Publications

Book

 

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

Publications

2017

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.

2016

80.
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.
79.
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.
78.
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.
77.
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.
76.
Eshel, G; Shepon, A; Noor, E; Milo, R (2016). Environmentally Optimal, Nutritionally Aware Beef Replacement Plant-Based Diets.  Environmental science & technology. 50.
75.
Sender, Ron; Fuchs, Shai; Milo, Ron (2016). Revised Estimates for the Number of Human and Bacteria Cells in the Body.  PLoS biology. 14.
74.
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.

media coverage: Haarretz

73.
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.
72.
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.

media coverage: F1000Prime

71.
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.
70.
Shamir, M; Bar-On, Y; Phillips, R; Milo, R (2016). SnapShot: Timescales in Cell Biology.  Cell. 164.
69.
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.

media coverage: The New York Times, Nature, Listen

2015

68.
Kaushansky, N; Eisenstein, M; Boura-Halfon, S; Hansen, BE; Nielsen, CH; Milo, R; Zeilig, G; Lassmann, H; Altmann, DM; Ben-Nun, A (2015). Role of a Novel Human Leukocyte Antigen-DQA1*01:02; DRB1*15:01 Mixed Isotype Heterodimer in the Pathogenesis of "Humanized" Multiple Sclerosis-like Disease.  JOURNAL OF BIOLOGICAL CHEMISTRY. 290:15260-15278.
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). 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

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. 153:432-445.
64.
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.
63.
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.

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.
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.
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.
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.
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.

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.
55.
Noor, E; Haraldsdottir, HS; Milo, R; Fleming, RMT (2013). Consistent Estimation of Gibbs Energy Using Component Contributions.  Plos Computational Biology. 9.
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.
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.
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.
51.
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.
50.
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.
49.
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.
48.
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.
47.
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.

2012

46.
Milo, R; Last, RL (2012). Achieving Diversity in the Face of Constraints: Lessons from Metabolism.  Science. 336:1663-1667.
45.
Noor, E; Lewis, NE; Milo, R (2012). A proof for loop-law constraints in stoichiometric metabolic networks.  Bmc Systems Biology. 6.
44.
Noor, E; Milo, R (2012). Efficiency in Evolutionary Trade-Offs.  Science. 336:1114-1115.
43.
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.
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.
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.
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.
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.
38.
Flamholz, A; Noor, E; Bar-Even, A; Milo, R (2012). eQuilibrator-the biochemical thermodynamics calculator.  Nucleic Acids Research. 40:D770-D775.
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.

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.
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.
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.
33.
Bar-Even, A; Noor, E; Flamholz, A; Buescher, JM; Milo, R (2011). Hydrophobicity and Charge Shape Cellular Metabolite Concentrations.  Plos Computational Biology. 7.
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.

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.
29.
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.
28.
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.
27.
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.
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.

2009

25.
Milo, R; Schuldiner, M (2009). Weizmann Young PI Forum: The Power of Peer Support.  Molecular Cell. 36:913-915.
24.
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.
23.
Milo, R (2009). What governs the reaction center excitation wavelength of photosystems I and II?.  Photosynthesis Research. 101:59-67.
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.

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.

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.
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.
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.
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.
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.

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.
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.
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.
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.

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.

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.
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.
8.
Itzkovitz, S; Milo, R; Kashtan, N; Newman, MEJ; Alon, U (2004). Reply to "Comment on 'Subgraphs in random networks' ".  Physical Review E. 70.
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.
6.
Kashtan, N; Itzkovitz, S; Milo, R; Alon, U (2004). Topological generalizations of network motifs.  Physical Review E. 70.
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.

2003

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

2002

2.
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.
1.
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.