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Cagliani R ,Forni D, Mozzi A, Fuchs R, Tussia-Cohen D, Arrigoni F , Pozzoli U , De Gioia L, Hagai T, Sironi M. Evolution of Virus-like Features and Intrinsically Disordered Regions in Retrotransposon-derived Mammalian Genes. Mol Biol Evol. 2024 Aug 2;41(8):msae154.
https://doi.org/10.1093/molbev/msae154
Cagliani R ,Forni D, Mozzi A, Fuchs R, Hagai T, Sironi M. Evolutionary analysis of ZAP and its cofactors identifies intrinsically disordered regions as central elements in host-pathogen interactions. Comput Struct Biotechnol J. August 01, 2024.
https://doi.org/10.1016/j.csbj.2024.07.022
Schneor L, Hagai T*. Evolutionary divergence of induced versus constitutive antiviral gene expression between primates and rodents. Preprint: bioRxiv.
https://doi.org/10.1101/2024.05.26.595927
Levinger R#, Tussia-Cohen D#, Friedman S, Lender Y, Nissan Y, Fraimovitch E, Gavriel Y, Tearle J, Kolodziejczyk AA, Gomes T, Kunowska N, Weinberg M, Donati G, James KR, Yovel Y, Hagai T*. Spatial and single-cell transcriptomics illuminate bat immunity and barrier tissue evolution. Preprint: bioRxiv
https://doi.org/10.1101/2023.10.30.564705
Schneor L#, Kaltenbach S#, Fridman S, Tussia-Cohen D, Nissan Y, Shuler G, Fraimovitch E, Weinberg M, Kolodziejczyk AA, Donati G, Teeling EC, Yovel Y, Hagai T*. Comparison of antiviral responses in two bat species reveals conserved and divergent innate immune pathways. iScience. 2023. 26,107435, August 18.
https://doi.org/10.1016/j.isci.2023.107435
Kumasaka N, Rostom R, Huang N, Polanski K, Meyer KB, Patel S, Boyd R, Gomez C, Barnett SN, Panousis NI, Schwartzentruber J, Ghoussaini M, Lyons PA, Calero-Nieto FJ, Göttgens B, Barnes JL, Worlock KB, Yoshida M, Nikolić MZ, Stephenson E, Reynolds G, Haniffa M, Marioni JC, Stegle O, Hagai T*, Teichmann SA*. Mapping interindividual dynamics of innate immune response at single-cell resolution. Nat Genet 2023 Jun;55(6):1066-1075. doi: 10.1038/s41588-023-01421-y.
https://www.nature.com/articles/s41588-023-01421-y
Levra Levron C, Watanabe M, Proserpio V, Piacenti G, Lauria A, Kaltenbach S, Tamburrini A, Nohara T, Anselmi F, Duval C, Elettrico L, Donna D, Conti L, Baev D, Natsuga K, Hagai T, Oliviero S, Donati G. Tissue memory relies on stem cell priming in distal undamaged areas.
Nat Cell Biol. 2023 Apr 20. doi: 10.1038/s41556-023-01120-0. PMID: 37081165
https://www.nature.com/articles/s41556-023-01120-0
Schneor L#, Kaltenbach S#, Fridman S, Nissan Y, Shuler G, Fraimovitch E, Weinberg M, Kolodziejczyk AA, Donati G, Teeling EC, Yovel Y, Hagai T*. A comparative analysis of the antiviral response in two bat species reveals conserved and divergent innate immune pathways. Preprint: bioRxiv
https://www.biorxiv.org/content/10.1101/2023.04.23.537989v1
Fraimovitch E, Hagai T*. Promoter evolution of mammalian gene duplicates.
BMC Biol. 2023 Apr 13;21(1):80. doi: 10.1186/s12915-023-01590-6. PMID: 37055747
https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-023-01590-6
Levron CL, Watanabe M, Proserpio V, Piacenti G, Lauria A, Kaltenbach S, Tamburrini A, Nohara T, Anselmi F, Duval C, Elettrico L, Donna D, Conti L, Baev D, Natsuga K, Hagai T, Oliviero S, Donati G. Lifelong tissue memory relies on spatially organised wound-distal progenitors. Preprint: bioRxiv
https://www.biorxiv.org/content/10.1101/2023.02.02.526841v1
Cohn O, Yankovitz G, Peshes-Yaloz N, Steuerman Y, Frishberg A, Brandes R, Mandelboim M, Hamilton JR, Hagai T, Amit I, Netea MG, Hacohen N, Iraqi FA, Bacharach E, Gat-Viks I. Distinct gene programs underpinning disease tolerance and resistance in influenza virus infection. Cell Syst. 2022 Dec 21;13(12):1002-1015.e9. doi: 10.1016/j.cels.2022.11.004. Epub 2022 Dec 13. PMID: 36516834
https://doi.org/10.1016/j.cels.2022.11.004
Shuler G, Hagai T*. Rapidly evolving viral motifs mostly target biophysically constrained binding pockets of host proteins.
