Publications

Book

 

Milo R, Phillips R (2016). Cell Biology by the Numbers (Garland Science). read online.

Publications

2019

92.
Flamholz A., Prywes N., Moran U., David D., Bar-On Y. M., Oltrogge L. M., Alves R., Savage D. & Milo R. (2019). Revisiting Trade-offs between Rubisco Kinetic Parameters.  Biochemistry. 58:(31)3365-3376.  Abstract
91.
Bar-On Y. M. & Milo R. (2019). Towards a quantitative view of the global ubiquity of biofilms.  Nature Reviews Microbiology. 17:(4)199-200.  Abstract
90.
Bar-On Y. M. & Milo R. (2019). The global mass and average rate of rubisco.  Proceedings Of The National Academy Of Sciences Of The United States Of America-Physical Sciences. 116:(10)4738-4743.  Abstract
89.
Weill U., Krieger G., Avihou Z., Milo R., Schuldiner M. & Davidi D. (2019). Assessment of GFP Tag Position on Protein Localization and Growth Fitness in Yeast.  Journal of Molecular Biology. 431:(3)636-641.  Abstract

2018

88.
Eshel G., Shepon A., Shaket T., Cotler B. D., Gilutz S., Giddings D., Raymo M. E. & Milo R. (2018). A model for 'sustainable' US beef production.  Nature Ecology and Evolution. 2:(1)81-85.  Abstract
87.
Davidi D., Longo L. M., Jablonska J., Milo R. & Tawfik D. S. (2018). A Bird's-Eye View of Enzyme Evolution: Chemical, Physicochemical, and Physiological Considerations.  Chemical Reviews. 118:(18)8786-8797.  Abstract
86.
Bar-On Y. M., Phillips R. & Milo R. (2018). The biomass distribution on Earth.  Proceedings Of The National Academy Of Sciences Of The United States Of America-Biological Sciences. 115:(25)6506-6511.  Abstract
85.
Shepon A., Eshel G., Noor E. & Milo R. (2018). The opportunity cost of animal based diets exceeds all food losses.  Proceedings Of The National Academy Of Sciences Of The United States Of America-Biological Sciences. 115:(15)3804-3809.  Abstract

2017

84.
Davidi D. & Milo R. (2017). Lessons on enzyme kinetics from quantitative proteomics.  Current Opinion in Biotechnology. 46:81-89.  Abstract
83.
Mahmoudabadi G., Milo R. & Phillips R. (2017). Energetic cost of building a virus.  Proceedings of the National Academy of Sciences of the United States of America. 114:(22)E4324-E4333.  Abstract
82.
Antonovsky N., Gleizer S. & Milo R. (2017). Engineering carbon fixation in E. coil: from heterologous RuBisCO expression to the Calvin-Benson-Bassham cycle: from heterologous RuBisCO expression to the Calvin-Benson-Bassham cycle.  Current Opinion in Biotechnology. 47:83-91.  Abstract
81.
Barenholz U., Davidi D., Reznik E., Bar-On Y., Antonovsky N., Noor E. & Milo R. (2017). Design principles of autocatalytic cycles constrain enzyme kinetics and force low substrate saturation at flux branch points.  eLife. 6.  Abstract
80.
Herz E., Antonovsky N., Bar-On Y., Davidi D., Gleizer S., Prywes N., Noda-Garcia L., Frisch K. L., Zohar Y., Wernick D. G., Savidor A., Barenholz U. & Milo R. (2017). The genetic basis for the adaptation of E-coli to sugar synthesis from CO2.  Nat Commun. 8.  Abstract

