Publications

See also GoogleScholar

Peer-reviewed publications (*corresponding author)

Wimmer JLE, Xavier JC, et al. (2021). Energy at Origins: Favorable Thermodynamics of Biosynthetic Reactions in the Last Universal Common Ancestor (LUCA) Frontiers in Microbiology, 12:793664.

Tria FDK, Brückner J, Skejo J, Xavier JC, Zimorski V, Gould SB, Garg SG, Martin WF (2021). Gene duplications trace mitochondria to the onset of eukaryote complexity. Genome Biology and Evolution, 13:evab055.

Xavier JC*, Gerhards RW, Wimmer JLE, Bruckner J1, Tria FDK, Martin WF. (2021) The metabolic network of the Last Bacterial Common Ancestor. Communications Biology, 4:413.

Wimmer JLE, Vieira AN, Xavier JC, Kleinermanns K, Martin WF, Preiner M. (2021) The Autotrophic Core: An Ancient Network of 404 Reactions Converts H2, CO2, and NH3 into Amino Acids, Bases, and Cofactors. Microorganisms, 9: 458.

Steel M, Xavier JC, Huson DH (2020). The structure of autocatalytic networks, with application to early biochemistry. Journal of the Royal Society Interface 2020, 17:20200488.

Xavier JC*, Hordijk W, Kauffman S, Steel M, Martin WF (2020). Autocatalytic chemical networks at the origin of metabolism. Proceedings of the Royal Society B, 287:20192377.

Lieven C, Beber ME, […], Xavier JC, et al (2020). MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology, 38:272-276.

Preiner M, […], Xavier JC* (2020). The future of origin of life research: bridging decades-old divisions. Life, 10:20.

Xavier JC* (2020). The early origin of cooperation. Nature Ecology and Evolution, 4:18-19.

Preiner M, Xavier JC*, Vieira AN, Kleinermanns K, Allen JF, Martin WF (2019). Catalysts, autocatalysis and the origin of metabolism. Interface Focus, 9:20190072.

Xavier JC*, Martin WF (2019). Sediment, methane and energy. Nature Microbiology, 4:547-549.

Steel M, Hordijk W, Xavier JC (2019). Autocatalytic networks in biology: structural theory and algorithms. Journal of the Royal Society Interface, 16:20180808.

Xavier JC, Patil KR, Rocha I (2018). Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes. PLoS Computational Biology, 14:e1006556.

Xavier JC*, Preiner M, Martin WF (2018). Something special about CO-dependent CO2 fixation. The FEBS Journal, 285:4181-4195.

Preiner M, Xavier JC, et al (2018). Serpentinization: connecting geochemistry, ancient metabolism and industrial hydrogenation. Life, 8:41.

Weiss MC, Preiner M, Xavier JC, Zimorski V, Martin WF (2018). The last universal common ancestor between ancient Earth chemistry and the onset of genetics. PLoS Genetics, 14:e1007518.

Kapust N,[…], Xavier JC*, Martin WF (2018). Failure to recover major events of gene flux in real biological data due to method misapplication. Genome biology and evolution, 10:1198-1209.

Gerlitz M, Knopp M, Kapust N, Xavier JC, Martin WF (2018). Elusive data underlying debate at the prokaryote-eukaryote divide. Biology Direct, 13:21.

Xavier JC, Patil KR, Rocha I (2017). Integration of biomass formulations of genome-scale metabolic models with experimental data reveals universally essential cofactors in prokaryotes. Metabolic Engineering, 39:200-208.

Xavier JC, Patil KR, Rocha I (2014). Systems biology perspectives on minimal and simpler cells. Microbiology and Molecular Biology Reviews, 78:487–509.

Preprints

Invited talks

Xavier, JC. Origin and early evolution of metabolic networks. Astrobiology and Planetary Exploration (APEX) Meeting Series, 2022 (online to UCL, UK).

Xavier, JC. Origin and early evolution of metabolic networks. German Aerospace Center, Aerospace Microbiology Research Group, 2021 (online to Köln, Germany).

