Barbara McClintock: A Geneticist, A Lonely Pioneer, A Warrior That Defied Her Time
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“There’s got to be a musical somewhere in the future of this.” — Robert Sapolsky
Blog posts
2023
Okay… so, what is protein design?
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In plain English: it’s “2dloFahplA” - AlphaFold2 reversed.
Learning RFdiffusion: build protein backbones with diffusion ML model
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Learning notes of the RFdiffusion software developed by the Baker group.
Smith-Waterman dynamics programming for calculating edit distance.
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The recursive method runs slow as it calls the same function many times. Dynamics programming address that by recording the answer for later calling.
Edit distance calculation: recursive edit distance of prefixes
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The edit distance of X and Y can be solved by looking at prefixes that are 1 character shorter, and solve the smaller edit distance problem recursively.
Coding example: Boyer-Moore Matching Algorithm
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Writing Boyer-Moore machtching from scratch in Python, implementing the bad character rule and the good suffix rule.
Coding example: index assited approximate matching: kmer, sorted list, pigeonhole principle and subsequence
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Here we implement the index assisted mathcing algorithm by recording substrings/subsequences of text T into a sorted list, and implement the approximate matching according to pigeonhole principle.
Approximate matching, hamming and edit distance, pigeonhole principle
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Exact matching algorithms like the naive, Boyer-Moore and index assisted matching can align a pattern P (sequence read) to a text T (genome).
Indexing the genome - index assisted pattern matching, sorted list & hash table, subsequences vs substrings
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The Boyer-Moore matching algorithm uses the bad character and the good suffix rules to skip futile alignments and speed up the search. It preprocesses the pattern P to build up look up tables for the two rules.
Boyer-Moore Matching Algorithm: The Art of Giving Up
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For searches that won’t yield a match, givng up faster saves us time, the same principle applies to life too :)
Naive Exact Matching Algorithm
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Naive exact match is a simple algorithm to solve alignment problems in genomics.
My First Marathon
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Life is good, and we often forget about that.
Huberman Podcast Notes: Dr. Elissa Epel - Control Stress for Healthy Eating, Metabolism & Aging
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Stress response can offer just what we need in a crisis, but it comes with a great cost.
The Sunscreen Song/Wear Sunscreen
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“Wear Sunscreen” was an essay written by Mary Schmich, published on Chicago Tribune in June 1997, in which the Pulitzer winning wise lady offered advice that I have benefitted greatly from.