2016

79.
Noor E., Flamholz A., Bar-Even A., Davidi D., Milo R. & Liebermeister W. (2016). The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization.  PLoS Computational Biology. 12:(11)  Abstract
78.
Shepon A., Eshel G., Noor E. & Milo R. (2016). Energy and protein feed-to-food conversion efficiencies in the US and potential food security gains from dietary changes.  Environmental Research Letters. 11:(10)  Abstract
77.
Mangan N. M., Flamholz A., Hood R. D., Milo R. & Savage D. F. (2016). pH determines the energetic efficiency of the cyanobacterial CO2 concentrating mechanism.  Proceedings of the National Academy of Sciences of the United States of America. 113:(36)E5354-E5362.  Abstract
76.
Sender R., Fuchs S. & Milo R. (2016). Revised Estimates for the Number of Human and Bacteria Cells in the Body.  PLoS Biology. 14:(8)e1002533.  Abstract
75.
Keren L., Hausser J., Lotan-Pompan M., Vainberg Slutskin S. I., Alisar H., Kaminski S., Weinberger A., Alon U., Milo R. & Segal E. (2016). Massively Parallel Interrogation of the Effects of Gene Expression Levels on Fitness.  Cell. 166:(5)1282-1294.e18.  Abstract
74.
Eshel G., Shepon A., Noor E. & Milo R. (2016). Environmentally Optimal, Nutritionally Aware Beef Replacement Plant-Based Diets.  Environmental Science & Technology. 50:(15)8164-8.  Abstract
73.
Antonovsky N., Gleizer S., Noor E., Zohar Y., Herz E., Barenholz U., Zelcbuch L., Amram S., Wides A., Tepper N., Davidi D., Bar-On Y., Bareia T., Wernick D. G., Shani I., Malitsky S., Jona G., Bar-Even A. & Milo R. (2016). Sugar Synthesis from CO2 in Escherichia coli.  Cell. 166:(1)115-125.  Abstract
72.
Zelcbuch L., Lindner S. N., Zegman Y., Slutskin I. V., Antonovsky N., Gleizer S., Milo R. & Bar-Even A. (2016). Pyruvate Formate-Lyase Enables Efficient Growth of Escherichia coli on Acetate and Formate.  Biochemistry. 55:(17)2423-2426.  Abstract
71.
Shamir M., Milo R. & Bar-On Y. (2016). SnapShot: Timescales in Cell Biology.  Cell. 164.
70.
Barenholz U., Keren L., Segal E. & Milo R. (2016). A Minimalistic Resource Allocation Model to Explain Ubiquitous Increase in Protein Expression with Growth Rate.  PLoS One. 11:(4)e0153344.  Abstract
69.
Davidi D., Barenholz U., Goldenfeld M. & Milo R. (2016). Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements.  PNAS. 113.  Abstract
68.
Sender R., Fuchs S. & Milo R. (2016). Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans.  Cell. 164:(3)337-340.  Abstract

2015

67.
Keren L., Van Dijk D. D., Weingarten-Gabbay S., Davidi D., Jona G., Weinberger A., Milo R. & Segal E. (2015). Noise in gene expression is coupled to growth rate.  Genome Research. 25:(12)1893-902.  Abstract
66.
Bar-Even A., Milo R., Noor E. & Tawfik D. (2015). The Moderately Efficient Enzyme: Futile Encounters and Enzyme Floppiness.  Biochemistry. 54:(32)
65.
Eshel G., Shepon A., Makov T. & Milo R. (2015). Partitioning United States' feed consumption among livestock categories for improved environmental cost assessments.  Journal of Agricultural Science. 153:(3)432-445.  Abstract
64.
Zelcbuch L., Razo-Mejia M., Herz E., Yahav S., Antonovsky N., Kroytoro H., Milo R. & Bar-Even A. (2015). An In Vivo Metabolic Approach for Deciphering the Product Specificity of Glycerate Kinase Proves that Both E. coli's Glycerate Kinases Generate 2-Phosphoglycerate.  PLoS One. 10:(3)  Abstract
63.
Eshel G., Shepon A., Makov T. & Milo R. (2015). Reply to Tichenor: Proposed update to beef greenhouse gas footprint is numerically questionable and well within current uncertainty bounds.  Proceedings of the National Academy of Sciences of the United States of America. 112:(8)E822-E823.

