A look at the structures of called BA.1 and BA.2. — You may have gotten word of a new SARS-CoV-2 “subvariant” to Omicron. In fact, there are a currently two, called BA.1 and BA.2. (Yes, the terminology and nomenclature are really confusing…) I have taken a quick look at the predicted structures for the receptor-binding domains (RBDs) of each subvariant. …

Distributing protein structure prediction generation using HyperDrive — Back in December, I published a couple posts here (post 1 and post 2) about using AlphaFold2 and RoseTTAFold to predict the receptor binding domain (RBD) of the SARS-CoV-2 Omicron variant. The motivation for this was due to fact that the actual structure of the RBD wasn’t yet available. (It…

Neutralizing antibodies still seem to bind to the RBD of B.1.1.529. So, we should still see some protection from vaccines. — Each time a new SARS-CoV-2 variant pops up in the news, there are two reactions that I have: “Here we go again…🙄” and “I wonder if this actually means anything? 🤔”. On Friday, I published a post on Medium that outlines how I used AlphaFold2 to predict the structure of…

How mutations in the B.1.1.529 variant may affect the receptor binding domain of the Spike protein. — It’s been a bit since we’ve heard much about a new COVID variant. With people starting to get their boosters and the holidays in full-swing, this seems like an inopportune time to hear about a new, “mega-mutated” variant: B.1.1.529. B.1.1.529 was first uploaded to GISAID on November 22nd (accession: EPI_ISL_6752027)…

If you’re an academic, scientist, business article contributor, or any other person that writes research-y things and attempts to have… — If you’re an academic, scientist, business article contributor, or any other person that writes research-y things and attempts to have them published in reputable journals, you’ve probably been scarred by the peer review process. Today, a scientific journal published an article I (and others) wrote about using machine learning to…

I was recently granted access to OpenAI’s GPT-3 API and had it generate 2 cookie recipes to compare to an existing recipe. — I was recently granted access to OpenAI’s GPT-3 API. This system provides state-of-the-art natural language intelligence for a variety of applications including text generation, translation, summarization, code generation, classification, and more. To read OpenAI’s GPT-3 post, visit: https://openai.com/blog/gpt-3-apps/.

What qualifies as a variant in terms of genomics and how does it relate to public health in this COVID-19 pandemic? — If you watch or read the news, there are a flurry of reports of SARS-CoV-2 variants popping up in the US and around the world. Some reports generalize and might say something like “The South African variant was found in South Carolina” or “The E484 variant was seen in Massachusetts”…

Cloud-based alignment and variant calling using the Microsoft Genomics service in Azure and the msgen R package. — The Microsoft Genomics service in Azure is a cloud-based implementation of the Burrows-Wheeler Aligner (BWA) and the Genome Analysis Toolkit (GATK) for alignment and variant calling. This service came was released a few years ago and currently provides a Python 2.7 CLI to submit workflows. This software takes in either…

Over the past couple weeks, friends and family have asked me questions about the “accuracy” of different COVID-19 tests. This video by… — Over the past couple weeks, friends and family have asked me questions about the “accuracy” of different COVID-19 tests. This video by #3Blue1Brown explains why accuracy isn’t really what you’re wanting to know. A better question would be: “Given a positive test result, what’s the probability I actually have COVID-19?”…