GAMA Miguel Angel
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miangoar.bsky.social
GAMA Miguel Angel
@miangoar.bsky.social
230 followers 180 following 110 posts
Biologist that navigate in the oceans of diversity through space-time

Protein evolution, metagenomics, AI/ML/DL

Website https://miangoaren.github.io/
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miangoar.bsky.social
GAMA Miguel Angel @miangoar.bsky.social · 10d
🧵1/3 I created this free 37-hour course, distributed across 10 lectures, to introduce AI-based protein design. For more information about the course and its specific topics, please visit the official course page:
miangoar.bsky.social
The 7th lecture is available on YouTube :) We will review how proteins emerge and diversify throughout evolution, considering mutations and molecular interactions
youtu.be/qaypRS8SX5M

Slides
drive.google.com/file/d/1BfQd...

English is available only via auto-translated subtitles
February 1, 2026 at 5:57 PM
Reposted by GAMA Miguel Angel
kacarlab.bsky.social
Our new paper, out today! We resurrected ancient nitrogenases first used by life on Earth 3 billion years ago. We combined synthetic biology and geology & validated their chemical #biosignature in rocks that helps reveal ancient life on Earth!(and beyond!)

Link: www.nature.com/articles/s41...
Resurrected nitrogenases recapitulate canonical N-isotope biosignatures over two billion years - Nature Communications
The study shows that nitrogenase enzymes have maintained stable isotope signatures over billions of years, revealing how ancient microbes shaped Earth’s nitrogen cycle and offering a new experimental ...
www.nature.com
January 30, 2026 at 9:12 PM
Reposted by GAMA Miguel Angel
watchclockwork.com
💪 NEW VIDEO:
Flying over the A-band of an atomic-scale model of a vertebrate muscle sarcomere. Let's explore the molecular mechanics that make your muscles work.

Rendered using @bradyajohnston.bsky.social 's molecular nodes

Model based on the incredible work of the @raunser-lab.bsky.social lab
January 31, 2026 at 3:00 PM
miangoar.bsky.social
The 6th lecture is now available on YouTube :) We’ll review how proteins adopt their 3D shape, how they perform their functions and how their activity is regulated
youtu.be/cZs8XtVYa5A

Slides
drive.google.com/file/d/1TpPj...

English is available only via auto-translated subtitles
January 31, 2026 at 5:55 PM
miangoar.bsky.social
The fifth lecture of the course is now available on YouTube :) We’ll review amino acid chemistry and how we organize and classify proteins
youtu.be/gE6qXwpBP_s

Slides
drive.google.com/file/d/1F99V...

For now, the English version is only available through the automatic translation of the subtitles
January 30, 2026 at 6:51 PM
miangoar.bsky.social
The fourth lecture of the course is now available on YouTube :) We will review how Transformers and modern LLMs work
youtu.be/vUpb6O6T2yQ

Slides
drive.google.com/file/d/1y2Vj...

For now, the English version is only available through the automatic translation of the subtitles.
January 29, 2026 at 6:03 PM
miangoar.bsky.social
The third lecture of the course is now available on YouTube :) We will review how neural networks work.
youtu.be/pAgL7NsCUMU

Slides
drive.google.com/file/d/1cazt...

For now, the English version is only available through the automatic translation of the subtitles.
January 28, 2026 at 6:23 PM
miangoar.bsky.social
The second lecture of the course is now available on YouTube :) We will review what AI is, its subfields and how to train a model.
youtu.be/Xx80O85-5rI

Slides
drive.google.com/file/d/1i-Jo...

For now, the English version is only available through the automatic translation of the subtitles.
January 27, 2026 at 5:03 PM
miangoar.bsky.social
The first lecture of the course is now available on YouTube :)
youtu.be/uMkZzKbnoJI

Slides
drive.google.com/file/d/1uDwe...

For now, the English version is only available through the automatic translation of the subtitles.
January 27, 2026 at 4:20 AM
miangoar.bsky.social
🧵1/3 I created this free 37-hour course, distributed across 10 lectures, to introduce AI-based protein design. For more information about the course and its specific topics, please visit the official course page:
January 22, 2026 at 9:16 PM
Reposted by GAMA Miguel Angel
jennyrohn.bsky.social
Cost of being female lead/corresponding author in biomedical sciences: "[T]he median amount of time spent under review is 7.4%–14.6% longer for female-authored articles than for male-authored articles" even in disciplines where women well-represented. #AcademicSky

journals.plos.org/plosbiology/...
Biomedical and life science articles by female researchers spend longer under review
Women are underrepresented in academia, especially in STEMM fields, at top institutions, and in senior positions. This study analyzes millions of biomedical and life science articles, revealing that f...
journals.plos.org
January 21, 2026 at 2:38 PM
Reposted by GAMA Miguel Angel
milot.bsky.social
My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring!
mirdita.org
Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning
Mirdita Lab builds scalable bioinformatics methods.
mirdita.org
January 20, 2026 at 11:07 AM
Reposted by GAMA Miguel Angel
cjjackson.bsky.social
www.biorxiv.org/content/10.6... most proteins are multi domain but our understanding of how architectures evolve is limited - we mapped 40K chitinases and show a stepwise “grammar” of domain gain/loss and localisation changes that predicts ecological strategy and physiological function.
www.biorxiv.org
January 20, 2026 at 3:20 AM
Reposted by GAMA Miguel Angel
miangoar.bsky.social
I just want to create hype and say that I made a 10-class course to introduce people to AI-driven protein design. It’s around 750 slides and will be freely available for anyone who wants to use them and, most importantly, improve them. Stay tuned :)
October 9, 2025 at 5:59 PM
miangoar.bsky.social
1/2 If you think that the Protein Data Bank is a representative DB, it is not. The data is highly biased. The CATH suggests that there are 1,472 protein folds, yet among the ~600k domains present in the PDB, ~39% are represented by the 10 most abundant folds (AKA superfolds).
January 16, 2026 at 6:35 PM
Reposted by GAMA Miguel Angel
claudiaalcar.bsky.social
Thrilled to introduce TEDLH, a library of profile HMMs built from TED’s structure-derived domain annotations of the AFDB.
Explore 765K HMMs capturing CATH superfamily diversity.

