Posts
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Argument against “DIY computational drug-discovery” trend in Bangladesh
I’m seeing a trend that bioscience students from Bangladesh (South Asia in general) are increasingly interested in publishing papers on computational drug design. Many bright students, undergrad or freshly graduated, are actually publishing drug designing related papers in good journals. I have also done similar projects. But now, I think it is a bad trend.…
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Phylogeny from multi-locus sequences aka MLSA
For one of my Ph.D. projects, I had to generate phylogeny from multi-locus sequence data. Often I have to repeat similar analyses and need to go back to the previous workflow to check what I actually did. I’m sharing the protocol here mainly to help my future self, and may be this is useful to…
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What is the alternative to the ‘junk DNA’ hypothesis?
After completing the human genome sequencing in the 2000s, much of our DNA, even more than half, was considered unnecessary. It was called “junk DNA,” “broken genes” trapped in the genome’s prison, and the DNA fossils of viruses that have been silenced. It was thought these destroyed DNA elements had no purpose and were unrelated…
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Clad-shift consistency of Dengue in Bangladesh
Last year I collaborated with cross-institution researchers from Bangladesh led by BCSIR on the severe Dengue outbreak in 2021. The study has been published in the BMC Virology Journal recently. Dengue remains a dangerous endemic disease causing many deaths and suffering in Bangladesh. My contribution was to analyze the phylodynamics of the Dengue virus (DENV).…
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Calculating Fst for haploid data in R
How to estimate the fixation index, FST, to test for population differentiation in R
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Quick PCA analysis from sequence alignment data in R
Sometimes you need to visualize SNP data from a small Fasta file. PCA analysis is a great way to look for any distribution pattern.
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How to make Co-phylogeny plot: easy tanglegram in R
Tanglegrams are co-phylogeny which is a very powerful visualization tool to examine co-evolution. Here is a tutorial on how to make them in R.
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The fascinating story of HIV origin
I have reviewed a paper by Sharp and Hahn (2011) in YouTube for my students in Evolution course (I am a TA for Spring 2020). This paper is a complete review on the fascinating origin of HIV and how AIDS becomes a pandemic.
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How to resolve conflict in Science: On FMDV classification problem
How a scholarly conflict on FMD virus classification between Bangladeshi and Chinese research-groups was resolved.
Learn Python for Bioinformatics
I have created a set of worksheets that give a quick overview of Python for Bioinformatics (as well as intro to UNIX). You just have to give it 3-6 hours, and you will know the essentials!