Weirauch Research Lab

Lu, X; Chen, X; Forney, C; Donmez, O; Miller, D; Parameswaran, S; Hong, T; Huang, Y; Pujato, M; Cazares, T; et al. Global discovery of lupus genetic risk variant allelic enhancer activity. Nature Communications. 2021; 12.

Liu, X; Hong, T; Parameswaran, S; Ernst, K; Marazzi, I; Weirauch, MT; Bass, JI F. Human Virus Transcriptional Regulators. Cell. 2020; 182:24-37.

Lambert, SA; Yang, AW H; Sasse, A; Cowley, G; Albu, M; Caddick, MX; Morris, QD; Weirauch, MT; Hughes, TR. Similarity regression predicts evolution of transcription factor sequence specificity. Nature Genetics. 2019; 51:981-989.

Harley, JB; Chen, X; Pujato, M; Miller, D; Maddox, A; Forney, C; Magnusen, AF; Lynch, A; Chetal, K; Yukawa, M; et al. Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity. Nature Genetics. 2018; 50:699-707.

Lambert, SA; Jolma, A; Campitelli, LF; Das, PK; Yin, Y; Albu, M; Chen, X; Taipale, J; Hughes, TR; Weirauch, MT. The Human Transcription Factors. Cell. 2018; 172:650-665.

Zhang, G; Feenstra, B; Bacelis, J; Liu, X; Muglia, LM; Juodakis, J; Miller, DE; Litterman, N; Jiang, P; Russell, L; et al. Genetic Associations with Gestational Duration and Spontaneous Preterm Birth. New England Journal of Medicine. 2017; 377:1156-1167.

Alipanahi, B; Delong, A; Weirauch, MT; Frey, BJ. Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning. Nature Biotechnology. 2015; 33:831-838.

Weirauch, MT; Yang, A; Albu, M; Cote, AG; Montenegro-Montero, A; Drewe, P; Najafabadi, HS; Lambert, SA; Mann, I; Cook, K; et al. Determination and inference of eukaryotic transcription factor sequence specificity. Cell. 2014; 158:1431-1443.

Ray, D; Kazan, H; Cook, KB; Weirauch, MT; Najafabadi, HS; Li, X; Gueroussov, S; Albu, M; Zheng, H; Yang, A; et al. A compendium of RNA-binding motifs for decoding gene regulation. Nature. 2013; 499:172-177.

Weirauch, MT; Cote, A; Norel, R; Annala, M; Zhao, Y; Riley, TR; Saez-Rodriguez, J; Cokelaer, T; Vedenko, A; Talukder, S; et al. Evaluation of methods for modeling transcription factor sequence specificity. Nature Biotechnology. 2013; 31:126-134.

Zhao, Y; Vartak, SV; Conte, A; Wang, X; Garcia, DA; Stevens, E; Kyoung Jung, S; Kieffer-Kwon, KR; Vian, L; Stodola, T; et al. "Stripe " transcription factors provide accessibility to co-binding partners in mammalian genomes. Molecular Cell. 2022; 82:3398-3411.e11.

Brusilovsky, M; Rochman, M; Shoda, T; Kotliar, M; Caldwell, JM; Mack, LE; Besse, JA; Chen, X; Weirauch, MT; Barski, A; et al. Vitamin D receptor and STAT6 interactome governs oesophageal epithelial barrier responses to IL-13 signalling. Gut. 2022.

Fagg, WS; Liu, N; Braunschweig, U; Pereira de Castro, KL; Chen, X; Ditmars, FS; Widen, SG; Donohue, JP; Modis, K; Russell, WK; et al. Definition of germ layer cell lineage alternative splicing programs reveals a critical role for Quaking in specifying cardiac cell fate. Nucleic Acids Research. 2022; 50:5313-5334.

Namjou, B; Lape, M; Malolepsza, E; DeVore, SB; Weirauch, MT; Dikilitas, O; Jarvik, GP; Kiryluk, K; Kullo, IJ; Liu, C; et al. Multiancestral polygenic risk score for pediatric asthma. Journal of Allergy and Clinical Immunology. 2022.

