Publications

Nov 19, 2021 Nat Commun.

COVID-19 genetic risk variants are associated with expression of multiple genes in diverse immune cell types.

Schmiedel BJ, Rocha J, Gonzalez-Colin C, Bhattacharyya S, Madrigal A, Ottensmeier CH, Ay F, Chandra V, Vijayanand P.

Aug 19, 2021 Genome Biol.

Chromatin lncRNA Platr10 controls stem cell pluripotency by coordinating an intrachromosomal regulatory network.

Du Z, Wen X, Wang Y, Jia L, Zhang S, Liu Y, Zhou L, Li H, Yang W, Wang C, Chen J, Hao Y, Salgado Figueroa D, Chen H, Li D, Chen N, Celik I, Zhu Y, Yan Z, Fu C, Liu S, Jiao B, Wang Z, Zhang H, Gülsoy G, Luo J, Qin B, Gao S, Kapranov P, Esteban MA, Zhang S, Li W, Ay F, Chen R, Hoffman AR, Cui J, Hu JF.

Aug 1, 2021 Nat Immunol.

Intratumoral follicular regulatory T cells curtail anti-PD-1 treatment efficacy.

Eschweiler S, Clarke J, Ramírez-Suástegui C, Panwar B, Madrigal A, Chee SJ, Karydis I, Woo E, Alzetani A, Elsheikh S, Hanley CJ, Thomas GJ, Friedmann PS, Sanchez-Elsner T, Ay F, Ottensmeier CH, Vijayanand P.

May 20, 2021 Bioinformatics.

ExTraMapper: Exon- and Transcript-level mappings for orthologous gene pairs.

Chakraborty A, Ay F, Davuluri RV.

May 1, 2021 Genome Res.

Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants.

Xia J, Venkat A, Bainbridge RE, Reese ML, Le Roch KG, Ay F, Boyle JP.

Apr 1, 2021 Nat Immunol.

The tumor suppressor kinase DAPK3 drives tumor-intrinsic immunity through the STING-IFN-β pathway.

Takahashi M, Lio CJ, Campeau A, Steger M, Ay F, Mann M, Gonzalez DJ, Jain M, Sharma S.

Apr 1, 2021 Genome Res.

Multi-cell type gene coexpression network analysis reveals coordinated interferon response and cross-cell type correlations in systemic lupus erythematosus.

Panwar B, Schmiedel BJ, Liang S, White B, Rodriguez E, Kalunian K, McKnight AJ, Soloff R, Seumois G, Vijayanand P, Ay F

Mar 30, 2021 J Health Popul Nutr.

A comparison of the different anthropometric indices for assessing malnutrition among older people in Turkey: a large population-based screening.

Başıbüyük GÖ, Ayremlou P, Saeidlou SN, Ay F, Dalkıran A, Simzari W, Vitályos GÁ, Bektaş Y.

Mar 15, 2021 Development.

Publications

COVID-19 genetic risk variants are associated with expression of multiple genes in diverse immune cell types.

Chromatin lncRNA Platr10 controls stem cell pluripotency by coordinating an intrachromosomal regulatory network.

Intratumoral follicular regulatory T cells curtail anti-PD-1 treatment efficacy.

ExTraMapper: Exon- and Transcript-level mappings for orthologous gene pairs.

Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants.

The tumor suppressor kinase DAPK3 drives tumor-intrinsic immunity through the STING-IFN-β pathway.

Multi-cell type gene coexpression network analysis reveals coordinated interferon response and cross-cell type correlations in systemic lupus erythematosus.

A comparison of the different anthropometric indices for assessing malnutrition among older people in Turkey: a large population-based screening.

Sox2-Evf2 lncRNA-mediated mechanisms of chromosome topological control in developing forebrain.

Severely ill COVID-19 patients display impaired exhaustion features in SARS-CoV-2-reactive CD8+ T cells.

Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants.

Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation.