Posts by Collection

portfolio

publications

1. Kontopoulos, D.-G., and Glykos, N.M. (2013). Pinda: A Web service for detection and analysis of intraspecies gene duplication events. Computer Methods and Programs in Biomedicine 111(3):711-714.
Abstract | Full text | Website | Source code | citation |

1. Morales, A.E., Dong, Y., Brown, T., Baid, K., Kontopoulos, D.-G., Gonzalez, V., Huang, Z., Ahmed, A.-W., Bhuinya, A., Hilgers, L., Winkler, S., Hughes, G., Li, X., Lu, P., Yang, Y., Kirilenko, B.M., Devanna, P., Lama, T.M., Nissan, Y., Pippel, M., Dávalos, L.M., Vernes, S.C., Puechmaille, S.J., Rossiter, S.J., Yossi, Y., Prescott, J.B., Kurth, A., Ray, D.A., Lim, B.K., Myers, E., Teeling, E.C., Banerjee, A., Irving, A.T., and Hiller, M. (2023). Reference-quality bat genomes illuminate adaptations to viral tolerance and disease resistance. Research Square.
Abstract | Full text |

2. Kontopoulos, D.-G., Levesque, D.L., and Hiller, M. (2023). Numerous independent gains of torpor and hibernation across endotherms, linked with adaptation to diverse environments. bioRxiv 2023.12.12.571278.
Abstract | Full text

2. Vlachakis, D., Kontopoulos, D.G., and Kossida, S. (2013). Space Constrained Homology Modelling: The Paradigm of the RNA-Dependent RNA Polymerase of Dengue (Type II) Virus. Computational and Mathematical Methods in Medicine 2013:108910.
Abstract | Full text | Website | Source code | citation |

3. Kontopoulou, T.,, Kontopoulos, D.G., Vaidakis, E., and Mousoulis, G.P. (2015). Adult Kawasaki disease in a European patient: a case report and review of the literature. Journal of Medical Case Reports 9:75.
Abstract | Full text | Dataset | citation |

3. Kontopoulos, D.-G., Patmanidis, I., Barraclough, T., and Pawar, S. (2024). Changes in flexibility but not in compactness underlie the thermal adaptation of prokaryotic adenylate kinases. bioRxiv 2024.09.04.611173.
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4. Kontopoulos, D.G., Vlachakis, D., Tsiliki, G., and Kossida, S. (2016). Structuprint: a scalable and extensible tool for two-dimensional representation of protein surfaces. BMC Structural Biology 16:4.
Abstract | Full text | Website | Source code | citation |

5. Kontopoulos, D.-G., Kontopoulou, T., Ho, H.-C., and García-Carreras, B. (2017). Towards a theoretically informed policy against a rakghoul plague outbreak. The Medical Journal of Australia 207(11):490-494.
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6. Kontopoulos, D.-G., García-Carreras, B., Sal, S., Smith, T.P., and Pawar, S. (2018). Use and misuse of temperature normalisation in meta-analyses of thermal responses of biological traits. PeerJ 6:e4363.
Abstract | Full text | Source code | citation |

7. Kumbhar, R., Vidal-Eychenié, S., Kontopoulos, D.-G., Larroque, M., Larroque, C., Basbous, J., Kossida, S., Ribeyre, C., and Constantinou, A. (2018). Recruitment of ubiquitin-activating enzyme UBA1 to DNA by poly(ADP-ribose) promotes ATR signalling. Life Science Alliance 1(3):e201800096.
Abstract | Full text | citation |

8. García-Carreras, B., Sal, S., Padfield, D., Kontopoulos, D.-G., Bestion, E., Schaum, C.-E., Yvon-Durocher, G., and Pawar, S. (2018). Role of carbon allocation efficiency in the temperature dependence of autotroph growth rates. PNAS 115(31):E7361-E7368.
Abstract | Full text | citation |

9. Kontopoulos, D.-G., van Sebille, E., Lange, M., Yvon-Durocher, G., Barraclough, T.G., and Pawar, S. (2020). Phytoplankton thermal responses adapt in the absence of hard thermodynamic constraints. Evolution 74(4):775-790.
[Top Cited Article 2020-2021 in Evolution]
Abstract | Full text | Data and code | citation |

10. Kontopoulos, D.-G., Smith, T.P., Barraclough, T.G., and Pawar, S. (2020). Adaptive evolution shapes the present-day distribution of the thermal sensitivity of population growth rate. PLOS Biology 18(10):e3000894.
Abstract | Full text | PLOS Showcase page | Code | Data | citation |

