Uri Alon - Publications

Affiliations: 
Weizmann Institute of Science, Rehovot, Israel 
Area:
Bioinformatics Biology, General Biophysics

82 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Adler M, Mayo A, Zhou X, Franklin RA, Meizlish ML, Medzhitov R, Kallenberger SM, Alon U. Principles of Cell Circuits for Tissue Repair and Fibrosis. Iscience. 23: 100841. PMID 32058955 DOI: 10.1016/J.Isci.2020.100841  0.396
2019 Adler M, Korem Kohanim Y, Tendler A, Mayo A, Alon U. Continuum of Gene-Expression Profiles Provides Spatial Division of Labor within a Differentiated Cell Type. Cell Systems. PMID 30638811 DOI: 10.1016/J.Cels.2018.12.008  0.319
2019 Hausser J, Mayo A, Keren L, Alon U. Central dogma rates and the trade-off between precision and economy in gene expression. Nature Communications. 10: 68. PMID 30622246 DOI: 10.1038/S41467-018-07391-8  0.358
2018 Adler M, Mayo A, Zhou X, Franklin RA, Jacox JB, Medzhitov R, Alon U. Endocytosis as a stabilizing mechanism for tissue homeostasis. Proceedings of the National Academy of Sciences of the United States of America. PMID 29429964 DOI: 10.1073/Pnas.1714377115  0.444
2018 Zhou X, Franklin RA, Adler M, Jacox JB, Bailis W, Shyer JA, Flavell RA, Mayo A, Alon U, Medzhitov R. Circuit Design Features of a Stable Two-Cell System. Cell. PMID 29398113 DOI: 10.1016/J.Cell.2018.01.015  0.454
2018 Adler M, Alon U. Fold-change detection in biological systems Current Opinion in Systems Biology. 8: 81-89. DOI: 10.1016/J.Coisb.2017.12.005  0.321
2017 Drayman N, Karin O, Mayo A, Danon T, Shapira L, Rafael D, Zimmer A, Bren A, Kobiler O, Alon U. Dynamic Proteomics of Herpes Simplex Virus Infection. Mbio. 8. PMID 29114028 DOI: 10.1128/Mbio.01612-17  0.337
2017 Harikumar A, Edupuganti RR, Sorek M, Azad GK, Markoulaki S, Sehnalová P, Legartová S, Bártová E, Farkash-Amar S, Jaenisch R, Alon U, Meshorer E. An Endogenously Tagged Fluorescent Fusion Protein Library in Mouse Embryonic Stem Cells. Stem Cell Reports. PMID 28966122 DOI: 10.1016/J.Stemcr.2017.08.022  0.338
2017 Zimmer A, Amar-Farkash S, Danon T, Alon U. Dynamic proteomics reveals bimodal protein dynamics of cancer cells in response to HSP90 inhibitor. Bmc Systems Biology. 11: 33. PMID 28270142 DOI: 10.1186/S12918-017-0410-8  0.34
2017 Adler M, Szekely P, Mayo A, Alon U. Optimal Regulatory Circuit Topologies for Fold-Change Detection. Cell Systems. PMID 28089543 DOI: 10.1016/J.Cels.2016.12.009  0.307
2016 Karin O, Swisa A, Glaser B, Dor Y, Alon U. Dynamical compensation in physiological circuits. Molecular Systems Biology. 12: 886. PMID 27875241 DOI: 10.15252/Msb.20167216  0.303
2016 Keren L, Hausser J, Lotan-Pompan M, Vainberg Slutskin I, Alisar H, Kaminski S, Weinberger A, Alon U, Milo R, Segal E. Massively Parallel Interrogation of the Effects of Gene Expression Levels on Fitness. Cell. PMID 27545349 DOI: 10.1016/J.Cell.2016.07.024  0.33
2015 Korem Y, Szekely P, Hart Y, Sheftel H, Hausser J, Mayo A, Rothenberg ME, Kalisky T, Alon U. Geometry of the Gene Expression Space of Individual Cells. Plos Computational Biology. 11: e1004224. PMID 26161936 DOI: 10.1371/Journal.Pcbi.1004224  0.331
