Dorado v2.0.0 part 2: assembly polishing
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Dorado v2.0.0: no more sup?
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Is Truth Absolutely Necessary for Science?
<p>These days, corporate entities are increasingly dominating research in basic science. This essay looks into how this will change the most cherised convention of science.</p> <!--more--> <p>Resear...
Batch Effect: To Correct or Not for Bulk RNA-seq Data
<p>A colleague sent me a PCA plot last week. Three replicates per condition, control vs KO of a gene. PC1 cleanly separated replicate 1 from replicate 2 from replicate 3. PC2 separated control vs KO. ...
Pawsitively prehistoric
First described from Laos in 2005, the Laotian rock rat Laonastes aenigmamus quickly gained fame as one of the most remarkable “living fossil” discoveries in modern mammalogy. A. Abramov (Zoological I...
Biology is Messy, Because Physicists Failed
<p>I came across an interesting blog post titled <a href="https://gptomics.com/blog/biology_is_messy.html#fn:7">Biology is Messy</a>. The main argument is that biology is not built on top of reduction...
Mathematical Side of AI and Its Applications in Biology
<p>Right now everyone is either enamored of or is completely turned off by AI. Speaking of being fed up, please check the students at University of Florida booing <a href="https://www.youtube.com/shor...
Gene Regulatory Network Reconstruction with Single-cell Data
<p>On the subject of reconstructing gene regulatory networks (GRNs) from RNAseq and scRNAseq data, I am working through a number of review papers and the techniques described therein.</p> <ol> <li>...
Scientific Questions (and Maybe Answers) for 2021-2038
<p>In an <a href="https://homolog.us/blogs/biology/2026/05/08/history-genetics-1949-today/">earlier post</a>, I divided the modern era of genetics into 18-year periods (eras). The discoveries of each ...
Organic
<p>When I hear the word organic, two thoughts immediately come up: organic search and organic chemistry. The latter comes up because it is ingrained in me that organic chemistry is one of the hardest ...