MuDCoD: multi-subject community detection in personalized dynamic gene networks from single-cell RNA sequencing.

Oct 3, 2023 Bioinformatics

MuDCoD: multi-subject community detection in personalized dynamic gene networks from single-cell RNA sequencing.

Şapcı AOB, Lu S, Yan S, Ay F, Tastan O, Keleş S.

Dec 9, 2023 J Invest Dermatol.

Integrative Keratinocyte Responses to TWEAK with IL-13 and IL-22 Reveal Pathogenic Transcriptomes Associated with Atopic Dermatitis

Gupta RK, Fung K, Figueroa DS, Ay F, Croft M

Nov 22, 2023 Cell

Lineage-specific 3D genome organization is assembled at multiple scales by IKAROS

Hu Y, Salgado Figueroa D, Zhang Z, Veselits M, Bhattacharyya S, Kashiwagi M, Clark MR, Morgan BA, Ay F, Georgopoulos K.

Nov 20, 2023 iScience

Atypical B cells consist of subsets with distinct functional profiles

Reyes RA, Batugedara G, Dutta P, Reers AB, Garza R, Ssewanyana I, Jagannathan P, Feeney ME, Greenhouse B, Bol S, Ay F, Bunnik EM

Nov 19, 2023 bioRxiv

Brd2 is dispensable for genome compartmentalization and replication timing

Hinojosa-Gonzalez L, Turner JL, Sasaki T, Ay F, Gilbert DM

Feb 17, 2024 J Autoimmun.

LIGHT signaling through LTβR and HVEM in keratinocytes promotes psoriasis and atopic dermatitis-like skin inflammation

Gupta RK, Figueroa DS, Fung K, Miki H, Miller J, Ay F, Croft M.

Feb 13, 2024 bioRxiv

Chromatin structure and var2csa – a tango in regulation of var gene expression in the human malaria parasite, Plasmodium falciparum?

Lenz T, Zhang X, Chakraborty A, Ardakany AR, Prudhomme J, Ay F, Deitsch K, Le Roch KG.

Nov 27, 2023 Research News

No IKAROS, no antibodies

Researchers map the genome to figure out how a protein called IKAROS controls healthy B cell development

Oct 31, 2023 Institute News

LJI kicks off partnership with San Diego’s Fleet Science Center

Fleet's Sharp Minds lecture series to feature immune system experts

Apr 3, 2023 Sci Rep

Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft

Dozmorov MG, Marshall MA, Rashid NS, Grible JM, Valentine A, Olex AL, Murthy K, Chakraborty A, Reyna J, Figueroa DS, Hinojosa-Gonzalez L, Da-Inn Lee E, Baur BA, Roy S, Ay F, Harrell JC.

Apr 21, 2023 Nat Commun

3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma

Okonechnikov K, Camgöz A, Chapman O, Wani S, Park DE, Hübner JM, Chakraborty A, Pagadala M, Bump R, Chandran S, Kraft K, Acuna-Hidalgo R, Reid D, Sikkink K, Mauermann M, Juarez EF, Jenseit A, Robinson JT, Pajtler KW, Milde T, Jäger N, Fiesel P, Morgan L, Sridhar S, Coufal NG, Levy M, Malicki D, Hobbs C, Kingsmore S, Nahas S, Snuderl M, Crawford J, Wechsler-Reya RJ, Davidson TB, Cotter J, Michaiel G, Fleischhack G, Mundlos S, Schmitt A, Carter H, Michealraj KA, Kumar SA, Taylor MD, Rich J, Buchholz F, Mesirov JP, Pfister SM, Ay F, Dixon JR, Kool M, Chavez L.

Feb 25, 2022 Sci Immunol

Single-cell eQTL analysis of activated T cell subsets reveals activation and cell type-dependent effects of disease-risk variants

Schmiedel BJ, Gonzalez-Colin C, Fajardo V, Rocha J, Madrigal A, Ramírez-Suástegui C, Bhattacharyya S, Simon H, Greenbaum JA, Peters B, Seumois G, Ay F, Chandra V, Vijayanand P