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



Niv Antonovsky; Shmuel Gleizer; Ron Milo (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
Uri Barenholz; Dan Davidi; Ed Reznik; Yinon Bar-On; Niv Antonovsky; Elad Noor; Ron Milo (2017). Design principles of autocatalytic cycles constrain enzyme kinetics and force low substrate saturation at flux branch points.  eLife. 6.  Abstract
Elad Herz; Niv Antonovsky; Yinon Bar-On et al. (2017). The genetic basis for the adaptation of E-coli to sugar synthesis from CO2.  Nat Commun. 8.  Abstract [All authors]
Dan Davidi; Ron Milo (2017). Lessons on enzyme kinetics from quantitative proteomics.  Current Opinion in Biotechnology. 46:81-89.  Abstract
Gita Mahmoudabadi; Ron Milo; Rob Phillips (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


Elad Noor; Abraham Flamholz; Arren Bar-Even; Dan Davidi; Ron Milo; W Liebermeister (2016). The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization.  PLOS Computational Biology. 12:(11)  Abstract
Alon Shepon; Gil Eshel; Elad Noor; Ron Milo (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
Niall M. Mangan; Avi Flamholz; Rachel D. Hood; Ron Milo; David F. Savage (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
Ron Sender; Shai Fuchs; Ron Milo (2016). Revised Estimates for the Number of Human and Bacteria Cells in the Body.  PLoS Biology. 14:(8)e1002533.  Abstract
Leeat Keren; Jean Hausser; Maya Lotan-Pompan et al. (2016). Massively Parallel Interrogation of the Effects of Gene Expression Levels on Fitness.  Cell. 166:(5)1282-1294.e18.  Abstract [All authors]
Gidon Eshel; Alon Shepon; Elad Noor; Ron Milo (2016). Environmentally Optimal, Nutritionally Aware Beef Replacement Plant-Based Diets.  Environmental Science & Technology. 50:(15)8164-8.  Abstract
Niv Antonovsky; Shmuel Gleizer; Elad Noor et al. (2016). Sugar Synthesis from CO2 in Escherichia coli.  Cell. 166:(1)115-125.  Abstract [All authors]
Lior Zelcbuch; Steffen N. Lindner; Yonatan Zegman; Ilya Vainberg Slutskin; Niv Antonovsky; Shmuel Gleizer; Ron Milo; Arren Bar-Even (2016). Pyruvate Formate-Lyase Enables Efficient Growth of Escherichia coli on Acetate and Formate.  Biochemistry. 55:(17)2423-2426.  Abstract
Maya Shamir; Ron Milo; Yinon Bar-On (2016). SnapShot: Timescales in Cell Biology.  CELL. 164.
Uri Barenholz; Leeat Keren; Eran Segal; Ron Milo (2016). A Minimalistic Resource Allocation Model to Explain Ubiquitous Increase in Protein Expression with Growth Rate.  PLoS One. 11:(4)e0153344.  Abstract
Dan Davidi; Uri Barenholz; Miki Goldenfeld; Ron Milo (2016). Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements.  PNAS. 113.  Abstract
Ron Sender; Shai Fuchs; Ron Milo (2016). Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans.  Cell. 164:(3)337-340.  Abstract


Leeat Keren; Dijk, David Van Dijk; Shira Weingarten-Gabbay; Dan Davidi; Ghil Jona; Adina Weinberger; Ron Milo; Eran Segal (2015). Noise in gene expression is coupled to growth rate.  Genome Research. 25:(12)1893-902.  Abstract
Arren Bar-Even; Ron Milo; Elad Noor; Dan Tawfik (2015). The Moderately Efficient Enzyme: Futile Encounters and Enzyme Floppiness.  BIOCHEMISTRY. 54:(32)
Gil Eshel; Alon Shepon; T. Makov; Ron Milo (2015). Partitioning United States' feed consumption among livestock categories for improved environmental cost assessments.  Journal of Agricultural Science. 153:(3)432-445.  Abstract
Lior Zelcbuch; Manuel Razo-Mejia; Elad Herz; Sagit Yahav; Niv Antonovsky; Hagar Kroytoro; Ron Milo; Arren Bar-Even (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
Gidon Eshel; Alon Shepon; Tamar Makov; Ron Milo (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.


