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Original Articles as a PI at the University of Pennsylvania

  1. Wang, W., Fasolino, M., Cattau, B., Goldman, N., Kong, W., Frederick, M., McCright, S., Kiani, K.,Fraietta, J.A., Vahedi,G.: “Joint Profiling of Chromatin Accessibility and CAR-T Integration Site Analysis at Population and Single-cell Levels”, PNAS, Feb 2020.

  2. Fasolino*, M., Goldman*, N., Wang, W., Cattau, B., Zhou, Y., Petrovic, J., Link, V.M., Cote, A., Chandra, A., Silverman, M., Joyce, E.F., Little, S.C., the HPAP Consortium, Kaestner, K.H., Naji, A., Raj, A., Henao-Mejia, J., Faryabi, R.B., and Vahedi, G.: “Genetic Variation in Type 1 Diabetes Reconfigures the 3D Chromatin Organization of T Cells and Alters Gene Expression”, Immunity, Feb 11 2020. * equal contributions. Featured on the cover.

  3. Schwartz GW, Zhou Y, Petrovic J, Fasolino M, Xu L, Pear WS, Vahedi G., Faryabi RB: “TooManyCells identifies and visualizes relationships of single-cell clades”, Nature Methods, March 2020.

  4. Sidoli S, Lopes M, Lund PJ, Goldman N., Fasolino M, Coradin M, Kulej K, Bhanu NV, Vahedi G, Garcia BA: A mass spectrometry-based assay using metabolic labeling to rapidly monitor chromatin accessibility of modified histone proteins., Scientific Reports volume 9, Article number: 13613, 2019.

  5. Chen Z, Ji Z, Ngiow SF, Manne S, Cai Z, Huang AC, Johnson J, Staupe RP, Bengsch B, Xu C, Yu S, Kurachi M, Herati RS, Vella LA, Baxter AE, Wu JE, Khan O, Beltra JC, Giles JR, Stelekati E, McLane LM, Lau CW, Yang X, Berger SL, Vahedi G, Ji H, Wherry EJ. :“TCF-1-Centered Transcriptional Network Drives an Effector versus Exhausted CD8 T Cell-Fate Decision.”, Immunity,2019 Nov 19;51(5):840-855.

  6. Choobdar, S., Ahsen, M.E., Crawford, J., Tomasoni, J., Fang, T., Lamparter, D., Lin, J., Hescott, B., Hu, X., Mercer, J., Natoli, T., Narayan, R., The DREAM Module Identification Challenge Consortium (Cai, S. and Vahedi, G.), Subramanian, A., Zhang, J.D., Stolovitzky, G., Kutalik, Z., Lage, K., Slonim D.K., Saez-Rodriguez, J., Cowen L.J., Bergmann, S., and Marbach, D.: Assessment of network module identification across complex diseases. Nature Methods, In press, September 2019.

  7. Vacchio M.S., Ciucci T., Gao Y., Watanabe, M., Balmaceno-Criss, M., McGinty, MT, Xiao HQ, McConkey C., Zhao, Y., Shetty, J., Tran B., Pepper, M., Vahedi, G., Jenkins, MK, McGavern, DB, Bosselut, R.: A Thpok-directed transcriptional circuitry promotes Bcl6 and Maf to orchestrate T follicular helper differentiation. Immunity, September 2019.

  8. Petrovic J., Zhou Y, Fasolino M, Goldman N, Schwartz G, Mumbach M, Nguyen S, Rome K, Sela, Y, Zapataro Z, Blacklow S, Kruhlak M, Aster J, Shi J, Joyce E, Little S, Vahedi G, Pear, WS, Faryabi RB: “Oncogenic Notch promotes long-range regulatory interactions within hyperconnected 3D cliques”. Molecular Cell 73, March 2019.

  9. Cai S., Georgakilas G., Johnson J.L., Vahedi G.. “A cosine similarity-based method to infer variability of chromatin accessibility at the single-cell level”, Frontiers in Genetics, August 2018.

