The hottest Bioinformatics Substack posts right now

And their main takeaways
Category
Top Technology Topics

Dear Shambolic Oligarchs: Here’s What I Did This Week

Viruses Must Die • 96 implied HN points • 25 Feb 25
🔬 Science Virology Molecular Biology Bioinformatics Vaccines Health Research
  1. There's a plan to create a vaccine for chickens using yeast to help them fight bird flu. This involves some complex science but aims to protect poultry.
  2. Efforts are underway to upload massive amounts of viral data to a federal cloud, making it easier for scientists to access crucial information. However, workplace issues are causing worries about delays.
  3. A colleague discovered a cancer treatment but was let go during a staff change, which highlights the challenges faced by dedicated scientists and the impact of workplace stress on their work.

Keeping up with the State-of-the-Art in TechBio

Kesav’s Lab • 9 implied HN points • 21 Feb 25
🕹 Technology Bioinformatics AI Automation Biotechnology Software
  1. The Nobel Prize in Chemistry was awarded for breakthroughs in understanding protein structures, which can lead to better medicines and solutions to major health challenges.
  2. There’s a growing community focused on TechBio, which merges technology and biology. Events like meetups can help people learn and connect over important topics.
  3. Staying informed about the latest in TechBio is important, and contributing to community newsletters helps track new tools and research developments.

GPU peak calling for epigenetics

LatchBio • 11 implied HN points • 21 Jan 25
🕹 Technology Bioinformatics Data Analysis Algorithms Computing Genetics
  1. Peak calling is crucial for analyzing epigenetic data like ATAC-seq and ChIP-seq. It helps scientists identify important regions in the genome related to gene expression and diseases.
  2. The MACS3 algorithm is a common tool used for peak calling but struggles with handling large data volumes efficiently. Improving its implementation with GPUs can speed up analyses significantly.
  3. By using GPUs, researchers have achieved about 15 times faster processing speeds for peak calling, which is vital as more genetic data is generated in the field.

An AWS For Sequencing?

ASeq Newsletter • 58 implied HN points • 16 Nov 24
🕹 Technology Bioinformatics Data Analysis Cloud Computing Software Development Genetics
  1. Bioinformatics companies often struggle to succeed on their own, but some are finding unique ways to add value by providing analysis of sequencing data from external service providers.
  2. Just like how companies can use AWS for their server needs, the idea is to create an AWS-like platform specifically for DNA sequencing, making services easier and more accessible.
  3. Building a platform for sequencing could lower barriers for businesses and encourage new applications in the field, opening up more opportunities for innovation.
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How to Engineer Therapeutic AAVs

LatchBio • 15 implied HN points • 14 Nov 24
🔬 Science Gene Therapy Bioinformatics Machine Learning
  1. Adeno-associated viruses (AAVs) are used for gene therapy because they can deliver therapeutic genes safely without causing disease in humans. They're like little delivery trucks that send important genetic information to specific parts of the body.
  2. Dyno Therapeutics created a new version of AAV called Dyno bCap1, which is much better at getting to the brain and avoiding the liver, showcasing how engineering can significantly improve these therapies.
  3. By using machine learning, scientists can design better AAVs by predicting how changes in their structure affect their ability to deliver genes. This makes the process smarter and helps create more effective treatments.

Product Digest: Latch Plots, Protein Engineering and GPU-enabled Bioinformatics

LatchBio • 12 implied HN points • 13 Nov 24
🕹 Technology Bioinformatics Machine Learning Data Visualization Software Development Protein engineering
  1. Latch Bio offers a new Protein Engineering Toolkit with over 16 tools that help create and analyze proteins. This means scientists can now design better drugs and enzymes more easily.
  2. The new software called Latch Plots makes it easier for scientists to visualize biological data. It allows them to create dynamic graphs and analyze data from various sources without much hassle.
  3. Using GPU technology in bioinformatics speeds up data processing significantly. This upgrade allows researchers to analyze large datasets quickly, which is essential for drug discovery and many research projects.

Horrors Of The Theoretical Maximum

ASeq Newsletter • 14 implied HN points • 30 Oct 24
🕹 Technology Bioinformatics Data Analysis Genomics Research Methods
  1. Vendors sometimes quote theoretical maximums for data output, which can be misleading. It's important to understand that these numbers might not reflect actual performance.
  2. Comparing different technologies can be complicated because they have different specifications and capabilities. Each technology, like PacBio, Oxford Nanopore, and Illumina, has its unique strengths and limitations.
  3. In the real world, the difference between what is theoretically possible and what is actually achieved can be significant. This means we should be cautious and not rely solely on theoretical figures.

GPU-enabled Bioinformatics

LatchBio • 9 implied HN points • 06 Nov 24
🕹 Technology Bioinformatics Data science AI Development Cloud Computing
  1. Bioinformatics is moving towards using GPUs to speed up data processing. This change can save a lot of time and money for researchers.
  2. New molecular techniques generate massive amounts of data that take too long to analyze without faster systems. Using GPUs can make these processes much quicker, especially for large datasets.
  3. There are now cloud platforms that make it easier to use GPU technology without needing special expertise or expensive hardware. This helps more teams access advanced analysis tools.

Functional protein mining with conformal guarantees

Axial • 14 implied HN points • 28 Nov 24
🔬 Science Bioinformatics Molecular Biology Machine Learning Genomics Proteomics
  1. A new method is developed for predicting protein functions using something called conformal prediction. This makes the predictions more reliable and provides a clear way to understand risks when selecting proteins.
  2. The approach helps in annotating genes and predicting enzyme functions more accurately without needing new training models. This is great for speeding up research in life sciences.
  3. It also offers a smart way to reduce the number of proteins needing full analysis, making the process quicker and cheaper while still keeping good accuracy.