Eapen, AA; Parameswaran, S; Forney, C; Edsall, LE; Miller, D; Donmez, O; Dunn, K; Lu, X; Granitto, M; Rowden, H; et al. Epigenetic and transcriptional dysregulation in CD4+ T cells in patients with atopic dermatitis. PLoS Genetics. 2022; 18.

Barreyro, L; Sampson, AM; Ishikawa, C; Hueneman, KM; Choi, K; Pujato, MA; Chutipongtanate, S; Wyder, M; Haffey, WD; O'Brien, E; et al. Blocking UBE2N abrogates oncogenic immune signaling in acute myeloid leukemia. Science Translational Medicine. 2022; 14.

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

Murrison, LB; Ren, X; Preusse, K; He, H; Kroner, J; Chen, X; Jenkins, S; Johansson, E; Biagini, JM; Weirauch, MT; et al. TSLP disease-associated genetic variants combined with airway TSLP expression influence asthma risk. Journal of Allergy and Clinical Immunology. 2022; 149:79-88.

Hou, G; Harley, IT W; Lu, X; Zhou, T; Xu, N; Yao, C; Qin, Y; Ouyang, Y; Ma, J; Zhu, X; et al. SLE non-coding genetic risk variant determines the epigenetic dysfunction of an immune cell specific enhancer that controls disease-critical microRNA expression. Nature Communications. 2021; 12.

Alizada, A; Khyzha, N; Wang, L; Antounians, L; Chen, X; Khor, M; Liang, M; Rathnakumar, K; Weirauch, MT; Medina-Rivera, A; et al. Conserved regulatory logic at accessible and inaccessible chromatin during the acute inflammatory response in mammals. Nature Communications. 2021; 12.

Lu, X; Chen, X; Forney, C; Donmez, O; Miller, D; Parameswaran, S; Hong, T; Huang, Y; Pujato, M; Cazares, T; et al. Global discovery of lupus genetic risk variant allelic enhancer activity. Nature Communications. 2021; 12.

Olafson, PU; Aksoy, S; Attardo, GM; Buckmeier, G; Chen, X; Coates, CJ; Davis, M; Dykema, J; Emrich, SJ; Friedrich, M; et al. The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control. BMC Biology. 2021; 19.

Singh, B; Maiti, GP; Zhou, X; Fazel-Najafabadi, M; Bae, SC; Sun, C; Terao, C; Okada, Y; Heng Chua, K; Kochi, Y; et al. Lupus Susceptibility Region Containing CDKN1B rs34330 Mechanistically Influences Expression and Function of Multiple Target Genes, Also Linked to Proliferation and Apoptosis. Arthritis and Rheumatology. 2021; 73:2303-2313.

Herman, EK; Greninger, A; van der Giezen, M; Ginger, ML; Ramirez-Macias, I; Miller, HC; Morgan, MJ; Tsaousis, AD; Velle, K; Vargová, R; et al. Genomics and transcriptomics yields a system-level view of the biology of the pathogen Naegleria fowleri. BMC Biology. 2021; 19.

Hong, T; Parameswaran, S; Donmez, OA; Miller, D; Forney, C; Lape, M; Saint Just Ribeiro, M; Liang, J; Edsall, LE; Magnusen, AF; et al. Epstein-Barr virus nuclear antigen 2 extensively rewires the human chromatin landscape at autoimmune risk loci. Genome Research. 2021.

Kiryluk, K; Sanchez-Rodriguez, E; Zhou, X; Zanoni, F; Liu, L; Mladkova, N; Khan, A; Marasa, M; Zhang, J; Balderes, O; et al. GWAS defines pathogenic signaling pathways and prioritizes drug targets for IgA nephropathy. 2021.

Felton, JM; Bouffi, C; Schwartz, JT; Schollaert, KL; Malik, A; Vallabh, S; Wronowski, B; Magier, AZ; Merlin, L; Barski, A; et al. Aiolos regulates eosinophil migration into tissues. Mucosal Immunology. 2021; 14:1271-1281.

Johnston, ME; Rivas, MP; Nicolle, D; Gorse, A; Gulati, R; Kumbaji, M; Weirauch, MT; Bondoc, A; Cairo, S; Geller, J; et al. Olaparib Inhibits Tumor Growth of Hepatoblastoma in Patient-Derived Xenograft Models. Hepatology. 2021; 74:2201-2215.

