Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks by Pelikan, Richard C., Kelly, Jennifer A., Fu, Yao, Lareau, Caleb A., Tessneer, Kandice L., Wiley, Graham B., Wiley, Mandi M., Glenn, Stuart B., Harley, John B., Guthridge, Joel M., James, Judith A., Aryee, Martin J., Montgomery, Courtney, Gaffney, Patrick M.

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An enhancer element harboring variants associated with systemic lupus erythematosus engages the TNFAIP3 promoter to influence A20 expression by Wang, Shaofeng, Wen, Feng, Wiley, Graham B, Kinter, Michael T, Gaffney, Patrick M

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RBPJ Mutations Identified in Two Families Affected by Adams-Oliver Syndrome by Hassed, Susan J., Wiley, Graham B., Wang, Shaofeng, Lee, Ji-Yun, Li, Shibo, Xu, Weihong, Zhao, Zhizhuang J., Mulvihill, John J., Robertson, James, Warner, James, Gaffney, Patrick M.

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Ecogenomics: using massively parallel pyrosequencing to understand virus ecology by ROOSSINCK, MARILYN J., SAHA, PRASENJIT, WILEY, GRAHAM B., QUAN, JIAXI, WHITE, JAMES D., LAI, HONGSHING, CHAVARRÍA, FELIPE, SHEN, GUOAN, ROE, BRUCE A.

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Regulatory polymorphisms modulate the expression of HLA class II molecules and promote autoimmunity by Raj, Prithvi, Rai, Ekta, Song, Ran, Khan, Shaheen, Wakeland, Benjamin E, Viswanathan, Kasthuribai, Arana, Carlos, Liang, Chaoying, Zhang, Bo, Dozmorov, Igor, Carr-Johnson, Ferdicia, Mitrovic, Mitja, Wiley, Graham B, Kelly, Jennifer A, Lauwerys, Bernard R, Olsen, Nancy J, Cotsapas, Chris, Garcia, Christine K, Wise, Carol A, Harley, John B, Nath, Swapan K, James, Judith A, Jacob, Chaim O, Tsao, Betty P, Pasare, Chandrashekhar, Karp, David R, Li, Quan Zhen, Gaffney, Patrick M, Wakeland, Edward K

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Cloning, characterization and expression analysis of porcine microRNAs by Reddy, Alavala Matta, Zheng, Yun, Jagadeeswaran, Guru, Macmil, Simone L, Graham, Wiley B, Roe, Bruce A, Desilva, Udaya, Zhang, Weixiong, Sunkar, Ramanjulu

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Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations by Satou, Yutaka, Mineta, Katsuhiko, Ogasawara, Michio, Sasakura, Yasunori, Shoguchi, Eiichi, Ueno, Keisuke, Yamada, Lixy, Matsumoto, Jun, Wasserscheid, Jessica, Dewar, Ken, Wiley, Graham B, Macmil, Simone L, Roe, Bruce A, Zeller, Robert W, Hastings, Kenneth E M, Lemaire, Patrick, Lindquist, Erika, Endo, Toshinori, Hotta, Kohji, Inaba, Kazuo

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Forward genetic screening identifies a small molecule that blocks Toxoplasma gondii growth by inhibiting both host- and parasite-encoded kinases by Brown, Kevin M, Suvorova, Elena, Farrell, Andrew, McLain, Aaron, Dittmar, Ashley, Wiley, Graham B, Marth, Gabor, Gaffney, Patrick M, Gubbels, Marc Jan, White, Michael, Blader, Ira J

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The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571 by Lee, Kyung-Bum, De Backer, Philippe, Aono, Toshihiro, Liu, Chi-Te, Suzuki, Shino, Suzuki, Tadahiro, Kaneko, Takakazu, Yamada, Manabu, Tabata, Satoshi, Kupfer, Doris M, Najar, Fares Z, Wiley, Graham B, Roe, Bruce, Binnewies, Tim T, Ussery, David W, D'Haeze, Wim, Herder, Jeroen Den, Gevers, Dirk, Vereecke, Danny, Holsters, Marcelle, Oyaizu, Hiroshi

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The genomics of autoimmune disease in the era of genome-wide association studies and beyond by Lessard, Christopher J, Ice, John A, Adrianto, Indra, Wiley, Graham B, Kelly, Jennifer A, Gaffney, Patrick M, Montgomery, Courtney G, Moser, Kathy L

