# Biology Published articles for Biology. This is one page of public article previews, not the complete archive. Follow Next page to continue. Summaries are not the original full articles. ## PottsMPNN uses machine learning to improve computational protein design DevFeed: [PottsMPNN uses machine learning to improve computational protein design]() Original publisher: [Read original article]() Author: Lillian Eden | Department of Biology Published: 2026-08-27T19:20:00Z Content type: news Language: en Sources: [MIT AI News]() Topics: [Machine learning](), [Artificial Intelligence]() Tags: [ai](), [ai-in-biology](), [amino-acids](), [amy-keating](), [artificial-intelligence](), [biological-engineering](), [biology](), [computational-protein-design](), [computer-science-and-technology](), [foster-birnbaum](), [machine-learning](), [mit-department-of-biology](), [native-sequence-recovery](), [novel-protein-design](), [pottsmpnn](), [proteins](), [research](), [school-of-engineering](), [school-of-science]() ### AI overview Researchers developed PottsMPNN, a machine-learning framework for computational protein design that incorporates physical principles governing protein structure and stability. The framework evaluates generated sequences by their likelihood of folding into desired structures and by its ability to predict mutation effects, rather than by how closely they match naturally occurring sequences. ### Source excerpt A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature. ## MCH2022: DNA and GPS/Galileo/GNSS Talks DevFeed: [MCH2022: DNA and GPS/Galileo/GNSS Talks]() Original publisher: [Read original article]() Published: 2022-07-27T11:41:11Z Content type: article Language: en Sources: [Bert Hubert's writings]() Topics: [navigation](), [Hacking]() Tags: [biology](), [dna](), [event](), [gnss](), [gps](), [talks](), [video]() ### AI overview A personal recap of MCH2022, a large Dutch hacker community campsite event, featuring two talks: one introducing DNA and genome editing, and another explaining GPS, Galileo, BeiDou, GLONASS, and the galmon.eu satellite-monitoring project. ### Source excerpt (scroll down for my two talks if you are in a hurry) As I write this I'm suffering from severe post-camp blues. Every four years the Dutch hacker community organizes a stupendously large multi-day campsite event, with ample international help. To a large extent, "everyone" is there. And this time, like every time, people who originally decided they could not make it.. show up by day two. Because the pull is just too strong. ## SkewDB: an open database of GC and other microbial skews DevFeed: [SkewDB: an open database of GC and other microbial skews]() Original publisher: [Read original article]() Published: 2021-08-30T12:19:18Z Content type: article Language: en Sources: [Bert Hubert's writings]() Topics: [Database](), [Replication](), [Open Source](), [Software]() Tags: [biology](), [database](), [dna](), [open-source](), [replication](), [software]() ### AI overview This article introduces SkewDB, an open downloadable database containing GC skew and other nucleotide skews for 28,000 bacterial chromosomes from the NCBI genomes service. It explains how GC skew relates to DNA replication and describes the database's potential for exploring and testing hypotheses. ### Source excerpt Hello and welcome to this introduction of the SkewDB. This open (downloadable) database contains details of GC skew, plus a dozen other skews, for all 28,000 bacterial chromosomes available through the NCBI genomes service. The database is created using the open source Antonie DNA software. There is also an online viewer that includes graphs. GC skew is the phenomenon where almost all circular chromosomes tend to have near equal amounts of G and C nucleotides, per strand, but where the leading replication strand contains an excess of G, and the lagging replication strand has an excess of C nucleotides. ## Why You Cannot Simply Print a Safe mRNA Vaccine DevFeed: [Why You Cannot Simply Print a Safe mRNA Vaccine]() Original publisher: [Read original article]() Published: 2021-03-30T13:46:36Z Content type: opinion Language: en Sources: [Bert Hubert's writings]() Topics: [processing]() Tags: [automated](), [biology](), [code](), [covid-19](), [dna](), [future](), [processing](), [quality-control](), [technology]() ### AI overview This post explains why knowing an mRNA vaccine's sequence does not make it possible to print a safe vaccine. Production requires complex biochemical processing, lipid nanoparticle packaging, extensive quality control, and sterile manufacturing. ### Source excerpt Brief post, in response to the many many many technical people that propose to print their own mRNA vaccines "now that the source is out there". I've spent a lot of time individually explaining why this is unlikely to happen any time soon, and I thought it a good idea to explain it here as well. Mountains of details on how the vaccines are actually produced can be found on this awesome page by Jonas Neubert and Cornelia Scheitz. ## The Genetic Code and Proteins of the Other Covid-19 Vaccines DevFeed: [The Genetic Code and Proteins of the Other Covid-19 Vaccines]() Original publisher: [Read original article]() Published: 2021-01-12T12:47:18Z Content type: article Language: en Sources: [Bert Hubert's writings]() Topics: [Reverse