2014

62.
Noor E., Bar-Even A., Flamholz A., Reznik E., Liebermeister W. & Milo R. (2014). Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism.  PLoS Computational Biology. 10:(2)  Abstract
61.
Eshel G., Shepon A., Makov T. & Milo R. (2014). Reply to Metson et al.: The importance of phosphorus perturbations.  Proceedings of the National Academy of Sciences of the United States of America. 111:(46)E4908-E4908.
60.
Flamholz A., Phillips R. & Milo R. (2014). The quantified cell.  Molecular Biology of the Cell. 25:(22)3497-3500.  Abstract
59.
Eshel G., Shepon A., Makov T. & Milo R. (2014). Land, irrigation water, greenhouse gas, and reactive nitrogen burdens of meat, eggs, and dairy production in the United States.  Proceedings of the National Academy of Sciences of the United States of America. 111:(33)11996-12001.  Abstract
58.
Liebermeister W., Noor E., Flamholz A., Davidi D., Bernhardt J. & Milo R. (2014). Visual account of protein investment in cellular functions.  Proceedings of the National Academy of Sciences of the United States of America. 111:(23)8488-8493.  Abstract
57.
Farkash-Amar S., Zimmer A., Eden E., Cohen A., Geva Zatorsky Z. N., Cohen L., Milo R., Sigal A., Danon T. & Alon U. (2014). Noise Genetics: Inferring Protein Function by Correlating Phenotype with Protein Levels and Localization in Individual Human Cells.  PLoS Genetics. 10:(3)  Abstract

2013

56.
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. (2013). Promoters maintain their relative activity levels under different growth conditions.  Molecular Systems Biology. 9.  Abstract
55.
Tepper N., Noor E., Amador-Noguez D., Haraldsdottir H. S., Milo R., Rabinowitz J., Liebermeister W. & Shlomi T. (2013). Steady-State Metabolite Concentrations Reflect a Balance between Maximizing Enzyme Efficiency and Minimizing Total Metabolite Load.  PLoS One. 8:(9)  Abstract
54.
Flamholz A., Noor E., Bar-Even A., Liebermeister W. & Milo R. (2013). Glycolytic strategy as a tradeoff between energy yield and protein cost.  Proceedings of the National Academy of Sciences of the United States of America. 110:(24)10039-10044.  Abstract
53.
Levin Karp K. A., Barenholz U., Bareia T., Dayagi M., Zelcbuch L., Antonovsky N., Noor E. & Milo R. (2013). Quantifying Translational Coupling in E. coli Synthetic Operons Using RBS Modulation and Fluorescent Reporters.  ACS Synthetic Biology. 2:(6)327-336.  Abstract
52.
Zelcbuch L., Antonovsky N., Bar-Even A., Levin Karp A., Barenholz U., Dayagi M., Liebermeister W., Flamholz A., Noor E., Amram S., Brandis A., Bareia T., Yofe I., Jubran H. & Milo R. (2013). Spanning high-dimensional expression space using ribosome-binding site combinatorics.  Nucleic Acids Research. 41:(9)  Abstract
51.
Shepon A., Israeli T., Eshel G. & Milo R. (2013). EcoTime-An intuitive quantitative sustainability indicator utilizing a time metric.  Ecological Indicators. 24:240-245.  Abstract
50.
Milo R. (2013). What is the total number of protein molecules per cell volume? A call to rethink some published values.  BioEssays. 35:(12)1050-1055.  Abstract
49.
Noor E., Flamholz A., Liebermeister W., Bar-Even A. & Milo R. (2013). A note on the kinetics of enzyme action: A decomposition that highlights thermodynamic effects.  FEBS Letters. 587:(17)2772-2777.  Abstract
48.
Bar-Even A., Noor E., Flamholz A. & Milo R. (2013). Design and analysis of metabolic pathways supporting formatotrophic growth for electricity-dependent cultivation of microbes.  Biochimica Et Biophysica Acta-Bioenergetics. 1827:(9-Aug)1039-1047.  Abstract
47.
Noor E., Haraldsdottir H. S., Milo R. & Fleming R. M. T. (2013). Consistent Estimation of Gibbs Energy Using Component Contributions.  PLoS Computational Biology. 9:(7)  Abstract

