Publications

Stripenn detects architectural stripes from chromatin conformation data using computer vision

Yoon, S., Chandra, A. and Vahedi, G.

Nature Communications

2022

Single-cell multi-omics analysis of human pancreatic islets reveals novel cellular states in type 1 diabetes

Fasolino M, Schwartz GW, Patil AR, Mongia A, Golson ML, Wang YJ, Morgan A, Liu C, Schug J, Liu J, Wu M, Traum D, Kondo A, May CL, Goldman N, Wang W, Feldman M, Moore JH, Japp AS, Betts MR; HPAP Consortium, Faryabi RB, Naji A, Kaestner KH, Vahedi G.

Nature Metabolism

2022

Transcription factors combine to paint the methylation landscape

Goldman, N., Chandra, A., and Vahedi, G.

Trends in Immunology

2021

BRD4 orchestrates genome folding to promote neural crest differentiation

Linares-Saldana R, Kim W, Bolar NA, Zhang H, Koch-Bojalad BA, Yoon S, Shah PP, Karnay A, Park DS, Luppino JM, Nguyen SC, Padmanabhan A, Smith CL, Poleshko A, Wang Q, Li L, Srivastava D, Vahedi G, Eom GH, Blobel GA, Joyce EF, Jain R.

Nat Genet. 2021 Oct;53(10):1480-1492

2021

BET bromodomain protein inhibition reverses chimeric antigen receptor extinction and reinvigorates exhausted T cells in chronic lymphocytic leukemia

Kong W, Dimitri A, Wang W, Jung IY, Ott CJ, Fasolino M, Wang Y, Kulikovskaya I, Gupta M, Yoder T, DeNizio JE, Everett JK, Williams EF, Xu J, Scholler J, Reich TJ, Bhoj VG, Haines KM, Maus MV, Melenhorst JJ, Young RM, Jadlowsky JK, Marcucci KT, Bradner JE, Levine BL, Porter DL, Bushman FD, Kohli RM, June CH, Davis MM, Lacey SF, Vahedi G, Fraietta JA.

J Clin Invest. 2021 Aug 16;131(16)

2021

Epigenetic scarring of exhausted T cells hinders memory differentiation upon eliminating chronic antigenic stimulation

Abdel-Hakeem, M., Manne, S., Beltra, J.C., Stelekati, E., Chen, C., Nzingha, K., Ali, M., Johnson, J.L., Giles, J., Mathew, D., Greenplate, A., Vahedi, G., and Wherry, E.J.

Nature Immunology

2021

Exome-wide evaluation of rare coding variants

Park J, Lucas AM, Zhang X, Chaudhary K, Cho JH, Nadkarni G, Dobbyn A, Chittoor G, Josyula NS, Katz N, Breeyear JH, Ahmadmehrabi S, Drivas TG, Chavali VRM, Fasolino M, Sawada H, Daugherty A, Li Y, Zhang C, Bradford Y, Weaver J, Verma A, Judy RL, Kember RL, Overton JD, Reid JG, Ferreira MAR, Li AH, Baras A, LeMaire SA, Shen YH, Naji A, Kaestner KH, Vahedi G, Edwards TL, Chen J, Damrauer SM, Justice AE, Do R, Ritchie MD, Rader DJ.

Nature Medicine

2021

The Identity of Human Tissue-Emigrant CD8+ T Cells

Buggert, M., Vella,L.A., Nguyen, S., Wu, V., Sekine, T., Perez-Potti1, A., Maldini, C., Manne, S., Darko, S., Ransier, A., Kuri-Cervantes, L., Japp, A.S., Brody, I., Ivarsson, M., Hertwig, L., Antel, J.P., Johnson, M.E., Okoye, A, Picker, L., Vahedi, G., Sparrelid, E., Llewellyn-Lacey, S., Gostick, E, Björkström1, N., Bar-Or, A., Dori, Y., Naji, A., Canaday, D.H., Laufer, T.M, Wells, A., Price, D.A., Frank, I., Douek, D.C., Wherry, E.J, Itkin, M., Betts, M.R.

Cell

2020