Hi! I am Yogi.
I am a freelance educator, facilitator, systems scientist, evolutionary biologist, and natural philosopher with an extremely transdisciplinary track record. My teaching and research bridges the worlds of science, mathematics, art, and philosophy.
Originally trained as a geneticist, I have spent my career exploring how living systems develop, evolve, and how they generate meaning—questions that connect the life sciences with human creativity.
I am interested in fundamental problems such as the limits of (genetic) reductionism, formal modelling, and mechanistic explanation in biology. My current projects deal with the use of models as epistemic tools, with causal flow in complex adaptive systems, and with the nature of organismic agency and creativity and their role in evolution.
I am a freelance educator, facilitator, systems scientist, evolutionary biologist, and natural philosopher with an extremely transdisciplinary track record. My teaching and research bridges the worlds of science, mathematics, art, and philosophy.
Originally trained as a geneticist, I have spent my career exploring how living systems develop, evolve, and how they generate meaning—questions that connect the life sciences with human creativity.
I am interested in fundamental problems such as the limits of (genetic) reductionism, formal modelling, and mechanistic explanation in biology. My current projects deal with the use of models as epistemic tools, with causal flow in complex adaptive systems, and with the nature of organismic agency and creativity and their role in evolution.
You can find most of my public lectures on my YouTube channel.
Together with artist Marcus Neustetter, I am currently writing a book about a 21st-century science that no longer views the world as a machine.
I offer courses and workshops that teach philosophy to researchers, survival and flourishing to young academics, and creativity to everyone.
I am a founding member of the arts & science collective The ZoNE in Vienna. I offer arts & science workshops, events, scouting, and consulting with Marcus, through The Perspective Studio.
In recent years, I have also developed an interest in promoting open science and in formulating an epistemology suitable for open inquiry and innovation.
Together with artist Marcus Neustetter, I am currently writing a book about a 21st-century science that no longer views the world as a machine.
I offer courses and workshops that teach philosophy to researchers, survival and flourishing to young academics, and creativity to everyone.
I am a founding member of the arts & science collective The ZoNE in Vienna. I offer arts & science workshops, events, scouting, and consulting with Marcus, through The Perspective Studio.
In recent years, I have also developed an interest in promoting open science and in formulating an epistemology suitable for open inquiry and innovation.
Crossing disciplinary boundaries between biology, mathematics, philosophy, and art is an essential aspect of my work.
Teaching and mentoring are my passions.
In addition, I gained valuable managerial experience in running an institute of advanced study. I have a talent for facilitating interdisciplinary interactions, and a proven track record for building a supportive, productive, and creative academic environment.
Teaching and mentoring are my passions.
In addition, I gained valuable managerial experience in running an institute of advanced study. I have a talent for facilitating interdisciplinary interactions, and a proven track record for building a supportive, productive, and creative academic environment.
PROFESSIONAL EXPERIENCE:
Freelance Researcher, Philosopher, and Educator (2017–), associated with the Complexity Science Hub (CSH) Vienna
Scholar (2023–2024), Ronin Institute
Project Leader (2022–2025), John Templeton Foundation, Project: "Pushing the Boundaries", Dept of Philosophy, Uni Vienna
Scientific Director (2015–2017), Konrad Lorenz Institute for Evolution & Cognition Research (KLI), Klosterneuburg, Austria
Group Leader (2008–2015), EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Barcelona
Postdoctoral Associate (2006–2008), University Museum of Zoology, University of Cambridge, UK
EDUCATION:
PhD, Graduate Program in Genetics (2005), Stony Brook University, NY
MSc in Holistic Science (2000), Schumacher College, Dartington, Devon
University Diploma in Biology (1999), Biocenter, University of Basel
Freelance Researcher, Philosopher, and Educator (2017–), associated with the Complexity Science Hub (CSH) Vienna
Scholar (2023–2024), Ronin Institute
Project Leader (2022–2025), John Templeton Foundation, Project: "Pushing the Boundaries", Dept of Philosophy, Uni Vienna
Scientific Director (2015–2017), Konrad Lorenz Institute for Evolution & Cognition Research (KLI), Klosterneuburg, Austria
Group Leader (2008–2015), EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Barcelona
Postdoctoral Associate (2006–2008), University Museum of Zoology, University of Cambridge, UK
EDUCATION:
PhD, Graduate Program in Genetics (2005), Stony Brook University, NY
MSc in Holistic Science (2000), Schumacher College, Dartington, Devon
University Diploma in Biology (1999), Biocenter, University of Basel
AWARDS & FELLOWSHIPS:
D'Alembert Fellow (2020/21), Université Paris-Saclay/Institut d´Études Avancées (IEA) de Paris
Fellow (2020). Stellenbosch Institute for Advanced Study (STIAS)
Dr. Chopin Visiting Fellowship (2019), Webster Private University, Vienna
Fellow (2018/19), Centre de Recherches Interdisciplinaires (CRI), Paris
Visiting Scholar (2017/18), Center for Systems Biology Dresden (CSBD)
Fellow (2014/15), Institute for Advanced Study/Wissenschaftskolleg zu Berlin
President's Medal (2013), Section: Cell Biology, Society for Experimental Biology (SEB)
D'Alembert Fellow (2020/21), Université Paris-Saclay/Institut d´Études Avancées (IEA) de Paris
Fellow (2020). Stellenbosch Institute for Advanced Study (STIAS)
Dr. Chopin Visiting Fellowship (2019), Webster Private University, Vienna
Fellow (2018/19), Centre de Recherches Interdisciplinaires (CRI), Paris
Visiting Scholar (2017/18), Center for Systems Biology Dresden (CSBD)
Fellow (2014/15), Institute for Advanced Study/Wissenschaftskolleg zu Berlin
President's Medal (2013), Section: Cell Biology, Society for Experimental Biology (SEB)
RESEARCH PUBLICATIONS:
Jaeger J, Rodrigues A (in preparation). Thinking about the Box: Models of Living Processes in the 21st Century.