Gidon Eshel; Alon Shepon; Tamar Makov; Ron Milo (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.
Avi Flamholz; Rob Phillips; Ron Milo (2014). The quantified cell.  Molecular Biology of the Cell. 25:(22)3497-3500.  Abstract
Gidon Eshel; Alon Shepon; Tamar Makov; Ron Milo (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
Wolfram Liebermeister; Elad Noor; Avi Flamholz; Dan Davidi; Joerg Bernhardt; Ron Milo (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
Shlomit Farkash-Amar; Anat Zimmer; Eran Eden et al. (2014). Noise Genetics: Inferring Protein Function by Correlating Phenotype with Protein Levels and Localization in Individual Human Cells.  PLoS Genetics. 10:(3)  Abstract [All authors]
Elad Noor; Arren Bar-Even; Abraham Flamholz; E Reznik; W Liebermeister; Ron Milo (2014). Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism.  PLoS Computational Biology. 10:(2)  Abstract


Leeat Keren; Ora Zackay; Maya Lotan-Pompan et al. (2013). Promoters maintain their relative activity levels under different growth conditions.  Molecular Systems Biology. 9.  Abstract [All authors]
Naama Tepper; Elad Noor; Daniel Amador-Noguez; Hulda S. Haraldsdottir; Ron Milo; Josh Rabinowitz; Wolfram Liebermeister; Tomer Shlomi (2013). Steady-State Metabolite Concentrations Reflect a Balance between Maximizing Enzyme Efficiency and Minimizing Total Metabolite Load.  PLoS One. 8:(9)  Abstract
Avi Flamholz; Elad Noor; Arren Bar-Even; Wolfram Liebermeister; Ron Milo (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
Karp, Ayelet Levin Karp; Uri Barenholz; Tasneem Bareia; Michal Dayagi; Lior Zelcbuch; Niv Antonovsky; Elad Noor; Ron Milo (2013). Quantifying Translational Coupling in E. coli Synthetic Operons Using RBS Modulation and Fluorescent Reporters.  ACS Synthetic Biology. 2:(6)327-336.  Abstract
Lior Zelcbuch; Niv Antonovsky; Arren Bar-Even et al. (2013). Spanning high-dimensional expression space using ribosome-binding site combinatorics.  Nucleic Acids Research. 41:(9)  Abstract [All authors]
Alon Shepon; Tamar Israeli; Gidon Eshel; Ron Milo (2013). EcoTime-An intuitive quantitative sustainability indicator utilizing a time metric.  Ecological Indicators. 24:240-245.  Abstract
Ron Milo (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
Elad Noor; Hulda S. Haraldsdottir; Ron Milo; Ronan M. T. Fleming (2013). Consistent Estimation of Gibbs Energy Using Component Contributions.  PLoS Computational Biology. 9:(7)  Abstract
Elad Noor; Avi Flamholz; Wolfram Liebermeister; Arren Bar-Even; Ron Milo (2013). A note on the kinetics of enzyme action: A decomposition that highlights thermodynamic effects.  FEBS Letters. 587:(17)2772-2777.  Abstract
Arren Bar-Even; Elad Noor; Avi Flamholz; Ron Milo (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


Avi Flamholz; Elad Noor; Arren Bar-Even; Ron Milo (2012). eQuilibrator-the biochemical thermodynamics calculator.  Nucleic Acids Research. 40:(D1)D770-D775.  Abstract
Elad Noor; Nathan E. Lewis; Ron Milo (2012). A proof for loop-law constraints in stoichiometric metabolic networks.  BMC Systems Biology. 6.  Abstract
Roi Adadi; Benjamin Volkmer; Ron Milo; Matthias Heinemann; Tomer Shlomi (2012). Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters.  PLoS Computational Biology. 8:(7)  Abstract
Elad Noor; Ron Milo (2012). Efficiency in Evolutionary Trade-Offs.  Science. 336:(6085)1114-1115.
Ron Milo; Robert L. Last (2012). Achieving Diversity in the Face of Constraints: Lessons from Metabolism.  Science. 336:(6089)1663-1667.  Abstract
Shlomit Farkash-Amar; Eran Eden; Ariel Cohen; Zatorsky, Naama Geva Zatorsky; Lydia Cohen; Ron Milo; Alex Sigal; Tamar Danon; Uri Alon (2012). Dynamic Proteomics of Human Protein Level and Localization across the Cell Cycle.  PLoS One. 7:(11)  Abstract
Arren Bar-Even; Avi Flamholz; Elad Noor; Ron Milo (2012). Thermodynamic constraints shape the structure of carbon fixation pathways.  Biochimica Et Biophysica Acta-Bioenergetics. 1817:(9)1646-1659.  Abstract
Elad Noor; Arren Bar-Even; Avi Flamholz; Yaniv Lubling; Dan Davidi; Ron Milo (2012). An integrated open framework for thermodynamics of reactions that combines accuracy and coverage.  Bioinformatics. 28:(15)2037-2044.  Abstract
Arren Bar-Even; Avi Flamholz; Elad Noor; Ron Milo (2012). Rethinking glycolysis: on the biochemical logic of metabolic pathways.  Nature Chemical Biology. 8:(6)509-517.  Abstract
Arren Bar-Even; Elad Noor; Ron Milo (2012). A survey of carbon fixation pathways through a quantitative lens.  Journal of Experimental Botany. 63:(6)2325-2342.  Abstract


