Publications

Book

 

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

Publications

2017

83.
Antonovsky, N; Gleizer, S; Milo, R (2017). Engineering carbon fixation in E. coil: from heterologous RuBisCO expression to the Calvin-Benson-Bassham cycle.  CURRENT OPINION IN BIOTECHNOLOGY. 47:83-91.  Abstract
82.
Davidi, D; Milo, R (2017). Lessons on enzyme kinetics from quantitative proteomics.  CURRENT OPINION IN BIOTECHNOLOGY. 46:81-89.  Abstract
81.
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:E4324-E4333.  Abstract
80.
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

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.  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.  Abstract
77.
Mangan, NM; Flamholz, A; Hood, RD; Milo, R; Savage, DF (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:E5354-E5362.  Abstract
76.
Keren, L; Hausser, J; Lotan-Pompan, M; Vainberg 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.  Abstract
75.
Eshel, G; Shepon, A; Noor, E; Milo, R (2016). Environmentally Optimal, Nutritionally Aware Beef Replacement Plant-Based Diets.  Environmental science & technology. 50.  Abstract
74.
Sender, Ron; Fuchs, Shai; Milo, Ron (2016). Revised Estimates for the Number of Human and Bacteria Cells in the Body.  PLoS biology. 14.  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, DG; Shani, I; Malitsky, S; Jona, G; Bar-Even, A; Milo, R (2016). Sugar Synthesis from CO2 in Escherichia coli.  CELL. 166:115-125.  Abstract

media coverage: Haarretz

72.
Zelcbuch, L; Lindner, SN; Zegman, Y; Slutskin, IV; Antonovsky, N; Gleizer, S; Milo, R; Bar-Even, A (2016). Pyruvate Formate-Lyase Enables Efficient Growth of Escherichia coli on Acetate and Formate.  BIOCHEMISTRY. 55:2423-2426.  Abstract
71.
Davidi, D; Noor, E; Liebermeister, W; Bar-Even, A; Flamholz, A; Tummler, K; Barenholz, U; Goldenfeld, M; Shlomi, T;Milo, R (2016). Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro k(cat) measurements.  PNAS. 113.  Abstract

media coverage: F1000Prime

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.  Abstract
69.
Shamir, M; Bar-On, Y; Phillips, R; Milo, R (2016). SnapShot: Timescales in Cell Biology.  Cell. 164.
68.
Sender, Ron; Fuchs, Shai; Milo, Ron (2016). Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans.  Cell. 164:337-340.  Abstract

media coverage: The New York Times, Nature, Listen

2015

67.
Bar-Even, Arren; Milo, Ron; Noor, Elad; Tawfik, Dan S. (2015). The Moderately Efficient Enzyme: Futile Encounters and Enzyme Floppiness.  BIOCHEMISTRY. 54.
66.
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. 153:432-445.  Abstract
65.
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:E822-E823.

media coverage: BBCNational GeographicListen

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.  Abstract
63.
Keren, L; van Dijk, 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. 25:1893-902.  Abstract

2014

62.
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. 111:11996-12001.  Abstract
61.
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. 111:8488-8493.  Abstract
60.
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:E4908.
59.
Flamholz, A; Phillips, R; Milo, R (2014). The quantified cell.  Molecular Biology Of The Cell. 25:3497-3500.  Abstract
58.
Farkash-Amar, S; Zimmer, A; Eden, E; Cohen, A; Geva-Zatorsky, 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.  Abstract
57.
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.  Abstract

2013

56.
Tepper, N; Noor, E; Amador-Noguez, D; Haraldsdottir, HS; 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.  Abstract
55.
Noor, E; Haraldsdottir, HS; Milo, R; Fleming, RMT (2013). Consistent Estimation of Gibbs Energy Using Component Contributions.  Plos Computational Biology. 9.  Abstract
54.
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
53.
Levin-Karp, 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. 2:327-336.  Abstract
52.
Milo, R (2013). What is the total number of protein molecules per cell volume? A call to rethink some published values.  Bioessays. 35:1050-1055.  Abstract
51.
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. 1827:1039-1047.  Abstract
50.
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. 110:10039-10044.  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. 587:2772-2777.  Abstract
48.
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.  Abstract
47.
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