  10. Buggert M, Nguyen S, Salgado-Montes de Oca G, Bengsch B, Darko S, Ransier A, Roberts ER, Del Alcazar D, Brody IB, Vella LA, Beura L, Wijeyesinghe S, Herati RS, Del Rio Estrada PM, Ablanedo-Terrazas Y, Kuri-Cervantes L, Sada Japp A, Manne S, Vartanian S, Huffman A, Sandberg JK, Gostick E, Nadolski G, Silvestri G, Canaday DH, Price DA, Petrovas C, Su LF, Vahedi G, Dori Y, Frank I, Itkin MG, Wherry EJ, Deeks SG, Naji A, Reyes-Terán G, Masopust D, Douek DC, Betts MR. “Identification and characterization of HIV-specific resident memory CD8+ T cells in human lymphoid tissue” Science Immunology, 3(24), June 2018.

  11. Zhao YT, Kwon DY, Johnson BS, Fasolino M, Lamonica JM, Kim YJ, Zhao BS, He C, Vahedi G, Kim TH, Zhou Z., “Long genes linked to autism spectrum disorders harbor broad enhancer-like chromatin domains.” Genome Research. May 2018.

  12. Johnson* J.L., Georgakilas* G., Petrovic* J., Kurachi M., Cai S., Harly C., Pear W.S., Bhandoola A., Wherry E.J., Vahedi G. “Lineage-determining transcription factor TCF-1 initiates the epigenetic identity of T cell development”, Immunity, February 2018, * equal contributions. Featured on the cover, received News and Views, highlighted in Nature Immunology, and discussed in a Press Release.

  13. Johnson, B.S., Zhao, Y., Fasolino, M., Lamonica, J.M, Kim, Y.J., Georgakilas, G., Wood, K.H., Bu, D., Cui, Y., Goffin, D., Vahedi, G., Kim, T.H., Zhou, Z., “Biotin tagging of MeCP2 reveals contextual insights into the Rett syndrome transcriptome”, Nature Medicine, September 2017.

  14. Pauken, K.E., Sammons, M.A., Odorizzi, P.M., Manne, S.K., Godec, J., Khan, O., Sen, D., Kurachi, M., Barnitz, R.A., Bengsch, B., Huang, A.C., Schenkel, J.M., Vahedi G., Haining, W.N., Berger, S.L., Wherry, E.J. “Impact of PD-1 blockade on epigenetic and transcriptional reprogramming of exhausted T cells”, Science, October 2016.

  15. Richard AC, Peters JE, Lee JC, Vahedi G, Schäffer AA, Siegel RM, Lyons PA, Smith KG.: “Targeted genomic analysis reveals widespread autoimmune disease association with regulatory variants in the TNF superfamily cytokine signalling network.”, Genome Medicine, 76(8), July 2016.

Original Articles as a postdoctoral fellow at the NIH

  1. Poholek, A., Jankovic, D., Villarino, A., Petermann, F., Hettinga, A., Shouval, D., Snapper, S., Kaech, S., Brooks, S., Vahedi, G., Sher, A., Kanno, Y., O'Shea, J.: “IL-10 induces a STAT3-dependent autoregulatory loop in TH2 cells that promotes Blimp-1 restriction of cell expansion via antagonism of STAT5 target genes”. Science Immunology, 1(5): November 2016.

  2. Jain R, Chen Y, Kanno Y, Joyce-Shaikh B, Vahedi G., Hirahara K, Blumenschein WM, Sukumar S, Haines CJ, Sadekova S, McClanahan TK, McGeachy MJ, O'Shea JJ, Cua DJ.: “Interleukin-23-Induced Transcription Factor Blimp-1 Promotes Pathogenicity of T Helper 17 Cells”. Immunity, 44(1), January 2016.

  3. Hirahara, K., Onodera, A., Villarino, A. V., Bonelli, M., Sciume, G., Laurence, A., Sun, H. W., Brooks, S. R., Vahedi, G., Shih, H. Y., Gutierrez-Cruz, G., Iwata, S., Suzuki, R., Mikami, Y., Okamoto, Y., Nakayama, T., Holland, S. M., Hunter, C. A., Kanno, Y., O'Shea, J. J.: “Asymmetric Action of STAT Transcription Factors Drives Transcriptional Outputs and Cytokine Specificity”. Immunity 42(5): 877-89, 2015.