Jaeger J, Hofmeyr J-H (in preparation). Life enmattered and enformed: the problem of embodiment.
Jaeger J, Loettgers A, Purkhauser K, Poledna P, Knuuttila T (in preparation). Radical emergence: the diachronic origin of novel levels of organization.
Jaeger J, DiFrisco, Monk N. The ontology of dynamical systems. (in preparation)
Jaeger J. Re-Engineering Wimsatt for Limited Beings. (commissioned for a special issue of Acta Biotheor, in preparation).
Jaeger J, DiFrisco J, Loettgers A (2025). Beyond networks: explaining dynamics in the natural and social sciences (2025). In: Modeling the Possible, Knuuttila T (ed.), Routledge, London (preprint).
Jaeger J, Riedl A, Djedovic A, Vervaeke J, Walsh D (2024). Naturalizing Relevance Realization: Why Agency and Cognition Are Fundamentally Not Computational. Front Psychol 15: 1362658 (preprint).
Jaeger J (2024). Ontogenesis, Organization, and Organismal Agency. In: Organismal Agency: Biological Concepts and Their Philosophical Foundations, Švorcová J (ed.), Spinger Nature, Cham (preprint).
Jaeger J (2024). The Fourth Perspective: Evolution and Organismal Agency. In: Organization in Biology, Mossio M (ed.), Springer, Berlin (preprint).
Jaeger J (2024). Artificial Intelligence is Algorithmic Mimicry: Why Artificial "Agents" Are Not (and Won't Be) Proper Agents. NBDT 1-21: 001c.94404 (preprint).
Jaeger J (2024). Assembly Theory: What it Does and What it Does Not Do. J Mol Evol 92: 87–92 (based on this original blog post).
Jaeger J., Masselot C., Greshake Tzovaras B., Senabre Hidalgo E., Santolini M (2023). An epistemology for democratic citizen science. Roy Soc Open Sci 10: 231100 (preprint).
Torri A, Jaeger J, Pradeu T, Saleh M-C (2022). The origin of RNA interference: adaptive or neutral evolution? PLoS Biol 20: e3001715.
Roli A, Jaeger J, Kauffman SA (2022). How organisms come to know the world: fundamental limits on artificial general intelligence. Front Ecol Evol 9: 806283 (preprint).
Crombach A, Jaeger J (2021). Life’s attractors continued: progress in understanding developmental systems through reverse engineering and in silico evolution. In: Evolutionary Systems Biology: Advances, Questions, and Opportunities, Crombach A (ed.), Springer Nature Switzerland, Cham (preprint).
Jaeger J, Monk N (2021). Dynamical modularity of the genotype-phenotype map. In: Evolutionary Systems Biology: Advances, Questions, and Opportunities, Crombach A (ed.), Springer Nature Switzerland, Cham (preprint).
Jaeger J, Monk N (2021). Dynamical modules in metabolism, cell and developmental biology. J Roy Soc Interface 11: 20210011 (preprint).
DiFrisco J, Jaeger J (2021). Homology of processes: developmental dynamics in comparative biology. J Roy Soc Interface 11: 20210007 (preprint).
DiFrisco J, Jaeger J (2020). Genetic causation in complex regulatory systems: an integrative dynamic perspective. BioEssays 42: 1900226.
