publications

2023

1. Inferring the differences in incubation-period and generation-interval distributions of the Delta and Omicron variants of SARS-CoV-2

   Sang Woo Park, Kaiyuan Sun, Sam Abbott, and 8 more authors

   Proceedings of the National Academy of Sciences, 2023
2. When to Lock, Not Whom: Managing Current and Future Epidemics Using Time-Based

   Yinon Bar-On, and Tanya Baron

   2023
3. Initial protection against SARS-CoV-2 omicron lineage infection in children and adolescents by BNT162b2 in Israel: an observational study

   Ofra Amir, Yair Goldberg, Micha Mandel, and 7 more authors

   The Lancet Infectious Diseases, 2023
4. The global biomass and number of terrestrial arthropods

   Yuval Rosenberg, Yinon M Bar-On, Amir Fromm, and 4 more authors

   Science advances, 2023
5. The global biomass of wild mammals

   Lior Greenspoon, Eyal Krieger, Ron Sender, and 8 more authors

   Proceedings of the National Academy of Sciences, 2023
6. Protection against Omicron BA. 1/BA. 2 severe disease 0–7 months after BNT162b2 booster

   Ofra Amir, Yair Goldberg, Micha Mandel, and 7 more authors

   Communications biology, 2023
7. Three phases of increasing complexity in estimating vaccine protection

   Ofra Amir, Yair Goldberg, Micha Mandel, and 5 more authors

   International Journal of Epidemiology, 2023
8. Systematic exploration of prokaryotic form I rubisco maximal carboxylation rates

   Benoit Pins, Lior Greenspoon, Yinon M Bar-On, and 8 more authors

   bioRxiv, 2023

2022

1. The unmitigated profile of COVID-19 infectiousness

   Ron Sender, Yinon Bar-On, Sang Woo Park, and 3 more authors

   Elife, 2022
2. Anthroponumbers. org: A quantitative database of human impacts on Planet Earth

   Griffin Chure, Rachel A Banks, Avi I Flamholz, and 6 more authors

   Patterns, 2022
3. Protection by a Fourth Dose of BNT162b2 against Omicron in Israel

   Yinon M Bar-On, Yair Goldberg, Micha Mandel, and 7 more authors

   New England Journal of Medicine, 2022
4. Protection following BNT162b2 booster in adolescents substantially exceeds that of a fresh 2-dose vaccine

   Ofra Amir, Yair Goldberg, Micha Mandel, and 6 more authors

   Nature communications, 2022
5. Protection and waning of natural and hybrid immunity to SARS-CoV-2

   Yair Goldberg, Micha Mandel, Yinon M Bar-On, and 6 more authors

   New England Journal of Medicine, 2022

2021

1. The total number and mass of SARS-CoV-2 virions

   Ron Sender, Yinon M Bar-On, Shmuel Gleizer, and 4 more authors

   Proceedings of the National Academy of Sciences, 2021
2. COVID-19: Erroneous modelling and its policy implications

   Yinon Bar-On, Tatiana Baron, Ron Milo, and 1 more author

   2021
3. The global ocean size spectrum from bacteria to whales

   Ian A Hatton, Ryan F Heneghan, Yinon M Bar-On, and 1 more author

   Science advances, 2021
4. The importance of time post-vaccination in determining the decrease in vaccine efficacy against SARS-CoV-2 variants of concern

   Yinon Bar On, Elad Noor, Noam Gottlieb, and 2 more authors

   Medrxiv, 2021
5. Protection of BNT162b2 vaccine booster against Covid-19 in Israel

   Yinon M Bar-On, Yair Goldberg, Micha Mandel, and 8 more authors

   New england journal of medicine, 2021
6. Waning immunity after the BNT162b2 vaccine in Israel

   Yair Goldberg, Micha Mandel, Yinon M Bar-On, and 7 more authors

   New England Journal of Medicine, 2021
7. Protection against Covid-19 by BNT162b2 booster across age groups

   Yinon M Bar-On, Yair Goldberg, Micha Mandel, and 6 more authors

   New England Journal of Medicine, 2021
8. Epidemiological dynamics in the Economic analysis of pandemic