Cell Reports. 2022, Volume 40, Issue 7, 111212, August 16
https://doi.org/10.1016/j.celrep.2022.111212
Cohn O, Yankovitz G, Peshes-Yaloz N, Steuerman Y, Frishberg A, Brandes R, Mandelboim M, Hamilton JR, Hagai T, Amit I, Netea MG, Hacohen N, Iraqi FA, Bacharach E, Gat-Viks I. Distinct gene programs underpinning ‘disease tolerance’ and ‘resistance’ in influenza virus infection. Preprint: bioRxiv
https://doi.org/10.1101/2022.03.22.485254
Shuler G, Hagai T*. Rapidly evolving viral motifs target biophysically constrained binding pockets of host proteins. Preprint: bioRxiv
https://doi.org/10.1101/2022.01.29.478279
Kumasaka N, Rostom R, Huang N, Polanski K, Meyer KB, Patel S, Boyd R, Gomez C, Barnett SN, Panousis NI, Schwartzentruber J, Ghoussaini M, Lyons PA, Calero-Nieto FJ, Göttgens B, Barnes JL, Worlock KB, Yoshida M, Nikolic MZ, Stephenson E, Reynolds G, Haniffa M, Marioni J, Stegle O, Hagai T*, Teichmann SA*. Mapping interindividual dynamics of innate immune response at single-cell resolution. Preprint: bioRxiv
https://doi.org/10.1101/2021.09.01.457774
Fraimovitch E, Hagai T*. Promoter architecture links gene duplication with transcriptional divergence. Preprint: bioRxiv
https://doi.org/10.1101/2021.07.03.450995
Dolan PT, Taguwa S, Rangel MA, Acevedo A, Hagai T, Andino R, Frydman J. Principles of dengue virus evolvability derived from genotype-fitness maps in human and mosquito cells. eLife. 2021 Jan 25;10:e61921.
https://doi.org/10.7554/eLife.61921
Reynolds G, Vegh P, Fletcher J, Poyner EFM, Stephenson E, Goh I, Botting RA, Huang N, Olabi B, Dubois A, Dixon D, Green K, Maunder D, Engelbert J, Efremova M, Polański K, Jardine L, Jones C, Ness T, Horsfall D, McGrath J, Carey C, Popescu DM, Webb S, Wang XN, Sayer B, Park JE, Negri VA, Belokhvostova D, Lynch MD, McDonald D, Filby A, Hagai T, Meyer KB, Husain A, Coxhead J, Vento-Tormo R, Behjati S, Lisgo S, Villani AC, Bacardit J, Jones PH, O’Toole EA, Ogg GS, Rajan N, Reynolds NJ, Teichmann SA, Watt FM, Haniffa M. Developmental cell programs are co-opted in inflammatory skin disease. Science. 2021 Jan 22;371(6527):eaba6500.
https://doi.org/10.1126/science.aba6500.
Davidson S, Efremova M, Riedel A, Mahata B, Pramanik J, Huuhtanen J, Kar G, Vento-Tormo R, Hagai T, Chen X, Haniffa MA, Shields JA & Teichmann SA. Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth. Cell Rep 2020: May 31(7)
https://doi.org/10.1016/j.celrep.2020.107628.
McCarthy DJ, Rostom R, Huang Y, Kunz DJ, Danecek P, Bonder MJ, Hagai T, Lyu R; HipSci Consortium, Wang W, Gaffney DJ, Simons BD, Stegle O, Teichmann SA. Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes. Nat Methods 2020 Mar16
https://doi.org/10.1038/s41592-020-0766-3
Dolan PT, Taguwa S, Rangel MA, Acevedo A, Hagai T, Andino R, Frydman J
Principles of dengue virus evolvability derived from genotype-fitness maps in human and mosquito cells. (under review) Preprint: bioRxiv
https://doi.org/10.1101/2020.02.05.936195
Davidson S, Efremova M, Riedel A, Mahata B, Pramanik J, Huuhtanen J, Kar G, Vento-Tormo R, Hagai T, Chen X, Haniffa MA, Shields JA & Teichmann SA. A dynamic stromal niche supports tumour growth during tumour evolution. (under review) Preprint: bioRxiv
http://doi.org/10.1101/467225
McCarthy DJ, Rostom R,Huang Y, Kunz DJ, Danecek P,Bonder MJ, Hagai T, HipSci Consortium, Wang W, Gaffney DJ, Simons BD, Stegle O& Teichmann SA. Cardelino: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants. (under review) Preprint: bioRxiv
http://doi.org/10.1101/413047
Hagai T*, Chen X, Miragaia RJ, Rostom R, Gomes T, Kunowska N, Henriksson J, Park J, Proserpio V, Donati G, Bossini-Castillo L, Braga FAV, Naamati G, Fletcher J, Stephenson E, Vegh P, Trynka G, Kondova I, Dennis M, Hanniffa M, Nourmohammad A, Lassig M & Teichmann SA*. (2018) Gene expression variability across cells and species shapes innate immunity. Nature Nov;563(7730):197-202
