The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed...
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A $k$-long sequence $P$ is a ($k$,$s$)-open-syncmer, $s\le k$, if $P[1,s]$ is the smallest among all $s$-mers in $P$. Suppose function $\phi$ is a bijective hash function of $k$-long sequences. $P$ is a random ($k$,$s$)-syncmer if $\phi(P)$ is an open syncmer. Because we often map $k$-mers to integers, $\phi$ can take the form of an invertible integer hash function. In practice, $\phi$ does not have to be a bijection. It can also map a sequence to an integer of a …
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The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed...
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The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed...
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A week ago, a company calling itself General Inception emerged from stealth as a new concept, which they call an “Igniter company”, to promote the formation of new life sciences company. As described to me in a phone conversation with General Inception CEO Paul Conley, General Inception provides a range of science and business expertise and support to enable embryonic ideas to condense into functional startups. The igniter metaphor Conley offered me is the spark plug of a car: it …
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The Only Thing Clear About Infinity Is It Is Now Complete Long Reads. Illumina told us a new name for Infinity -- Illumina Complete Long Reads -- and an initial pair of products, but didn't reveal anything new about the underlying tech. They threw out a number of claims, but very vague ones. Particularly confusing is that it "isn't synthetic reads". If not, then what is it? Read more »
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The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed...
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Command-line interface, or CLI in brief, specifies how a user interacts with a program on the command line. Torsten Seemann wrote a good article on creating CLI. This blog post adds a few more suggestions. 1. Keep the backward compatibility of CLI as much as possible Backward compatibility here means users can upgrade and run a tool without changing the command lines they used in the past. This implies we should not remove or change the meaning of an existing …
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The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed...
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A couple of weeks ago I sat down for coffee with a pair of MGI representatives - American Region CEO Yongwei Zhang and Director, Global Business Development Damon Zhang. Since I hadn’t been at AGBT 2022 (my 2023 application already filed!). Yongwei and I had planned to try to catch up the next time he was in Boston area, so I braved our current subway issues (not one, but two major lines shut for extended maintenance!) and covered a range …
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The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed...
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The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed...
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This was once a guest post by Karol Estrada, who was a postdoctoral research fellow in the Analytic and Translational Research Unit at Massachusetts General Hospital and the Broad Institute of MIT and Harvard. It was written in memory of Laura Riba. We have briefly summarised her thoughts and findings from that post below. Karol … A Rare Variant in Mexico with Far-reaching Implications Read More »
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The common notion running through molecular biology is that the information present in DNA is transferred to RNA and then to protein. Back in 2010, researchers made a potentially ground-breaking observation. They found that within any given individual, there are tens of thousands of places where transcribed RNA does not match the template … Notes on the Evidence for Extensive RNA Editing in Humans Read More »
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In May 2019, it was reported in an article that over ten thousand sequence mismatches were observed between messenger RNA and DNA from the same individuals. More recently, three technical comments were published by Science surrounding this article. It was concluded that at least 90% of the Li et al. RDD sites are technical artifacts. … Questioning the Evidence for Non-Canonical RNA Editing in Humans Read More »
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A little while back, Razib Khan used data from 23andMe to explore his family’s genetic history. He previously published his findings and summarized them. Today, I’m going to fill you in on what he had to say! Khan was interested in genetics, anthropology, and history, mainly how we have changed the way lineages are marked … My Personal Genome: What Razib Khan Had to Say Read More »
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Alzheimer’s disease is a form of dementia that impacts the brain and results in memory loss. In recent years we have been able to study it and its risk factors to calculate the chances of you being affected by the disease. Today we are going to look at how that risk is calculated. Most people … Calculating your Alzheimer’s Risk Read More »
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At the annual Advances in Genome Biology and Technology (AGBT) conference held in Florida during 2012, there were many exciting announcements and developments in the world of DNA sequencing technology. An especially cool piece of news came from the team at Oxford Nanopore, the stars of our piece on cluster sequencing, about their (then) brand … Making Sequencing Simpler With Nanopores Read More »
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I agreed to make my 23andMe genotyping results available publicly as part of GNZ because I knew that the results were slightly dull, and I’m not majorly at high or low risk for any diseases. I was also very unsurprised to find out that I have blue eyes and that I was identified to … Testing Possibilities About My Ancestry Read More »
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It’s been over eight years since Oxford Nanopore presented the first ever nanopore sequencing data at the AGBT conference in February 2012, where they provided an overview of the hardware and software behind the GridION and MinION systems. Even today Oxford Nanopore could be seen as a dark horse. Their GridION platform is used … Cluster Sequencing with Oxford Nanopore’s GridION System Read More »
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It is usually thought that we can confidently say that if our genotyping results say that we carry a certain genetic variant, that we actually do carry that variant. However, why does this not mean that we can be confident about the prediction about disease risks? There are many risks and benefits associated with population … How Well Can a Screening Test Predict Disease Risk? Read More »
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Researching your family history is a fascinating experience. Even if you find out that your ancestors led very normal lives. Just being able to see the name and life milestones of your great-great-great-great-great (etc) grandmother is exciting. It’s amazing to be able to track your ancestry. But it can also be a confusing process. This … Best Genealogy Software Read More »
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The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed...
go to blog
The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed...
go to blog
I ran into an annoying problem last night and was quite steamed, but had the discipline to wait until morning to vent publicly about it. Now I'm more in a morose mood on the subject, not furious but still quite frustrated. The quick version of what happened is I'm belatedly trying to go through some nicely documented reproducible analysis code to explore some concerns I have with the analysis, and the code is working on an SRA entry -- and …
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The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed...
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Singular Genomics reported earnings last week and delivered an unpleasant surprise: inability of suppliers to make timely deliveries of key (but unspecified) hardware components have slowed G4 instrument production to a very slow crawl. Given the lively competition in the desktop short read space, this is a serious setback for Singular's commercial launch. Read more »
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Biostar Herald
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