Proto Bioengineering
@protobio.bsky.social
Learn to code for science.
"Everything simple is false. Everything complex is unusable." - Paul Valery
Learn at https://medium.com/@protobioengineering
(Banner: Nicolas Thomas, Unsplash)
"Everything simple is false. Everything complex is unusable." - Paul Valery
Learn at https://medium.com/@protobioengineering
(Banner: Nicolas Thomas, Unsplash)
Reposted by Proto Bioengineering
My first editorial in @science.org was published today: what to do (and, importantly, what NOT to do) when your grants are suddenly cut or research funding is uncertain. Please read and share!
#AcademicSky #Science #Astronomy
www.science.org/doi/10.1126/...
#AcademicSky #Science #Astronomy
www.science.org/doi/10.1126/...
Weathering budget cuts: Lessons from NASA
The current uncertainty and cuts to science funding affect universities, research facilities, and laboratories across the United States, but this situation is not unprecedented. Under pressure to fund...
www.science.org
January 8, 2026 at 11:28 PM
My first editorial in @science.org was published today: what to do (and, importantly, what NOT to do) when your grants are suddenly cut or research funding is uncertain. Please read and share!
#AcademicSky #Science #Astronomy
www.science.org/doi/10.1126/...
#AcademicSky #Science #Astronomy
www.science.org/doi/10.1126/...
Reposted by Proto Bioengineering
Celebrating 25 years of Xenbase—the world’s largest database for African clawed frog (Xenopus laevis) and tadpole research. Learn how Aaron Zorn, PhD, and team are driving breakthroughs in genetics and regenerative medicine: scienceblog.cincinnatichildrens.org/25-years-lat...
@xenbase.bsky.social
@xenbase.bsky.social
25 Years Later, Xenbase Still Supporting Scientific Leaps - Research Horizons
scienceblog.cincinnatichildrens.org
January 6, 2026 at 9:19 PM
Celebrating 25 years of Xenbase—the world’s largest database for African clawed frog (Xenopus laevis) and tadpole research. Learn how Aaron Zorn, PhD, and team are driving breakthroughs in genetics and regenerative medicine: scienceblog.cincinnatichildrens.org/25-years-lat...
@xenbase.bsky.social
@xenbase.bsky.social
Reposted by Proto Bioengineering
⏰ Apply to Summer by Design 2026!
This program for Ph.D. students and postdocs, running June 8–17 in Toronto, explores the full technology translation continuum in #RegenerativeMedicine.
Gain the skills to take innovations from the lab to patient impact. ✨
🔗 stemcellnetwork.ca/training/wor...
This program for Ph.D. students and postdocs, running June 8–17 in Toronto, explores the full technology translation continuum in #RegenerativeMedicine.
Gain the skills to take innovations from the lab to patient impact. ✨
🔗 stemcellnetwork.ca/training/wor...
January 6, 2026 at 7:52 PM
⏰ Apply to Summer by Design 2026!
This program for Ph.D. students and postdocs, running June 8–17 in Toronto, explores the full technology translation continuum in #RegenerativeMedicine.
Gain the skills to take innovations from the lab to patient impact. ✨
🔗 stemcellnetwork.ca/training/wor...
This program for Ph.D. students and postdocs, running June 8–17 in Toronto, explores the full technology translation continuum in #RegenerativeMedicine.
Gain the skills to take innovations from the lab to patient impact. ✨
🔗 stemcellnetwork.ca/training/wor...
