TAU's Single Cell Genomics Core enables scientists to pursue their research with cutting-edge analysis tools and services. Below are recent publications of studies that made use of our services.


Single-cell transcriptomic analysis of oral masticatory and lining mucosa-derived mesenchymal stromal cells

Ilan Pinkhasov, Liron Kabakov, Carlos E Nemcovsky, Miron Weinreb, Pnina Schlesinger, Omer Bender, Maayan Gal, Daniel Z Bar, Evgeny Weinberg.

J Clin Periodontol, 2023 Jun;50(6):807-818. doi: 10.1111/jcpe.13799


Frequent aneuploidy in primary human T cells after CRISPR–Cas9 cleavage

Alessio David Nahmad, Eli Reuveni, Ella Goldschmidt, Tamar Tenne, Meytal Liberman, Miriam Horovitz-Fried, Rami Khosravi, Hila Kobo, Eyal Reinstein, Asaf Madi, Uri Ben-David, Adi Barzel. 

Nature Biotechnology, volume 40, pages1807–1813 (2022)


Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes.

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.

Nat Methods. 2020 Apr;17(4):414-421. 


Inferring cellular heterogeneity of associations from single cell genomics

Maya Levy, Amit Frishberg, Irit Gat-Viks, Inferring cellular heterogeneity of associations from single cell genomics, Bioinformatics, , btaa151,


Checkpoint blockade immunotherapy induces dynamic changes in novel subsets of PD-1-CD8+ tumor-infiltrating T cells.

Kurtulus S*, Madi A*, Escobar J, Klapholz M, Nyman J, Pawlak M, Dionne D, Xia J, Rozenblatt-Rosen O, Kuchroo VK, Regev A, Anderson AC.

Immunity 2019 Jan 15;50(1):181-194.e6.


Linking cell dynamics with gene coexpression networks to characterize key events in chronic virus infections.

Pedragosa M, Riera G, Casella V, Esteve-Codina A, Steuerman Y, Seth C, Bocharov G, Heath S, Gat-Viks I, Argilaguet J, Meyerhans A.

Front Immunol. 2019 May 3;10:1002.


Cell composition analysis of bulk genomics using single-cell data.

Frishberg A, Peshes-Yaloz N, Cohn O, Rosentul D, Steuerman Y, Valadarsky L, Yankovitz G, Mandelboim M, Iraqi FA, Amit I, Mayo L, Bacharach E, Gat-Viks I.

Nat Methods. 2019 Apr;16(4):327-332.


Global modulation in DNA epigenetics during pro-inflammatory macrophage activation.

Jain N, Shahal T, Gabrieli T, Gilat N, Torchinsky D, Michaeli Y, Vogel V, Ebenstein Y.

Epigenetics. 2019 Jul 8:1-11.


5-Hydroxymethylcytosine as a clinical biomarker: Fluorescence-based assay for high-throughput epigenetic quantification in human tissues.

Margalit S, Avraham S, Shahal T, Michaeli Y, Gilat N, Magod P, Caspi M, Loewenstein S, Lahat G, Friedmann-Morvinski D, Kariv R, Rosin-Arbesfeld R, Zirkin S, Ebenstein Y.

Int J Cancer. 2019 Jun 18.


Long-read single-molecule maps of the functional methylome.

Sharim H, Grunwald A, Gabrieli T, Michaeli Y, Margalit S, Torchinsky D, Arielly R, Nifker G, Juhasz M, Gularek F, Almalvez M, Dufault B, Chandra SS, Liu A, Bhattacharya S, Chen YW, Vilain E, Wagner KR, Pevsner J, Reifenberger J, Lam ET, Hastie AR, Cao H, Barseghyan H, Weinhold E, Ebenstein Y.

Genome Res. 2019 Apr;29(4):646-656.


Analytical epigenetics: single-molecule optical detection of DNA and histone modifications.

Heck C, Michaeli Y, Bald I, Ebenstein Y.

Curr Opin Biotechnol. 2019 Feb;55:151-158


Microfluidic DNA combing for parallel single-molecule analysis.

Wu S, Jeffet J, Grunwald A, Sharim H, Gilat N, Torchinsky D, Zheng Q, Zirkin S, Xu L, Ebenstein Y.

Nanotechnology. 2019 Jan 25;30(4):045101


Dissection of influenza infection in vivo by single-cell RNA sequencing.

Steuerman Y, Cohen M, Peshes-Yaloz N, Valadarsky L, Cohn O, David E, Frishberg A, Mayo L, Bacharach E, Amit I, Gat-Viks I.

Cell Syst. 2018 Jun 27;6(6):679-691.e4.


Cell type transcriptome atlas for the planarian Schmidtea mediterranea.

Fincher CT, Wurtzel O, de Hoog T, Kravarik KM, Reddien PW.

Science. 2018 May 25;360(6391).


Induction and transcriptional regulation of the co-inhibitory gene module in T cells.

Chihara N, Madi A, Kondo T, Zhang H, Acharya N, Singer M, Nyman J, Marjanovic ND, Kowalczyk MS, Wang C, Kurtulus S, Law T, Etminan Y, Nevin J, Buckley CD, Burkett PR, Buenrostro JD, Rozenblatt-Rosen O, Anderson AC, Regev A, Kuchroo VK.

Nature. 2018 Jun;558(7710):454-459. doi: 10.1038/s41586-018-0206-z. 


DNA methylation dynamics during embryonic development and postnatal maturation of the mouse auditory sensory epithelium.

Yizhar-Barnea O, Valensisi C, Jayavelu ND, Kishore K, Andrus C, Koffler-Brill T, Ushakov K, Perl K, Noy Y, Bhonker Y, Pelizzola M, Hawkins RD, Avraham KB.

Sci Rep. 2018 Nov 26;8(1):17348. 


T cell receptor repertoires of mice and humans are clustered in similarity networks around conserved public CDR3 sequences.

Madi A, Poran A, Shifrut E, Reich-Zeliger S, Greenstein E, Zaretsky I, Arnon T, Laethem FV, Singer A, Lu J, Sun PD, Cohen IR, Friedman N.

Elife. 2017 Jul 21;6.


Single cell analysis of the inner ear sensory organs.

Yizhar-Barnea O, Avraham KB.

Int J Dev Biol. 2017;61(3-4-5):205-213



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