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Genome-wide DNA methylation maps in follicular lymphoma cells determined by methylation-enriched bisulfite sequencing by Choi, Jeong-Hyeon, Li, Yajun, Guo, Juyuan, Pei, Lirong, Rauch, Tibor A, Kramer, Robin S, Macmil, Simone L, Wiley, Graham B, Bennett, Lynda B, Schnabel, Jennifer L, Taylor, Kristen H, Kim, Sun, Xu, Dong, Sreekumar, Arun, Pfeifer, Gerd P, Roe, Bruce A, Caldwell, Charles W, Bhalla, Kapil N, Shi, Huidong

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Dysregulated long non-coding RNA in Sjögren’s disease impacts both interferon and adaptive immune responses by Joachims, Michelle L, Khatri, Bhuwan, Li, Chuang, Tessneer, Kandice L, Ice, John A, Stolarczyk, Anna M, Means, Nicolas, Grundahl, Kiely M, Glenn, Stuart B, Kelly, Jennifer A, Lewis, David M, Radfar, Lida, Stone, Donald U, Guthridge, Joel M, James, Judith A, Scofield, R Hal, Wiley, Graham B, Wren, Jonathan D, Gaffney, Patrick M, Montgomery, Courtney G, Sivils, Kathy L, Rasmussen, Astrid, Farris, A Darise, Adrianto, Indra, Lessard, Christopher J

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High-throughput sequence analysis of Ciona intestinalis SL trans-spliced mRNAs: alternative expression modes and gene function correlates by Matsumoto, Jun, Dewar, Ken, Wasserscheid, Jessica, Wiley, Graham B, Macmil, Simone L, Roe, Bruce A, Zeller, Robert W, Satou, Yutaka, Hastings, Kenneth E M

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The Medicago genome provides insight into the evolution of rhizobial symbioses by Debellé, Frédéric, Geurts, Rene, Cannon, Steven B., Udvardi, Michael K., Mayer, Klaus F. X., Gouzy, Jérôme, Van de Peer, Yves, Proost, Sebastian, Cook, Douglas R., Meyers, Blake C., Spannagl, Manuel, De Mita, Stéphane, Krishnakumar, Vivek, Gundlach, Heidrun, Zhou, Shiguo, Mudge, Joann, Bharti, Arvind K., Murray, Jeremy D., Naoumkina, Marina A., Rosen, Benjamin, Silverstein, Kevin A. T., Tang, Haibao, Rombauts, Stephane, Zhao, Patrick X., Zhou, Peng, Barbe, Valérie, Bardou, Philippe, Bechner, Michael, Bellec, Arnaud, Berger, Anne, Bidwell, Shelby, Bisseling, Ton, Choisne, Nathalie, Denny, Roxanne, Dai, Xinbin, Dudez, Anne-Marie, Farmer, Andrew D., Fouteau, Stéphanie, Franken, Carolien, Gibelin, Chrystel, Gish, John, Goldstein, Steven, González, Alvaro J., Green, Pamela J., Hua, Axin, Humphray, Sean J., Jing, Yi, Jöcker, Anika, Kenton, Steve M., Kim, Dong-Jin, Klee, Kathrin, Lai, Hongshing, Lang, Chunting, Lin, Shaoping, Macmil, Simone L., Magdelenat, Ghislaine, McCorrison, Jamison, Monaghan, Erin L., Mun, Jeong-Hwan, Najar, Fares Z., Nicholson, Christine, Noirot, Céline, Poulain, Julie, Prion, Florent, Qu, Chunmei, Retzel, Ernest F., Riddle, Claire, Sallet, Erika, Samain, Sylvie, Samson, Nicolas, Sanders, Iryna, Saurat, Olivier, Schiex, Thomas, Segurens, Béatrice, Severin, Andrew J., Sherrier, D. Janine, Shi, Ruihua, Sims, Sarah, Singer, Susan R., Sinharoy, Senjuti, Sterck, Lieven, Wang, Bing-Bing, Wang, Keqin, Wang, Mingyi, Wang, Xiaohong, Warfsmann, Jens, White, Doug D., Wiley, Graham B., Wincker, Patrick, Xing, Yanbo, Yang, Limei, Yao, Ziyun, Ying, Fu, Zuber, Antoine, Dénarié, Jean, Dixon, Richard A., Schwartz, David C., Rogers, Jane, Quétier, Francis, Roe, Bruce A.