Speaking of AI, check out AlphaFold, a database of protein structures that have been successfully guessed by AI (and regular experiments). One obstacle in science is knowing how the trillions of proteins in us do their jobs or how they're shaped. AI is helping with that. #ai
alphafold.ebi.ac.uk
alphafold.ebi.ac.uk
AlphaFold Protein Structure Database
AlphaFold Protein Structure Database
alphafold.ebi.ac.uk
January 6, 2026 at 8:55 PM
Speaking of AI, check out AlphaFold, a database of protein structures that have been successfully guessed by AI (and regular experiments). One obstacle in science is knowing how the trillions of proteins in us do their jobs or how they're shaped. AI is helping with that. #ai
alphafold.ebi.ac.uk
alphafold.ebi.ac.uk
We're going to steal ML and AI back from the grifters and actually use it for science, so help me, God. #science #learntocode #biomedicalengineering #bioinformatics
AI guys are like we can’t use it to cure cancer but we can suck all the joy and purpose out of life so that dying isn’t sad
January 6, 2026 at 8:29 PM
We're going to steal ML and AI back from the grifters and actually use it for science, so help me, God. #science #learntocode #biomedicalengineering #bioinformatics
Reposted by Proto Bioengineering
A modular organ-on-a-chip system enables precise simulation of drug-induced muscle and kidney injury, allowing real-time observation of inter-organ interactions and toxic responses in a lab setting. doi.org/hbhxsq
Organ-on-a-chip simulates drug-triggered muscle and kidney injury
Rhabdomyolysis is a condition in which muscle damage—often caused by drug intake—can lead to impaired kidney function and acute kidney failure.
medicalxpress.com
January 6, 2026 at 4:30 PM
A modular organ-on-a-chip system enables precise simulation of drug-induced muscle and kidney injury, allowing real-time observation of inter-organ interactions and toxic responses in a lab setting. doi.org/hbhxsq
Free online textbook for learning computation genomics in R. Covers beginner R, ChIP-seq, RNA-seq, DNA methylation, and more.
compgenomr.github.io/book/
#genomics #r #learntocode #biomedicalengineering #dna #rna
compgenomr.github.io/book/
#genomics #r #learntocode #biomedicalengineering #dna #rna
Computational Genomics with R
A guide to computationa genomics using R. The book covers fundemental topics with practical examples for an interdisciplinery audience
compgenomr.github.io
January 6, 2026 at 7:24 PM
Free online textbook for learning computation genomics in R. Covers beginner R, ChIP-seq, RNA-seq, DNA methylation, and more.
compgenomr.github.io/book/
#genomics #r #learntocode #biomedicalengineering #dna #rna
compgenomr.github.io/book/
#genomics #r #learntocode #biomedicalengineering #dna #rna
Which programming language should you actually learn? This is like asking whether you should learn Spanish, French, or Cantonese. It is all relative, but this article will help you finally decide.
medium.com/@protobioeng...
#learntocode #biomedicalengineering #science #gradschool
medium.com/@protobioeng...
#learntocode #biomedicalengineering #science #gradschool
Which Programming Language Should You Actually Learn?
The final article to settle the argument.
medium.com
January 5, 2026 at 5:35 PM
Which programming language should you actually learn? This is like asking whether you should learn Spanish, French, or Cantonese. It is all relative, but this article will help you finally decide.
medium.com/@protobioeng...
#learntocode #biomedicalengineering #science #gradschool
medium.com/@protobioeng...
#learntocode #biomedicalengineering #science #gradschool
Hey, yo, you can shoot lasers at cancer to tell if its cancer or not. Between this and MR spectroscopy, there are avenues for getting better at detecting cancer without even opening a person up. #medicine #medicalimaging #oncology #biomedicalengineering
How do melanomas vs non-melanoma carcinomas reflect laser signals? New research shows each produces distinguishable patterns.
Free access til Feb 1: www.dl.begellhouse.com/journals/648...
#SkinCancerDetection #BiomedicalOptics
Free access til Feb 1: www.dl.begellhouse.com/journals/648...
