Americans. Scientific Reports. 2024; 14(1):14009.

Lewis, ACF; Chisholm, RL; Connolly, JJ; Esplin, ED; Glessner, J; Gordon, A; Green, RC; Hakonarson, H; Harr, M; Holm, IA; Sterling, R; Terek, S; Wei, W-Q; Fullerton, SM. Managing differential performance of polygenic risk scores across groups: Real-world experience of the eMERGE Network. American Journal of Human Genetics. 2024; 111(6):999-1005.

Dourson, AJ; Fadaka, AO; Warshak, AM; Paranjpe, A; Weinhaus, B; Queme, LF; Hofmann, MC; Evans, HM; Donmez, OA; Forney, C; Weirauch, MT; Kottyan, LC; Lucas, D; Deepe, GS; Jankowski, MP. Macrophage memories of early-life injury drive neonatal nociceptive priming. Cell reports. 2024; 43(5):114129.

Virolainen, SJ; Satish, L; Biagini, JM; Chaib, H; Chang, WC; Dexheimer, PJ; Dixon, MR; Dunn, K; Fletcher, D; Forney, C; Shook, M; Weirauch, MT; Khurana Hershey, GK; Kottyan, LC. Filaggrin loss-of-function variants are associated with atopic dermatitis phenotypes in a diverse, early-life prospective cohort. JCI Insight. 2024; 9(9).

Viel, KCMF; Parameswaran, S; Donmez, OA; Forney, CR; Hass, MR; Yin, C; Jones, SH; Prosser, HK; Diouf, AA; Gittens, OE; Gewurz, B; Zhao, B; Kottyan, LC; Weirauch, MT. Shared and distinct interactions of type 1 and type 2 Epstein-Barr Nuclear Antigen 2 with the human genome. BMC Genomics. 2024; 25(1):273.

Lennon, NJ; Kottyan, LC; Kachulis, C; Abul-Husn, NS; Arias, J; Belbin, G; Below, JE; Berndt, SI; Chung, WK; Cimino, JJ; Weng, C; Wiesner, GL; Yin, X; Kenny, EE. Selection, optimization and validation of ten chronic disease polygenic risk scores for clinical implementation in diverse US populations. Nature Medicine. 2024; 30(2):480-487.

Shook, MS; Lu, X; Chen, X; Parameswaran, S; Edsall, L; Trimarchi, MP; Ernst, K; Granitto, M; Forney, C; Donmez, OA; Diouf, AA; Vonhandorf, A; Rothenberg, ME; Weirauch, MT; Kottyan, LC. Systematic identification of genotype-dependent enhancer variants in eosinophilic esophagitis. American Journal of Human Genetics. 2024; 111(2):280-294.

Dai, D; Gu, S; Han, X; Ding, H; Jiang, Y; Zhang, X; Yao, C; Hong, S; Zhang, J; Shen, Y; Kottyan, LC; Weirauch, MT; Vinuesa, CG; Shen, N. The transcription factor ZEB2 drives the formation of age-associated B cells. Science. 2024; 383(6681):413-421.

Chehade, M; Wright, BL; Atkins, D; Aceves, SS; Ackerman, SJ; Assa'ad, AH; Bauer, M; Collins, MH; Commins, SP; Davis, CM; Wechsler, J; Zimmermann, N; Furuta, GT; Rothenberg, ME. Breakthroughs in understanding and treating eosinophilic gastrointestinal diseases presented at the CEGIR/TIGERs Symposium at the 2022 American Academy of Allergy, Asthma & Immunology Meeting. Journal of Allergy and Clinical Immunology. 2023; 152(6):1382-1393.

Meibers, HE; Warrick, KA; Vonhandorf, A; Vallez, CN; Kawarizadeh, K; Saha, I; Donmez, O; Jain, VG; Kottyan, LC; Weirauch, MT; Pasare, C. Effector memory T cells induce innate inflammation by triggering DNA damage and a non-canonical STING pathway in dendritic cells. Cell reports. 2023; 42(10):113180.