Jaeger J, Verd B (2020). Dynamic positional information: patterning mechanism vs. precision in gradient-driven systems. Curr Top Dev Biol 137: 219–246.
Anderson G, Verd B & Jaeger J (2020). Drawing to extend Waddington’s Epigenetic Landscape. Leonardo 53: 1–14.
DiFrisco J, Jaeger J (2019). Beyond networks: mechanism and process in evo-devo. Biol Philos 34: 54.
Verd B, Monk N & Jaeger J (2019). Modularity, criticality and evolvability of a developmental gene regulatory network. eLIFE 8: e42832.
Jaeger J (2019). Dynamic structures in evo-devo: from morphogenetic fields to evolving organisms. In: Perspectives on Evolutionary and Developmental Biology: Essays for Alessandro Minelli, Fusco G (ed.), Padova Univ Press, Padova, Italy (preprint).
Verd B, Clark E, Wotton KR, Janssens H, Jiménez-Guri E, Crombach A & Jaeger J (2018). A damped oscillator imposes temporal order on posterior gap gene expression in Drosophila. PLOS Biol 16: e2003174.
Fraire-Zamora JJ, Jaeger J, Solon J (2018). Two consecutive microtubule-based epithelial seaming events mediate dorsal closure in the scuttle fly Megaselia abdita. eLIFE 7: e33807.
Jaeger J (2018). Shift happens: the developmental and evolutionary dynamics of the gap gene system. Curr Op Syst Biol 11: 65–73.
Verd B, Crombach A & Jaeger J (2017). Dynamic maternal gradients control timing and shift-rates for Drosophila gap gene expression. PLOS Comp Biol 13: e1005285.
Jaeger J (2017). The importance of being dynamic: systems biology beyond the hairball. In: Philosophy of Systems Biology: Perspectives from Philosophers and Scientists, Green S (ed.), Springer, Berlin.
Crombach A, Wotton KR, Jiménez-Guri E & Jaeger J (2016). Gap gene regulatory dynamics evolve along a genotype network. Mol Biol Evol 33: 1293–1307.
Hoermann A, Cicin-Sain D & Jaeger J (2016). A quantitative validated model reveals two phases of transcriptional regulation for the gap gene giant in Drosophila. Dev Biol 411: 325–38.
Wotton KR, Jiménez-Guri E, Crombach A, Janssens H, Alcaine Colet A, Lemke S, Schmidt-Ott U & Jaeger J (2015). Quantitative system drift compensates for altered maternal inputs to the gap gene network of the scuttle fly Megaselia abdita. eLIFE 4: e04785.
Wotton KR, Jiménez-Guri E & Jaeger J (2015). Maternal co-ordinate gene regulation and axis polarity in the scuttle fly Megaselia abdita. PLOS Genetics 11: e1005042.
Cicin-Sain D, Hermoso Pulido A, Crombach A, Wotton KR, Jiménez-Guri E, Taly J-F, Roma G & Jaeger J (2015). SuperFly: a comparative database for quantified spatio-temporal gene expression patterns in early dipteran embryos. Nucl Acids Res 43 (Database Issue): D752–6.
Green S, Fagan M & Jaeger J (2015). Explanatory integration challenges in evolutionary systems biology. Biol Theory 10: 18–35.
Jaeger J, Laubichler M & Callebaut W (2015). The comet cometh: evolving developmental systems. Biol Theory 10: 36–49. (This is a critical reply to Duboule D (2010). The evo-devo comet. EMBO Rep 11: 489.)
Villaverde AF, Henriques D, Smallbone K, Bongard S, Schmid J, Cicin-Sain D, Crombach A, Saez-Rodriguez J, Mauch K, Balsa-Canto E, Mendes P, Jaeger J & Banga JR (2015). BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. BMC Syst Biol 9: 8.
Jaeger J & Monk N (2015). Everything flows: a process perspective on life. EMBO Rep 16: 1064–7. (See also: Jaeger J, Monk N (2022). The flow of substance: a reply to Horsting & Hartjes. EMBO Rep 23: e55642.)
Jaeger J & Monk N (2014). Bioattractors: dynamical systems theory and the evolution of regulatory processes. J Physiol 592: 2267–81.
Crombach A, García-Solache M & Jaeger J (2014). Evolution of early development in dipterans: reverse-engineering the gap gene network in the moth midge Clogmia albipunctata (Psychodidae). BioSystems 123: 75–85.
Verd B, Crombach A & Jaeger J (2014). Classification of transient behaviours in a time-dependent toggle switch model. BMC Syst Biol 8: 43.
Jiménez-Guri E, Wotton KR, Gavilán B & Jaeger J (2014). A staging scheme for the development of the moth midge Clogmia albipunctata. PLoS ONE 9: e84422.