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BAC-Pool Sequencing and Analysis of Large Segments of A12 and D12 Homoeologous Chromosomes in Upland Cotton by Buyyarapu, Ramesh, Kantety, Ramesh V, Yu, John Z, Xu, Zhanyou, Kohel, Russell J, Percy, Richard G, Macmil, Simone, Wiley, Graham B, Roe, Bruce A, Sharma, Govind C, Wei, Zhi

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Variants on the UBE2L3/YDJC Autoimmune Disease Risk Haplotype Increase UBE2L3 Expression by Modulating CCCTC‐Binding Factor and YY1 Binding by Gopalakrishnan, Jaanam, Tessneer, Kandice L., Fu, Yao, Pasula, Satish, Pelikan, Richard C., Kelly, Jennifer A., Wiley, Graham B., Gaffney, Patrick M.

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Role of Systemic Lupus Erythematosus Risk Variants With Opposing Functional Effects as a Driver of Hypomorphic Expression of TNIP1 and Other Genes Within a Three‐Dimensional Chroma... by Pasula, Satish, Tessneer, Kandice L., Fu, Yao, Gopalakrishnan, Jaanam, Pelikan, Richard C., Kelly, Jennifer A., Wiley, Graham B., Wiley, Mandi M., Gaffney, Patrick M.

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Identification of IRF8, TMEM39A, and IKZF3-ZPBP2 as Susceptibility Loci for Systemic Lupus Erythematosus in a Large-Scale Multiracial Replication Study by Lessard, Christopher J., Adrianto, Indra, Ice, John A., Wiley, Graham B., Kelly, Jennifer A., Glenn, Stuart B., Adler, Adam J., Li, He, Rasmussen, Astrid, Williams, Adrienne H., Ziegler, Julie, Comeau, Mary E., Marion, Miranda, Wakeland, Benjamin E., Liang, Chaoying, Ramos, Paula S., Grundahl, Kiely M., Gallant, Caroline J., Alarcón, Graciela S., Anaya, Juan-Manuel, Bae, Sang-Cheol, Boackle, Susan A., Brown, Elizabeth E., Chang, Deh-Ming, Cho, Soo-Kyung, Criswell, Lindsey A., Edberg, Jeffrey C., Freedman, Barry I., Gilkeson, Gary S., Jacob, Chaim O., James, Judith A., Kamen, Diane L., Kimberly, Robert P., Kim, Jae-Hoon, Martin, Javier, Merrill, Joan T., Niewold, Timothy B., Park, So-Yeon, Petri, Michelle A., Pons-Estel, Bernardo A., Ramsey-Goldman, Rosalind, Reveille, John D., Scofield, R. Hal, Song, Yeong Wook, Stevens, Anne M., Tsao, Betty P., Vila, Luis M., Vyse, Timothy J., Yu, Chack-Yung, Guthridge, Joel M., Kaufman, Kenneth M., Harley, John B., Wakeland, Edward K., Langefeld, Carl D., Gaffney, Patrick M., Montgomery, Courtney G., Moser, Kathy L.

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Cloning and characterization of small RNAs from Medicago truncatula reveals four novel legume-specific microRNA families by Jagadeeswaran, Guru, Zheng, Yun, Li, Yong-Fang, Shukla, Lata I, Matts, Jessica, Hoyt, Peter, Macmil, Simone L, Wiley, Graham B, Roe, Bruce A, Zhang, Weixiong, Sunkar, Ramanjulu

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Single-cell analysis of glandular T cell receptors in Sjögren's syndrome by Joachims, Michelle L, Leehan, Kerry M, Lawrence, Christina, Pelikan, Richard C, Moore, Jacen S, Pan, Zijian, Rasmussen, Astrid, Radfar, Lida, Lewis, David M, Grundahl, Kiely M, Kelly, Jennifer A, Wiley, Graham B, Shugay, Mikhail, Chudakov, Dmitriy M, Lessard, Christopher J, Stone, Donald U, Scofield, R Hal, Montgomery, Courtney G, Sivils, Kathy L, Thompson, Linda F, Farris, A Darise

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