Publications

See also articles in Hebrew.

 

Y. Elyahu, I. Hekselman, I. Eizenberg-Magar, O. Berner, I. Strominger, M. Schiller, K. Mittal, A. Nemirovsky, E. Eremenko, A. Vital, E. Simonovsky, V. Chalifa-Caspi, N. Friedman, E. Yeger-Lotem, and A. Monsonego
Aging Promotes Reorganization of the CD4 T Cell Landscape toward Extreme Regulatory and Effector Phenotypes.
Science Advances 5(8): eaaw8330., Aug. 2019

L. De Mattos-Arruda, S. Sammut, E. Ross, R. Bashford-Rogers, E. Greenstein, H. Markus, S. Morganella, Y. Teng, Y. Maruvka, B. Pereira, O. M. Rueda, S. Chin, T. Contente-Cuomo, Regina Mayor, Alexandra Arias, H. Raza Ali, Wei Cope, Daniel Tiezzi, Aliakbar Dariush, Tauanne Dias Amarante, D. Reshef, N. Ciriaco, E. Martinez-Saez, V. Peg, S. Ramon Y Cajal, J. Cortes, G. Vassiliou, G. Getz, S. Nik-Zainal, M. Murtaza, N. Friedman, F. Markowetz, J. Seoane, and C. Caldas
The Genomic and Immune Landscapes of Lethal Metastatic Breast Cancer.
Cell Reports 27(9):2690-2708.e10, May 2019

D. Schneidman-Duhovny, N. Khuri, G. Qiang Dong, M.B. Winter, E. Shifrut, N. Friedman, C.S. Craik, K.P. Pratt, P. Paz, F. Aswad, and A. Sali
Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition.
PLoS One, vol. 13, no. 11, p. e0206654, Nov. 2018

S. Kalaora, Y. Wolf, T. Feferman, E. Barnea, E. Greenstein, D. Reshef, I. Tirosh, A. Reuben, S. Patkar, R. Levy, J. Quinkhardt, T. Omokoko, N. Qutob, O. Golani, J. Zhang, X. Mao, X. Song, C. Bernatchez, C. Haymaker, M.-A. Forget, C. Creasy, P. Greenberg, B. W. Carter, Z. A. Cooper, S. A. Rosenberg, M. Lotem, U. Sahin, G. Shakhar, E. Ruppin, J. A. Wargo, N. Friedman, A. Admon, and Y. Samuels
Combined analysis of antigen presentation and T-cell recognition reveals restricted immune responses in melanoma.
Cancer Discovery, vol. 8, no. 11, pp. 1366–75, Sep. 2018

M. Polonsky, J. Rimer, A. Kern-Perets, I. Zaretsky, S. Miller, C. Bornstein, E. David, N. M. Kopelman, G. Stelzer, Z. Porat, B. Chain, and N. Friedman
Induction of CD4 T cell memory by local cellular collectivity.
Science, vol. 360, no. 6394, Jun. 2018

S. Adutler-Lieber, N. Friedman, and B. Geiger
Expansion and antitumor cytotoxicity of T-cells are augmented by substrate-bound CCL21 and intercellular adhesion molecule 1.
Front. Immunol., vol. 9, pp. 1303, Jun. 2018

S. Adutler-Lieber, I. Zaretsky, H. Sabany, E. Kartvelishvily, O. Golani, B. Geiger, and N. Friedman
Substrate-bound CCL21 and ICAM1 combined with soluble IL-6 collectively augment the expansion of antigen-specific murine CD4(+) T cells.
Blood Adv., vol. 1, no. 15, pp. 1016–1030, Jun. 2017

I. Eizenberg-Magar, J. Rimer, I. Zaretsky, D. Lara-Astiaso, S. Reich-Zeliger, and N. Friedman
Diverse continuum of CD4+ T-cell states is determined by hierarchical additive integration of cytokine signals.
Proc. Natl. Acad. Sci. , vol. 114, no. 31, pp. E6447–E6456, Aug. 2017

See also: I. Eizenberg-Magar, J. Rimer, and N. Friedman
Cells combine cytokine signals in a hierarchical-additive manner.
In Principles of Systems Biology, Cell Syst., vol. 5, no. 3, pp. 158–160, Apr. 2018