Wotton KR, Jiménez-Guri E, García Matheu B & Jaeger J (2014). A staging scheme for the development of the scuttle fly Megaselia abdita. PLoS ONE 9: e84421.
Janssens H, Siggens K, Cicin-Sain D, Jiménez-Guri E, Musy M, Akam M & Jaeger J (2013). A quantitative atlas of Even-Skipped and Hunchback expression in Clogmia albipunctata (Diptera: Psychodidae) blastoderm embryos. EvoDevo 5: 1.
Becker K, Balsa-Canto E, Cicin-Sain D, Hoermann A, Janssens H, Banga JR, Jaeger J (2013). Reverse-engineering post-transcriptional regulation of gap genes in Drosophila melanogaster. PLoS Comp Biol 9: e1003281.
Janssens H, Crombach A, Wotton KR, Cicin-Sain D, Surkova S, Lim CL, Samsonova M, Akam M & Jaeger J (2013). Lack of tailless leads to an increase in expression variability in Drosophila embryos. Dev Biol 377: 305–317.
Jiménez-Guri E, Huerta-Cepas J, Cozzuto L, Wotton KR, Kang H, Himmelbauer H, Roma G, Gabaldón T, Jaeger J (2013). Comparative transcriptomics of early dipteran development. BMC Genomics 14: 123.
Jaeger J & Monk N (2013). Keeping the gene in its place. In: The Intuitive Way of Knowing: A Tribute to Brian Goodwin, Lambert D & Chetland C (eds), Floris, Edinburgh (Full Text PDF).
Crombach A, Wotton KR, Cicin-Sain D, Ashyraliyev M & Jaeger J (2012). Efficient reverse-engineering of a developmental gene regulatory network. PLoS Comp Biol 8: e1002589.
Crombach A, Cicin-Sain D, Wotton KR & Jaeger J (2012). Medium-throughput processing of whole mount in situ hybridisation experiments into gene expression domains. PLoS ONE 7: e46658.
Jaeger J & Crombach A (2012). Life’s attractors: understanding developmental systems through reverse engineering and in silico evolution. In: Evolutionary Systems Biology, Soyer O (ed.), Springer, Berlin.
Jaeger J, Irons D & Monk N (2012). The inheritance of process: a dynamical systems approach. J Exp Zool (Mol Dev Evol) 318B: 591–612.
Jaeger J, Manu & Reinitz J (2012). Drosophila blastoderm patterning. Curr Op Genes Dev 22: 533–41.
Jaeger J (2011). The gap gene network. Cell Mol Life Sci 68: 243–74
García-Solache M, Jaeger J & Akam M (2010). A systematic analysis of the gap gene system in the moth midge Clogmia albipunctata. Dev Biol 344: 308–18.
Jostins L & Jaeger J (2010). Reverse engineering a gene network using an asynchronous parallel evolution strategy. BMC Syst Biol 4:17.
Jaeger J (2009). Modelling the Drosophila embryo. Mol BioSyst 5: 1549–68.
Ashyraliyev M, Siggens K, Janssens H, Blom J, Akam M & Jaeger J (2009). Gene circuit analysis of the terminal gap gene huckebein. PLoS Comp Biol 5: e10000548.
Jaeger J, Irons D & Monk N (2008). Regulative feedback in pattern formation: towards a general relativistic theory of positional information. Development 135: 3175–83.
Jaeger J, Sharp DH & Reinitz J (2007). Known maternal gradients are not sufficient for the establishment of gap domains in Drosophila melanogaster. Mech Dev 124: 108–28.
Jaeger J & Reinitz J (2006). On the dynamic nature of positional information. BioEssays 28: 1102–11.
Janssens H, Hou S, Jaeger J, Kim A-R, Myasnikova E, Sharp DH & Reinitz J (2006). Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene. Nat Genet 38: 1159–65.
Perkins TJ, Jaeger J, Reinitz J & Glass L (2006). Reverse engineering the gap gene network of Drosophila melanogaster. PLoS Comp Biol 2: e51.
Jaeger J, Surkova S, Blagov M, Janssens H, Kosman D, Kozlov KN, Manu, Myasnikova E, Vanario-Alonso CE, Samsonova M, Sharp DH & Reinitz J (2004). Dynamic control of positional information in the early Drosophila embryo. Nature 430: 368–71.
Jaeger J, Blagov M, Kosman D, Kozlov KN, Manu, Myasnikova E, Surkova S, Vanario-Alonso, CE, Samsonova M, Sharp DH & Reinitz J (2004). Dynamical analysis of regulatory interactions in the gap gene system of Drosophila melanogaster. Genetics
167: 1721–37.
