# DNA Published articles for DNA. This is one page of public article previews, not the complete archive. Follow Next page to continue. Summaries are not the original full articles. ## 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. ## How an Independent Researcher Got the SkewDB Paper Published DevFeed: [How an Independent Researcher Got the SkewDB Paper Published]() Original publisher: [Read original article]() Published: 2022-01-25T12:50:28Z Content type: opinion Language: en Sources: [Bert Hubert's writings]() Topics: [Database](), [data-processing]() Tags: [academic](), [advice](), [blog](), [dna](), [paper](), [publication](), [research]() ### AI overview An independent researcher describes how a series of blog posts led to the acceptance of the SkewDB paper by Nature Scientific Data. The article shares practical advice on journal selection, preprints, public data and software, reproducibility, manuscript preparation, and reviewer responses. ### Source excerpt And we're back! As noted in part 1 and part 2 I thought it might be possible that I had discovered something interesting in biology. Lacking an academic peer group, I had decided to use a series of blog posts to gather feedback and to keep myself honest. I'm very pleased to report that this process worked! I just received word that Nature Scientific Data has formally accepted my paper "SkewDB, a comprehensive database of GC and 10 other skews for over 30,000 chromosomes and plasmids" for publication! ## 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. ## A Science Experiment: part 2 DevFeed: [A Science Experiment: part 2]() Original publisher: [Read original article]() Published: 2021-08-26T12:50:28Z Content type: article Language: en Sources: [Bert Hubert's writings]() Topics: [Database](), [dataset](), [data](), [Jupyter Notebook](), [Software](), [jupyter]() Tags: [blog](), [data](), [database](), [dataset](), [dna](), [experiment](), [jupyter](), [jupyter-notebook](), [science](), [software]() ### AI overview This second installment describes SkewDB, an open database of GC/TA and other skews across 25,000 bacterial chromosomes, along with open-source software and a Jupyter notebook for exploring it. The author reports tentative findings about Firmicute skew prediction and unusual bacterial chromosome patterns, while emphasizing that the results require scientific review. ### Source excerpt And we're back! As noted in part 1, there is the possibility I've discovered something interesting in biology. Lacking an academic peer group, I'm using a series of blog posts to gather feedback and to keep myself honest. Because chances continue to be high that as an outsider I am deluding myself. The full backstory can be found in part 1 without which this installment will not make much sense. ## Documenting a Possible Biology Discovery as an Experiment DevFeed: [Documenting a Possible Biology Discovery as an Experiment]() Original publisher: [Read original article]() Published: 2021-08-19T07:27:09Z Content type: opinion Language: en Sources: [Bert Hubert's writings]() Topics: [Computing]() Tags: [computing](), [discovery](), [discussion](), [dna](), [science]() ### AI overview The author reflects on the uncertainty of making a possible discovery in biology as an outsider, describes the value of academic peer feedback, and begins documenting the discovery process to solicit input and maintain pressure to continue. ### Source excerpt So, I think I may have discovered something interesting in biology! Professional scientists know this feeling all too well. Exhilarated that it looks like you might be the first person ever to know something, but worried sick that it might not be real. Also, you might be fooling yourself - and you are the easiest person to fool. And even if it is real, does it even mean something? Or did you effectively discover that hot things are not cold? ## 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. ## Understanding DNA Through a Programmer's Perspective DevFeed: [Understanding DNA Through a Programmer's Perspective]() Original publisher: [Read original article]() Published: 2021-01-09T13:33:46Z Content type: article Language: en Sources: [Bert Hubert's writings]() Topics: [Code](), [Script](), [Perl](), [Unix](), [browsers]() Tags: [article](), [book](), [code](), [dna](), [firefox](), [perl](), [presentation](), [revision](), [unix](), [updated]() ### AI overview A computer programmer explains DNA using programming concepts, comparing the genome to source or byte-compiled code executed by a virtual machine. The article describes DNA as a four-symbol digital language and explains how codons encode amino acids. ### Source excerpt Updates: 12th of September 2021: I'm writing a book on DNA! If you want to become a beta reader, or have suggestions, I'd love to hear from you! 8th of January 2021: This article has been revised and updated, scientifically and in terms of dead links. Revision made by Tomás Simões (@putadagravidade / tomasprsimoes@gmail.com). Feel free to contact me if I made a mistake. 25th of August 2017: This page has led to a two-hour presentation called DNA: The code of Life as presented at SHA 2017. ## Merekayasa Balik Kode Sumber Vaksin SARS-CoV-2 BioNTech/Pfizer DevFeed: [Merekayasa Balik Kode Sumber Vaksin SARS-CoV-2 BioNTech/Pfizer]() Original publisher: [Read original article]() Published: 2020-12-29T10:12:20Z Content type: article Language: id Sources: [Bert Hubert's writings]() Topics: [Code](), [digital]() Tags: [code](), [codex](), [covid-19](), [digital](), [dna](), [flash](), [health](), [printer](), [source]() ### AI overview This Indonesian-language article examines the mRNA source code of the BioNTech/Pfizer SARS-CoV-2 vaccine, also identified as BNT162b2, Tozinameran, and Comirnaty. It explains how the digital sequence is used in vaccine production and compares biological DNA and RNA with computer storage and memory. ### Source excerpt (artikel asli ditulis oleh Bert Hubert) Selamat datang! Pada artikel ini, kita akan mengamati kode sumber dari vaksin mRNA BioNTech/Pfizer SARS-CoV-2 berdasarkan ciri-ciri. Saya menghaturkan terima kasih banyak kepada sejumlah besar orang yang meluangkan waktu untuk mempratinjau artikel ini untuk memastikan keterbacaan dan ketepatan. Seluruh kesalahan tetaplah milik saya, namun saya akan dengan senang hati menerima tanggapan Anda segera pada bert@hubertnet.nl atau @bert_hu_bert* Pernyataan ini mungkin agak mengejutkan - vaksin adalah sebuah cairan yang disuntikkan ke lengan. ## 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! ## Amateur SARS/2019-NCoV RNA Comparison DevFeed: [Amateur SARS/2019-NCoV RNA Comparison]() Original publisher: [Read original article]() Published: 2020-01-24T12:42:01Z Content type: article Language: en Sources: [Bert Hubert's writings]() Topics: [Algorithms, Complexity](), [Computing](), [JavaScript]() Tags: [algorithm](), [algorithms](), [alignment](), [comparison](), [computing](), [covid-19](), [dna](), [javascript]() ### AI overview A rough comparison of the reported SARS and 2019-nCoV genomes using the Needleman-Wunsch alignment algorithm. The author says the amateur comparison found about 80% identity, while noting that this result does not establish what the similarity means. ### Source excerpt Here is a rough comparison between the reported genomes of SARS and 2019-nCoV ("Wuhan virus"). This is the output of an old but still interesting 'alignment' algorithm called Needleman-Wunsch. In the world of computing we use 'diff' for this purpose, DNA has some specific aspects which are incorporated into the alignment algorithms. Many years ago I wrote a JavaScript demonstration of this algorithm, which can be found here. ## 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.