www.biorxiv.org/content/10.6...
Construction of TEDLH from TED domain annotations.
January 9, 2026 at 8:44 AM
Reposted by GAMA Miguel Angel
hecklab.bsky.social
🕷️Spiders in your blood? Don’t worry, these are protein molecules of C4BP protein, part of your immune system. Just like real spiders, they grab prey with their “legs.” Watch them in action! Intrigued, check the paper of @tkadava.bsky.social doi.org/10.1016/j.mc... @bijvoet-centre.bsky.social
September 4, 2025 at 2:27 PM
Reposted by GAMA Miguel Angel
archaeal.bsky.social
youtu.be/Jy_boPdY0zo?...
The Origins of Complex Life | Searching for the Asgards
YouTube video by Schmidt Ocean
youtu.be
November 26, 2025 at 8:29 PM
Reposted by GAMA Miguel Angel
dzyla.bsky.social
Proteins are dynamic structures, but structural biology often shows them as static snapshots. Inspired by long-exposure photography and generative art, I built ProteinCHAOS, an artistic tool inspired by molecular dynamics to capture protein flexibility over time, much like long-exposure images.
November 23, 2025 at 11:18 PM
Reposted by GAMA Miguel Angel
hansonmark.bsky.social
We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing:

a 🧵 1/n

Drain: arxiv.org/abs/2511.04820
Strain: direct.mit.edu/qss/article/...
Oligopoly: direct.mit.edu/qss/article/...
A table showing profit margins of major publishers. A snippet of text related to this table is below. 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. A figure detailing the drain on researcher time. 1. The four-fold drain 1.2 Time The number of papers published each year is growing faster than the scientific workforce, with the number of papers per researcher almost doubling between 1996 and 2022 (Figure 1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material has aligned well with the competitive prestige culture in which publications help secure jobs, grants, promotions, and awards. To the extent that this growth is driven by a pressure for profit, rather than scholarly imperatives, it distorts the way researchers spend their time. The publishing system depends on unpaid reviewer labour, estimated to be over 130 million unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of peer-review for decades, but the scale of the problem is now worse, with editors reporting widespread difficulties recruiting reviewers. The growth in publications involves not only the authors’ time, but that of academic editors and reviewers who are dealing with so many review demands. Even more seriously, the imperative to produce ever more articles reshapes the nature of scientific inquiry. Evidence across multiple fields shows that more papers result in ‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow progress until one considers how it affects researchers’ time. While rewards remain tied to volume, prestige, and impact of publications, researchers will be nudged away from riskier, local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized. What looks like productivity often masks intellectual exhaustion built on a demoralizing, narrowing scientific vision. A table of profit margins across industries. The section of text related to this table is below: 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. The costs of inaction are plain: wasted public funds, lost researcher time, compromised scientific integrity and eroded public trust. Today, the system rewards commercial publishers first, and science second. Without bold action from the funders we risk continuing to pour resources into a system that prioritizes profit over the advancement of scientific knowledge.
November 11, 2025 at 11:52 AM
miangoar.bsky.social
I strongly recommend making cat-based diagrams to illustrate complex topics in protein science: "Figure 4 considers [...] invariance and equivariance with respect to translations and rotations in 3D. For illustration purposes, the figure includes a series of cat cartoons in 2D."
October 24, 2025 at 5:47 AM
miangoar.bsky.social
I just want to create hype and say that I made a 10-class course to introduce people to AI-driven protein design. It’s around 750 slides and will be freely available for anyone who wants to use them and, most importantly, improve them. Stay tuned :)
October 9, 2025 at 5:59 PM
Reposted by GAMA Miguel Angel
claudiaalcar.bsky.social
Happy to share Piecing Together the History of Protein Folds From a Fragmented Evolutionary Record 🧪
It appears as part of a Special Section in @genomebiolevol.bsky.social organized by @cpuentelelievre.bsky.social @proteinmechanic.bsky.social and J. Douglas

doi.org/10.1093/gbe/...
Piecing Together the History of Protein Folds From a Fragmented Evolutionary Record
Abstract. Protein folds are structural units defined by the number, type, arrangement, and orientation of their core secondary structural elements. The uni
doi.org
September 15, 2025 at 7:52 AM
Reposted by GAMA Miguel Angel
evodivmet.bsky.social
🫡
September 12, 2025 at 1:10 AM
Reposted by GAMA Miguel Angel
sberry.bsky.social
This is a very cool ancestral reconstruction study by @krishnareddy.bsky.social et al. that I recommend reading! @rachellegaudet.bsky.social and I thought it was so interesting that we wrote a News & Views about it, check it out: rdcu.be/eCfyl
August 26, 2025 at 4:28 AM