#SkinCancerDetection #BiomedicalOptics
January 5, 2026 at 5:27 PM
Hey, yo, you can shoot lasers at cancer to tell if its cancer or not. Between this and MR spectroscopy, there are avenues for getting better at detecting cancer without even opening a person up. #medicine #medicalimaging #oncology #biomedicalengineering
Reposted by Proto Bioengineering
This was thought provoking 🧠
Doesn't invalidate computational approaches but a clear-eyed view of the limits/assumptions, and an eloquent description of why neurobiology is endlessly fascinating
Doesn't invalidate computational approaches but a clear-eyed view of the limits/assumptions, and an eloquent description of why neurobiology is endlessly fascinating
When we try to formalize a neuron computationally, we don't translate biology into code—we perform a violent collapse.
www.ocrampal.com/what-a-neuro...
#philosophy #science #psychology #AI #intelligence #physics #biology #philmind #philsci #philsky #philpsy #neurosky #neuroskyence
www.ocrampal.com/what-a-neuro...
#philosophy #science #psychology #AI #intelligence #physics #biology #philmind #philsci #philsky #philpsy #neurosky #neuroskyence
What a Neuron Teaches Us About Computation's Limits
When we try to formalize a neuron computationally, we don't translate biology into code—we perform a violent collapse. We lock causation into fixed arrows when biology lives in causal ambiguity. We sy...
www.ocrampal.com
January 4, 2026 at 5:02 PM
This was thought provoking 🧠
Doesn't invalidate computational approaches but a clear-eyed view of the limits/assumptions, and an eloquent description of why neurobiology is endlessly fascinating
Doesn't invalidate computational approaches but a clear-eyed view of the limits/assumptions, and an eloquent description of why neurobiology is endlessly fascinating
When we teach, we multiply not only the people around us but ourselves. #scienceeducation #teaching #biology #biomedicalengineering
January 4, 2026 at 4:35 PM
When we teach, we multiply not only the people around us but ourselves. #scienceeducation #teaching #biology #biomedicalengineering
People in mosh pits end up behaving like particles in fluids, with vortices and other stereotyped patterns. #fluiddynamics #neuroscience #engineering #psychology
www.youtube.com/shorts/1weOV...
www.youtube.com/shorts/1weOV...
The physics of mosh pits
YouTube video by The Rest Is Science
www.youtube.com
January 3, 2026 at 10:14 PM
People in mosh pits end up behaving like particles in fluids, with vortices and other stereotyped patterns. #fluiddynamics #neuroscience #engineering #psychology
www.youtube.com/shorts/1weOV...
www.youtube.com/shorts/1weOV...
Reposted by Proto Bioengineering
I have been exploring neural circuits of emotion in the brain lately, which led me to write this primer on the amygdala over the holidays!
Amygdala Structure, Function, and Clinically Relevant Pathways
This content is also available on my website: https://logancollinsblog.com/2026/01/02/amygdala-structure-function-and-clinically-relevant-pathways/
substack.com
January 3, 2026 at 12:32 AM
I have been exploring neural circuits of emotion in the brain lately, which led me to write this primer on the amygdala over the holidays!
AI that speeds up science > AI that replaces artists
#biology #biomedicalengineering #ai #machinelearning
#biology #biomedicalengineering #ai #machinelearning
BioTrouble: A Multi-Agent Workflow for Troubleshooting Molecular Biology Techniques [new]
AI workflow aids researchers in resolving molecular biology experimental issues, leveraging RAG and learning from user interactions.
AI workflow aids researchers in resolving molecular biology experimental issues, leveraging RAG and learning from user interactions.
January 3, 2026 at 4:25 PM
AI that speeds up science > AI that replaces artists
#biology #biomedicalengineering #ai #machinelearning
#biology #biomedicalengineering #ai #machinelearning
What keeps the world spinning is the niche little work done day to day. Chipping away at problems, big or small, makes us and our world better. If it seems like a waste of time, remember that "our work works on us more than we work on it" (Alex Hormozi, paraphrased). #work
medium.com/westenberg/t...
medium.com/westenberg/t...