2012

46.
Flamholz A., Noor E., Bar-Even A. & Milo R. (2012). eQuilibrator: the biochemical thermodynamics calculator.  Nucleic Acids Research. 40:(D1)D770-D775.  Abstract
45.
Farkash-Amar S., Eden E., Cohen A., Geva Zatorsky Z. N., Cohen L., Milo R., Sigal A., Danon T. & Alon U. (2012). Dynamic Proteomics of Human Protein Level and Localization across the Cell Cycle.  PLoS One. 7:(11)  Abstract
44.
Noor E., Lewis N. E. & Milo R. (2012). A proof for loop-law constraints in stoichiometric metabolic networks.  BMC Systems Biology. 6.  Abstract
43.
Bar-Even A., Flamholz A., Noor E. & Milo R. (2012). Thermodynamic constraints shape the structure of carbon fixation pathways.  Biochimica Et Biophysica Acta-Bioenergetics. 1817:(9)1646-1659.  Abstract
42.
Noor E., Bar-Even A., Flamholz A., Lubling Y., Davidi D. & Milo R. (2012). An integrated open framework for thermodynamics of reactions that combines accuracy and coverage.  Bioinformatics. 28:(15)2037-2044.  Abstract
41.
Adadi R., Volkmer B., Milo R., Heinemann M. & Shlomi T. (2012). Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters.  PLoS Computational Biology. 8:(7)  Abstract
40.
Bar-Even A., Flamholz A., Noor E. & Milo R. (2012). Rethinking glycolysis: on the biochemical logic of metabolic pathways.  Nature Chemical Biology. 8:(6)509-517.  Abstract
39.
Noor E. & Milo R. (2012). Efficiency in Evolutionary Trade-Offs.  Science. 336:(6085)1114-1115.
38.
Milo R. & Last R. L. (2012). Achieving Diversity in the Face of Constraints: Lessons from Metabolism.  Science. 336:(6089)1663-1667.  Abstract
37.
Bar-Even A., Noor E. & Milo R. (2012). A survey of carbon fixation pathways through a quantitative lens.  Journal of Experimental Botany. 63:(6)2325-2342.  Abstract

2011

36.
Hart Y., Mayo A. E., Milo R. & Alon U. (2011). Robust Control of PEP Formation Rate in the Carbon Fixation Pathway of C-4 Plants by a Bifunctional Enzyme.  BMC Systems Biology. 5.  Abstract
35.
Sigal A., Kim J. T., Balazs A. B., Dekel E., Mayo A., Milo R. & Baltimore D. (2011). Cell-to-cell spread of HIV permits ongoing replication despite antiretroviral therapy.  Nature. 477:(7362)95-U100.  Abstract
34.
Bar-Even A., Noor E., Flamholz A., Buescher J. M. & Milo R. (2011). Hydrophobicity and Charge Shape Cellular Metabolite Concentrations.  PLoS Computational Biology. 7:(10)  Abstract
33.
Bar-Even A., Noor E., Savir Y., Liebermeister W., Davidi D., Tawfik D. & Milo R. (2011). The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters.  Biochemistry. 50:(21)4402-4410.  Abstract
32.
Alperovitch-Lavy A., Sharon I., Rohwer F., Aro E., Glaser F., Milo R., Nelson N. & Beja O. (2011). Reconstructing a puzzle: existence of cyanophages containing both photosystem-I and photosystem-II gene suites inferred from oceanic metagenomic datasets.  Environmental Microbiology. 13:(1)24-32.  Abstract

