All Stories

  1. Naturalizing relevance realization: why agency and cognition are fundamentally not computational

    Article • Frontiers in Psychology, June 2024, Frontiers

    Dr Johannes Jaeger

  2. Assembly Theory: What It Does and What It Does Not Do

    Article • Journal of Molecular Evolution, March 2024, Springer Science + Business Media

    Dr Johannes Jaeger

  3. Artificial intelligence is algorithmic mimicry: why artificial “agents” are not (and won’t be) proper agents

    Article • Neurons Behavior Data analysis and Theory, February 2024, Neurons Behavior Data Analysis and Behavior

    Dr Johannes Jaeger

  4. Naturalizing Relevance Realization: Why agency and cognition are fundamentally not computational

    Article • December 2023, Center for Open Science

    Dr Johannes Jaeger

  5. Beyond Networks: Explaining Dynamics in the Natural and Social Sciences

    Article • December 2023, Center for Open Science

    Dr Johannes Jaeger

  6. Drawing to Extend Waddington's Epigenetic Landscape

    Article • October 2023, Intellect

    Dr Johannes Jaeger

  7. The flow of substance: a reply to Horsting & Hartjes

    Article • EMBO Reports, July 2022, Springer Science + Business Media

    Dr Johannes Jaeger

  8. Ontogenesis, Organization, and Organismal Agency

    Article • June 2022, Center for Open Science

    Dr Johannes Jaeger

  9. An Epistemology for Democratic Citizen Science

    Article • June 2022, Center for Open Science

    Dr Johannes Jaeger

  10. How Organisms Come to Know the World: Fundamental Limits on Artificial General Intelligence

    Article • Frontiers in Ecology and Evolution, January 2022, Frontiers

    Dr Johannes Jaeger

  11. How organisms come to know the world: fundamental limits on artificial general intelligence

    Article • October 2021, Center for Open Science

    Dr Johannes Jaeger

  12. Homology of process: developmental dynamics in comparative biology

    Article • Interface Focus, April 2021, Royal Society Publishing

    Dr Johannes Jaeger

  13. Dynamical modules in metabolism, cell and developmental biology

    Article • Interface Focus, April 2021, Royal Society Publishing

    Dr Johannes Jaeger

  14. The Fourth Perspective: Evolution and Organismal Agency

    Article • February 2021, Center for Open Science

    Dr Johannes Jaeger

  15. Dynamical Modules in Metabolism, Cell and Developmental Biology

    Article • February 2021, Center for Open Science

    Dr Johannes Jaeger

  16. Dynamic structures in evo-devo: From morphogenetic fields to evolving organisms

    Article • February 2021, Center for Open Science

    Dr Johannes Jaeger

  17. Dynamical Modularity of the Genotype-Phenotype Map

    Article • February 2021, Center for Open Science

    Dr Johannes Jaeger

  18. Genetic Causation in Complex Regulatory Systems: An Integrative Dynamic Perspective

    Article • BioEssays, May 2020, Wiley

    Dr Johannes Jaeger

  19. Dynamic positional information: Patterning mechanism versus precision in gradient-driven systems

    Article • January 2020, Elsevier

    Dr Johannes Jaeger

  20. Beyond networks: mechanism and process in evo-devo

    Article • Biology & Philosophy, November 2019, Springer Science + Business Media

    Dr Johannes Jaeger

  21. Modularity, criticality, and evolvability of a developmental gene regulatory network

    Article • eLife, June 2019, eLife

    Dr Johannes Jaeger

  22. Drawing to Extend Waddington’s Epigenetic Landscape

    Article • Leonardo, February 2019, The MIT Press

    Dr Johannes Jaeger

  23. Shift happens: The developmental and evolutionary dynamics of the gap gene system

    Article • Current Opinion in Systems Biology, August 2018, Elsevier

    Dr Johannes Jaeger

  24. Two consecutive microtubule-based epithelial seaming events mediate dorsal closure in the scuttle fly Megaselia abdita

    Article • eLife, March 2018, eLife

    Dr Johannes Jaeger

  25. A damped oscillator imposes temporal order on posterior gap gene expression in Drosophila

    Article • PLoS Biology, February 2018, PLOS

    Dr Johannes Jaeger

  26. tarsal-less is expressed as a gap gene but has no gap gene phenotype in the moth midge Clogmia albipunctata .