The Rime of the Ancient Maintainer
Why Maintenance Culture Matters
medium.com
January 1, 2026 at 8:50 PM
What keeps the world spinning is the niche little work done day to day. Chipping away at problems, big or small, makes us and our world better. If it seems like a waste of time, remember that "our work works on us more than we work on it" (Alex Hormozi, paraphrased). #work
medium.com/westenberg/t...
medium.com/westenberg/t...
Reposted by Proto Bioengineering
Now seems as good a time as any to remind people that the guy who wrote “Pretty Fly For a White Guy” earned a PhD in molecular biology.
We all contain multitudes.
We all contain multitudes.
December 31, 2025 at 2:24 AM
Now seems as good a time as any to remind people that the guy who wrote “Pretty Fly For a White Guy” earned a PhD in molecular biology.
We all contain multitudes.
We all contain multitudes.
Reposted by Proto Bioengineering
Have genome data that needs assembling? The Galaxy Training Network offers a comprehensive collection of tutorials to guide you through every step in an accessible, browser-based environment.
training.galaxyproject.org/training-mat...
training.galaxyproject.org/training-mat...
Assembly / Tutorial List
DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' ...
training.galaxyproject.org
December 9, 2025 at 12:43 PM
Have genome data that needs assembling? The Galaxy Training Network offers a comprehensive collection of tutorials to guide you through every step in an accessible, browser-based environment.
training.galaxyproject.org/training-mat...
training.galaxyproject.org/training-mat...
Reposted by Proto Bioengineering
USC biomedical engineers have found a way to make a solid tumor paint a target on its own back in order to train the body’s immune system to find and destroy it. Learn more: https://viterbischool.usc.edu/news/2025/11/tricking-tumors-into-marking-themselves-for-destruction/
Tricking Tumors into Marking Themselves for Destruction - USC Viterbi | School of Engineering
New research from the USC Viterbi School of Engineering harnesses focused ultrasound to reprogram solid tumors, making them more effective targets for immune cells.
viterbischool.usc.edu
December 30, 2025 at 6:08 PM
USC biomedical engineers have found a way to make a solid tumor paint a target on its own back in order to train the body’s immune system to find and destroy it. Learn more: https://viterbischool.usc.edu/news/2025/11/tricking-tumors-into-marking-themselves-for-destruction/
Reposted by Proto Bioengineering
The National Institutes of Health has agreed to evaluate grant applications that were wrongfully frozen due to the Trump administration’s ideological purge of biomedical research.
December 30, 2025 at 2:51 PM
The National Institutes of Health has agreed to evaluate grant applications that were wrongfully frozen due to the Trump administration’s ideological purge of biomedical research.
A scientific image forgery detection competition is going on on Kaggle for the next two weeks. Check out the code that people are writing to automate the detection of scientific fraud. Recod.ai is giving away $55,000 in prizes, which is neato.
www.kaggle.com/competitions...
#science #forensics #ml
www.kaggle.com/competitions...
#science #forensics #ml
Recod.ai/LUC - Scientific Image Forgery Detection
Develop methods that can accurately detect and segment copy-move forgeries within biomedical research images.
www.kaggle.com
December 30, 2025 at 4:24 PM
A scientific image forgery detection competition is going on on Kaggle for the next two weeks. Check out the code that people are writing to automate the detection of scientific fraud. Recod.ai is giving away $55,000 in prizes, which is neato.
www.kaggle.com/competitions...
#science #forensics #ml
www.kaggle.com/competitions...
#science #forensics #ml
Reposted by Proto Bioengineering
This review presents a framework for high‑performance artificial #SensorySystems, spanning #nanomaterial processing to device integration, highlighting coating/printing methods, human‑sense applications, and future #AI integration.
#OpenAccess in #IJEM: doi.org/10.1088/2631...
#OpenAccess in #IJEM: doi.org/10.1088/2631...
December 28, 2025 at 2:34 PM
This review presents a framework for high‑performance artificial #SensorySystems, spanning #nanomaterial processing to device integration, highlighting coating/printing methods, human‑sense applications, and future #AI integration.