  4. Yang, X. P., Jiang, K., Hirahara, K., Vahedi, G., Afzali, B., Sciume, G., Bonelli, M., Sun, H. W., Jankovic, D., Kanno, Y., Sartorelli, V., O'Shea, J. J., Laurence, A.: “EZH2 is crucial for both differentiation of regulatory T cells and T effector cell expansion”. Sci Rep, 5: 10643, 2015.

  5. Vahedi, G., Kanno, Y., Furumoto, Y., Jiang, K., Parker, S. C., Erdos, M. R., Davis, S. R., Roychoudhuri, R., Restifo, N. P., Gadina, M., Tang, Z., Ruan, Y., Collins, F. S., Sartorelli, V., O'Shea, J. J., “Super-enhancers delineate disease-associated regulatory nodes in T cells”. Nature, 2015.

  6. Steward-Tharp, S. M., Laurence, A., Kanno, Y., Kotlyar, A., Villarino, A. V., Sciume, G., Kuchen, S., Resch, W., Wohlfert, E. A., Jiang, K., Hirahara, K., Vahedi, G., Sun, H. W., Feigenbaum, L., Milner, J. D., Holland, S. M., Casellas, R., Powrie, F., O'Shea, J. J., “A mouse model of HIES reveals pro- and anti-inflammatory functions of STAT3”, Blood, 123(19): 2978-87, 2014.

  7. Nakayamada, S., Poholek, A. C., Lu, K. T., Takahashi, H., Kato, M., Iwata, S., Hirahara, K., Cannons, J. L., Schwartzberg, P. L., Vahedi, G., Sun, H. W., Kanno, Y., O'Shea, J. J., “Type I IFN induces binding of STAT1 to Bcl6: divergent roles of STAT family transcription factors in the T follicular helper cell genetic program”, J Immunol, 192(5): 2156-66, 2014.

  8. Kanno, T., Kanno, Y., LeRoy, G., Campos, E., Sun, H. W., Brooks, S. R., Vahedi, G., Heightman, T. D., Garcia, B. A., Reinberg, D., Siebenlist, U., O'Shea, J. J., Ozato, K., “BRD4 assists elongation of both coding and enhancer RNAs by interacting with acetylated histones”. Nat Struct Mol Biol, 21(12): 1047-57, 2014.

  9. Roychoudhuri, R., Hirahara, K., Mousavi, K., Clever, D., Klebanoff, C. A., Bonelli, M., Sciume, G., Zare, H., Vahedi, G., Dema, B., Yu, Z., Liu, H., Takahashi, H., Rao, M., Muranski, P., Crompton, J. G., Punkosdy, G., Bedognetti, D., Wang, E., Hoffmann, V., Rivera, J., Marincola, F. M., Nakamura, A., Sartorelli, V., Kanno, Y., Gattinoni, L., Muto, A., Igarashi, K., O'Shea, J. J., Restifo, N. P., “BACH2 represses effector programs to stabilize T(reg)-mediated immune homeostasis”. Nature, 498(7455): 506-10, 2013.

  10. Adamson, A., Ghoreschi, K., Rittler, M., Chen, Q., Sun, H. W., Vahedi, G., Kanno, Y., Stetler-Stevenson, W. G., O'Shea, J. J., Laurence, A., “Tissue inhibitor of metalloproteinase 1 is preferentially expressed in Th1 and Th17 T-helper cell subsets and is a direct STAT target gene”. PLoS One, 8(3): e59367, 2013.

  11. Vahedi, G., Takahashi, H., Nakayamada, S., Sun, H. W., Sartorelli, V., Kanno, Y., O'Shea, J. J., “STATs shape the active enhancer landscape of T cell populations”. Cell, 151(5): 981-93, 2012.

  12. Sciume, G., Hirahara, K., Takahashi, H., Laurence, A., Villarino, A. V., Singleton, K. L., Spencer, S. P., Wilhelm, C., Poholek, A. C., Vahedi, G., Kanno, Y., Belkaid, Y., O'Shea, J. J., “Distinct requirements for T-bet in gut innate lymphoid cells”. J Exp Med, 209(13): 2331-8, 2012.