2012

46.
Noor, E; Lewis, NE; Milo, R (2012). A proof for loop-law constraints in stoichiometric metabolic networks.  Bmc Systems Biology. 6.  Abstract
45.
Noor, E; Milo, R (2012). Efficiency in Evolutionary Trade-Offs.  Science. 336:1114-1115.
44.
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.  Abstract
43.
Milo, R; Last, RL (2012). Achieving Diversity in the Face of Constraints: Lessons from Metabolism.  Science. 336:1663-1667.  Abstract
42.
Bar-Even, A; Flamholz, A; Noor, E; Milo, R (2012). Rethinking glycolysis: on the biochemical logic of metabolic pathways.  Nature Chemical Biology. 8:509-517.  Abstract
41.
Farkash-Amar, S; Eden, E; Cohen, A; Geva-Zatorsky, 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.  Abstract
40.
Bar-Even, A; Flamholz, A; Noor, E; Milo, R (2012). Thermodynamic constraints shape the structure of carbon fixation pathways.  Biochimica Et Biophysica Acta-Bioenergetics. 1817:1646-1659.  Abstract
39.
Bar-Even, A; Noor, E; Milo, R (2012). A survey of carbon fixation pathways through a quantitative lens.  Journal Of Experimental Botany. 63:2325-2342.  Abstract
38.
Flamholz, A; Noor, E; Bar-Even, A; Milo, R (2012). eQuilibrator-the biochemical thermodynamics calculator.  Nucleic Acids Research. 40:D770-D775.  Abstract
37.
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. 28:2037-2044.  Abstract

2011

36.
Sigal, A; Kim, JT; Balazs, AB; Dekel, E; Mayo, A; Milo, R; Baltimore, D (2011). Cell-to-cell spread of HIV permits ongoing replication despite antiretroviral therapy.  Nature. 477:95-U100.  Abstract
35.
Alperovitch-Lavy, A; Sharon, I; Rohwer, F; Aro, EM; 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. 13:24-32.  Abstract
34.
Hart, Y; Mayo, AE; 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
33.
Bar-Even, A; Noor, E; Flamholz, A; Buescher, JM; Milo, R (2011). Hydrophobicity and Charge Shape Cellular Metabolite Concentrations.  Plos Computational Biology. 7.  Abstract
32.
Bar-Even, A; Noor, E; Savir, Y; Liebermeister, W; Davidi, D; Tawfik, DS; Milo, R (2011). The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters.  Biochemistry. 50:4402-4410.  Abstract

2010

31.
Moran, U; Phillips, R; Milo, R (2010). SnapShot: Key Numbers in Biology.  Cell. 141:1262.
30.
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
29.
Geva-Zatorsky, N; Cohen, AA; Eden, E; Dekel, E; Frenkel-Morgenstern, M; Issaeva, I; Danon, T; Cohen, L; Perzov, N; Milo, R; Sigal, A; Alon, U (2010). Dynamics proteomics of individual cancer cells in response to drugs.  Febs Journal. 277:281.
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. 107:3475-3480.  Abstract
27.
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. 39:809-820.  Abstract
26.
Bar-Even, A; Noor, E; Lewis, NE; Milo, R (2010). Design and analysis of synthetic carbon fixation pathways.  Proceedings Of The National Academy Of Sciences Of The United States Of America. 107:8889-8894.  Abstract