#OpenAccess in #IJEM: doi.org/10.1088/2631...
#OpenAccess in #IJEM: doi.org/10.1088/2631...
Reposted by Proto Bioengineering
1/ 🧠 Is there a "hidden" brain signal that protects against age-related memory decline? Our new paper in @neurobiology-aging.bsky.social explores how periodic (oscillatory) and aperiodic (non-oscillatory) EEG activity may be a key biomarker for cognitive resilience in older adults. 🧵
December 29, 2025 at 6:22 PM
1/ 🧠 Is there a "hidden" brain signal that protects against age-related memory decline? Our new paper in @neurobiology-aging.bsky.social explores how periodic (oscillatory) and aperiodic (non-oscillatory) EEG activity may be a key biomarker for cognitive resilience in older adults. 🧵
Reposted by Proto Bioengineering
🧬 Key Biological Databases in Bioinformatics
From GenBank & UniProt to KEGG, GEO, and Ensembl — these databases power modern genomics, transcriptomics, and multi-omics research.
Perfect for students, researchers & early-career scientists 👩🔬👨🔬
#Bioinformatics #Genomics #MolecularBiology #PhDLife
From GenBank & UniProt to KEGG, GEO, and Ensembl — these databases power modern genomics, transcriptomics, and multi-omics research.
Perfect for students, researchers & early-career scientists 👩🔬👨🔬
#Bioinformatics #Genomics #MolecularBiology #PhDLife
December 29, 2025 at 4:11 PM
🧬 Key Biological Databases in Bioinformatics
From GenBank & UniProt to KEGG, GEO, and Ensembl — these databases power modern genomics, transcriptomics, and multi-omics research.
Perfect for students, researchers & early-career scientists 👩🔬👨🔬
#Bioinformatics #Genomics #MolecularBiology #PhDLife
From GenBank & UniProt to KEGG, GEO, and Ensembl — these databases power modern genomics, transcriptomics, and multi-omics research.
Perfect for students, researchers & early-career scientists 👩🔬👨🔬
#Bioinformatics #Genomics #MolecularBiology #PhDLife
Reposted by Proto Bioengineering
The paper submission deadline for the 11th International Conference on Biomedical Robotics and Biomechatronics (BioRob 2026) is coming up fast.
Don't miss the January 10th deadline!
Learn more and submit your paper: https://2026.ieeebiorob.org/call-for-papers/?utm_source=bluesky&utm_medium=social
Don't miss the January 10th deadline!
Learn more and submit your paper: https://2026.ieeebiorob.org/call-for-papers/?utm_source=bluesky&utm_medium=social
December 28, 2025 at 6:48 PM
The paper submission deadline for the 11th International Conference on Biomedical Robotics and Biomechatronics (BioRob 2026) is coming up fast.
Don't miss the January 10th deadline!
Learn more and submit your paper: https://2026.ieeebiorob.org/call-for-papers/?utm_source=bluesky&utm_medium=social
Don't miss the January 10th deadline!
Learn more and submit your paper: https://2026.ieeebiorob.org/call-for-papers/?utm_source=bluesky&utm_medium=social
A Dozen Resources for Learning Bioinformatics from Scratch:
medium.com/@protobioeng...
#bioinformatics #python #biology #biomedicalengineering #learntocode #r #tidyverse
medium.com/@protobioeng...
#bioinformatics #python #biology #biomedicalengineering #learntocode #r #tidyverse
A Dozen Resources for Learning Bioinformatics from Scratch
How and where to learn bioinformatics, from big topics to small.
medium.com
December 28, 2025 at 8:45 PM
A Dozen Resources for Learning Bioinformatics from Scratch:
medium.com/@protobioeng...
#bioinformatics #python #biology #biomedicalengineering #learntocode #r #tidyverse
medium.com/@protobioeng...
#bioinformatics #python #biology #biomedicalengineering #learntocode #r #tidyverse