Author: Arafat
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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.
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Note for First-Year Graduate Student
Few tips for new graduate-students to make shift from undergrad mindset to become an independent researcher.
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Statement of Purpose
[This is a writeup from 2016. Caution! If you are willing to apply in US for higher study and planning to write SOP soon, I’ll suggest not to read this write-up, because it may bias you. And do not use this format as your SOP. Your SOP is supposed to be unique. Better, write your…
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Show Your Work
Show Your Work Sometimes we are practitioner of a field, professionals or artists do not feel easy to show our own work, the process of work, what we are learning, sharing our work with more general people. This book encourage and provide some guidelines for that, because time has been changed in this connected world.…
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Python for Bioinformatics: An Online Course from Me!
I teach an on-line course ‘Python/Biopython for Bioinformatics’ in cBLAST. This is three month’s course, I use biological examples showing how we use Python to handle and analyze biological data. The video lectures are in Bangla, and video’s are both slides and screen-casts of coding. Center for Bioinformatics Learning Advancement and Systematic Training, or cBLAST,…