Publications

 

  1. Feldman S, Ner-Gaon H, Treister E, Shay T (2024). Comparison and development of cross-study normalization methods for inter-species transcriptional analysis. PLoS One. 2024 Sep. doi: 10.1371/journal.pone.0307997. eCollection 2024
  2. Shani Talia Gal-Oz, Baysoy A, Vijaykumar B, Mostafavi S, Benoist C, Shay T, Immunological Genome Project (2024). Microheterogeneity in the Kinetics and Sex-Specific Response to Type I IFN. J Immunol. 2024 Jul 1;213(1):96-104. doi: 10.4049/jimmunol.2300453.
  3. Shani Talia Gal-Oz, Shay T (2023). Genetics of Sex Differences in Immunity. Curr Top Microbiol Immunol. 2023;441:1-19. doi: 10.1007/978-3-031-35139-6_1.
  4. Hadas Ner-Gaon, Ronnie Peleg, Roi Gazit, Anat Reiner-Benaim, Tal Shay (2023). Mapping the splicing landscape of the human immune system. Front. Immunol. Volume 14 | https://doi.org/10.3389/fimmu.2023.1116392
  5. Lucy Androsiuk, Tal Shay, Shay Tal (2023). Characterization of the Environmental Plasmidome of the Red Sea. Microbiol Spectr. 11(4). doi:10.1128/spectrum.00400-23
  6. Muhammad Tibi, Stav Biton, Hannah Hochgerner, Zhige Lin, Shachar Givon, Osnat Ophir, Tal Shay, Thomas Mueller, Ronen Segev, Amit Zeisel (2023). A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial struchture and cell types. bioRxiv. doi:https://doi.org/10.1101/2023.06.19.545605
  7. Alev Baysoy, Kumba Seddu, Tamara Salloum, Caleb A Dawson, Juliana J Lee, Liang Yang, Shani Gal-Oz, Hadas Ner-Gaon, Julie Tellier, Alberto Millan, Alexander Sasse, Brian Brown, Lewis L Lanier, Tal Shay, Stephen Nutt, Daniel Dwyer, Christophe Benoist, Immunological Genome Project Consortium (2023). The interweaved signatures of common-gamma-chain cytokines across immunologic lineages. J Exp Med. 3;220(7):e20222052.doi: 10.1084/jem.20222052
  8. Shani Talia Gal-Oz, Shay T (2022). Immune Sexual Dimorphism: Connecting the Dots. Physiology (Bethesda). 2022 Mar 1;37(2):55-68. doi: 10.1152/physiol.00006.2021. Epub 2021 Sep 13.
  9. Nufar Grinshpan, Faiza A.A. Abyed, Melody Wahl, Hadas Ner-Gaon, Rivka Manor, Amir Sagi, Tal Shay (2022). The transcriptional landscape of the giant freshwater prawn: Embryonic development and early sexual differentiation mechanisms. Front. Endocrinol. Volume 13 | https://doi.org/10.3389/fendo.2022.1059936
  10. Edy Y. Kim, Hadas Ner-Gaon, Jack Varon, Aidan M. Cullen, Jingyu Guo, Jiyoung Choi, Diana Barragan-Bradford, Angelica Higuera, Mayra Pinilla-Vera, Samuel A.P. Short, Antonio J. Arciniegas-Rubio, Tomoyoshi Tamura, David E. Leaf, Rebecca M. Baron, Tal Shay, Michael B. Brenner (2020). Post-sepsis immunosuppression depends on NKT cell regulation of mTOR/IFNγ in NK cells. J Clin Invest. https://doi.org/10.1172/JCI128075
  11. Shani Talia Gal-Oz, Barbara Maier, Hideyuki Yoshida, Kumba Seddu, Nitzan Elbaz, Charles Czysz, Or Zuk, Barbara E. Stranger, Hadas Ner-Gaon, Tal Shay (2019). ImmGen report: sexual dimorphism in the immune system transcriptome. Nature Communications10(1).
  12. Lieberman Y, Rokach L, Shay T (2018). CaSTLe – Classification of single cells by transfer learning: Harnessing the power of publicly available single cell RNA sequencing experiments to annotate new experiments. PLoS ONE 13(10)
  13. Kohlgruber AC, Gal-Oz ST, LaMarche NM, Shimazaki M, Duquette D, Nguyen HN, Mina AI, Paras T, Tavakkoli A, von Andrian U, Banks AS, Shay T, Brenner MB, Lynch L (2018). γδ T cells producing interleukin-17A regulate adipose regulatory T cell homeostasis and thermogenesis. Nat Immunol. 19(5).
  14. Mukherjee D, Ignatowska-Jankowska BM, Itskovits E, Gonzales BJ, Turm H, Izakson L, Haritan D, Bleistein N, Cohen C, Amit I, Shay T, Grueter B, Zaslaver A, Citri A (2018). Salient experiences are represented by unique transcriptional signatures in the mouse brain. Elife.