   Yinon Bar-On, Tanya Baron, Ofer Cornfeld, and 2 more authors

   2021

2020

1. SARS-CoV-2 (COVID-19) by the numbers

   Yinon M Bar-On, Avi Flamholz, Rob Phillips, and 1 more author

   elife, 2020
2. Adaptive cyclic exit strategies from lockdown to suppress COVID-19 and allow economic activity

   Omer Karin, Yinon M Bar-On, Tomer Milo, and 8 more authors

   MedRxiv, 2020
3. A quantitative compendium of COVID-19 epidemiology

   Yinon M Bar-On, Ron Sender, Avi I Flamholz, and 2 more authors

   arXiv preprint arXiv:2006.01283, 2020
4. Highly active rubiscos discovered by systematic interrogation of natural sequence diversity

   Dan Davidi, Melina Shamshoum, Zhijun Guo, and 8 more authors

   The EMBO journal, 2020
5. COVID-19: Looking for the Exit

   Uri Alon, Tanya Baron, Yinon Bar-On, and 4 more authors

   COVID-19: Looking for the Exit, 2020
6. Quantitative clarification of key questions about COVID-19 epidemiology

   Yinon M Bar-On, Ron Sender, Avi I Flamholz, and 2 more authors

   arXiv preprint arXiv:2007.05362, 2020
7. Draft genome sequence of the redox-active enteric bacterium Citrobacter portucalensis strain MBL

   Lev M Tsypin, Scott H Saunders, Yinon Bar-On, and 2 more authors

   Microbiology Resource Announcements, 2020
8. Engineering microbes to produce fuel, commodities, and food from CO2

   Shmuel Gleizer, Yinon M Bar-On, Roee Ben-Nissan, and 1 more author

   Cell Reports Physical Science, 2020
9. Global human-made mass exceeds all living biomass

   Emily Elhacham, Liad Ben-Uri, Jonathan Grozovski, and 2 more authors

   Nature, 2020
10. Phenzine Oxidizer Enrichment and Isolation

    Lev Tsypin, Yinon Bar-On, Scott Saunders, and 2 more authors

    2020

2019

1. Revisiting trade-offs between Rubisco kinetic parameters

   Avi I Flamholz, Noam Prywes, Uri Moran, and 6 more authors

   Biochemistry, 2019
2. The global mass and average rate of rubisco

   Yinon M Bar-On, and Ron Milo

   Proceedings of the National Academy of Sciences, 2019
3. Towards a quantitative view of the global ubiquity of biofilms

   Yinon M Bar-On, and Ron Milo

   Nature Reviews Microbiology, 2019
4. Evolthon: A community endeavor to evolve lab evolution

   Sivan Kaminski Strauss, Dvir Schirman, Ghil Jona, and 8 more authors

   PLoS biology, 2019
5. Conversion of Escherichia coli to generate all biomass carbon from CO2

   Shmuel Gleizer, Roee Ben-Nissan, Yinon M Bar-On, and 8 more authors

   Cell, 2019
6. The biomass composition of the oceans: a blueprint of our blue planet

   Yinon M Bar-On, and Ron Milo

   Cell, 2019

2018

1. The biomass distribution on Earth

   Yinon M Bar-On, Rob Phillips, and Ron Milo

   Proceedings of the National Academy of Sciences, 2018

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   A census of the biomass on Earth is key for understanding the structure and dynamics of the biosphere. However, a global, quantitative view of how the biomass of different taxa compare with one another is still lacking. Here, we assemble the overall biomass composition of the biosphere, establishing a census of the ≈550 gigatons of carbon (Gt C) of biomass distributed among all of the kingdoms of life. We find that the kingdoms of life concentrate at different locations on the planet; plants (≈450 Gt C, the dominant kingdom) are primarily terrestrial, whereas animals (≈2 Gt C) are mainly marine, and bacteria (≈70 Gt C) and archaea (≈7 Gt C) are predominantly located in deep subsurface environments. We show that terrestrial biomass is about two orders of magnitude higher than marine biomass and estimate a total of ≈6 Gt C of marine biota, doubling the previous estimated quantity. Our analysis reveals that the global marine biomass pyramid contains more consumers than producers, thus increasing the scope of previous observations on inverse food pyramids. Finally, we highlight that the mass of humans is an order of magnitude higher than that of all wild mammals combined and report the historical impact of humanity on the global biomass of prominent taxa, including mammals, fish, and plants.