    Article • February 2018, Cold Spring Harbor Laboratory Press

    Dr Johannes Jaeger

  27. Non-canonical dorsoventral patterning in the moth midge Clogmia albipunctata

    Article • EvoDevo, November 2017, Springer Science + Business Media

    Dr Johannes Jaeger

  28. Dynamic Maternal Gradients Control Timing and Shift-Rates for Drosophila Gap Gene Expression

    Article • PLoS Computational Biology, February 2017, PLOS

    Dr Johannes Jaeger

  29. A quantitative validated model reveals two phases of transcriptional regulation for the gap gene giant in Drosophila

    Article • Developmental Biology, March 2016, Elsevier

    Dr Johannes Jaeger

  30. Gap Gene Regulatory Dynamics Evolve along a Genotype Network

    Article • Molecular Biology and Evolution, January 2016, Oxford University Press (OUP)

    Dr Johannes Jaeger

  31. Everything flows: A process perspective on life

    Article • EMBO Reports, August 2015, EMBO

    Dr Johannes Jaeger

  32. Gap gene regulatory dynamics evolve along a genotype network

    Article • August 2015, Cold Spring Harbor Laboratory Press

    Dr Johannes Jaeger

  33. Maternal Co-ordinate Gene Regulation and Axis Polarity in the Scuttle Fly Megaselia abdita

    Article • PLoS Genetics, March 2015, PLOS

    Dr Johannes Jaeger

  34. High-resolution gene expression data from blastoderm embryos of the scuttle fly Megaselia abdita

    Article • Scientific Data, March 2015, Springer Science + Business Media

    Dr Johannes Jaeger

  35. BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology

    Article • BMC Systems Biology, February 2015, Springer Science + Business Media

    Dr Johannes Jaeger, Professor Julio Saez-Rodriguez

  36. The Comet Cometh: Evolving Developmental Systems

    Article • Biological Theory, February 2015, Springer Science + Business Media

    Dr Johannes Jaeger

  37. Quantitative system drift compensates for altered maternal inputs to the gap gene network of the scuttle fly Megaselia abdita

    Article • eLife, January 2015, eLife

    Dr Johannes Jaeger

  38. SuperFly: a comparative database for quantified spatio-temporal gene expression patterns in early dipteran embryos

    Article • Nucleic Acids Research, November 2014, Oxford University Press (OUP)

    Dr Johannes Jaeger

  39. Evolution of early development in dipterans: Reverse-engineering the gap gene network in the moth midge Clogmia albipunctata (Psychodidae)

    Article • Biosystems, September 2014, Elsevier

    Dr Johannes Jaeger

  40. Explanatory Integration Challenges in Evolutionary Systems Biology

    Article • Biological Theory, July 2014, Springer Science + Business Media

    Dr Johannes Jaeger

  41. Bioattractors: dynamical systems theory and the evolution of regulatory processes

    Article • The Journal of Physiology, May 2014, Wiley

    Dr Johannes Jaeger

  42. A Staging Scheme for the Development of the Scuttle Fly Megaselia abdita

    Article • PLOS One, January 2014, PLOS

    Dr Johannes Jaeger

  43. A Staging Scheme for the Development of the Moth Midge Clogmia albipunctata

    Article • PLOS One, January 2014, PLOS

    Dr Johannes Jaeger

  44. Classification of transient behaviours in a time-dependent toggle switch model

    Article • BMC Systems Biology, January 2014, Springer Science + Business Media

    Dr Johannes Jaeger

  45. A quantitative atlas of Even-skipped and Hunchback expression in Clogmia albipunctata (Diptera: Psychodidae) blastoderm embryos

    Article • EvoDevo, January 2014, Springer Science + Business Media

    Dr Johannes Jaeger

  46. Reverse-Engineering Post-Transcriptional Regulation of Gap Genes in Drosophila melanogaster

    Article • PLoS Computational Biology, October 2013, PLOS

    Dr Johannes Jaeger

  47. Lack of tailless leads to an increase in expression variability in Drosophila embryos

    Article • Developmental Biology, May 2013, Elsevier

    Dr Johannes Jaeger

  48. Evolution and expression of BMP genes in flies

    Article • Development Genes and Evolution, April 2013, Springer Science + Business Media