Engineering](), [Code]() Tags: [biology](), [covid](), [covid-19](), [dna](), [proteins](), [research]() ### AI overview The article compares genetic differences among major SARS-CoV-2 vaccines, focusing on mRNA and viral-vector vaccines and how they express modified or unmodified Spike protein. It lists products including BioNTech/Pfizer, Moderna, CureVac, Oxford/AstraZeneca, Janssen, and Sputnik V. ### Source excerpt Translations: 中文, 日本語 As a followup to Reverse Engineering the source code of the BioNTech/Pfizer SARS-CoV-2 Vaccine, here is a look at the genetic code behind some of the other vaccines. I recommend at least skimming the earlier post before delving into this one, unless you are already fluent in modified mRNA bases and protein expression mechanics. To get an extremely full background on all vaccine work, I kindly refer you to excellent posts from Derek Lowe and Hilda Bastian. ## Vitamin D Research and Potential Implications for COVID-19 DevFeed: [Vitamin D Research and Potential Implications for COVID-19]() Original publisher: [Read original article]() Published: 2020-05-30T15:52:44Z Content type: opinion Language: en Sources: [Bert Hubert's writings]() Topics: [data](), [Internet]() Tags: [biology](), [covid](), [covid-19](), [health](), [opinion](), [public-health](), [research]() ### AI overview This commentary reviews polarized research and expert views on vitamin D, sunlight, and COVID-19. It presents the author's view that avoiding vitamin D deficiency may be important during the pandemic while acknowledging that evidence remains incomplete and contested. ### Source excerpt Welcome to this post, in which we'll be taking a trip through the wild and bumpy ride that has been Vitamin D & sunlight research over the past few decades, and what it might mean for COVID-19. As with my previous post, before any non-specialist attempts to write something on COVID-19, we should wonder: are any actual experts already writing on this, and if not, why not. Enough badly informed stuff has already been published by amateurs that before posting we should be certain we are actually being helpful. ## How qRT-PCR detects COVID-19 genetic material DevFeed: [How qRT-PCR detects COVID-19 genetic material]() Original publisher: [Read original article]() Published: 2020-05-22T15:18:33Z Content type: tutorial Language: en Sources: [Bert Hubert's writings]() Topics: [real-time]() Tags: [biology](), [covid-19](), [dna](), [healthcare](), [real-time]() ### AI overview An explainer of qRT-PCR, the laboratory method used to detect specific COVID-19 genetic material in virus tests. ### Source excerpt This post is dedicated to lab technicians everywhere doing the difficult work institutes and hospitals rely on to investigate disease and keep us healthy. Lab work requires high precision, deep understanding, is physically demanding, and can even be dangerous. Although our healthcare systems & universities would come to a grinding halt without lab technicians, they are often almost literally invisible somewhere far away. Thank you all for your hard work! ## On the Pan-Genome DevFeed: [On the Pan-Genome]() Original publisher: [Read original article]() Published: 2019-07-12T07:10:21Z Content type: article Language: en Sources: [Bert Hubert's writings]() Topics: [Computing](), [file](), [format]() Tags: [biology](), [computing](), [dna](), [file](), [format](), [formats]() ### AI overview This article explains how human genome references represent a mixture of people rather than one individual and how the FASTA file format cannot encode population-level genetic variation in a single sequence. It introduces the pan-genome as a broader representation that captures genes found in some but not all organisms. ### Source excerpt In this post I want to shine a light on an important development within the world of DNA which shows how much DNA and the world of computing are now intertwined. It turns out we share important problems, like in this case: file formats. Note: I expect to be posting more DNA material as part of my efforts to write a book on this fascinating subject. If you enjoy reading about DNA, you might like the links/presentations/videos found on this page. ## DNA: The Code of Life DevFeed: [DNA: The Code of Life]() Original publisher: [Read original article]() Published: 2017-08-12T18:01:03Z Content type: article Language: en Sources: [Bert Hubert's writings]() Topics: [Code](), [Computing](), [Programming]() Tags: [3d](), [biology](), [code](), [digital](), [dna](), [programming](), [proteins]() ### AI overview A brief introduction to presentations arguing that DNA in living cells can be usefully described and studied with computer terminology. It covers DNA's digital representation, genes, redundancy, the relationship between DNA, RNA and proteins, ribosomes, codons, and biological function calls. ### Source excerpt DNA: The Code of Life At the most magical SHA2017 gathering I gave two presentations, "DNA: The Code of Life" and the followup, "DNA: More greatest hits" (slides). The first presentation was recorded by the wonderful CCC C3VOC streaming crew, the second one by my friend Bart Smit (who is also wonderful). Without making this post too long, I want to thank everyone who helped me do this presentation -- a lot of people contributed time, advice, recording abilities, great questions and enthusiasm.