Kuang, Y; Pyo, A; Eafergan, N; Cain, B; Gutzwiller, LM; Axelrod, O; Gagliani, EK; Weirauch, MT; Kopan, R; Kovall, RA; et al. Enhancers with cooperative Notch binding sites are more resistant to regulation by the Hairless co-repressor. PLoS Genetics. 2021; 17.

Felton, JM; Vallabh, S; Parameswaran, S; Edsall, LE; Ernst, K; Wronowski, B; Malik, A; Kotliar, M; Weirauch, MT; Barski, A; et al. Epigenetic Analysis of the Chromatin Landscape Identifies a Repertoire of Murine Eosinophil-Specific PU.1-Bound Enhancers. Journal of Immunology. 2021; 207:1044-1054.

Korinfskaya, S; Parameswaran, S; Weirauch, MT; Barski, A. Runx Transcription Factors in T Cells-What Is Beyond Thymic Development?. Frontiers in Immunology. 2021; 12.

Hass, MR; Brissette, D; Parameswaran, S; Pujato, M; Donmez, O; Kottyan, LC; Weirauch, MT; Kopan, R. Runx1 shapes the chromatin landscape via a cascade of direct and indirect targets. PLoS Genetics. 2021; 17.

Zhu, T; Zhang, X; Chen, X; Brown, AP; Weirauch, MT; Guilbert, TW; Khurana Hershey, GK; Biagini, JM; Ji, H. Nasal DNA methylation differentiates severe from non-severe asthma in African-American children. Allergy: European Journal of Allergy and Clinical Immunology. 2021; 76:1836-1845.

Johansson, E; Martin, LJ; He, H; Chen, X; Weirauch, MT; Kroner, JW; Khurana Hershey, GK; Biagini, JM. Second-hand smoke and NFE2L2 genotype interaction increases paediatric asthma risk and severity. Clinical and Experimental Allergy. 2021; 51:801-810.

Moreno-Fernandez, ME; Giles, DA; Oates, JR; Chan, CC; Damen, MS M A; Doll, JR; Stankiewicz, TE; Chen, X; Chetal, K; Karns, R; et al. PKM2-dependent metabolic skewing of hepatic Th17 cells regulates pathogenesis of non-alcoholic fatty liver disease. Cell Metabolism. 2021; 33:1187-1204.e9.

Ho, JS Y; Mok, BW Y; Campisi, L; Jordan, T; Yildiz, S; Parameswaran, S; Wayman, JA; Gaudreault, NN; Meekins, DA; Indran, SV; et al. TOP1 inhibition therapy protects against SARS-CoV-2-induced lethal inflammation. Cell. 2021; 184:2618-2632.e17.

Yin, X; Kim, K; Suetsugu, H; Bang, SY; Wen, L; Koido, M; Ha, E; Liu, L; Sakamoto, Y; Jo, S; et al. Meta-analysis of 208370 East Asians identifies 113 susceptibility loci for systemic lupus erythematosus. Annals of the Rheumatic Diseases. 2021; 80:632-640.

Schott, G; Munoz, GG; Trevino, N; Chen, X; Weirauch, MT; Gregory, SG; Bradrick, SS; Blanco, MA G. U2AF2 binds IL7R exon 6 ectopically and represses its inclusion. RNA. 2021.

Chidambaran, V; Zhang, X; Pilipenko, V; Chen, X; Wronowski, B; Geisler, K; Martin, LJ; Barski, A; Weirauch, MT; Ji, H. Methylation quantitative trait locus analysis of chronic postsurgical pain uncovers epigenetic mediators of genetic risk. Epigenomics. 2021; 13:613-630.

Santiago, IJ; Zhang, D; Saras, A; Pontillo, N; Xu, C; Chen, X; Weirauch, MT; Mistry, M; Ginty, DD; Pecot, MY; et al. Drosophila Fezf functions as a transcriptional repressor to direct layer-specific synaptic connectivity in the fly visual system. Proceedings of the National Academy of Sciences of the United States of America. 2021; 118.