2015 Friedlander T, Mayo AE, Tlusty T, Alon U. Evolution of bow-tie architectures in biology. Plos Computational Biology. 11: e1004055. PMID 25798588 DOI: 10.1371/Journal.Pcbi.1004055  0.305
2014 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. 158: 1022-32. PMID 25171404 DOI: 10.1016/J.Cell.2014.07.033  0.335
2014 Adler M, Mayo A, Alon U. Logarithmic and power law input-output relations in sensory systems with fold-change detection. Plos Computational Biology. 10: e1003781. PMID 25121598 DOI: 10.1371/Journal.Pcbi.1003781  0.302
2014 Rothschild D, Dekel E, Hausser J, Bren A, Aidelberg G, Szekely P, Alon U. Linear superposition and prediction of bacterial promoter activity dynamics in complex conditions. Plos Computational Biology. 10: e1003602. PMID 24809350 DOI: 10.1371/Journal.Pcbi.1003602  0.309
2014 Farkash-Amar S, Zimmer A, Eden E, Cohen A, Geva-Zatorsky N, Cohen L, Milo R, Sigal A, Danon T, Alon U. Noise genetics: inferring protein function by correlating phenotype with protein levels and localization in individual human cells. Plos Genetics. 10: e1004176. PMID 24603725 DOI: 10.1371/Journal.Pgen.1004176  0.668
2013 Keren L, Zackay O, Lotan-Pompan M, Barenholz U, Dekel E, Sasson V, Aidelberg G, Bren A, Zeevi D, Weinberger A, Alon U, Milo R, Segal E. Promoters maintain their relative activity levels under different growth conditions. Molecular Systems Biology. 9: 701. PMID 24169404 DOI: 10.1038/Msb.2013.59  0.311
2013 Szekely P, Sheftel H, Mayo A, Alon U. Evolutionary tradeoffs between economy and effectiveness in biological homeostasis systems. Plos Computational Biology. 9: e1003163. PMID 23950698 DOI: 10.1371/Journal.Pcbi.1003163  0.307
2013 Hart Y, Mayo AE, Shoval O, Alon U. Comparing apples and oranges: fold-change detection of multiple simultaneous inputs. Plos One. 8: e57455. PMID 23469195 DOI: 10.1371/Journal.Pone.0057455  0.303
2013 Hart Y, Alon U. The utility of paradoxical components in biological circuits. Molecular Cell. 49: 213-21. PMID 23352242 DOI: 10.1016/J.Molcel.2013.01.004  0.311
2012 Farkash-Amar S, Eden E, Cohen A, Geva-Zatorsky N, Cohen L, Milo R, Sigal A, Danon T, Alon U. Dynamic proteomics of human protein level and localization across the cell cycle. Plos One. 7: e48722. PMID 23144944 DOI: 10.1371/Journal.Pone.0048722  0.663
2012 Sasson V, Shachrai I, Bren A, Dekel E, Alon U. Mode of regulation and the insulation of bacterial gene expression. Molecular Cell. 46: 399-407. PMID 22633488 DOI: 10.1016/J.Molcel.2012.04.032  0.33
2012 Hart Y, Antebi YE, Mayo AE, Friedman N, Alon U. Design principles of cell circuits with paradoxical components. Proceedings of the National Academy of Sciences of the United States of America. 109: 8346-51. PMID 22562798 DOI: 10.1073/Pnas.1117475109  0.361
2012 Geva-Zatorsky N, Issaeva I, Mayo A, Cohen A, Dekel E, Danon T, Cohen L, Liron Y, Alon U, Eden E. Using bleach-chase to measure protein half-lives in living cells. Nature Protocols. 7: 801-11. PMID 22461069 DOI: 10.1038/Nprot.2012.028  0.366
