Homolog.us - Frontier in Bioinformatics

Rules of the Genomes

What are the rules of the genomes? What patterns do the genome sequences follow? What biochemical and evolutionary mechanisms are behind these patterns? Are newly published genomes and pangenomes displaying many exceptions to the rules, or do they all confirm the expected patterns?

The Best of 2021

Now that we are on the very last day of 2021, it is not too late to review the positives of the year. I picked four categories (humor, science, society, technology) and shortlisted a tiny subset from many deserving candidates.

Devastating Impact of Climate Change Around the World

Climate Change is taking a devastating toll on the lives of people around the world. This week, two students from Anderson High School died in their sleep. The school district canceled the final exams to help the grieving community. Separately, in Europe, three soccer players left game this week because of heart conditions. Also, 33-year old Argentine striker Sergio Aguero playing for Barcelona announced retirement from soccer due to heart condition. In Silicon valley, 43 year old Tyson Clark from Google Ventures and 44 year old Ryan Popple also died in their sleep.

Did They Fake Their Entire NGS Experiment?

In NGS experiments, when the researchers encounter issues with genome assembly or analysis, they go back to the raw data composed of sequencing reads. In a latest preprint submitted to zenodo, Steven C. Quay did exactly that for a seminal paper and concluded - “The alternative conclusion is that this sample was not a fecal specimen but was contrived. The data cannot, however, distinguish between a non-fecal specimen that came from true field work on the one hand and a specimen created de novo in the laboratory on the other hand.” This is no simple matter, because the entire world had been running like headless chicken for the last two years relying on the genome assembly submitted in the paper.

Another Unusual Connection Between Covid and AIDS

In early 2020, Prashant Pradhan and collaborators posted a preprint titled “Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag” in biorxiv. Based on the released emails from NIH under FOIA, we now know that this article and its coverage in zerohedge upset Fauci so much that he immediately convened an urgent meeting of virologists and several health bureaucrats from US, UK and Europe. All details of this meeting had been redacted, but the virologists present in the meeting fast-tracked a Nature Medicine paper claiming the virus definitely came from animals even though they described it as lab-engineered in their private emails. This paper was then used for over one year to censor all counter-arguments. Especially, biorxiv retracted the preprint due to intense pressure and thus destroyed its reputation as a preprint server for good.

A Disturbing Rise in Heart Attacks Explained

All over the world, people are noticing disturbing rises in heart-related problems among the young and healthy. This year, seventy five prominent athletes died suddenly of heart attack, and many others were sent to hospitals often in the middle of the matches. The problem has become so noticeable that this compiled video of athletes falling on the ground with heart problem went viral. In Australia, a top player with the Adelaide Crows was diagosed with pericarditis. In India, 29 year old former Indian U-19 cricket team captain died after suffering a cardiac arrest and so did 66 year old former cricket player Yashpal Sharma.

Leaky Vaccines, Freaky Mutants and Viral Quasiparticle Swarms

NIH Director Francis Collins Plans to Change Name to Avoid Scandal

A newly leaked classified document revealed that scandal-ridden Francis Collins plans to change his name to continue running the NIH. He got the idea by observing Facebook CEO Mark Zuckerberg, who is rebranding himself to be a reptilian.

Oxford Nanopore IPO Takes Place on the Same Day UK Runs out of Petrol

Dishonest Trevor Bedford Wins Howard Hughes and MacArthur Awards

US establishment biologists are so tone-deaf that they gave Trevor Bedford both Howard Hughes and MacArthur awards. These same people also scream at the top of their lungs - “Trust the experts”. Here is what I got by trusting “experts” like Trevor Bedford.

Is It Time to Retract All Papers from Zhengli Shi and Peter Daszak?

This DEFUSE Grant Proposal is the Scariest Document I Have Ever Read

Yesterday, an explosive set of leaked documents on the origin of SARS-CoV-2 virus got released by DRASTIC. People following the topic are describining them as “worse than the Chernobyl in the biology field”. In my opinion, this release changed the entire understanding of the origin of the pandemic and exposed a group of people as extremely wicked, shockingly evil and vile (sorry to borrow the movie name). Let me explain why.

Three Major Breakthroughs on the Origin of Covid

The scientists looking for the true origin of the Wuhan flu are excited about three major developments over the last few weeks. Let me list them here.

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).

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