Song, R; Gao, Y; Dozmorov, I; Malladi, V; Saha, I; McDaniel, MM; Parameswaran, S; Liang, C; Arana, C; Zhang, B; et al. IRF1 governs the differential interferon-stimulated gene responses in human monocytes and macrophages by regulating chromatin accessibility. Cell Reports. 2021; 34.

Miraldi, ER; Chen, X; Weirauch, MT. Deciphering cis-regulatory grammar with deep learning. Nature Genetics. 2021; 53:266-268.

Oatman, N; Dasgupta, N; Arora, P; Choi, K; Gawali, MV; Gupta, N; Parameswaran, S; Salomone, J; Reisz, JA; Lawler, S; et al. Mechanisms of stearoyl CoA desaturase inhibitor sensitivity and acquired resistance in cancer. Science advances. 2021; 7.

Stone, HK; Parameswaran, S; Eapen, AA; Chen, X; Harley, JB; Devarajan, P; Weirauch, MT; Kottyan, L. Comprehensive Review of Steroid-Sensitive Nephrotic Syndrome Genetic Risk Loci and Transcriptional Regulation as a Possible Mechanistic Link to Disease Risk. Kidney International Reports. 2021; 6:187-195.

Kottyan, LC; Trimarchi, MP; Lu, X; Caldwell, JM; Maddox, A; Parameswaran, S; Lape, M; D'Mello, RJ; Bonfield, M; Ballaban, A; et al. Replication and meta-analyses nominate numerous eosinophilic esophagitis risk genes. Journal of Allergy and Clinical Immunology. 2021; 147:255-266.

Petrany, MJ; Swoboda, CO; Sun, C; Chetal, K; Chen, X; Weirauch, MT; Salomonis, N; Millay, DP. Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers. Nature Communications. 2020; 11.

Sirvent, S; Vallejo, AF; Davies, J; Clayton, K; Wu, Z; Woo, J; Riddell, J; Chaudhri, VK; Stumpf, P; Nazlamova, LA; et al. Genomic programming of IRF4-expressing human Langerhans cells. Nature Communications. 2020; 11.

Sparks, ME; Bansal, R; Benoit, JB; Blackburn, MB; Chao, H; Chen, M; Cheng, S; Childers, C; Dinh, H; Doddapaneni, HV; et al. Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest. BMC Genomics. 2020; 21.

Scott, MJ; Benoit, JB; Davis, RJ; Bailey, ST; Varga, V; Martinson, EO; Hickner, PV; Syed, Z; Cardoso, GA; Torres, TT; et al. Genomic analyses of a livestock pest, the New World screwworm, find potential targets for genetic control programs. Communications Biology. 2020; 3.

Stevens, ML; Zhang, Z; Johansson, E; Ray, S; Jagpal, A; Ruff, BP; Kothari, A; He, H; Martin, LJ; Ji, H; et al. Disease-associated KIF3A variants alter gene methylation and expression impacting skin barrier and atopic dermatitis risk. Nature Communications. 2020; 11.

Rotenberg, D; Baumann, AA; Ben-Mahmoud, S; Christiaens, O; Dermauw, W; Ioannidis, P; Jacobs, CG C; Vargas Jentzsch, IM; Oliver, JE; Poelchau, MF; et al. Genome-enabled insights into the biology of thrips as crop pests. BMC Biology. 2020; 18.

Finch, G; Nandyal, S; Perretta, C; Davies, B; Rosendale, AJ; Holmes, CJ; Gantz, JD; Spacht, DE; Bailey, ST; Chen, X; et al. Multi-level analysis of reproduction in an Antarctic midge identifies female and male accessory gland products that are altered by larval stress and impact progeny viability. Scientific Reports. 2020; 10.

Elliott, KH; Chen, X; Salomone, J; Chaturvedi, P; Schultz, PA; Balchand, SK; Servetas, JD; Zuniga, A; Zeller, R; Gebelein, B; et al. Gli3 utilizes Hand2 to synergistically regulate tissue-specific transcriptional networks. eLife. 2020; 9.