2012 Silander OK, Nikolic N, Zaslaver A, Bren A, Kikoin I, Alon U, Ackermann M. A genome-wide analysis of promoter-mediated phenotypic noise in Escherichia coli. Plos Genetics. 8: e1002443. PMID 22275871 DOI: 10.1371/Journal.Pgen.1002443  0.7
2012 Silander OK, Nikolic N, Zaslaver A, Bren A, Kikoin I, Alon U, Ackermann M. Correction: A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli Plos Genetics. 8. DOI: 10.1371/Annotation/73Cf6E53-2141-4918-926B-8D07B073884D  0.667
2011 Madar D, Dekel E, Bren A, Alon U. Negative auto-regulation increases the input dynamic-range of the arabinose system of Escherichia coli. Bmc Systems Biology. 5: 111. PMID 21749723 DOI: 10.1186/1752-0509-5-111  0.369
2011 Eden E, Geva-Zatorsky N, Issaeva I, Cohen A, Dekel E, Danon T, Cohen L, Mayo A, Alon U. Proteome half-life dynamics in living human cells. Science (New York, N.Y.). 331: 764-8. PMID 21233346 DOI: 10.1126/Science.1199784  0.374
2011 Shoval O, Alon U, Sontag E. Symmetry Invariance for Adapting Biological Systems Siam Journal On Applied Dynamical Systems. 10: 857-886. DOI: 10.1137/100818078  0.359
2010 Issaeva I, Cohen AA, Eden E, Cohen-Saidon C, Danon T, Cohen L, Alon U. Generation of double-labeled reporter cell lines for studying co-dynamics of endogenous proteins in individual human cells. Plos One. 5: e13524. PMID 20975952 DOI: 10.1371/Journal.Pone.0013524  0.401
2010 Shoval O, Goentoro L, Hart Y, Mayo A, Sontag E, Alon U. Fold-change detection and scalar symmetry of sensory input fields. Proceedings of the National Academy of Sciences of the United States of America. 107: 15995-6000. PMID 20729472 DOI: 10.1073/Pnas.1002352107  0.304
2010 Geva-Zatorsky N, Dekel E, Batchelor E, Lahav G, Alon U. Fourier analysis and systems identification of the p53 feedback loop. Proceedings of the National Academy of Sciences of the United States of America. 107: 13550-5. PMID 20622152 DOI: 10.1073/Pnas.1001107107  0.773
2010 Shachrai I, Zaslaver A, Alon U, Dekel E. Cost of unneeded proteins in E. coli is reduced after several generations in exponential growth. Molecular Cell. 38: 758-67. PMID 20434381 DOI: 10.1016/J.Molcel.2010.04.015  0.689
2010 Frenkel-Morgenstern M, Cohen AA, Geva-Zatorsky N, Eden E, Prilusky J, Issaeva I, Sigal A, Cohen-Saidon C, Liron Y, Cohen L, Danon T, Perzov N, Alon U. Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells. Nucleic Acids Research. 38: D508-12. PMID 19820112 DOI: 10.1093/Nar/Gkp808  0.652
2009 Goentoro L, Shoval O, Kirschner MW, Alon U. The incoherent feedforward loop can provide fold-change detection in gene regulation. Molecular Cell. 36: 894-9. PMID 20005851 DOI: 10.1016/J.Molcel.2009.11.018  0.329
2009 Cohen-Saidon C, Cohen AA, Sigal A, Liron Y, Alon U. Dynamics and variability of ERK2 response to EGF in individual living cells. Molecular Cell. 36: 885-93. PMID 20005850 DOI: 10.1016/J.Molcel.2009.11.025  0.65
2009 Zaslaver A, Kaplan S, Bren A, Jinich A, Mayo A, Dekel E, Alon U, Itzkovitz S. Invariant distribution of promoter activities in Escherichia coli. Plos Computational Biology. 5: e1000545. PMID 19851443 DOI: 10.1371/Journal.Pcbi.1000545  0.695