  15. Ner-Gaon H, Melchior A, Golan N, Ben-Haim Y and Shay T (2017). JingleBells: A Repository of Immune-Related Single-Cell RNA-Sequencing Datasets. J. Immunol. 198(9): 3375.
  16. Goldstein O, Meyer K, Greenshpan Y, Bujanover N, Feigin M, Ner-Gaon H, Shay T and Gazit R (2017). Mapping Whole-Transcriptome Splicing in Mouse Hematopoietic Stem Cells. Step Cell Reports. 8(1): 163.
  17. Kurscheid S, Bady P, Sciuscio D, Samarzija I, Shay T, Vassallo I, van Criekinge W, Daniel R, van den Bent M, Marosi C, Weller M, Mason W, Domany E, Stupp R, Delorenzi M and Hegi M (2015). Chromosome 7 gain and DNA hypermethylation at the HOXA10 locus are associated with expression of a stem cell related HOX-signature in glioblastoma. Genome Biology 16(1): 16.
  18. Shay T, Lederer JA, and Benoist C (2014). Genomic responses to inflammation in mouse models mimic humans: We concur, apples to oranges comparisons won’t do. PNAS published ahead of print December 24.
  19. Jojic V, Shay T, Sylvia K, Zuk O, Sun X, Kang J, Regev A, Koller D and the ImmGen Consortium (2013). Identification of transcriptional regulators in the mouse immune system. Nature Immunology 14(6): 633-643.
  20. Shay T and Kang J (2013). Immunological Genome project and systems immunology. Trends in Immunology 34(12):602-609.
  21. Shay T, Jojic V, Zuk O, Rothamel K, Puyraimond-Zemmour D, Feng T, Wakamatsu E, Benoist C, Koller D, Regev A and the ImmGen Consortium (2013). Conservation and divergence in the transcriptional programs of human and mouse immune systems. PNAS 110(8): 2946-2951.
  22. Gazit R, Garrison BS, Rao TN, Shay T, Costello J, Ericson J, Kim F, Collins JJ, Regev A, Wagers AJ, Rossi DJ and the ImmGen Consortium (2013). Transcriptome Analysis Identifies Regulators of Hematopoietic Stem and Progenitor Cells. Stem Cell Reports 1(3): 266-280.
  23. Cohen NR, Brennan PJ, Shay T, Watts GF, Brigl M, Kang J and Brenner MB (2013). Shared and distinct transcriptional programs underlie the hybrid nature of iNKT cells. Nature Immunology 14(1): 90-99.
  24. Gautier EL, Shay T, Miller J, Greter M, Jakubzick C, Ivanov S, Helft J, Chow A, Elpek KG, Gordonov S, Mazloom AR, Ma’ayan A, Chua W-J, Hansen TH, Turley SJ, Merad M and Randolph GJ (2012). Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages. Nature Immunology 13(11): 1118-1128.
  25. Miller JC, Brown BD, Shay T, Gautier EL, Jojic V, Cohain A, Pandey G, Leboeuf M, Elpek KG, Helft J, Hashimoto D, Chow A, Price J, Greter M, Bogunovic M, Bellemare-Pelletier A, Frenette PS, Randolph GJ, Turley SJ and Merad M (2012). Deciphering the transcriptional network of the dendritic cell lineage. Nature Immunology 13(9): 888-899.
  26. Tarcic G, Avraham R, Pines G, Amit I, Shay T, Lu Y, Zwang Y, Katz M, Ben-Chetrit N, Jacob-Hirsch J, Virgilio L, Rechavi G, Mavrothalassitis G, Mills GB, Domany E and Yarden Y (2012). EGR1 and the ERK-ERF axis drive mammary cell migration in response to EGF. FASEB Journal 26(4): 1582-1592.
  27. Novershtern N, Subramanian A, Lawton LN, Mak RH, Haining WN, McConkey ME, Habib N, Yosef N, Chang CY, Shay T, Frampton GM, Drake AC, Leskov I, Nilsson B, Preffer F, Dombkowski D, Evans JW, Liefeld T, Smutko JS, Chen J, Friedman N, Young RA, Golub TR, Regev A and Ebert BL (2011). Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell 144(2): 296-309.
  28. Lambiv WL, Vassallo I, Delorenzi M, Shay T, Diserens AC, Misra A, Feuerstein B, Murat A, Migliavacca E, Hamou MF, Sciuscio D, Burger R, Domany E, Stupp R and Hegi ME (2011). The Wnt inhibitory factor 1 (WIF1) is targeted in glioblastoma and has a tumor suppressing function potentially by induction of senescence. Neuro-oncology 13(7): 736-747.