Maezawa, S; Sakashita, A; Yukawa, M; Chen, X; Takahashi, K; Alavattam, KG; Nakata, I; Weirauch, MT; Barski, A; Namekawa, SH. Super-enhancer switching drives a burst in gene expression at the mitosis-to-meiosis transition. Nature Structural Biology. 2020; 27:978-988.

Mukherjee, S; Chaturvedi, P; Rankin, SA; Fish, MB; Wlizla, M; Paraiso, KD; MacDonald, M; Chen, X; Weirauch, MT; Blitz, IL; et al. Sox17 and β-catenin co-occupy Wnt-responsive enhancers to govern the endoderm gene regulatory network. eLife. 2020; 9.

Liu, X; Hong, T; Parameswaran, S; Ernst, K; Marazzi, I; Weirauch, MT; Bass, JI F. Human Virus Transcriptional Regulators. Cell. 2020; 182:24-37.

Rajaram, S; Canaday, LM; Ochayon, DE; Rangel, KM; Ali, A; Gyurova, IE; Krishnamurthy, D; Fletcher, JS; Reighard, SD; Cox, A; et al. The Promise and Peril of Natural Killer Cell Therapies in Pulmonary Infection. Immunity. 2020; 52:887-889.

Moncrieffe, H; Dunn, K; Huang, Y; Chen, X; Langefeld, CD; Weirauch, MT; Harley, JB; Kottyan, LC; Thompson, SD. 4277 Functional consequences of the juvenile idiopathic arthritis risk variant at 1q24.3. Journal of Clinical and Translational Science. 2020; 4:95-96.

Jennings, EC; Korthauer, MW; Hendershot, JM; Bailey, ST; Weirauch, MT; Ribeiro, JM C; Benoit, JB. Molecular mechanisms underlying milk production and viviparity in the cockroach, Diploptera punctata. Insect Biochemistry and Molecular Biology. 2020; 120.

Hong, T; Parameswaran, S; Donmez, O; Miller, D; Forney, C; Lape, M; Ribeiro, MS J; Liang, J; Edsall, L; Magnusen, A; et al. Epstein-Barr virus nuclear antigen 2 (EBNA2) extensively rewires the human chromatin landscape at autoimmune risk loci. 2020.

Ji, H; Zhang, X; Myers, JB; Chen, X; Weirauch, M; Guilbert, T; Hershey, GK. DNA methylation Variation Associated with the Severity of Childhood Asthma. Journal of Allergy and Clinical Immunology. 2020; 145.

Emadi, B; Carter, M; Eswar, S; Chen, X; Laurynenka, V; Parameswaran, S; Kaufman, KM; Namjou, B; Kottyan, LC; Weirauch, M; et al. P136 EPSTEIN-BARR VIRUS TRANSCRIPTION CO-FACTORS BIND TO MANY INFLAMMATORY BOWEL DISEASE RISK LOCI. Gastroenterology. 2020; 158:s49-s50.

Yukawa, M; Jagannathan, S; Vallabh, S; Kartashov, AV; Chen, X; Weirauch, MT; Barski, A. AP-1 activity induced by co-stimulation is required for chromatin opening during T cell activation. Journal of Experimental Medicine. 2020; 217.

Kottyan, LC; Parameswaran, S; Weirauch, MT; Rothenberg, ME; Martin, LJ. The genetic etiology of eosinophilic esophagitis. Journal of Allergy and Clinical Immunology. 2020; 145:9-15.

Panfilio, KA; Jentzsch, IM V; Benoit, JB; Erezyilmaz, D; Suzuki, Y; Colella, S; Robertson, HM; Poelchau, MF; Waterhouse, RM; Ioannidis, P; et al. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. Genome Biology. 2019; 20.

Burleson, JD; Siniard, D; Yadagiri, VK; Chen, X; Weirauch, MT; Ruff, BP; Brandt, EB; Hershey, GK K; Ji, H. TET1 contributes to allergic airway inflammation and regulates interferon and aryl hydrocarbon receptor signaling pathways in bronchial epithelial cells. Scientific Reports. 2019; 9.

Liu, X; Helenius, D; Skotte, L; Beaumont, RN; Wielscher, M; Geller, F; Juodakis, J; Mahajan, A; Bradfield, JP; Lin, FT; et al. Variants in the fetal genome near pro-inflammatory cytokine genes on 2q13 associate with gestational duration. Nature Communications. 2019; 10.

