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Todd Oakley

🧵 New paper! We’re excited to release OPTICS: software that immediately predicts color sensitivity from any opsin protein sequence. In other words: give OPTICS any opsin sequence, and it predicts the wavelength of light the pigment is most sensitive to 🌈👁️ academic.oup.com/mbe/advance-...

Accessible and Robust Machine Learning Approaches to Improve the Opsin Genotype-Phenotype MapAbstract. Predicting phenotypes from genetic variation is a central challenge in biology. Here, machine learning (ML) offers great promise, but its use isacademic.oup.com
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2 прямых ответов · 11 сообщений

Todd Oakley

We are on a long road toward a big goal: predicting phenotype from genotype For vision, one key phenotype we are starting with is spectral sensitivity - the color of light a visual pigment “sees” best

Ответ для Todd Oakley
Todd Oakley

The story actually began with a failed grant proposal 😅 Even though the proposal was never funded, it forced us to think hard about what the field needed: better organized data, better tools, and more accessible ways to predict functions from gene sequences

Ответ для Todd Oakley
Todd Oakley

We started building the Visual Physiology Opsin Database, bringing together opsins and measured visual pigment sensitivities, giving us training data for machine learning. Published with collaborators from GW who built deepBreaks, the engine that powers OPTICS academic.oup.com/gigascience/...

Discovering genotype–phenotype relationships with machine learning and the Visual Physiology Opsin Database (VPOD)AbstractBackground. Predicting phenotypes from genetic variation is foundational for fields as diverse as bioengineering and global change biology, highligacademic.oup.com
Ответ для Todd Oakley
Todd Oakley

First author Seth Frazer has also built a very nice interface for exploring VPOD here: visphys.eemb.ucsb.edu It makes the database much easier to search, visualize, and use. If you know of data we missed, you can upload it there, and we will verify and add it to the next version

VPOD Explorervisphys.eemb.ucsb.edu
Ответ для Todd Oakley
Todd Oakley

Now we are releasing the Opsin Phenotype Tool for Inference of Color Sensitivity OPTICS 🎉 The most flexible way to use it is in Python, and Seth Frazer has done a terrific job with the documentation. github.com/VisualPhysio...

GitHub - VisualPhysiologyDB/optics: An open-source tool that predicts the Opsin Phenotype (λmax) from unaligned opsin amino-acid sequences.An open-source tool that predicts the Opsin Phenotype (λmax) from unaligned opsin amino-acid sequences. - VisualPhysiologyDB/opticsgithub.com
Ответ для Todd Oakley
Ответ для Todd Oakley
Todd Oakley

Why are we excited? Because this gives us a practical genotype–phenotype map for opsins. We can now make informed predictions about visual sensitivity very quickly and easily, even when physiology is hard to measure directly.

Ответ для Todd Oakley
Todd Oakley

Colleagues around the world are already using these approaches to predict opsin phenotypes in krill, fishes, and other amazing organisms. It is opening the door to asking how visual systems evolve across environments and across the tree of life. 🌊🐟🦐

Ответ для Todd Oakley
Todd Oakley

We are also using simulations of opsin evolution to ask how things like epistasis shape phenotypic diversity. In other words: how do molecular changes interact with each other to affect how visual systems evolve?

Ответ для Todd Oakley
Todd Oakley

OPTICS is out now, and we’re excited to see what people do with it. Stay tuned for more developments — and please get in touch if you have ideas, questions, cool opsins, or organisms with mysterious visual worlds! 🌈👁️✨

Jo Wolfe, PhD

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