  13. Hirahara, K., Ghoreschi, K., Yang, X. P., Takahashi, H., Laurence, A., Vahedi, G., Sciume, G., Hall, A. O., Dupont, C. D., Francisco, L. M., Chen, Q., Tanaka, M., Kanno, Y., Sun, H. W., Sharpe, A. H., Hunter, C. A., O'Shea, J. J., “Interleukin-27 priming of T cells controls IL-17 production in trans via induction of the ligand PD-L1”, Immunity, 36(6): 1017-30, 2012.

  14. Yang, X. P., Ghoreschi, K., Steward-Tharp, S. M., Rodriguez-Canales, J., Zhu, J., Grainger, J. R., Hirahara, K., Sun, H. W., Wei, L., Vahedi, G., Kanno, Y., O'Shea, J. J., Laurence, A., “Opposing regulation of the locus encoding IL-17 through direct, reciprocal actions of STAT3 and STAT5”, Nat Immunol, 12(3): 247-54, 2011.

  15. Nakayamada, S., Kanno, Y., Takahashi, H., Jankovic, D., Lu, K. T., Johnson, T. A., Sun, H. W., Vahedi, G., Hakim, O., Handon, R., Schwartzberg, P. L., Hager, G. L., O'Shea, J. J., “Early Th1 cell differentiation is marked by a Tfh cell-like transition”, Immunity, 35(6): 919-31, 2011.

  16. Wei*, L., Vahedi*, G., Sun, H. W., Watford, W. T., Takatori, H., Ramos, H. L., Takahashi, H., Liang, J., Gutierrez-Cruz, G., Zang, C., Peng, W., O'Shea, J. J., Kanno, Y., “Discrete roles of STAT4 and STAT6 transcription factors in tuning epigenetic modifications and transcription during T helper cell differentiation”, Immunity, 32(6): 840-51, 2010 Notes: *equal contributing authors.

  17. Durant, L., Watford, W. T., Ramos, H. L., Laurence, A., Vahedi, G., Wei, L., Takahashi, H., Sun, H. W., Kanno, Y., Powrie, F., O'Shea, J. J., “Diverse targets of the transcription factor STAT3 contribute to T cell pathogenicity and homeostasis”, Immunity, 32(5): 605-15, 2010.

Original Articles as a graduate student at Texas A&M University

  1. Vahedi, G., Ivanov, I. V., Dougherty, E. R., “Inference of Boolean networks under constraint on bidirectional gene relationships”. IET Syst Biol, 3(3): 191-202, 2009.

  2. Vahedi, G., Faryabi, B., Chamberland, J. F., Datta, A., Dougherty, E. R., “Sampling-rate-dependent probabilistic Boolean networks”. J Theor Biol, 261(4): 540-7, 2009.

  3. Vahedi, G., Faryabi, B., Chamberland, J. F., Datta, A., Dougherty, E. R., “Optimal intervention strategies for cyclic therapeutic methods”, IEEE Trans Biomed Eng, 56(2): 281-91, 2009.

  4. Faryabi, B., Vahedi, G., Chamberland, JF, Datta, A, Dougherty, ER, “Intervention in Context-Sensitive Probabilistic Boolean Networks Revisited”, EURASIP Journal on Bioinformatics and Systems Biology, 2009(1): 360864, 2009.

  5. Faryabi, B., Vahedi, G., Chamberland, J. F., Datta, A., Dougherty, E. R., “Intervention in context-sensitive probabilistic Boolean networks revisited”, EURASIP J Bioinform Syst Biol, Page: 360864, 2009.

  6. Vahedi, G., Faryabi, B., Chamberland, J. F., Datta, A., Dougherty, E. R., “Intervention in gene regulatory networks via a stationary mean-first-passage-time control policy”, IEEE Trans Biomed Eng, 55(10): 2319-31, 2008.