11. Kordas, R.L., Pawar, S., Kontopoulos, D.-G., Woodward, G., and O’Gorman, E.J. (2022). Metabolic plasticity can amplify ecosystem responses to global warming. Nature Communications 13:2161.
Abstract | Full text | Data and code | citation |

12. Smith, T.P., Mombrikotb, S., Ransome, E., Kontopoulos, D.-G., Pawar, S., and Bell, T. (2022). Latent functional diversity may accelerate microbial community responses to temperature fluctuations. eLife 11:e80867.
Abstract | Full text | Data and code | citation |

13. Kirilenko, B.M., Munegowda, C., Osipova, E., Jebb, D., Sharma, V., Blumer, M., Morales, A.E., Ahmed, A.-W., Kontopoulos, D.-G., Hilgers, L., Lindblad-Toh, K., Karlsson, E.K., Zoonomia Consortium, and Hiller, M. (2023). Integrating gene annotation with orthology inference at scale. Science 380(6643):eabn3107.
Abstract | Full text | Preprint | Source code | citation |

14. Pawar, S., Huxley, P.J., Smallwood, T.R.C., Nesbit, M.L., Chan, A.H.H., Shocket, M.S., Johnson, L.R., Kontopoulos, D.-G., and Cator, L.J. (2024). Variation in temperature of peak trait performance constrains adaptation of arthropod populations to climatic warming. Nature Ecology & Evolution 8:500-510.
Abstract | Full text | Data and code | citation |

15. Kontopoulos, D.-G., Sentis, A., Daufresne, M., Glazman, N., Dell, A.I., and Pawar, S. (2024). No universal mathematical model for thermal performance curves across traits and taxonomic groups. Nature Communications 15:8855.
Abstract | Full text | Code | Data | citation |

talks

1. Kontopoulos, D.-G., and Glykos, N.M. Pinda: a Web Service for Detection and Analysis of Intraspecies Gene Duplications.

2. Kontopoulos, D.-G., Yvon-Durocher, G., Chen, B., and Pawar, S. Γενικά μοτίβα θερμικής προσαρμογής μεταξύ των ειδών του φυτοπλαγκτού [General patterns of thermal adaptation among phytoplankton].

3. Kontopoulos, D.-G., Yvon-Durocher, G., Allen, A.P., Chen, B., Thomas, M.K., and Pawar, S. Phylogenetic constraints and environmental drivers of thermal adaptation among the phytoplankton.

4. Kontopoulos, D.-G., Yvon-Durocher, G., and Pawar, S. Deep-time macroevolution of thermal sensitivity of growth rate among phytoplankton.

5. Kontopoulos, D.-G., Yvon-Durocher, G., and Pawar, S. Deep-time macroevolution of thermal sensitivity of growth rate among phytoplankton.

6. Kontopoulos, D.-G., Yvon-Durocher, G., and Pawar, S. Niche convergence in the macroevolution of the thermal sensitivity of phytoplankton growth rate.

7. Kontopoulos, D.-G., van Sebille, E., Lange, M., Yvon-Durocher, G., and Pawar, S. Trait correlations vs environmental drivers in the evolution of phytoplankton thermal responses.

1. Trait correlations vs environmental drivers in the evolution of phytoplankton thermal responses.

8. Kontopoulos, D.-G., van Sebille, E., Lange, M., Yvon-Durocher, G., Barraclough, T.G., and Pawar, S. Non-random adaptive evolution of the thermal sensitivity of growth rate among phytoplankton.

9. Kontopoulos, D.-G., Patmanidis, I., Barraclough, T.G., and Pawar, S. Nonsynonymous mutations are more detrimental at high temperatures; a prokaryote-wide study of adenylate kinases.

2. Deep‑time evolution of physiological responses to temperature changes.

3. Deep‑time evolution of biological responses to temperature changes.

10. Kontopoulos, D.-G., Levesque, D.L, and Hiller, M. Physiological, ecological, and genomic underpinnings of daily torpor and hibernation across mammals and birds.

4. Evolution of ecophysiological responses to temperature changes.

11. Kontopoulos, D.-G., Ahmed, A.‑W., Bein, B., and Hiller, M. The impact of phylogenetic diversity on the strength of gene‑ trait associations.

teaching