A. Madi, A. Poran, E. Shifrut, S. Reich-Zeliger, E. Greenstein, I. Zaretsky, T. Arnon, F. Van Laethem, A. Singer, J. Lu, P. D. Sun, I. R. Cohen, and N. Friedman
T cell receptor repertoires of mice and humans are clustered in similarity networks around conserved public CDR3 sequences.
Elife, vol. 6, p. e22057, 2017

N. Tickotsky, T. Sagiv, J. Prilusky, E. Shifrut, and N. Friedman
McPAS-TCR: A manually-curated catalogue of pathology-associated T cell receptor sequences.
Bioinformatics, 2017

M. Cinelli, Sun Yuxin, K. Best, J. M. Heather, S. Reich-Zeliger, E. Shifrut, N. Friedman, J. Shawe-Taylor, and B. Chain
Feature selection using a one dimensional naïve Bayes’ classifier increases the accuracy of support vector machine classification of CDR3 repertoires.
Bioinformatics, vol. 33, no. 7, pp. 951–955, Apr. 2017

Y. Sun, K. Best, M. Cinelli, J. M. Heather, S. Reich-Zeliger, E. Shifrut, N. Friedman, J. Shawe-Taylor, and B. Chain
Specificity, privacy, and degeneracy in the CD4 T cell receptor repertoire following immunization.
Frontiers in Immunology , vol. 8. p. 430, 2017

Y. Wolf, A. Shemer, M. Polonsky, M. Gross, A. Mildner, S. Yona, E. David, K.-W. Kim, T. Goldmann, I. Amit, M. Heikenwalder, S. Nedospasov, M. Prinz, N. Friedman, and S. Jung
Autonomous TNF is critical for in vivo monocyte survival in steady state and inflammation.
J. Exp. Med., Mar. 2017.

Setty M, Tadmor MD, Reich-Zeliger S, Angel O, Salame TM, Kathail P, Choi K, Bendall S, Friedman N and Pe'er D
Wishbone identifies bifurcating developmental trajectories from single-cell data.
Nat Biotech, vol. 34, no. 6, pp. 637–645, Jun. 2016.

Heather JM, Best K, Oakes T, Gray ER, Roe JK, Thomas N, Friedman N, Noursadeghi M and Chain B
Dynamic perturbations of the T-Cell receptor repertoire in chronic HIV infection and following antiretroviral therapy.
Frontiers in Immunology , vol. 6. p. 644, 2016

Polonsky M, Chain B, Friedman N
Clonal expansion under the microscope: studying lymphocyte activation and differentiation using live-cell imaging.
Immunol Cell Biol, vol. 94, no. 3. Australasian Society for Immunology Inc., pp. 242–249, Mar-2016.

Zlotnikov-Klionsky Y, Nathansohn-Levi B, Shezen E, Rosen C, Kagan S, Bar-On L, Jung S, Shifrut E, Reich-Zeliger S, Friedman N, Aharoni R, Arnon R, Yifa O, Aronovich A, Reisner Y.
Perforin-positive dendritic cells exhibit an immuno-regulatory role in metabolic syndrome and autoimmunity.
Immunity, vol. 43, no. 4, pp. 776–787, Oct. 2015.  See also research highlight.

Hart Y, Reich-Zeliger S, Antebi YE, Zaretsky I, Mayo AE, Alon U, Friedman N
Paradoxical signaling by a secreted molecule leads to homeostasis of cell levels.
Cell, vol. 158, no. 5, pp. 1022–1032, Aug. 2014.

Thomas N, Best K, Cinelli M, Reich-Zeliger S, Gal H, Shifrut E, Madi A, Friedman N, Shawe-Taylor J, Chain B
Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence.
Bioinforma. , vol. 30, no. 22, pp. 3181–3188, Nov. 2014.

Shipony Z, Mukamel Z, Cohen NM, Landan G, Chomsky E, Zeliger SR, Fried YC, Ainbinder E, Friedman N, Tanay A
Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells.
Nature, vol. 513, no. 7516, pp. 115–119, Sep. 2014.

Madi A, Shifrut E, Reich-Zeliger S, Gal H, Best K, Ndifon W, Chain B, Cohen IR, Friedman N
T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity.
Genome Res., vol. 24, pp. 1603-1612, Oct. 2014.

Adutler-Lieber S, Zaretsky I, Platzman I, Deeg J, Friedman N, Spatz JP, Geiger B
Engineering of synthetic cellular microenvironments: Implications for immunity.
J. Autoimmun., vol. 54, pp. 100–111, Nov. 2014.