Haas, KM; Mcgregor, MJ; Bouhaddou, M; Polacco, BJ; Kim, E-Y; Nguyen, TT; Newton, BW; Urbanowski, M; Kim, H; Williams, MAP; Hultquist, JF; Kaake, RM; García-Sastre, A; Krogan, NJ. Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets. Nature Communications. 2023; 14(1):6030.

Wang, L; Rossi, RM; Chen, X; Chen, J; Runyon, J; Chawla, M; Miller, D; Forney, C; Lynch, A; Zhang, X; Kottyan, LC; Weirauch, MT; Zhang, G; Muglia, LJ. A functional mechanism for a non-coding variant near AGTR2 associated with risk for preterm birth. BMC Medicine. 2023; 21(1):258.

Kiryluk, K; Sanchez-Rodriguez, E; Zhou, X-J; Zanoni, F; Liu, L; Mladkova, N; Khan, A; Marasa, M; Zhang, JY; Balderes, O; Novak, J; Scolari, F; Zhang, H; Gharavi, AG. Genome-wide association analyses define pathogenic signaling pathways and prioritize drug targets for IgA nephropathy. Nature Genetics. 2023; 55(7):1091-1105.

Song, J; Forrest, N; Gordon, A; Kottyan, L; Mittendorf, KF; Wei, W-Q; Ramsey-Goldman, R; Walunas, T; Kho, A. Utilization of electronic health record data to evaluate the association of urban environment with systemic lupus erythematosus symptoms. Rheumatology. 2023; 62(6):e180-e181.

Gautam, Y; Caldwell, J; Kottyan, L; Chehade, M; Dellon, ES; Rothenberg, ME; Mersha, TB. Genome-wide admixture and association analysis identifies African ancestry-specific risk loci of eosinophilic esophagitis in African Americans. Journal of Allergy and Clinical Immunology. 2023; 151(5):1337-1350.

Linder, JE; Allworth, A; Bland, HT; Caraballo, PJ; Chisholm, RL; Clayton, EW; Crosslin, DR; Dikilitas, O; Divietro, A; Esplin, ED; Weng, C; Wiesner, GL; Wiley, K; Peterson, JF. Returning integrated genomic risk and clinical recommendations: The eMERGE study. Genetics in Medicine. 2023; 25(4):100006.

Wang, C; Liu, X; Liang, J; Narita, Y; Ding, W; Li, D; Zhang, L; Wang, H; Leong, MML; Hou, I; Zeng, M-S; Jiang, S; Teng, M; Zhao, B. A DNA tumor virus globally reprograms host 3D genome architecture to achieve immortal growth. Nature Communications. 2023; 14(1):1598.

Xiao, B; Velez Edwards, DR; Lucas, A; Drivas, T; Gray, K; Keating, B; Weng, C; Jarvik, GP; Hakonarson, H; Kottyan, L; Luo, Y; Kim, D; Ritchie, M; Verma, SS. Inference of Causal Relationships Between Genetic Risk Factors for Cardiometabolic Phenotypes and Female-Specific Health Conditions. Journal of the American Heart Association. 2023; 12(5):e026561.

Virolainen, SJ; Vonhandorf, A; Viel, KCMF; Weirauch, MT; Kottyan, LC. Gene-environment interactions and their impact on human health. Genes and Immunity. 2023; 24(1):1-11.

Hui, D; Xiao, B; Dikilitas, O; Freimuth, RR; Irvin, MR; Jarvik, GP; Kottyan, L; Kullo, I; Limdi, NA; Liu, C; Wei, W-Q; Verma, S; Kim, D; Ritchie, MD. Quantifying factors that affect polygenic risk score performance across diverse ancestries and age groups for body mass index. Pacific Symposium on Biocomputing. 2023; 28:437-448.

Cazares, TA; Rizvi, FW; Iyer, B; Chen, X; Kotliar, M; Bejjani, AT; Wayman, JA; Donmez, O; Wronowski, B; Parameswaran, S; Kottyan, LC; Barski, A; Weirauch, MT; Prasath, VBS; Miraldi, ER. maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. PLoS Computational Biology. 2023; 19(1):e1010863.