2. Ribosome self-assembly leads to overlapping reproduction cycles and increases growth rate

   Rami Pugatch, and Yinon M Bar-On

   arXiv preprint arXiv:1807.02771, 2018

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   In permissive environments, E. coli can double its dry mass every 21 minutes. During this time, ribosomes, RNA polymerases, and the proteome are all doubled. Yet, the question of how to relate bacterial doubling time to other biologically relevant time scales in the growth process remains illusive, due to the complex temporal nesting pattern of these processes. In particular, the relation between the cell’s doubling time and the ribosome assembly time is not known. Here we develop a model that connects growth rate to ribosome assembly time and show that the existence of a self-assembly step increases the overall growth rate, because during ribosome self-assembly existing ribosomes can start a new round of reproduction, by making a new batch of ribosomal proteins prior to the completion of the previous round. This overlapping of ribosome reproduction cycles increases growth rate beyond the serial-limit that is typically assumed to hold. Using recent data from ribosome profiling and well known measurements of the average translation rate, rigid bounds on the in-vivo ribosome self-assembly time are set, which are robust to the assumptions regarding the biological noises involved. At 21 minutes doubling time, the ribosome assembly time is found to be approximately 6 minutes — three fold larger than the common estimate. We further use our model to explain the detrimental effect of a recently discovered ribosome assembly inhibitor drug, and predict the effect of limiting the expression of ribosome assembly chaperons on the overall growth rate.

2017

1. Design principles of autocatalytic cycles constrain enzyme kinetics and force low substrate saturation at flux branch points

   Uri Barenholz, Dan Davidi, Ed Reznik, and 4 more authors

   Elife, 2017

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   A set of chemical reactions that require a metabolite to synthesize more of that metabolite is an autocatalytic cycle. Here, we show that most of the reactions in the core of central carbon metabolism are part of compact autocatalytic cycles. Such metabolic designs must meet specific conditions to support stable fluxes, hence avoiding depletion of intermediate metabolites. As such, they are subjected to constraints that may seem counter-intuitive: the enzymes of branch reactions out of the cycle must be overexpressed and the affinity of these enzymes to their substrates must be relatively weak. We use recent quantitative proteomics and fluxomics measurements to show that the above conditions hold for functioning cycles in central carbon metabolism of E. coli. This work demonstrates that the topology of a metabolic network can shape kinetic parameters of enzymes and lead to seemingly wasteful enzyme usage.

2. The genetic basis for the adaptation of E. coli to sugar synthesis from CO2

   Elad Herz, Niv Antonovsky, Yinon Bar-On, and 8 more authors

   Nature communications, 2017

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   Understanding the evolution of a new metabolic capability in full mechanistic detail is challenging, as causative mutations may be masked by non-essential "hitchhiking" mutations accumulated during the evolutionary trajectory. We have previously used adaptive laboratory evolution of a rationally engineered ancestor to generate an Escherichia coli strain able to utilize CO2 fixation for sugar synthesis. Here, we reveal the genetic basis underlying this metabolic transition. Five mutations are sufficient to enable robust growth when a non-native Calvin–Benson–Bassham cycle provides all the sugar-derived metabolic building blocks. These mutations are found either in enzymes that affect the efflux of intermediates from the autocatalytic CO2 fixation cycle toward biomass (prs, serA, and pgi), or in key regulators of carbon metabolism (crp and ppsR). Using suppressor analysis, we show that a decrease in catalytic capacity is a common feature of all mutations found in enzymes. These findings highlight the enzymatic constraints that are essential to the metabolic stability of autocatalytic cycles and are relevant to future efforts in constructing non-native carbon fixation pathways.