2010

31.
Noor E., Eden E., Milo R. & Alon U. (2010). Central Carbon Metabolism as a Minimal Biochemical Walk between Precursors for Biomass and Energy.  Molecular Cell. 39:(5)809-820.  Abstract
30.
Moran U., Phillips R. & Milo R. (2010). SnapShot: Key Numbers in Biology.  Cell. 141:(7)1262-1262.
29.
Bar-Even A., Noor E., Lewis N. E. & Milo R. (2010). Design and analysis of synthetic carbon fixation pathways.  Proceedings of the National Academy of Sciences of the United States of America. 107:(19)8889-8894.  Abstract
28.
Savir Y., Noor E., Milo R. & Tlusty T. (2010). Cross-species analysis traces adaptation of Rubisco toward optimality in a low-dimensional landscape.  Proceedings of the National Academy of Sciences of the United States of America. 107:(8)3475-3480.  Abstract
27.
Milo R., Jorgensen P., Moran U., Weber G. & Springer M. (2010). BioNumbers-the database of key numbers in molecular and cell biology.  Nucleic Acids Research. 38:D750-D753.  Abstract

2009

26.
Phillips R. & Milo R. (2009). A feeling for the numbers in biology.  Proceedings of the National Academy of Sciences of the United States of America. 106:(51)21465-21471.  Abstract
25.
Milo R. & Schuldiner M. (2009). Weizmann Young PI Forum: The Power of Peer Support.  Molecular Cell. 36:(6)913-915.
24.
Milo R. (2009). What governs the reaction center excitation wavelength of photosystems I and II?.  Photosynthesis Research. 101:(1)59-67.  Abstract
23.
Cohen A., Kalisky T., Mayo A., Geva Zatorsky Z. N., Danon T., Issaeva I., Kopito R. B., Perzov N., Milo R., Sigal A. & Alon U. (2009). Protein Dynamics in Individual Human Cells: Experiment and Theory.  PLoS One. 4:(4)  Abstract

2008

22.
Cohen A. A., Geva Zatorsky Z. N., Eden E., Frenkel-Morgenstern M., Issaeva I., Sigal A., Milo R., Cohen-Saidon C., Kam Z., Cohen L., Liron Y., Danon T., Perzov N. & Alon U. (2008). Dynamic Proteomics of Individual Cancer Cells in Response to a Drug.  Science. 322:(5907)1511-1516.  Abstract
21.
Sangster T. A., Salathia N., Undurraga S., Milo R., Schelienberg K., Lindquist S. & Queitsch C. (2008). HSP90 affects the expression of genetic variation and developmental stability in quantitative traits.  Proceedings Of The National Academy Of Sciences Of The United States Of America-Biological Sciences. 105:(8)2963-2968.  Abstract

2007

20.
Milo R., Hou J. H., Springer M., Brenner M. P. & Kirschner M. W. (2007). The relationship between evolutionary and physiological variation in hemoglobin.  Proceedings Of The National Academy Of Sciences Of The United States Of America-Biological Sciences. 104:(43)16998-17003.  Abstract
19.
Shinar G., Milo R., Martinez M. R. & Alon U. (2007). Input-output robustness in simple bacterial signaling systems.  Proceedings of the National Academy of Sciences of the United States of America. 104:(50)19931-19935.  Abstract
18.
Spiegel I., Adamsky K., Eshed Y., Milo R., Sabanay H., Sarig-Nadir O., Horresh I., Scherer S. S., Rasband M. N. & Peles E. (2007). A central role for Necl4 ( SynCAM4) in Schwann cell- axon interaction and myelination.  Nature Neuroscience. 10:(7)861-869.  Abstract
17.
Zaidel-Bar R., Milo R., Kam Z. & Geiger B. (2007). A paxillin tyrosine phosphorylation switch regulates the assembly and form of cell-matrix adhesions.  Journal of Cell Science. 120:(1)137-148.  Abstract
16.
Sigal A., Danon T., Cohen A., Milo R., Geva Zatorsky Z. N., Lustig G., Liron Y., Alon U. & Perzov N. (2007). Generation of a fluorescently labeled endogenous protein library in living human cells.  Nature Protocols. 2:(6)1515-1527.  Abstract
15.
Milo R. (2007). Dynamic proteomics in mammalian cells: capabilities and challenges.  Molecular BioSystems. 3:(8)542-546.  Abstract