2009 Kashtan N, Parter M, Dekel E, Mayo AE, Alon U. Extinctions in heterogeneous environments and the evolution of modularity. Evolution; International Journal of Organic Evolution. 63: 1964-75. PMID 19473401 DOI: 10.1111/J.1558-5646.2009.00684.X  0.303
2009 Cohen AA, Kalisky T, Mayo A, Geva-Zatorsky N, Danon T, Issaeva I, Kopito RB, Perzov N, Milo R, Sigal A, Alon U. Protein dynamics in individual human cells: experiment and theory. Plos One. 4: e4901. PMID 19381343 DOI: 10.1371/Journal.Pone.0004901  0.674
2009 Alon U. Design principles of biological circuits Biophysical Journal. 96. DOI: 10.1016/J.Bpj.2008.12.974  0.311
2008 Cohen AA, Geva-Zatorsky N, Eden E, Frenkel-Morgenstern M, Issaeva I, Sigal A, Milo R, Cohen-Saidon C, Liron Y, Kam Z, Cohen L, Danon T, Perzov N, Alon U. Dynamic proteomics of individual cancer cells in response to a drug. Science (New York, N.Y.). 322: 1511-6. PMID 19023046 DOI: 10.1126/Science.1160165  0.644
2008 Kaplan S, Bren A, Dekel E, Alon U. The incoherent feed-forward loop can generate non-monotonic input functions for genes. Molecular Systems Biology. 4: 203. PMID 18628744 DOI: 10.1038/Msb.2008.43  0.374
2008 Kaplan S, Bren A, Zaslaver A, Dekel E, Alon U. Diverse two-dimensional input functions control bacterial sugar genes. Molecular Cell. 29: 786-92. PMID 18374652 DOI: 10.1016/J.Molcel.2008.01.021  0.707
2007 Shinar G, Milo R, Martínez MR, Alon U. Input output robustness in simple bacterial signaling systems. Proceedings of the National Academy of Sciences of the United States of America. 104: 19931-5. PMID 18077424 DOI: 10.1073/Pnas.0706792104  0.318
2007 Rosenfeld N, Young JW, Alon U, Swain PS, Elowitz MB. Accurate prediction of gene feedback circuit behavior from component properties. Molecular Systems Biology. 3: 143. PMID 18004276 DOI: 10.1038/Msb4100185  0.609
2007 Kalisky T, Dekel E, Alon U. Cost-benefit theory and optimal design of gene regulation functions. Physical Biology. 4: 229-45. PMID 17991990 DOI: 10.1088/1478-3975/4/4/001  0.37
2007 Sigal A, Danon T, Cohen A, Milo R, Geva-Zatorsky N, Lustig G, Liron Y, Alon U, Perzov N. Generation of a fluorescently labeled endogenous protein library in living human cells. Nature Protocols. 2: 1515-27. PMID 17571059 DOI: 10.1038/Nprot.2007.197  0.643
2007 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, et al. A module of negative feedback regulators defines growth factor signaling. Nature Genetics. 39: 503-12. PMID 17322878 DOI: 10.1038/Ng1987  0.325
2006 Sigal A, Milo R, Cohen A, Geva-Zatorsky N, Klein Y, Liron Y, Rosenfeld N, Danon T, Perzov N, Alon U. Variability and memory of protein levels in human cells. Nature. 444: 643-6. PMID 17122776 DOI: 10.1038/Nature05316  0.744
2006 Frankenstein Z, Alon U, Cohen IR. The immune-body cytokine network defines a social architecture of cell interactions. Biology Direct. 1: 32. PMID 17062134 DOI: 10.1186/1745-6150-1-32  0.309
2006 Zaslaver A, Mayo A, Ronen M, Alon U. Optimal gene partition into operons correlates with gene functional order. Physical Biology. 3: 183-9. PMID 17021382 DOI: 10.1088/1478-3975/3/3/003  0.689