Birth of protein folds and functions in the virome

Axial • 14 implied HN points • 24 Nov 24
🔬 Science Virology Genetics Molecular Biology Bioinformatics
  1. A lot of viral proteins have unique structures, showing there's still much to discover in the viral world. More than half of these proteins are structurally different from anything we've seen before.
  2. Some viral proteins are surprisingly similar to human proteins, which allows viruses to trick our cells. This understanding could lead to new ways to combat viral infections.
  3. Using advanced techniques to study protein structures is really powerful. It can reveal function and relationships that traditional methods might miss, helping us understand viruses better.

4 Reads Per Cluster! Simultaneously Paired End-Sequencing!

ASeq Newsletter • 36 implied HN points • 31 Jan 24
🔬 Science Genetics Bioinformatics Sequencing Biotechnology
  1. Illumina has a method to potentially double their instruments' throughput, but it may come with a slight decrease in accuracy.
  2. By simultaneously reading both the forward and reverse strands, Illumina can achieve four reads per cluster, doubling the throughput.
  3. Implementing the simultaneous paired-end sequencing approach may be challenging without sacrificing accuracy, but it opens up opportunities for increased throughput in the future.

Codon Digest: GPT-4 Controls a Robot

Asimov Press • 90 implied HN points • 16 Apr 23
🔬 Science Biotechnology Genetic Engineering Bioinformatics Microbiology Biology
  1. GPT-4 controlled a lab robot to conduct chemical reactions, showcasing the potential of using natural language to automate experiments.
  2. Skin microbes were engineered to activate the immune system to fight tumors when applied to the skin, offering a novel cancer treatment approach.
  3. Tobacco plants were genetically modified to produce moth sex pheromones, providing a natural way to repel male moths from crops and protect them.

Rapid proteome-wide prediction of lipid-interacting proteins through ligand-guided structural genomics

Axial • 7 implied HN points • 05 Jan 25
🔬 Science Biology Genomics Machine Learning Proteomics Bioinformatics
  1. Researchers developed a new tool called SLiPP that helps quickly find proteins that interact with lipids. This is important because lipids play key roles in cell functions and diseases.
  2. SLiPP uses machine learning to distinguish between protein pockets likely to bind lipids and those that won't. This makes it easier to identify potential targets for drug discovery.
  3. The tool has been successfully tested on different organisms, showing it can accurately predict lipid-binding proteins. This helps scientists explore new areas in lipid biology and disease research.

What The H*ll Is PPMSeq?

ASeq Newsletter • 21 implied HN points • 17 Feb 24
🔬 Science Biotechnology Genomics Sequencing Bioinformatics
  1. PPMSeq is a duplex sequencing technique that ensures high accuracy reads by reading both forward and reverse strands of a double-stranded sequence.
  2. Ultima's PPMSeq works by amplifying both strands on the same bead and utilizing a tag to identify their presence, with errors causing radical dephasing which is taken care of by downstream software.
  3. Approaches to implementing PPMSeq on Ultima's platform involve reading both strands in both directions simultaneously or keeping the product on beads in the same orientation, each with its own challenges and considerations.

Native Snakemake Support on LatchBio

LatchBio • 20 implied HN points • 14 Sep 23
🕹 Technology Bioinformatics Cloud Computing Workflow management Data Management Infrastructure
  1. Bioinformaticians face challenges in developing specialized scientific workflows due to managing large files and deploying academic tools.
  2. Snakemake, a Python-based framework, offers advantages over Nextflow in terms of Python readability, debuggability, and configuration simplicity.
  3. LatchBio now provides native support for Snakemake, enabling bioinformaticians to leverage graphical interfaces, managed infrastructure, and downstream analysis solutions.

Data Science Weekly - Issue 8

Data Science Weekly Newsletter • 19 implied HN points • 16 Jan 14
🕹 Technology Data science Machine Learning Artificial Intelligence Big Data Bioinformatics
  1. US military scientists have figured out how to identify a small group of people who can spread messages effectively through networks. This group acts like a 'seed' to amplify the message to a larger audience.
  2. Data science is becoming crucial in various industries, like banking and healthcare, to help solve problems and improve services. Understanding data can give companies a competitive edge.
  3. Learning about data science is more accessible than ever, with resources like free eBooks and tutorials available online. This makes it easier for anyone interested to start their journey in the field.

Classical-to-Quantum Sequence Encoding in Genomics

Quantum Formalism • 0 implied HN points • 13 Apr 23
🔬 Science Genomics Quantum Computing Bioinformatics Machine Learning
  1. A special webinar on classical-to-quantum sequence encoding in genomics will take place tomorrow at 4 pm GMT with key insights presented by the team working on QF's data encoding challenge.
  2. The webinar abstract highlights innovative methods that combine diverse fields like Electrical Engineering, Information Theory, and Neural Networks to create efficient data encoding schemes for genomics.
  3. The research explores utilizing lossless compression, wavelet-based encoding, and information entropy in developing classical-to-quantum data encoding methods, offering implications for the future of bioinformatics and quantum computing.

The Hidden Heroes of the Genome

Nano Thoughts • 0 implied HN points • 18 Dec 24
🔬 Science Genetics Molecular Biology Biotechnology Health Bioinformatics
  1. Long non-coding RNAs (lncRNAs) were once thought to be useless 'junk DNA,' but they actually play important roles in regulating our genes and maintaining cellular stability.
  2. Recent advancements in lncRNA research are leading to better cancer diagnostics and new treatments, showing their potential as key players in medicine.
  3. The study of lncRNAs challenges our old views of genetics and shows that biological systems are much more complex and interconnected than we previously thought.