Levin, MG; Tsao, NL; Singhal, P; Liu, C; Vy, HMT; Paranjpe, I; Backman, JD; Bellomo, TR; Bone, WP; Biddinger, KJ; Joseph, J; Sun, YV; Voight, BF; Damrauer, SM. Genome-wide association and multi-trait analyses characterize the common genetic architecture of heart failure. Nature Communications. 2022; 13(1):6914.

Liu, L; Khan, A; Sanchez-Rodriguez, E; Zanoni, F; Li, Y; Steers, N; Balderes, O; Zhang, J; Krithivasan, P; Ledesma, RA; Ionita-Laza, I; Novak, J; Gharavi, AG; Kiryluk, K. Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits. Nature Communications. 2022; 13(1):6859.

Namjou, B; Lape, M; Malolepsza, E; Devore, SB; Weirauch, MT; Dikilitas, O; Jarvik, GP; Kiryluk, K; Kullo, IJ; Liu, C; Biagini, JM; Khurana Hershey, GK; Martin, LJ; Kottyan, L. Multiancestral polygenic risk score for pediatric asthma. Journal of Allergy and Clinical Immunology. 2022; 150(5):1086-1096.

Sawyer, RP; Stone, HK; Salim, H; Lu, X; Weirauch, MT; Kottyan, L. Frontotemporal degeneration genetic risk loci and transcription regulation as a possible mechanistic link to disease risk. Medicine (United Kingdom). 2022; 101(41):e31078.

Ge, T; Irvin, MR; Patki, A; Srinivasasainagendra, V; Lin, Y-F; Tiwari, HK; Armstrong, ND; Benoit, B; Chen, C-Y; Choi, KW; Lebo, MS; Meigs, JB; Limdi, NA; Karlson, EW. Development and validation of a trans-ancestry polygenic risk score for type 2 diabetes in diverse populations. Genome Medicine. 2022; 14(1):70.

Eapen, AA; Parameswaran, S; Forney, C; Edsall, LE; Miller, D; Donmez, O; Dunn, K; Lu, X; Granitto, M; Rowden, H; Devonshire, AL; Rothenberg, ME; Weirauch, MT; Kottyan, LC. Epigenetic and transcriptional dysregulation in CD4+ T cells in patients with atopic dermatitis. PLoS Genetics. 2022; 18(5):e1009973.

Kim, E; Forney, C; Viel, K; O’Brien, M; Nelson, C; Gecaine, P; Zabeti, A; Weirauch, M; Kottyan, L. Enrichment of Epstein Barr Virus in patients with Multiple Sclerosis. Journal of Immunology. 2022; 208(Supplement_1):104.09-104.09.

Zhou, T; Zhu, X; Ye, Z; Wang, Y-F; Yao, C; Xu, N; Zhou, M; Ma, J; Qin, Y; Shen, Y; Kottyan, LC; Weirauch, MT; Hou, G; Shen, N. Lupus enhancer risk variant causes dysregulation of IRF8 through cooperative lncRNA and DNA methylation machinery. Nature Communications. 2022; 13(1):1855.

Xiao, B; Edwards, DV; Lucas, A; Drivas, T; Gray, K; Keating, B; Weng, C; Jarvik, G; Hakonarson, H; Kottyan, L; Luo, Y; Kim, D; Ritchie, M; Verma, S. Inference of causal relationships between genetic risk factors for cardiometabolic phenotypes and female-specific health conditions. Res Sq. 2022.

Bray, D; Hook, H; Zhao, R; Keenan, JL; Penvose, A; Osayame, Y; Mohaghegh, N; Chen, X; Parameswaran, S; Kottyan, LC; Weirauch, MT; Siggers, T. CASCADE: high-throughput characterization of regulatory complex binding altered by non-coding variants. Cell Genomics. 2022; 2(2).