2006 Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U. A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nature Methods. 3: 623-8. PMID 16862137 DOI: 10.1038/Nmeth895  0.707
2006 Sigal A, Milo R, Cohen A, Geva-Zatorsky N, Klein Y, Alaluf I, Swerdlin N, Perzov N, Danon T, Liron Y, Raveh T, Carpenter AE, Lahav G, Alon U. Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins. Nature Methods. 3: 525-31. PMID 16791210 DOI: 10.1038/Nmeth892  0.762
2006 Geva-Zatorsky N, Rosenfeld N, Itzkovitz S, Milo R, Sigal A, Dekel E, Yarnitzky T, Liron Y, Polak P, Lahav G, Alon U. Oscillations and variability in the p53 system. Molecular Systems Biology. 2: 2006.0033. PMID 16773083 DOI: 10.1038/Msb4100068  0.783
2006 Rosenfeld N, Perkins TJ, Alon U, Elowitz MB, Swain PS. A fluctuation method to quantify in vivo fluorescence data. Biophysical Journal. 91: 759-66. PMID 16648159 DOI: 10.1529/Biophysj.105.073098  0.601
2006 Mayo AE, Setty Y, Shavit S, Zaslaver A, Alon U. Plasticity of the cis-regulatory input function of a gene. Plos Biology. 4: e45. PMID 16602820 DOI: 10.1371/Journal.Pbio.0040045  0.694
2006 Shinar G, Dekel E, Tlusty T, Alon U. Rules for biological regulation based on error minimization. Proceedings of the National Academy of Sciences of the United States of America. 103: 3999-4004. PMID 16537475 DOI: 10.1073/Pnas.0506610103  0.308
2006 Mangan S, Itzkovitz S, Zaslaver A, Alon U. The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli. Journal of Molecular Biology. 356: 1073-81. PMID 16406067 DOI: 10.1016/J.Jmb.2005.12.003  0.733
2005 Kalir S, Mangan S, Alon U. A coherent feed‐forward loop with a SUM input function prolongs flagella expression in Escherichia coli Molecular Systems Biology. 1. PMID 16729041 DOI: 10.1038/Msb4100010  0.369
2005 Dekel E, Mangan S, Alon U. Environmental selection of the feed-forward loop circuit in gene-regulation networks. Physical Biology. 2: 81-8. PMID 16204860 DOI: 10.1088/1478-3975/2/2/001  0.329
2005 Kashtan N, Alon U. Spontaneous evolution of modularity and network motifs. Proceedings of the National Academy of Sciences of the United States of America. 102: 13773-8. PMID 16174729 DOI: 10.1073/Pnas.0503610102  0.302
2005 Dekel E, Alon U. Optimality and evolutionary tuning of the expression level of a protein. Nature. 436: 588-92. PMID 16049495 DOI: 10.1038/Nature03842  0.329
2005 Friedman N, Vardi S, Ronen M, Alon U, Stavans J. Precise temporal modulation in the response of the SOS DNA repair network in individual bacteria. Plos Biology. 3: e238. PMID 15954802 DOI: 10.1371/Journal.Pbio.0030238  0.376
2005 Rosenfeld N, Young JW, Alon U, Swain PS, Elowitz MB. Gene regulation at the single-cell level. Science (New York, N.Y.). 307: 1962-5. PMID 15790856 DOI: 10.1126/Science.1106914  0.668
2004 Kalir S, Alon U. Using a quantitative blueprint to reprogram the dynamics of the flagella gene network. Cell. 117: 713-20. PMID 15186773 DOI: 10.1016/J.Cell.2004.05.010  0.377
2004 Zaslaver A, Mayo AE, Rosenberg R, Bashkin P, Sberro H, Tsalyuk M, Surette MG, Alon U. Just-in-time transcription program in metabolic pathways. Nature Genetics. 36: 486-91. PMID 15107854 DOI: 10.1038/Ng1348  0.7
