natural philosophy on a laptop
From the diverse life forms we observe on Earth, a question often arises: what generates this biodiversity?
My curiosity lies on the other side of the coin: what limits biodiversity?
One factor is the process of development that creates these organisms in the first place. But exactly how - and are findings in model systems generally shared across Earth’s diverse life forms?
As a doctoral researcher at the Max Planck Institute for Biology (Tübingen, Germany), I seek answers to these biological questions through bioinformatics research using brown algae as a model system.
bioinformatics
Contributions to open-source bioinformatic software applications.
orthologr provides a framework to perform large scale comparative genomics studies with R.
myTAI introduces procedures summarised under the term evolutionary transcriptomics to integrate gene age information into classical gene expression analysis in R.
phylomapr enables quick retrieval of precomputed gene age maps (phylomaps) in R.
GenEra estimates gene-family founder events (i.e., the age of the last common ancestor of protein-coding gene families) through the reimplementation of genomic phylostratigraphy at the tree of life scale.
…in the field
I am not just bound to my computer. Here are some of my biological adventures.
Algal sample collection in St. Abbs, Scotland.
publications
Barrera-Redondo, J., Lotharukpong, J. S., Drost, H-G., & Coelho, S. M. (2023). Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra. Genome Biology, 24(1), 54.
Manley, B. F., Lotharukpong, J. S., Barrera-Redondo, J., Llewellyn, T., Yildirir, G., Sperschneider, J., … & Dallaire, A. (2023). A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis. G3: Genes, Genomes, Genetics, 13(6), jkad077.
Lotharukpong, J. S., Zheng, M., Luthringer, R., Liesner, D., Drost, H-G., & Coelho, S. M. (2024). A transcriptomic hourglass in brown algae. Nature 635, 129–135
See also on google scholar
media
The Node (https://thenode.biologists.com/):
European Reference Genome Atlas (ERGA) (https://www.erga-biodiversity.eu/):
Max Planck Press Office:
Braunalgen entwickeln sich nach Sanduhr-Modell (see also in English)