  7. Faryabi, B., Vahedi, G., Chamberland, J. F., Datta, A., Dougherty, E. R., “Optimal constrained stationary intervention in gene regulatory networks”, EURASIP J Bioinform Syst Biol, Page: 620767, 2008.

  8. Vahedi, G., Kaler, K., Backhouse, C. J., “An integrated method for mutation detection using on-chip sample preparation, single-stranded conformation polymorphism, and heteroduplex analysis”, Electrophoresis, 25(14): 2346-56, 2004.

Review Articles

  1. Fasolino M and Vahedi G., “GR Extinguishes Inflamed Chromatin, and NF-kB Evacuates”. Immunity, August 2017.

  2. Johnson JL and Vahedi G., “Epigenome: a dynamic vehicle for transmitting and recording cytokine signalling”. CSHL Perspectives, Cold Spring Harbor Laboratory Press, 2017.

  3. Johnson JL and Vahedi G., “Exploiting Chromatin Biology to Understand Immunology.”, Methods Enzymol., 2016;574:365-83.

  4. Paiano JJ, Johnson JL, Vahedi G., “Enhancing our understanding of enhancers in T helper cells”, Eur J Immun., 2015 November.

  5. Witte S, O'Shea JJ, Vahedi G., “Super-enhancers: Asset management in immune cell genomes”, Trends Immunol., 2015 Aug 12.

  6. Vahedi, G., Richard, A. C., O'Shea, J. J., “Enhancing the understanding of asthma”, Nat Immunol, 15(8): 701-3, 2014.

  7. Shih, H. Y., Sciume, G., Poholek, A. C., Vahedi, G., Hirahara, K., Villarino, A. V., Bonelli, M., Bosselut, R., Kanno, Y., Muljo, S. A., O'Shea, J. J., “Transcriptional and epigenetic networks of helper T and innate lymphoid cells”, Immunol Rev, 261(1): 23-49, 2014.

  8. Bonelli, M., Shih, H. Y., Hirahara, K., Singelton, K., Laurence, A., Poholek, A., Hand, T., Mikami, Y., Vahedi, G., Kanno, Y., O'Shea, J. J., “Helper T cell plasticity: impact of extrinsic and intrinsic signals on transcriptomes and epigenomes”, Curr Top Microbiol Immunol, 381: 279-326, 2014.

  9. Vahedi, G., Kanno, Y., Sartorelli, V., O'Shea, J. J., “Transcription factors and CD4 T cells seeking identity: masters, minions, setters and spikers”, Immunology, 139(3): 294-8, 2013.

  10. Vahedi, G., C. Poholek A, Hand, T. W., Laurence, A., Kanno, Y., O'Shea, J. J., Hirahara, K., “Helper T-cell identity and evolution of differential transcriptomes and epigenomes”, Immunol Rev, 252(1): 24-40, 2013.

  11. Hirahara, K., Poholek, A., Vahedi, G., Laurence, A., Kanno, Y., Milner, J. D., O'Shea, J. J., “Mechanisms underlying helper T-cell plasticity: implications for immune-mediated disease”. J Allergy Clin Immunol, 131(5): 1276-87, 2013.

  12. Kanno, Y., Vahedi, G., Hirahara, K., Singleton, K., O'Shea, J. J., “Transcriptional and epigenetic control of T helper cell specification: molecular mechanisms underlying commitment and plasticity” Annu Rev Immunol, 30: 707-31, 2012.

  13. O'Shea, J. J., Lahesmaa, R., Vahedi, G., Laurence, A., Kanno, Y., “Genomic views of STAT function in CD4+ T helper cell differentiation”, Nat Rev Immunol, 11(4): 239-50, 2011.

  14. Hirahara, K., Vahedi, G., Ghoreschi, K., Yang, X. P., Nakayamada, S., Kanno, Y., O'Shea, J. J., Laurence, A., “Helper T-cell differentiation and plasticity: insights from epigenetics”, Immunology, 134(3): 235-45, 2011.

  15. Faryabi, B., Vahedi, G., Datta, A., Chamberland, J. F., Dougherty, E. R., “Recent advances in intervention in Markovian regulatory networks”, Curr Genomics, 10(7): 463-77, 2009.