3. Converting air into sugar: the design and in-vivo evolution of an E. coli strain capable using CO 2 as a source of biomass production

   Ghil Jona, Niv Antonovsky, Shmuel Gleizer, and 8 more authors

   In Recent Advances in Fermentation Technology (RAFT tm), 2017

2016

1. Opportunistic use of banana flower bracts by Glossophaga soricina

   Meghan Murphy, Elizabeth L Clare, Jens Rydell, and 4 more authors

   Acta Chiropterologica, 2016

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   The evolution of cue reception and cue production is well documented. The ability of species to use cues they did not evolve with is important in understanding flexibility in behaviour. We observed Neotropical nectar-feeding bats (Glossophaga soricina) feeding at Old World banana flowers (Musa acuminata) in a Belize garden. The flowers produce a rich source of nectar that is exposed as a bract lifts before dusk. We tested the hypothesis that the bracts serve as beacons to foraging bats and discuss this approach and the use of acoustic information by bats feeding at flowers. We ensonified a bract with cues like those of echolocating G. soricina, which revealed the production of strong echoes from the bract. Additionally, the removal of bracts from the flowers influenced the bats’ flower-visiting behaviour. We suggest that the bats use the echoes from the bract opportunistically as a cue to find the nectar source. Our findings provide an example of an interaction between a plant and flower visitor not reflecting a shared evolutionary past.

2. Sugar synthesis from CO2 in Escherichia coli

   Niv Antonovsky, Shmuel Gleizer, Elad Noor, and 8 more authors

   Cell, 2016

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   Can a heterotrophic organism be evolved to synthesize biomass from CO2 directly? So far, non-native carbon fixation in which biomass precursors are synthesized solely from CO2 has remained an elusive grand challenge. Here, we demonstrate how a combination of rational metabolic rewiring, recombinant expression, and laboratory evolution has led to the biosynthesis of sugars and other major biomass constituents by a fully functional Calvin-Benson-Bassham (CBB) cycle in E. coli. In the evolved bacteria, carbon fixation is performed via a non-native CBB cycle, while reducing power and energy are obtained by oxidizing a supplied organic compound (e.g., pyruvate). Genome sequencing reveals that mutations in flux branchpoints, connecting the non-native CBB cycle to biosynthetic pathways, are essential for this phenotype. The successful evolution of a non-native carbon fixation pathway, though not yet resulting in net carbon gain, strikingly demonstrates the capacity for rapid trophic-mode evolution of metabolism applicable to biotechnology.

3. SnapShot: timescales in cell biology

   Maya Shamir, Yinon Bar-On, Rob Phillips, and 1 more author

   Cell, 2016

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   Can a heterotrophic organism be evolved to synthesize biomass from CO2 directly? So far, non-native carbon fixation in which biomass precursors are synthesized solely from CO2 has remained an elusive grand challenge. Here, we demonstrate how a combination of rational metabolic rewiring, recombinant expression, and laboratory evolution has led to the biosynthesis of sugars and other major biomass constituents by a fully functional Calvin-Benson-Bassham (CBB) cycle in E. coli. In the evolved bacteria, carbon fixation is performed via a non-native CBB cycle, while reducing power and energy are obtained by oxidizing a supplied organic compound (e.g., pyruvate). Genome sequencing reveals that mutations in flux branchpoints, connecting the non-native CBB cycle to biosynthetic pathways, are essential for this phenotype. The successful evolution of a non-native carbon fixation pathway, though not yet resulting in net carbon gain, strikingly demonstrates the capacity for rapid trophic-mode evolution of metabolism applicable to biotechnology.

2013

1. It’s not black or white - on the range of vision and echolocation in echolocating bats

   Arjan Boonman, Yinon Bar-On, Noam Cvikel, and 1 more author

   Frontiers in physiology, 2013

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   Around 1000 species of bats in the world use echolocation to navigate, orient, and detect insect prey. Many of these bats emerge from their roost at dusk and start foraging when there is still light available. It is however unclear in what way and to which extent navigation, or even prey detection in these bats is aided by vision. Here we compare the echolocation and visual detection ranges of two such species of bats which rely on different foraging strategies (Rhinopoma microphyllum and Pipistrellus kuhlii). We find that echolocation is better than vision for detecting small insects even in intermediate light levels (1–10 lux), while vision is advantageous for monitoring far-away landscape elements in both species. We thus hypothesize that, bats constantly integrate information acquired by the two sensory modalities. We suggest that during evolution, echolocation was refined to detect increasingly small targets in conjunction with using vision. To do so, the ability to hear ultrasonic sound is a prerequisite which was readily available in small mammals, but absent in many other animal groups. The ability to exploit ultrasound to detect very small targets, such as insects, has opened up a large nocturnal niche to bats and may have spurred diversification in both echolocation and foraging tactics.