Attardo, GM; Abd-Alla, AM M; Acosta-Serrano, A; Allen, JE; Bateta, R; Benoit, JB; Bourtzis, K; Caers, J; Caljon, G; Christensen, MB; et al. Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes. Genome Biology. 2019; 20.

Oatman, N; Dasgupta, N; Choi, K; Gawali, M; Gupta, N; Parameswaran, S; Lawler, S; Brennan, C; Wu, J; Sallans, L; et al. CBMT-05. GENETIC AND EPIGENETIC MECHANISMS REGULATING SCD INHIBITOR SENSITIVITY IN GLIOBLASTOMA. Neuro-Oncology. 2019; 21:vi33-vi33.

Chidambaran, V; Zhang, X; Geisler, K; Stubbeman, BL; Chen, X; Weirauch, MT; Meller, J; Ji, H. Enrichment of Genomic Pathways Based on Differential DNA Methylation Associated With Chronic Postsurgical Pain and Anxiety in Children: A Prospective, Pilot Study. Journal of Pain. 2019; 20:771-785.

Lambert, SA; Yang, AW H; Sasse, A; Cowley, G; Albu, M; Caddick, MX; Morris, QD; Weirauch, MT; Hughes, TR. Similarity regression predicts evolution of transcription factor sequence specificity. Nature Genetics. 2019; 51:981-989.

Miller, DE; Forney, C; Rochman, M; Cranert, S; Habel, J; Rymer, J; Lynch, A; Schroeder, C; Lee, J; Sauder, A; et al. Genetic, Inflammatory, and Epithelial Cell Differentiation Factors Control Expression of Human Calpain-14. G3: Genes, Genomes, Genetics. 2019; 9:729-736.

Miller, DE; Forney, C; Rochman, M; Cranert, S; Habel, J; Rymer, J; Lynch, A; Schroeder, C; Lee, J; Sauder, A; et al. Genetic, Inflammatory, and Epithelial Cell Differentiation Factors Control Expression of Human Calpain-14. G3: Genes, Genomes, Genetics. 2019; 9:729-736.

Meibers, HE; Finch, G; Gregg, RT; Glenn, S; Assani, KD; Jennings, EC; Davies, B; Rosendale, AJ; Holmes, CJ; Gantz, JD; et al. Sex- and developmental-specific transcriptomic analyses of the Antarctic mite, Alaskozetes antarcticus, reveal transcriptional shifts underlying oribatid mite reproduction. Polar Biology. 2019; 42:357-370.

Eapen, A; Parameswaran, S; Forney, C; Miller, D; Donmez, O; Dunn, K; Chawla, M; Sauder, A; Fjellman, E; Pujato, M; et al. NFκB transcription factor binding is altered at many Atopic Dermatitis disease loci. Journal of Allergy and Clinical Immunology. 2019; 143.

Marletaz, F; Firbas, PN; Maeso, I; Tena, JJ; Bogdanovic, O; Perry, M; Wyatt, CD R; de la Calle-Mustienes, E; Bertrand, S; Burguera, D; et al. Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature. 2018; 564:64-70.

Schoville, SD; Chen, YH; Andersson, MN; Benoit, JB; Bhandari, A; Bowsher, JH; Brevik, K; Cappelle, K; Chen, MM; Childers, AK; et al. A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae). Scientific Reports. 2018; 8.

Zhang, C; Seo, J; Murakami, K; Salem, ES B; Bernhard, E; Borra, VJ; Choi, K; Yuan, CL; Chan, CC; Chen, X; et al. Hepatic Ago2-mediated RNA silencing controls energy metabolism linked to AMPK activation and obesity-associated pathophysiology. Nature Communications. 2018; 9.

Valanejad, L; Cast, A; Wright, M; Bissig, K; Karns, R; Weirauch, MT; Timchenko, N. PARP1 activation increases expression of modified tumor suppressors and pathways underlying development of aggressive hepatoblastoma. Communications Biology. 2018; 1.