Jaeger J & Goodwin BC (2001). A cellular oscillator model for periodic pattern formation. J Theor Biol 213: 171–81.
Jaeger J, Rodrigues A (in preparation). Thinking about the Box: Models of Living Processes in the 21st Century.
Jaeger J, Hofmeyr J-H (in preparation). Life enmattered and enformed: the problem of embodiment.
Jaeger J, Loettgers A, Purkhauser K, Poledna P, Knuuttila T (in preparation). Radical emergence: the diachronic origin of novel levels of organization.
Jaeger J, DiFrisco, Monk N. The ontology of dynamical systems. (in preparation)
Jaeger J. Re-Engineering Wimsatt for Limited Beings. (commissioned for a special issue of Acta Biotheor, in preparation).
Jaeger J, DiFrisco J, Loettgers A (2025). Beyond networks: explaining dynamics in the natural and social sciences (2025). In: Modeling the Possible, Knuuttila T (ed.), Routledge, London (preprint).
Jaeger J, Riedl A, Djedovic A, Vervaeke J, Walsh D (2024). Naturalizing Relevance Realization: Why Agency and Cognition Are Fundamentally Not Computational. Front Psychol 15: 1362658 (preprint).
Jaeger J (2024). Ontogenesis, Organization, and Organismal Agency. In: Organismal Agency: Biological Concepts and Their Philosophical Foundations, Švorcová J (ed.), Spinger Nature, Cham (preprint).
Jaeger J (2024). The Fourth Perspective: Evolution and Organismal Agency. In: Organization in Biology, Mossio M (ed.), Springer, Berlin (preprint).
Jaeger J (2024). Artificial Intelligence is Algorithmic Mimicry: Why Artificial "Agents" Are Not (and Won't Be) Proper Agents. NBDT 1-21: 001c.94404 (preprint).
Jaeger J (2024). Assembly Theory: What it Does and What it Does Not Do. J Mol Evol 92: 87–92 (based on this original blog post).
Jaeger J., Masselot C., Greshake Tzovaras B., Senabre Hidalgo E., Santolini M (2023). An epistemology for democratic citizen science. Roy Soc Open Sci 10: 231100 (preprint).
Torri A, Jaeger J, Pradeu T, Saleh M-C (2022). The origin of RNA interference: adaptive or neutral evolution? PLoS Biol 20: e3001715.
Roli A, Jaeger J, Kauffman SA (2022). How organisms come to know the world: fundamental limits on artificial general intelligence. Front Ecol Evol 9: 806283 (preprint).
Crombach A, Jaeger J (2021). Life’s attractors continued: progress in understanding developmental systems through reverse engineering and in silico evolution. In: Evolutionary Systems Biology: Advances, Questions, and Opportunities, Crombach A (ed.), Springer Nature Switzerland, Cham (preprint).
Jaeger J, Monk N (2021). Dynamical modularity of the genotype-phenotype map. In: Evolutionary Systems Biology: Advances, Questions, and Opportunities, Crombach A (ed.), Springer Nature Switzerland, Cham (preprint).
Jaeger J, Monk N (2021). Dynamical modules in metabolism, cell and developmental biology. J Roy Soc Interface 11: 20210011 (preprint).
DiFrisco J, Jaeger J (2021). Homology of processes: developmental dynamics in comparative biology. J Roy Soc Interface 11: 20210007 (preprint).
DiFrisco J, Jaeger J (2020). Genetic causation in complex regulatory systems: an integrative dynamic perspective. BioEssays 42: 1900226.
Jaeger J, Verd B (2020). Dynamic positional information: patterning mechanism vs. precision in gradient-driven systems. Curr Top Dev Biol 137: 219–246.
Anderson G, Verd B & Jaeger J (2020). Drawing to extend Waddington’s Epigenetic Landscape. Leonardo 53: 1–14.
DiFrisco J, Jaeger J (2019). Beyond networks: mechanism and process in evo-devo. Biol Philos 34: 54.
Verd B, Monk N & Jaeger J (2019). Modularity, criticality and evolvability of a developmental gene regulatory network. eLIFE 8: e42832.
Jaeger J (2019). Dynamic structures in evo-devo: from morphogenetic fields to evolving organisms. In: Perspectives on Evolutionary and Developmental Biology: Essays for Alessandro Minelli, Fusco G (ed.), Padova Univ Press, Padova, Italy (preprint).
Verd B, Clark E, Wotton KR, Janssens H, Jiménez-Guri E, Crombach A & Jaeger J (2018). A damped oscillator imposes temporal order on posterior gap gene expression in Drosophila. PLOS Biol 16: e2003174.