Xavier, JC. Universally-essential biomolecules and collective autocatalysis: the emergence of metabolism. Physics of Emergent Behaviour III, Imperial College London, 2021 (online to London, UK).

Xavier, JC. Metabolic networks and the origin of life. Complexity Webinar Series, CoMuNe Lab, 2021 (online to Rome, Italy).

Xavier, JC. Autocatalytic Networks at the Origin of Metabolism. Heidelberg Initiative for the Origins of Life (HIFOL) Colloquium Series, 2021 (online to Heidelberg, Germany).

Xavier, JC. Flux, autocatalysis and self-organization: modelling fundamental cellular properties with applications in biotechnology and the origin of life. GEE Special Seminar @UCL, 2021 (online to London, UK).

Xavier, JC. Reflections on the origin of cells by a biologists’ advocate. Origins of life: The possible and the actual – SFI Working Group, 2021 (online to Santa Fe, U.S.A.)

Xavier, JC. Small molecules driving autocatalysis in prokaryotic metabolism. Small Organic Molecules: Chemical Space, Reactions, Catalysis and Autocatalysis, 2020 (online to Oxford, UK).

Xavier, JC. Earth’s first bioreactors: from bioengineering to the origin of life. 11th Symposium on Bioengineering, 2020 (online to Porto, Portugal).

Xavier, JC. Autocatalytic networks in ancient bacterial and archaeal metabolism. Thirty Years of Complex Thinking: A Celebration of Stuart Kauffman’s Contributions to the Field of Complex Systems, 2019. Santa Fe, U.S.A.

Xavier, JC. From bioengineering to systems biology and back: an insider’s perspective. 5th Symposium on Bioengineering, 2013. Porto, Portugal.

Conference presentations

Xavier JC. Autocatalytic networks at the origin of metabolism. Oral presentation. II Interdisciplinary Origin of Life Meeting for Early-career researchers, 2020 (online to Glasgow, UK).

Xavier JC. Autocatalytic networks in ancient bacterial and archaeal metabolism. Oral presentation. 30/80 meeting: Alkaline vents 30th/Mike Russell’s 80th, 2019. Granada, Spain.

Xavier JC. Autocatalysis in global metabolism and ancient life. Oral presentation. I Interdisciplinary Origin of Life Meeting for Early-career researchers, 2018. Düsseldorf, Germany.

Xavier JC, Preiner M, Martin WF. CO-dependent CO2 ­fixation: unique, ancient and ancestral in biochemistry. Poster presentation. SMBE Conference, 2018 . Tokyo, Japan.

Xavier JC, Liu F, Ramalho F, Rocha I. Standardization, completion and new predictions of 121 manually curated genome-scale prokaryotic models. Poster presentation. XI Copenhagen Biosciences Conference, Data-driven Biotechnology, Novo Nordisk Foundation, 2017. Hillerød, Denmark.

Xavier JC, Patil KR, Rocha I. Universally essential cofactors in prokaryotes. Oral presentation. IV Constraint-Based Reconstruction and Analysis Conference, 2015. Heidelberg, Germany.

Xavier JC, Patil KR, Rocha I. Integration of biomass functions of genome-scale metabolic models with experimental data reveals universally essential cofactors in prokaryotes. Poster presentation. Metabolic Pathways Analysis Conference, Biochemical Society, 2015. Braga, Portugal.

Xavier JC, Patil KR, Rocha I. Standardization and comparison of the biomass objective functions of manually curated genome-scale metabolic models. Poster presentation. III Constraint-Based Reconstruction and Analysis (COBRA) Conference, 2014. Virginia, U.S.A.

Xavier JC, Patil KR, Rocha I. Systematic comparison of essential reactions in manually curated genome scale metabolic models. Poster presentation. III Copenhagen Biosciences Conferences, Cell Factories and Biosustainability, Novo Nordisk Foundation, 2013. Hillerød, Denmark.

Xavier JC, Patil KR, Rocha I. Analysis of minimal metabolic networks through whole-cell in silico modelling of prokaryotes. Poster presentation. XI Jornadas de Bioinformatica, 2012. Barcelona, Spain.