Yuval Hart; Avraham E. Mayo; Ron Milo; Uri Alon (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
Alex Sigal; Jocelyn T. Kim; Alejandro B. Balazs; Erez Dekel; Avi Mayo; Ron Milo; David Baltimore (2011). Cell-to-cell spread of HIV permits ongoing replication despite antiretroviral therapy.  Nature. 477:(7362)95-U100.  Abstract
Ariella Alperovitch-Lavy; Itai Sharon; Forest Rohwer; Eva-Mari Aro; Fabian Glaser; Ron Milo; Nathan Nelson; Oded Beja (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
Arren Bar-Even; Elad Noor; Avi Flamholz; Joerg M. Buescher; Ron Milo (2011). Hydrophobicity and Charge Shape Cellular Metabolite Concentrations.  PLoS Computational Biology. 7:(10)  Abstract
Arren Bar-Even; Elad Noor; Yonatan Savir; Wolfram Liebermeister; Dan Davidi; Dan Tawfik; Ron Milo (2011). The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters.  Biochemistry. 50:(21)4402-4410.  Abstract


Zatorsky, Naama Geva Zatorsky; A. A. Cohen; Eran Eden et al. (2010). Dynamics proteomics of individual cancer cells in response to drugs.  FEBS Journal. 277:281-281.  Abstract [All authors]
Yonatan Savir; Elad Noor; Ron Milo; Tsvi Tlusty (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
Uri Moran; Rob Phillips; Ron Milo (2010). SnapShot: Key Numbers in Biology.  Cell. 141:(7)1262-1262.
Ron Milo; Paul Jorgensen; Uri Moran; Griffin Weber; Michael Springer (2010). BioNumbers-the database of key numbers in molecular and cell biology.  Nucleic Acids Research. 38:D750-D753.  Abstract
Elad Noor; Eran Eden; Ron Milo; Uri Alon (2010). Central Carbon Metabolism as a Minimal Biochemical Walk between Precursors for Biomass and Energy.  Molecular Cell. 39:(5)809-820.  Abstract
Arren Bar-Even; Elad Noor; Nathan E. Lewis; Ron Milo (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


Rob Phillips; Ron Milo (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
Ron Milo; Maya Schuldiner (2009). Weizmann Young PI Forum: The Power of Peer Support.  Molecular Cell. 36:(6)913-915.
Ron Milo (2009). What governs the reaction center excitation wavelength of photosystems I and II?.  Photosynthesis Research. 101:(1)59-67.  Abstract
Ariel Cohen; Tomer Kalisky; Avi Mayo et al. (2009). Protein Dynamics in Individual Human Cells: Experiment and Theory.  PLoS One. 4:(4)  Abstract [All authors]


A. A. Cohen; Zatorsky, Naama Geva Zatorsky; Eran Eden et al. (2008). Dynamic Proteomics of Individual Cancer Cells in Response to a Drug.  Science. 322:(5907)1511-1516.  Abstract [All authors]


Guy Shinar; Ron Milo; Maria Rodriguez Martinez; Uri Alon (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
Ron Milo (2007). The relationship between evolutionary and physiological variation in hemoglobin.  PNAS. 104.  Abstract
Ivo Spiegel; Konstantin Adamsky; Yael Eshed et al. (2007). A central role for Necl4 ( SynCAM4) in Schwann cell- axon interaction and myelination.  Nature Neuroscience. 10:(7)861-869.  Abstract [All authors]
Ronen Zaidel-Bar; Ron Milo; Zvi Kam; Benjamin Geiger (2007). A paxillin tyrosine phosphorylation switch regulates the assembly and form of cell-matrix adhesions.  Journal of Cell Science. 120:(1)137-148.  Abstract
Alex Sigal; Tamar Danon; Ariel Cohen; Ron Milo; Zatorsky, Naama Geva Zatorsky; Gila Lustig; Yuvalal Liron; Uri Alon; Natalie Perzov (2007). Generation of a fluorescently labeled endogenous protein library in living human cells.  Nature Protocols. 2:(6)1515-1527.  Abstract


Alex Sigal; Ron Milo; Ariel Cohen et al. (2006). Variability and memory of protein levels in human cells.  Nature. 444:(7119)643-646.  Abstract [All authors]
A Sigal; Ron Milo; Ayala Cohen et al. (2006). Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins.  Nature Methods. 3:(7)525-531.  Abstract [All authors]
Shalev Itzkovitz; Ron Milo; Nadav Kashtan; Reuven Levitt; Amir Lahav; Uri Alon (2006). Recurring harmonic walks and network motifs in Western music.  Advances in Complex Systems. 9:(2-Jan)121-132.  Abstract
Zatorsky, Naama Geva Zatorsky; Nitzan Rosenfeld; Shalev Itzkovitz et al. (2006). Oscillations and variability in the p53 system.  Molecular Systems Biology. 2.  Abstract [All authors]


Shalev Itzkovitz; R Levitt; N Kashtan; Ron Milo; M Itzkovitz; Uri Alon (2005). Coarse-graining and self-dissimilarity of complex networks.  Physical Review E. 71:(1)  Abstract


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


Shalev Itzkovitz; Ron Milo; N Kashtan; G Ziv; Uri Alon (2003). Subgraphs in random networks.  Physical Review E. 68:(2)  Abstract


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