Homolog.us - Frontier in Bioinformatics

Pushback against Using PCA, tSNE and UMAP in Biology

Biologists Want Any Criticism of Them Legally Labeled as "Hate Crime"

Things are not going well with our friends in biology. In a new paper published in PLoS Biology, a bigshot from Baylor College of Medicine called for all criticisms of biologists be legally labeled as “hate crimes”. He appears to be upset that people found out about the sponsorship of Wuhan lab by Fauci and Daszak to make new and deadly coronaviruses.

BMJ Criticizes "Sir" Jeremy Farrar in Scathing Articles

Lately “Sir” Jeremy Farrar, the disgraced director of Wellcome Trust, is not having a good time. In a pair of scathing articles (here and here), British medical journal BMJ criticized his efforts of covering up the origin of the covid virus. If similar articles were posted merely two months back by “fringe” bioinformatics sites like ours, they would be discredited as “conspiracy theories” and blocked by the Silicon valley giants. Given that UK’s oldest medical journal wrote on this topic in its editorial, the wind must be blowing in a different direction.

Shotgun Development Biology

In an earlier post, I wrote about five open problems in bioinformatics. In the next several posts, I will select each of them and discuss in some detail. The current post is on the shotgun development biology experiments and related challenges.

Top Five Open Problems in Bioinformatics (2021)

In twitter, a number of researchers are discussing about the open problems in bioinformatics. Therefore, I wanted to share a set of unsolved problems I am curious about. Please tweet your suggestions in reply to this tweet, and I will add them below with your name.

Genome Assembly Experts - Was RaTG13 Fraudulently Constructed?

I like to make our readers be aware of the Chinese publications from where the claim that the virus came from bat originated. The key sequence to understand the origin of Covid is RaTG13, which you can download from here. You can also download the raw data files from NCBI SRA (SRX7724752 and SRX8357956).

Covid Coverup Party (CCP) Invades Zenodo

Over the last eighteen months, biologists funded by the NIH participated in a massive coverup of the origin of the covid virus. Now that they are exposed, these people are acting rather strangely, reminding me of cockroaches running away from the shining light. We like to provide our readers with a detailed overview so that they can get entertained by the actions of these lowly creatures. I have not been so amused ever since Dan Graur vanquised the ENCODE team in 2013 (check “On the Immortality of Television Sets: “Function” in the Human Genome According to the Evolution-Free Gospel of ENCODE”), but ENCODE, to its credit, did not get anyone killed (apart from science itself).

Biorxiv Fails Spectacularly as a Preprint Server

In the early days of Biorxiv, I was a strong supporter of the fledgling preprint server (see here and here. After using the physics preprint server (Arxiv) in my past life, I thought Biorxiv would become something similar and encourage the biologists to collaborate openly. Although I had lingering doubts about the biologists switching from their secretive mode of worrying about getting scooped to sharing openly, never did I expect the preprint server itself to turn into a gated community.

Important Covid-related Datasets Disappeared from NCBI SRA

The origin of SARS coronavirus causing the pandemic is still a mystery due to paucity of early data. This is puzzling because Wuhan, where the pandemic started, is equipped with world-class virology labs. A recent finding by Jesse Bloom, a virologist from Fred Hutch, suggests that we are likely being deliberately misled. By checking the internet caches, he recovered an entire set of early measurements deleted from the NCBI SRA database in March 2020, possibly based on an order from the Chinese government. Incorporating these early measurements point to a progenitor of SARS-Cov2 different from the commonly accepted one.

Discover Novel Viruses Without Leaving Your Couch

Over the last year, you probably saw news articles about how the Wuhan researchers collected bat poops from the remote caves of Yunnan province and found novel viruses. One of those viruses matched closely with the SARS-Cov2 (or that is what they claimed) giving us some idea about the origin of the pandemic. We will talk about this origin question in a later post. This one is about a much easier way to discover new viruses that you can safely try at home. A group of bioinformaticians discovered two novel coronaviruses without leaving their sofa or kissing the posterior of any bat or other dirty animal.

Pangolin - Guilty or Not Guilty?

This is a short post highlighting two recent papers making contradictory claims. Are they both correct?

Did SARS-1.0 Come from Bats through Civets?

“If you tell a lie big enough and keep repeating it, people will eventually come to believe it.”

Strains of SARS-CoV-2

In the previous post, we covered the basics of genetic analysis. The tools discussed there will go a long way to help you follow various scientific discussions involving SARS-CoV-2 genetic data. Today we will quickly review that post, and then look into different “strains” of SARS-CoV-2 coronavirus.

Is Wuhan Coronavirus a Bioweapon?

Over the last few weeks, I received many questions related to genetics of the new coronavirus. Some of them are about genome-based tracking of this virus by the nexttrain team. Others are on claims about two strains of the virus (“L” and “R”), whether the virus is mutating rapidly into more deadly form, how the tests are made, how scientist know that it came from bat or pangolin and finally whether it is a bioweapon.

Illumina Offers to Donate Pacbio Patents, But Will That Save Oxford Nanopore?

A couple of warnings before we begin - (i) this article is for entertainment purpose only and no part of it should be considered an investment advice, (ii) we have no financial position in the mentioned companies.

Woodford's WEIF Dead, Oxford Nanopore IPO Doubtful

A couple of warnings before we begin - (i) this article is for entertainment purpose only and no part of it should be considered an investment advice, (ii) we have no financial position in the mentioned companies.

Pacbio Releases HiFi Data on Drosophila, Rice and Those Pesky Little Creatures (aka Humans)

All Against All Fight Breaks Out among the Sequencing Businesses

A couple of warnings before we begin - (i) this article is for entertainment purpose only and no part of it should be considered an investment advice, (ii) we have no financial position in the mentioned companies.

Debugging RNAseq - (iv) Effective Length and TPM

In previous two posts on RNAseq concepts (here and here), we explained the inner workings of programs like Kallisto and Salmon based on a simple example. We also created a small simulated set identical to the example, ran Kallisto on it and got results matching theory.

Debugging RNAseq - (iii) Expectation Maximization Hands on

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