Modur, V; Singh, N; Mohanty, V; Chung, E; Muhammad, B; Choi, K; Chen, X; Chetal, K; Ratner, N; Salomonis, N; et al. Defective transcription elongation in a subset of cancers confers immunotherapy resistance. Nature Communications. 2018; 9.

Muench, DE; Ferchen, K; Velu, CS; Pradhan, K; Chetal, K; Chen, X; Weirauch, MT; Colmenares, C; Verma, A; Salomonis, N; et al. SKI controls MDS-associated chronic TGF-β signaling, aberrant splicing, and stem cell fitness. Blood. 2018; 132:e24-e34.

Bernstein, DI; Lummus, ZL; Kesavalu, B; Yao, J; Kottyan, L; Miller, D; Cartier, A; Cruz, M; Lemiere, C; Munoz, X; et al. Genetic variants with gene regulatory effects are associated with diisocyanate-induced asthma. Journal of Allergy and Clinical Immunology. 2018; 142:959-969.

Grimes, H; Venkatasubramanian, M; Chou, C; Olsson, A; Chen, X; Chetal, K; Newkold, T; Kulkarni, A; Meyers, K; Weirauch, M; et al. 3050 Global Unsupervised Splicing Analysis of Leukemia Reveals a Persistent Prognostic Signature That Precurses Oncogenesis. Experimental Hematology. 2018; 64.

Zhang, X; Chen, X; Weirauch, MT; Zhang, X; Burleson, JD; Brandt, EB; Ji, H. Diesel exhaust and house dust mite allergen lead to common changes in the airway methylome and hydroxymethylome. Environmental Epigenetics. 2018; 4.

Patel, ZH; Lu, X; Miller, D; Forney, CR; Lee, J; Lynch, A; Schroeder, C; Parks, L; Magnusen, AF; Chen, X; et al. A plausibly causal functional lupus-associated risk variant in the STAT1-STAT4 locus. Human Molecular Genetics. 2018; 27:2392-2404.

Chhipa, RR; Fan, Q; Anderson, J; Muraleedharan, R; Huang, Y; Ciraolo, G; Chen, X; Waclaw, R; Chow, LM; Khuchua, Z; et al. AMP kinase promotes glioblastoma bioenergetics and tumour growth. Nature Cell Biology. 2018; 20:823-835.

Boni, AC; Ambrosio, DL; Cupertino, FB; Montenegro-Montero, A; Virgilio, S; Freitas, FZ; Corrocher, FA; Goncalves, RD; Yang, A; Weirauch, MT; et al. Neurospora crassa developmental control mediated by the FLB-3 transcription factor. Mycological Research. 2018; 122:570-582.

Zhang, G; Feenstra, B; Bacelis, J; Liu, X; Muglia, LM; Juodakis, J; Miller, DE; Litterman, N; Jiang, PP; Russell, L; et al. Genetic Associations With Gestational Duration and Spontaneous Preterm Birth. 2018; 38.

Harley, JB; Chen, X; Pujato, M; Miller, D; Maddox, A; Forney, C; Magnusen, AF; Lynch, A; Chetal, K; Yukawa, M; et al. Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity. Nature Genetics. 2018; 50:699-707.

Zhang, X; Biagini Myers, JM; Burleson, JD; Ulm, A; Bryan, KS; Chen, X; Weirauch, MT; Baker, TA; Kovacic, MS B; Ji, H. Nasal DNA methylation is associated with childhood asthma. Epigenomics. 2018; 10:629-641.

Zandvakili, A; Campbell, I; Gutzwiller, LM; Weirauch, MT; Gebelein, B. Degenerate Pax2 and Senseless binding motifs improve detection of low-affinity sites required for enhancer specificity. PLoS Genetics. 2018; 14.

Zhang, G; Feenstra, B; Bacelis, J; Liu, X; Muglia, LM; Juodakis, J; Miller, DE; Litterman, N; Jiang, PP; Russell, L; et al. Genetic Associations With Gestational Duration and Spontaneous Preterm Birth. 2018; 38.

Lambert, SA; Jolma, A; Campitelli, LF; Das, PK; Yin, Y; Albu, M; Chen, X; Taipale, J; Hughes, TR; Weirauch, MT. The Human Transcription Factors. Cell. 2018; 172:650-665.