    Dr Johannes Jaeger

  49. Comparative transcriptomics of early dipteran development

    Article • BMC Genomics, January 2013, Springer Science + Business Media

    Dr Johannes Jaeger

  50. Drosophila blastoderm patterning

    Article • Current Opinion in Genetics & Development, December 2012, Elsevier

    Dr Johannes Jaeger

  51. The Inheritance of Process: A Dynamical Systems Approach

    Article • Journal of Experimental Zoology Part B Molecular and Developmental Evolution, October 2012, Wiley

    Dr Johannes Jaeger

  52. Medium-Throughput Processing of Whole Mount In Situ Hybridisation Experiments into Gene Expression Domains

    Article • PLOS One, September 2012, PLOS

    Dr Johannes Jaeger

  53. Efficient Reverse-Engineering of a Developmental Gene Regulatory Network

    Article • PLoS Computational Biology, July 2012, PLOS

    Dr Johannes Jaeger

  54. Life’s Attractors

    Article • January 2012, Springer Science + Business Media

    Dr Johannes Jaeger

  55. A matter of timing and precision

    Article • Molecular Systems Biology, November 2010, EMBO

    Dr Johannes Jaeger

  56. The gap gene network

    Article • Cellular and Molecular Life Sciences, October 2010, Springer Science + Business Media

    Dr Johannes Jaeger

  57. A systematic analysis of the gap gene system in the moth midge Clogmia albipunctata

    Article • Developmental Biology, August 2010, Elsevier

    Dr Johannes Jaeger

  58. Neither fish nor fowl

    Article • BioEssays, June 2010, Wiley

    Dr Johannes Jaeger

  59. Reverse engineering a gene network using an asynchronous parallel evolution strategy

    Article • BMC Systems Biology, March 2010, Springer Science + Business Media

    Dr Johannes Jaeger

  60. Gene Circuit Analysis of the Terminal Gap Gene huckebein

    Article • PLoS Computational Biology, October 2009, PLOS

    Dr Johannes Jaeger

  61. Getting the Measure of Positional Information

    Article • PLoS Biology, March 2009, PLOS

    Dr Johannes Jaeger

  62. Modelling the Drosophila embryo

    Article • Molecular BioSystems, January 2009, Royal Society of Chemistry

    Dr Johannes Jaeger

  63. Parameter estimation and determinability analysis applied to Drosophila gap gene circuits

    Article • BMC Systems Biology, September 2008, Springer Science + Business Media

    Dr Johannes Jaeger

  64. Regulative feedback in pattern formation: towards a general relativistic theory of positional information

    Article • Development, August 2008, The Company of Biologists

    Dr Johannes Jaeger

  65. Known maternal gradients are not sufficient for the establishment of gap domains in Drosophila melanogaster

    Article • Mechanisms of Development, February 2007, Elsevier

    Dr Johannes Jaeger

  66. Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene

    Article • Nature Genetics, September 2006, Springer Science + Business Media

    Dr Johannes Jaeger

  67. On the dynamic nature of positional information

    Article • BioEssays, January 2006, Wiley

    Dr Johannes Jaeger

  68. Reverse Engineering the Gap Gene Network of Drosophila melanogaster

    Article • PLoS Computational Biology, January 2006, PLOS

    Dr Johannes Jaeger

  69. A high-throughput method for quantifying gene expression data from early Drosophila embryos

    Article • Development Genes and Evolution, April 2005, Springer Science + Business Media

    Dr Johannes Jaeger

  70. Pattern formation and nuclear divisions are uncoupled in Drosophila segmentation: comparison of spatially discrete and continuous models

    Article • Physica D Nonlinear Phenomena, October 2004, Elsevier

    Dr Johannes Jaeger

  71. Functional divergence between eyeless and twin of eyeless in Drosophila melanogaster

    Article • Development, August 2004, The Company of Biologists

    Dr Johannes Jaeger

  72. Dynamical Analysis of Regulatory Interactions in the Gap Gene System of Drosophila melanogaster

    Article • Genetics, August 2004, Genetics Society of America

    Dr Johannes Jaeger

  73. Dynamic control of positional information in the early Drosophila embryo

    Article • July 2004, Nature

    Dr Johannes Jaeger

  74. A Cellular Oscillator Model for Periodic Pattern Formation

    Article • Journal of Theoretical Biology, November 2001, Elsevier

    Dr Johannes Jaeger

  75. Molecular basis for the inhibition of Drosophila eye development by Antennapedia

    Article • The EMBO Journal, February 2001, Wiley

    Dr Johannes Jaeger