Fraire-Zamora JJ, Jaeger J, Solon J (2018). Two consecutive microtubule-based epithelial seaming events mediate dorsal closure in the scuttle fly Megaselia abdita. eLIFE 7: e33807.
Jaeger J (2018). Shift happens: the developmental and evolutionary dynamics of the gap gene system. Curr Op Syst Biol 11: 65–73.
Verd B, Crombach A & Jaeger J (2017). Dynamic maternal gradients control timing and shift-rates for Drosophila gap gene expression. PLOS Comp Biol 13: e1005285.
Jaeger J (2017). The importance of being dynamic: systems biology beyond the hairball. In: Philosophy of Systems Biology: Perspectives from Philosophers and Scientists, Green S (ed.), Springer, Berlin.
Crombach A, Wotton KR, Jiménez-Guri E & Jaeger J (2016). Gap gene regulatory dynamics evolve along a genotype network. Mol Biol Evol 33: 1293–1307.
Hoermann A, Cicin-Sain D & Jaeger J (2016). A quantitative validated model reveals two phases of transcriptional regulation for the gap gene giant in Drosophila. Dev Biol 411: 325–38.
Wotton KR, Jiménez-Guri E, Crombach A, Janssens H, Alcaine Colet A, Lemke S, Schmidt-Ott U & Jaeger J (2015). Quantitative system drift compensates for altered maternal inputs to the gap gene network of the scuttle fly Megaselia abdita. eLIFE 4: e04785.
Wotton KR, Jiménez-Guri E & Jaeger J (2015). Maternal co-ordinate gene regulation and axis polarity in the scuttle fly Megaselia abdita. PLOS Genetics 11: e1005042.
Cicin-Sain D, Hermoso Pulido A, Crombach A, Wotton KR, Jiménez-Guri E, Taly J-F, Roma G & Jaeger J (2015). SuperFly: a comparative database for quantified spatio-temporal gene expression patterns in early dipteran embryos. Nucl Acids Res 43 (Database Issue): D752–6.
Green S, Fagan M & Jaeger J (2015). Explanatory integration challenges in evolutionary systems biology. Biol Theory 10: 18–35.
Jaeger J, Laubichler M & Callebaut W (2015). The comet cometh: evolving developmental systems. Biol Theory 10: 36–49. (This is a critical reply to Duboule D (2010). The evo-devo comet. EMBO Rep 11: 489.)
Villaverde AF, Henriques D, Smallbone K, Bongard S, Schmid J, Cicin-Sain D, Crombach A, Saez-Rodriguez J, Mauch K, Balsa-Canto E, Mendes P, Jaeger J & Banga JR (2015). BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. BMC Syst Biol 9: 8.
Jaeger J & Monk N (2015). Everything flows: a process perspective on life. EMBO Rep 16: 1064–7. (See also: Jaeger J, Monk N (2022). The flow of substance: a reply to Horsting & Hartjes. EMBO Rep 23: e55642.)
Jaeger J & Monk N (2014). Bioattractors: dynamical systems theory and the evolution of regulatory processes. J Physiol 592: 2267–81.
Crombach A, García-Solache M & Jaeger J (2014). Evolution of early development in dipterans: reverse-engineering the gap gene network in the moth midge Clogmia albipunctata (Psychodidae). BioSystems 123: 75–85.
Verd B, Crombach A & Jaeger J (2014). Classification of transient behaviours in a time-dependent toggle switch model. BMC Syst Biol 8: 43.
Jiménez-Guri E, Wotton KR, Gavilán B & Jaeger J (2014). A staging scheme for the development of the moth midge Clogmia albipunctata. PLoS ONE 9: e84422.
Wotton KR, Jiménez-Guri E, García Matheu B & Jaeger J (2014). A staging scheme for the development of the scuttle fly Megaselia abdita. PLoS ONE 9: e84421.
Janssens H, Siggens K, Cicin-Sain D, Jiménez-Guri E, Musy M, Akam M & Jaeger J (2013). A quantitative atlas of Even-Skipped and Hunchback expression in Clogmia albipunctata (Diptera: Psychodidae) blastoderm embryos. EvoDevo 5: 1.
Becker K, Balsa-Canto E, Cicin-Sain D, Hoermann A, Janssens H, Banga JR, Jaeger J (2013). Reverse-engineering post-transcriptional regulation of gap genes in Drosophila melanogaster. PLoS Comp Biol 9: e1003281.
Janssens H, Crombach A, Wotton KR, Cicin-Sain D, Surkova S, Lim CL, Samsonova M, Akam M & Jaeger J (2013). Lack of tailless leads to an increase in expression variability in Drosophila embryos. Dev Biol 377: 305–317.