http://doi.org/10.1038/s41586-018-0657-2
Mor N, Rais Y, Sheban D, Peles S, Aguilera-Castrejon A, Zviran A, Elinger D, Viukov S, Geula S, Krupalnik V, Zerbib M, Chomsky E, Lasman L, Shani T, Bayerl J, Gafni O, Hanna S, Buenrostro JD, Hagai T, Masika H, Vainorius G, Bergman Y, Greenleaf WJ, Esteban MA, Elling U, Levin Y, Massarwa R, Merbl Y, Novershtern N & Hanna JH. (2018) Neutralizing Gatad2a-Chd4-Mbd3/NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency. Cell Stem Cell 23(3):412-425
http://doi.org/10.1016/j.stem.2018.07.004
Miragaia RJ, Teichmann, SA, Hagai T. (2017) Single-cell insights into transcriptomic diversity in immunity. Curr Opin Sys Bio 5:63-71
http://doi.org/10.1016/j.coisb.2017.08.003
Y Gavrilov, Hagai T & Levy Y. (2015) Nonspecific yet decisive: Ubiquitination can affect the native‐state dynamics of the modified protein. Protein Science 24 (10): 1580-1592
http://doi.org/10.1002/pro.268
Gitlin L, Hagai T, LaBarbera A, Solovey M & Andino R. (2014) Rapid evolution of virus sequences and functions through intrinsically disordered regions. PLoS Pathogens 10 (12): e1004529
http://doi.org/10.1371/journal.ppat.1004529
Hagai T, Azia A, Babu MM & Andino R. (2014) Use of host-like peptide motifs in viral proteins is a prevalent strategy in host-virus interactions. Cell Reports 7(5):1729-39
http://doi.org/10.1016/j.celrep.2014.04.052
Tsvetkov P, MyersN, EliavR, Adamovich Y, Hagai T, Adler J, NavonA & Shaul Y. (2014). NADH binds and stabilizes the 26S proteasomes independent of ATP. J Biol Chem 289(16):11272-81
http://doi.org/10.1074/jbc.M113.537175
Rais Y, Zviran A, Geula S, Gafni O, Chomsky E, Viukov S, AlFatah Mansour A, Caspi I, Krupalnik V, Zerbib M, Maza I, Mor N, Baran D, Weinberger L, Jaitin DA, Lara-Astiaso D, Blecher-Gonen R, Shipony Z, Mukamel Z, Hagai T, Gilad S, Amann-Zalcenstein D, Tanay A, Amit I, Novershtern N & Hanna JH. (2013). Deterministic direct reprogramming of somatic cells to pluripotency. Nature 502, 65–70
http://doi.org/10.1038/nature1257
Dagan S, Hagai T, Gavrilov Y, Kapon R, Levy Y & Reich Z. (2013). Stabilization of a protein conferred by an increase in folded state entropy. Proc Natl Acad Sci U S A 110, 10628-33
http://doi.org/10.1073/pnas.1302284110
Hagai T, Azia A, Trizac E & Levy Y. (2012). Modulation of folding kinetics of repeat proteins: Interplay between intra- and inter-domain interactions. Biophys J 103, 1555-1565
http://doi.org/10.1016/j.bpj.2012.08.018
Hagai T, Toth-Petroczy A, Azia A & Levy Y. (2012). The origins and evolution of ubiquitination sites. Mol Biosyst 8, 1865-77
http://doi.org/10.1039/c2mb25052g
Hagai T, Azia A, Toth-Petroczy A & Levy Y. (2011). Intrinsic disorder in ubiquitination substrates. J Mol Biol 412, 319-24
http://doi.org/10.1016/j.jmb.2011.07.024
Hagai T & Levy Y. (2010). Ubiquitin not only serves as a tag but also assists degradation by inducing protein unfolding. Proc Natl Acad Sci U S A 107, 2001-6
http://doi.org/10.1073/pnas.0912335107
Shental D, Arviv O, Hagai T & Y Levy. (2010). Folding of conjugated proteins. Annu Rep Comput Chem 6, 263-277.
http://doi.org/10.1016/S1574-1400(10)06013-5
Hagai T & Levy Y. (2008). Folding of elongated proteins: conventional or anomalous? J Am Chem Soc 130, 14253-62
http://doi.org/10.1021/ja804280p
Hagai T, Cohen M & Bloch G. (2007). Genes encoding putative Takeout/juvenile hormone binding proteins in the honeybee (Apis mellifera) and modulation by age and juvenile hormone of the takeout-like gene GB19811. Insect Biochem Mol Biol 37, 689-701
http://doi.org/10.1016/j.ibmb.2007.04.002