Rimer J, Cohen IR, Friedman N
Do all creatures possess an acquired immune system of some sort?
BioEssays, vol. 36, no. 3, pp. 273–281, 2014.

Shifrut E, Baruch K, Gal H, Ndifon W, Deczkowska A, Schwartz M, Friedman N
CD4+ T cell-receptor repertoire diversity is compromised in the spleen but not in the bone-marrow of aged mice due to private and sporadic clonal expansions.
Front. Immunol., vol. 4, p. 379, Nov. 2013.

Waysbort N, Russ D, Chain BM, Friedman N
Coupled IL-2-dependent extracellular feedbacks govern two distinct consecutive phases of CD4 T cell activation.
J. Immunol. 2013 Dec 15;191(12):5822–30.

Antebi YE, Reich-Zeliger S, Hart Y, Mayo A, Eizenberg I, Rimer J, Putheti P, Pe’er D, Friedman N
Mapping Differentiation under mixed culture conditions reveals a tunable continuum of T cell fates.
PLoS Biol, vol. 11, no. 7, p. e1001616, Jul. 2013.

Yissachar N, Sharar Fischler T, Cohen AA, Reich-Zeliger S, Russ D, Shifrut E, Porat Z, Friedman N
Dynamic response diversity of NFAT isoforms in individual living cells.
Mol. Cell, vol. 49, no. 2, pp. 322–330, Jan. 2013.

Friedman N
Studying gene expression at the level of the single cell.
Briefings Funct. Genomics , vol. 12, no. 2, pp. 73–74, Mar. 2013.

Baruch K, Ron-Harel N, Gal H, Deczkowska A, Shifrut E, Ndifon W, Mirlas-Neisberg N, Cardon M, Vaknin I, Cahalon L, Berkutzki T, Mattson MP, Gomez-Pinilla F, Friedman N, Schwartz M
CNS-specific immunity at the choroid plexus shifts toward destructive Th2 inflammation in brain aging.
Proc. Natl. Acad. Sci. U. S. A. 2013 Feb 5;110(6):2264–9.

Polonsky M, Zaretsky I, Friedman N
Dynamic single-cell measurements of gene expression in primary lymphocytes: challenges, tools and prospects.
Brief. Funct. Genomics. 2013 Mar 17;12(2):99–108.

Savir Y, Waysbort N, Antebi YE, Tlusty T, Friedman N
Balancing speed and accuracy of polyclonal T cell activation: a role for extracellular feedback.
BMC Syst. Biol. 2012 Jan 24;6(2):111.

Zaretsky I, Polonsky M, Shifrut E, Reich-Zeliger S, Antebi Y, Aidelberg G, Waysbort N, Friedman N
Monitoring the dynamics of primary T cell activation and differentiation using long term live cell imaging in microwell arrays.
Lab Chip. 2012 Dec 7;12(23):5007–15.

Ndifon W, Gal H, Shifrut E, Aharoni R, Yissachar N, Waysbort N, Reich-Zeliger S, Arnon R, Friedman N
Chromatin conformation governs T-cell receptor Jβ gene segment usage.
Proc. Natl. Acad. Sci. U. S. A. 2012 Sep 25;109(39):15865–70.

Hart Y, Antebi YE, Mayo AE, Friedman N, Alon U
Design principles of cell circuits with paradoxical components.
Proc. Natl. Acad. Sci. U. S. A. 2012 May 22;109(21):8346–51.

Aharoni R, Eilam R, Stock A, Vainshtein A, Shezen E, Gal H, Friedman N, Arnon R
Glatiramer acetate reduces Th-17 inflammation and induces regulatory T-cells in the CNS of mice with relapsing-remitting or chronic EAE.
J. Neuroimmunol. 2010 Aug 25;225(1-2):100–11.

Friedman N, Cai L, Xie XS
Linking stochastic dynamics to population distribution: an analytical framework of gene expression.
Phys. Rev. Lett. 2006 Oct;97(16):168302.

Cai L, Friedman N, Xie XS
Stochastic protein expression in individual cells at the single molecule level.
Nature. 2006 Mar 16;440(7082):358–62.

מאמרים בעברית

ניר פרידמן, לראות את היער מבעד לעצים. אודיסאה, גליון 29, אוקטובר 2015