2009

25.
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. 106:21465-21471.  Abstract
24.
Milo, R (2009). What governs the reaction center excitation wavelength of photosystems I and II?.  Photosynthesis Research. 101:59-67.  Abstract
23.
Milo, R; Schuldiner, M (2009). Weizmann Young PI Forum: The Power of Peer Support.  Molecular Cell. 36:913-915.
22.
Cohen, AA; Kalisky, T; Mayo, A; Geva-Zatorsky, N; Danon, T; Issaeva, I; Kopito, RB; Perzov, N; Milo, R; Sigal, A; Alon, U (2009). Protein Dynamics in Individual Human Cells: Experiment and Theory.  Plos One. 4.  Abstract

2008

21.
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 (2008). Dynamic Proteomics of Individual Cancer Cells in Response to a Drug.  Science. 322:1511-1516.  Abstract

2007

20.
Milo, Ron; Hou, J. H.; Springer, M, Brenner, M. P.; Kirschner, M. W. (2007). The relationship between evolutionary and physiological variation in hemoglobin.  PNAS. 104.  Abstract
19.
Spiegel, I; Adamsky, K; Eshed, Y; Milo, R; Sabanay, H; Sarig-Nadir, O; Horresh, I; Scherer, SS; Rasband, MN; Peles, E (2007). A central role for Necl4 ( SynCAM4) in Schwann cell- axon interaction and myelination.  Nature Neuroscience. 10:861-869.  Abstract
18.
Shinar, G; Milo, R; Martinez, MR; Alon, U (2007). Input-output robustness in simple bacterial signaling systems.  Proceedings Of The National Academy Of Sciences Of The United States Of America. 104:19931-19935.  Abstract
17.
Sigal, A; Danon, T; Cohen, A; Milo, R; Geva-Zatorsky, N; Lustig, G; Liron, Y; Alon, U; Perzov, N (2007). Generation of a fluorescently labeled endogenous protein library in living human cells.  Nature Protocols. 2:1515-1527.  Abstract
16.
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. 120:137-148.  Abstract

2006

15.
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 (2006). Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins.  Nature Methods. 3:525-531.  Abstract
14.
Geva-Zatorsky, 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
13.
Sigal, A; Milo, R; Cohen, A; Geva-Zatorsky, N; Klein, Y; Liron, Y; Rosenfeld, N; Danon, T; Perzov, N; Alon, U (2006). Variability and memory of protein levels in human cells.  Nature. 444:643-646.  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. 9:121-132.  Abstract

2005

11.
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.  Abstract

2004

10.
de Rosbo, NK; Kaye, JF; Eisenstein, M; Mendel, W; Hoeftberger, R; Lassmann, H; Milo, R; Ben-Nun, A (2004). The myelin-associated oligodendrocytic basic protein region MOBP15-36 encompasses the immunodominant major encephalitogenic epitope(s) for SJL/J mice and predicted epitope(s) for multiple sclerosis-associated HLA-DRB1*1501.  Journal Of Immunology. 173:1426-1435.  Abstract
9.
Yeger-Lotem, E; Sattath, S; Kashtan, N; Itzkovitz, S; Milo, R; Pinter, RY; 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. 101:5934-5939.  Abstract
8.
Itzkovitz, S; Milo, R; Kashtan, N; Newman, MEJ; Alon, U (2004). Reply to "Comment on 'Subgraphs in random networks' ".  Physical Review E. 70.  Abstract
7.
Kashtan, N; Itzkovitz, S; Milo, R; Alon, U (2004). Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs.  Bioinformatics. 20:1746-1758.  Abstract
6.
Kashtan, N; Itzkovitz, S; Milo, R; Alon, U (2004). Topological generalizations of network motifs.  Physical Review E. 70.  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.
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. 303:1538-1542.  Abstract

2003

3.
Itzkovitz, S; Milo, R; Kashtan, N; Ziv, G; Alon, U (2003). Subgraphs in random networks.  Physical Review E. 68.  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. 298:824-827.  Abstract
1.
Shen-Orr, SS; Milo, R; Mangan, S; Alon, U (2002). Network motifs in the transcriptional regulation network of Escherichia coli.  Nature Genetics. 31:64-68.  Abstract