Jiménez-Guri E, Huerta-Cepas J, Cozzuto L, Wotton KR, Kang H, Himmelbauer H, Roma G, Gabaldón T, Jaeger J (2013). Comparative transcriptomics of early dipteran development. BMC Genomics 14: 123.
Jaeger J & Monk N (2013). Keeping the gene in its place. In: The Intuitive Way of Knowing: A Tribute to Brian Goodwin, Lambert D & Chetland C (eds), Floris, Edinburgh (Full Text PDF).
Crombach A, Wotton KR, Cicin-Sain D, Ashyraliyev M & Jaeger J (2012). Efficient reverse-engineering of a developmental gene regulatory network. PLoS Comp Biol 8: e1002589.
Crombach A, Cicin-Sain D, Wotton KR & Jaeger J (2012). Medium-throughput processing of whole mount in situ hybridisation experiments into gene expression domains. PLoS ONE 7: e46658.
Jaeger J & Crombach A (2012). Life’s attractors: understanding developmental systems through reverse engineering and in silico evolution. In: Evolutionary Systems Biology, Soyer O (ed.), Springer, Berlin.
Jaeger J, Irons D & Monk N (2012). The inheritance of process: a dynamical systems approach. J Exp Zool (Mol Dev Evol) 318B: 591–612.
Jaeger J, Manu & Reinitz J (2012). Drosophila blastoderm patterning. Curr Op Genes Dev 22: 533–41.
Jaeger J (2011). The gap gene network. Cell Mol Life Sci 68: 243–74
García-Solache M, Jaeger J & Akam M (2010). A systematic analysis of the gap gene system in the moth midge Clogmia albipunctata. Dev Biol 344: 308–18.
Jostins L & Jaeger J (2010). Reverse engineering a gene network using an asynchronous parallel evolution strategy. BMC Syst Biol 4:17.
Jaeger J (2009). Modelling the Drosophila embryo. Mol BioSyst 5: 1549–68.
Ashyraliyev M, Siggens K, Janssens H, Blom J, Akam M & Jaeger J (2009). Gene circuit analysis of the terminal gap gene huckebein. PLoS Comp Biol 5: e10000548.
Jaeger J, Irons D & Monk N (2008). Regulative feedback in pattern formation: towards a general relativistic theory of positional information. Development 135: 3175–83.
Jaeger J, Sharp DH & Reinitz J (2007). Known maternal gradients are not sufficient for the establishment of gap domains in Drosophila melanogaster. Mech Dev 124: 108–28.
Jaeger J & Reinitz J (2006). On the dynamic nature of positional information. BioEssays 28: 1102–11.
Janssens H, Hou S, Jaeger J, Kim A-R, Myasnikova E, Sharp DH & Reinitz J (2006). Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene. Nat Genet 38: 1159–65.
Perkins TJ, Jaeger J, Reinitz J & Glass L (2006). Reverse engineering the gap gene network of Drosophila melanogaster. PLoS Comp Biol 2: e51.
Jaeger J, Surkova S, Blagov M, Janssens H, Kosman D, Kozlov KN, Manu, Myasnikova E, Vanario-Alonso CE, Samsonova M, Sharp DH & Reinitz J (2004). Dynamic control of positional information in the early Drosophila embryo. Nature 430: 368–71.
Jaeger J, Blagov M, Kosman D, Kozlov KN, Manu, Myasnikova E, Surkova S, Vanario-Alonso, CE, Samsonova M, Sharp DH & Reinitz J (2004). Dynamical analysis of regulatory interactions in the gap gene system of Drosophila melanogaster. Genetics
167: 1721–37.
Jaeger J & Goodwin BC (2001). A cellular oscillator model for periodic pattern formation. J Theor Biol 213: 171–81.
GRANTS/PROJECTS
From Dec 2022 to Aug 2025, I was leading the project "Pushing the Boundaries: Agency, Evolution, and the Dynamic Emergence of Expanding Possibilities" (with co-leader Tarja Knuuttila), hosted at the Department of Philosophy of the University of Vienna. This project was funded by the John Templeton Foundation (Grant ID: 62581). You can read more about it in this blog post.
I've coordinated an FP7 project called "BioPreDyn: From Data to Models - New Bioinformatics Methods and Tools for Data-Driven, Predictive Dynamic Modelling in Biotechnological Applications" (2011–2015). It turned out to be a great project, but I swear I'll never do anything like this again.
I participated as a partner in a number of other European projects, including two ComplexityNET/ERANet grants that investigated multi-objective optimization (MOPDEV), and heart development in Drosophila (MODHEART), and a recent H2020 project on "Citizen Science for Monitoring Climate Impacts and Achieving Climate Resilience (Crowd4SDG)".