2006

14.
Sigal A., Milo R., Cohen A., Geva Zatorsky Z. N., Klein Y., Liron Y., Rosenfeld N., Danon T., Perzov N. & Alon U. (2006). Variability and memory of protein levels in human cells.  Nature. 444:(7119)643-646.  Abstract
13.
Sigal A., Milo R., Cohen A., Geva Zatorsky Z. N., Klein Y. A., Alaluf I., Swerdlin N., Perzov N., Danon T., Liron Y., Raveh T., Carpenter A., Lahav G. & Alon U. (2006). Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins.  Nature Methods. 3:(7)525-531.  Abstract
12.
Itzkovitz S., Milo R., Kashtan N., Levitt R., Lahav A. & Alon U. (2006). Recurring harmonic walks and network motifs in Western music.  Advances in Complex Systems. 9:(2-Jan)121-132.  Abstract
11.
Geva Zatorsky Z. N., Rosenfeld N., Itzkovitz S., Milo R., Sigal A., Dekel E., Yarnitzky T., Liron Y., Polak P., Lahav G. & Alon U. (2006). Oscillations and variability in the p53 system.  Molecular Systems Biology. 2.  Abstract

2005

10.
Itzkovitz S., Levitt R., Kashtan N., Milo R., Itzkovitz M. & Alon U. (2005). Coarse-graining and self-dissimilarity of complex networks.  Physical Review E. 71:(1)  Abstract

2004

9.
Itzkovitz S., Milo R., Kashtan N., Newman M. & Alon U. (2004). Reply to "Comment on 'Subgraphs in random networks' ".  Physical Review E. 70:(5)  Abstract
8.
Kashtan N., Itzkovitz S., Milo R. & Alon U. (2004). Topological generalizations of network motifs.  Physical Review E. 70:(3)  Abstract
7.
Kashtan N., Itzkovitz S., Milo R. & Alon U. (2004). Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs.  Bioinformatics. 20:(11)1746-1758.  Abstract
6.
Yeger-Lotem E., Sattath S., Kashtan N., Itzkovitz S., Milo R., Pinter R., Alon U. & Margalit H. (2004). 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:(16)5934-5939.  Abstract
5.
Milo R., Itzkovitz S., Kashtan N., Levitt R. & Alon U. (2004). Response to comment on "network motifs: Simple building blocks of complex networks" and "superfamilies of evolved and designed networks".  Science. 305:(5687)
4.
Milo R., Itzkovitz S., Kashtan N., Levitt R., Shen-Orr S., Ayzenshtat I., Sheffer M. & Alon U. (2004). Superfamilies of evolved and designed networks.  Science. 303:(5663)1538-1542.  Abstract

2003

3.
Itzkovitz S., Milo R., Kashtan N., Ziv G. & Alon U. (2003). Subgraphs in random networks.  Physical Review E. 68:(2)  Abstract

2002

2.
Milo R., Shen-Orr S., Itzkovitz S., Kashtan N., Chklovskii D. & Alon U. (2002). Network motifs: Simple building blocks of complex networks.  Science. 298:(5594)824-827.  Abstract
1.
Shen-Orr S., Milo R., Mangan S. & Alon U. (2002). Network motifs in the transcriptional regulation network of Escherichia coli.  Nature Genetics. 31:(1)64-68.  Abstract