2004 Yeger-Lotem E, Sattath S, Kashtan N, Itzkovitz S, Milo R, Pinter RY, Alon U, Margalit H. Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proceedings of the National Academy of Sciences of the United States of America. 101: 5934-9. PMID 15079056 DOI: 10.1073/Pnas.0306752101  0.347
2004 Lahav G, Rosenfeld N, Sigal A, Geva-Zatorsky N, Levine AJ, Elowitz MB, Alon U. Dynamics of the p53-Mdm2 feedback loop in individual cells. Nature Genetics. 36: 147-50. PMID 14730303 DOI: 10.1038/Ng1293  0.771
2003 Mangan S, Zaslaver A, Alon U. The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks. Journal of Molecular Biology. 334: 197-204. PMID 14607112 DOI: 10.1016/J.Jmb.2003.09.049  0.716
2003 Mangan S, Alon U. Structure and function of the feed-forward loop network motif. Proceedings of the National Academy of Sciences of the United States of America. 100: 11980-5. PMID 14530388 DOI: 10.1073/Pnas.2133841100  0.353
2003 Setty Y, Mayo AE, Surette MG, Alon U. Detailed map of a cis-regulatory input function. Proceedings of the National Academy of Sciences of the United States of America. 100: 7702-7. PMID 12805558 DOI: 10.1073/Pnas.1230759100  0.344
2003 Rosenfeld N, Alon U. Response delays and the structure of transcription networks. Journal of Molecular Biology. 329: 645-54. PMID 12787666 DOI: 10.1016/S0022-2836(03)00506-0  0.623
2002 Rosenfeld N, Elowitz MB, Alon U. Negative autoregulation speeds the response times of transcription networks. Journal of Molecular Biology. 323: 785-93. PMID 12417193 DOI: 10.1016/S0022-2836(02)00994-4  0.641
2002 Ronen M, Rosenberg R, Shraiman BI, Alon U. Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics. Proceedings of the National Academy of Sciences of the United States of America. 99: 10555-60. PMID 12145321 DOI: 10.1073/Pnas.152046799  0.37
2002 Shen-Orr SS, Milo R, Mangan S, Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nature Genetics. 31: 64-8. PMID 11967538 DOI: 10.1038/Ng881  0.322
2001 Kalir S, McClure J, Pabbaraju K, Southward C, Ronen M, Leibler S, Surette MG, Alon U. Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria. Science (New York, N.Y.). 292: 2080-3. PMID 11408658 DOI: 10.1126/Science.1058758  0.334
2001 Barkai N, Alon U, Leibler S. Robust amplification in adaptive signal transduction networks Comptes Rendus De L'Academie Des Sciences - Series Iv: Physics, Astrophysics. 2: 871-877. DOI: 10.1016/S1296-2147(01)01230-6  0.328
2000 Lev Bar-Or R, Maya R, Segel LA, Alon U, Levine AJ, Oren M. Generation of oscillations by the p53-Mdm2 feedback loop: a theoretical and experimental study. Proceedings of the National Academy of Sciences of the United States of America. 97: 11250-5. PMID 11016968 DOI: 10.1073/Pnas.210171597  0.325
1999 Alon U, Surette MG, Barkai N, Leibler S. Robustness in bacterial chemotaxis. Nature. 397: 168-71. PMID 9923680 DOI: 10.1038/16483  0.349
1998 Alon U, Camarena L, Surette MG, Aguera y Arcas B, Liu Y, Leibler S, Stock JB. Response regulator output in bacterial chemotaxis. The Embo Journal. 17: 4238-48. PMID 9687492 DOI: 10.1093/Emboj/17.15.4238  0.343
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