  29. Zwang Y, Sas-Chen A, Drier Y, Shay T, Avraham R, Lauriola M, Shema E, Lidor-Nili E, Jacob-Hirsch J, Amariglio N, Lu Y, Mills GB, Rechavi G, Oren M, Domany E and Yarden Y (2011). Two phases of mitogenic signaling unveil roles for p53 and EGR1 in elimination of inconsistent growth signals. Molecular Cell 42(4): 524-535.
  30. Valenti F, Fausti F, Biagioni F, Shay T, Fontemaggi G, Domany E, Yaffe MB, Strano S, Blandino G and Di Agostino S (2011). Mutant p53 oncogenic functions are sustained by Plk2 kinase through an autoregulatory feedback loop. Cell Cycle 10(24).
  31. Nadav-Dagan L, Shay T, Dezorella N, Naparstek E, Domany E, Katz BZ and Geiger B (2010). Adhesive interactions regulate transcriptional diversity in malignant B cells. Molecular Cancer Research 8(4): 482-493.
  32. Amit I, Garber M, Chevrier N, Leite AP, Donner Y, Eisenhaure T, Guttman M, Grenier JK, Li W, Zuk O, Schubert LA, Birditt B, Shay T, Goren A, Zhang X, Smith Z, Deering R, McDonald RC, Cabili M, Bernstein BE, Rinn JL, Meissner A, Root DE, Hacohen N and Regev A (2009). Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science 326(5950): 257-263.
  33. Kim HD, Shay T, O’Shea EK and Regev A (2009). Transcriptional regulatory circuits: predicting numbers from alphabets. Science 325(5939): 429-432.
  34. Shay T, Lambiv WL, Reiner-Benaim A, Hegi ME and Domany E (2009). Combining chromosomal arm status and significantly aberrant genomic locations reveals new cancer subtypes. Cancer Informatics 7: 91-104.
  35. Fontemaggi G, Dell’Orso S, Trisciuoglio D, Shay T, Melucci E, Fazi F, Terrenato I, Mottolese M, Muti P, Domany E, Del Bufalo D, Strano S and Blandino G (2009). The execution of the transcriptional axis mutant p53, E2F1 and ID4 promotes tumor neo-angiogenesis. Nature Structural and Molecular Biology 16(10): 1086-1093.
  36. Murat A, Migliavacca E, Gorlia T, Lambiv WL, Shay T, Hamou MF, de Tribolet N, Regli L, Wick W, Kouwenhoven MC, Hainfellner JA, Heppner FL, Dietrich PY, Zimmer Y, Cairncross JG, Janzer RC, Domany E, Delorenzi M, Stupp R and Hegi ME (2008). Stem cell-related “self-renewal” signature and high epidermal growth factor receptor expression associated with resistance to concomitant chemoradiotherapy in glioblastoma. Journal of Clinical Oncology 26(18): 3015-3024.
  37. Naffar-Abu-Amara S, Shay T, Galun M, Cohen N, Isakoff SJ, Kam Z and Geiger B (2008). Identification of novel pro-migratory, cancer-associated genes using quantitative, microscopy-based screening. PLoS One 3(1): e1457.
  38. Amit I, Citri A, Shay T, Lu Y, Katz M, Zhang F, Tarcic G, Siwak D, Lahad J, Jacob-Hirsch J, Amariglio N, Vaisman N, Segal E, Rechavi G, Alon U, Mills GB, Domany E and Yarden Y (2007). A module of negative feedback regulators defines growth factor signaling. Nature Genetics 39(4): 503-512.
  39. Fainaru O, Shay T, Hantisteanu S, Goldenberg D, Domany E and Groner Y (2007). TGFbeta-dependent gene expression profile during maturation of dendritic cells. Genes and Immunity 8(3): 239-244.
  40. Katz M, Amit I, Citri A, Shay T, Carvalho S, Lavi S, Milanezi F, Lyass L, Amariglio N, Jacob-Hirsch J, Ben-Chetrit N, Tarcic G, Lindzen M, Avraham R, Liao YC, Trusk P, Lyass A, Rechavi G, Spector NL, Lo SH, Schmitt F, Bacus SS and Yarden Y (2007). A reciprocal tensin-3-cten switch mediates EGF-driven mammary cell migration. Nature Cell Biology 9(8): 961-969.
  41. Ben-Zeev E, Kowalsman N, Ben-Shimon A, Segal D, Atarot T, Noivirt O, Shay T and Eisenstein M (2005). Docking to single-domain and multiple-domain proteins: old and new challenges. Proteins 60(2): 195-201.
  42. Shay T, Naffar-Abu-Amara S, Paran Y, Zamir E, Liron Y, Geiger B and Kam Z (2004). Cell-Based Screening for Function. IEEE – International Symposium on Biomedical Imaging 2: 1243-1246.