| Homepage | https://himmellab.org |
| ORCiD | https://orcid.org/0000-0001-7876-6960 |
| Google Scholar | https://scholar.google.com/citations?user=mrkxmMUAAAAJ&hl=en |
In Fall '26 the Himmel Lab will open at NJIT Biological Sciences. I'm beyond stoked!
Interested in a PhD/postdoc in the function/evolution/origins of the senses (computation or experimentation)? Message me and come join a great department in the NY metro! Sharing is appreciated. Info: himmellab.org
I'll be at the European Symposium for Insect Taste and Olfaction and the CSHL Neurobiology of Drosophila meetings later this year, if anyone wants to meet up in person.
Looking for the last universal common ancestor of all living organisms https://phys.org/news/2023-11-universal-common-ancestor.html
ATP synthase evolution on a cross-braced dated tree of life: Tara Mahendrarajah et al. https://www.nature.com/articles/s41467-023-42924-w
"the ancestors of current #archaea lived between 3.37 and 3.95 billion years ago. This makes it younger than the ancestor of all #bacteria... This suggests that earlier archaea either died out, or they live somewhere hidden on Earth where we have not found them yet"
LUCA, the "last universal common ancestor" of all living organisms, lived 4.32–4.52 billion years ago, according to a study from NIOZ biologists Tara Mahendrarajah and senior author Anja Spang, with collaborating partners from Universities in Bristol, Hungary, and Tokyo. Their research is published in Nature Communications.
Now out in Current Biology - our attempt at detecting protein homologs in the post-protein folding age.
Insect ORs and GRs are particularly difficult to work with because of rapid evolution and huge sequence divergence. By combining structure and sequence based searches, we surprisingly found homologs across the tree of life. Cryptic proteins as old as LUCA?
https://doi.org/10.1016/j.cub.2023.10.008
#phylogenetics #alphafold #evolution #ionchannels #olfaction #smell #gustation #taste #drosophila #asgard #LUCA
Structural phylogenetics -- a great preprint now out by Dave Moi et al, describing their elegant approach and implementation.
We were very lucky to be able to work with Foldtree, and Dave, on our recent 7TMIC paper, prior to Foldtree's release. We found it very informative when working with an extremely difficult protein superfamily!
https://www.biorxiv.org/content/10.1101/2023.09.19.558401v2
#phylogenetics #alphafold #foldseek #bioinformatics #evolution
Another great variation on alpha fold….I am still reeling from the structural insights that are now possible…very cool!
Latest preprint with @[email protected] studying insect OR evolution: we've found homologs across the entire tree of life! Insect receptors are just a majorly expanded branch of a 4 billion year old protein superfamily...
https://doi.org/10.1101/2023.08.30.555482
#phylogenetics #alphafold #esm #huggingface #LECA #LUCA #7TMIC #chemosensation #smell #taste #olfaction #insects #evolution #neuroscience
MSA diversity is key for AlphaFold2's accuracy. Larger databases == better results. So, we generated MSAs from 22 peta-bytes of SRA data and show that ColabFold could have improved from rank 11 to 3 at CASP15.
Congratulations to my undergrad students Sewon Lee and Gyuri Kim who did the work during their internship in only 6 months with help of Eli Levy Karin, @milotmirdita, Sukhwan Park, Artem Babaian, Rayan Chikhi and Andriy Kryshtafovych.
📄 https://www.biorxiv.org/content/10.1101/2023.07.10.548308v1
💾 https://doi.org/10.5281/zenodo.8126538
Lukas VFN 🇪🇺
Marc Robinson-Rechavi
Josh Brickman
Jennifer J. Bussell Ph.D.
Martin Steinegger