In addition, I managed to somehow secure continuous financial support from the Spanish and/or Catalan government for my research group in Barcelona in the time right after the 2008 financial crisis, which was a fun time to do science in Spain... No kidding.
From Dec 2022 to Aug 2025, I was leading the project "Pushing the Boundaries: Agency, Evolution, and the Dynamic Emergence of Expanding Possibilities" (with co-leader Tarja Knuuttila), hosted at the Department of Philosophy of the University of Vienna. This project was funded by the John Templeton Foundation (Grant ID: 62581). You can read more about it in this blog post.
I've coordinated an FP7 project called "BioPreDyn: From Data to Models - New Bioinformatics Methods and Tools for Data-Driven, Predictive Dynamic Modelling in Biotechnological Applications" (2011–2015). It turned out to be a great project, but I swear I'll never do anything like this again.
I participated as a partner in a number of other European projects, including two ComplexityNET/ERANet grants that investigated multi-objective optimization (MOPDEV), and heart development in Drosophila (MODHEART), and a recent H2020 project on "Citizen Science for Monitoring Climate Impacts and Achieving Climate Resilience (Crowd4SDG)".
In addition, I managed to somehow secure continuous financial support from the Spanish and/or Catalan government for my research group in Barcelona in the time right after the 2008 financial crisis, which was a fun time to do science in Spain... No kidding.
TEACHING/SUPERVISING/MENTORING:
I worked as a substitute science teacher for middle schoolers at the local Galemo Montessori School (Sep – Dec 2022).
Over the last twenty years, I've designed and taught a wide range of mainly graduate-level courses at institutions like Stony Brook University, the University of Cambridge, the Center for Genomic Regulation (CRG) in Barcelona, the École Normale Supérieure (ENS), Oxford Brookes University, the Instituto Gulbenkian de Ciência near Lisbon, the CRI/LPI Paris, IST Austria, and (as a recurring guest lecturer/Gastprofessor) at the University of Vienna.
I used to co-organize the Summer School in Systems Biology at the CRG in Barcelona (2011–2014), and I was the director of the biannual Venice Summer School in Evolutionary Systems Biology (2011, 2013, 2015, 2017, 2019, 2022 - postponed due to COVID19, 2023, and 2025).
Apart from continuing to serve as supervisor to graduate students across fields from molecular biology to mathematical modelling, philosophy, artificial intelligence, and cognitive science, I have acted and am acting as mentor to numerous students and researchers who have chosen to take up particularly unusual academic or non-academic career paths.
I worked as a substitute science teacher for middle schoolers at the local Galemo Montessori School (Sep – Dec 2022).
Over the last twenty years, I've designed and taught a wide range of mainly graduate-level courses at institutions like Stony Brook University, the University of Cambridge, the Center for Genomic Regulation (CRG) in Barcelona, the École Normale Supérieure (ENS), Oxford Brookes University, the Instituto Gulbenkian de Ciência near Lisbon, the CRI/LPI Paris, IST Austria, and (as a recurring guest lecturer/Gastprofessor) at the University of Vienna.
I used to co-organize the Summer School in Systems Biology at the CRG in Barcelona (2011–2014), and I was the director of the biannual Venice Summer School in Evolutionary Systems Biology (2011, 2013, 2015, 2017, 2019, 2022 - postponed due to COVID19, 2023, and 2025).
Apart from continuing to serve as supervisor to graduate students across fields from molecular biology to mathematical modelling, philosophy, artificial intelligence, and cognitive science, I have acted and am acting as mentor to numerous students and researchers who have chosen to take up particularly unusual academic or non-academic career paths.
OTHER:
I was a founding member and organizer for the Junior European Drosophila Investigators (JEDI).
I was an editor for PLoS ONE (from 2008 to 2015) and, therefore, have seen all nine circles of peer-review hell. I had a much better experience being the biology editor of Philosophy, Theory, and Practice in Biology (PTPbio) (from 2018 to 2023), still the only open-access journal in the philosophy of biology.
I am a member of the scientific advisory board of the PhD Programme in Theoretical & Evolutionary Biology at Charles University in Prague.
I was a founding member and organizer for the Junior European Drosophila Investigators (JEDI).
I was an editor for PLoS ONE (from 2008 to 2015) and, therefore, have seen all nine circles of peer-review hell. I had a much better experience being the biology editor of Philosophy, Theory, and Practice in Biology (PTPbio) (from 2018 to 2023), still the only open-access journal in the philosophy of biology.
I am a member of the scientific advisory board of the PhD Programme in Theoretical & Evolutionary Biology at Charles University in Prague.
You can download my full CV here, and find an up-to-date list of publications at my Google Scholar Profile or ORCID.