amulyagarimella

Papers for today's journal club

1. On the genetic basis of tail-loss evolution in humans and apes | Nature
   1. Summary: A mobile DNA sequence could explain tail loss in humans and apes
2. Formation of memory assemblies through the DNA-sensing TLR9 pathway | Nature
   1. Summary: Innate immunity in neurons makes memories persist
   2. Summary 2: Memories are made by breaking DNA — and fixing it

All submitted papers

Thank you to everyone who submitted a paper!! <3

• Diffusion models in protein structure and docking

amulyagarimella

• Noise2Noise: Learning Image Restoration without Clean Data
• Discovery of a structural class of antibiotics with explainable deep learning | Nature
• Sequence modeling and design from molecular to genome scale with Evo | bioRxiv
• Glia Accumulate Evidence that Actions Are Futile and Suppress Unsuccessful Behavior
• Organoids grown from amniotic fluid could shed light on rare diseases
• SegmentNT: annotating the genome at single-nucleotide resolution with DNA foundation models | bioRxiv
• [Integrating deep learning and unbiased automated high-content screening to identify complex disease signatures in human fibroblasts | Nature Communications](https://www.nature.com/articles/s414

amulyagarimella

I'm flipping to a random section of Molecular Biology of the Cell and riffing on it. Let me know what you think of this type of post!

Today: The RNA world and the origins of life (pp365 - 373) You can find my full notes on the MBC reading, as well as the full text of this post, here.

MBC Summary

The RNA world hypothesis states that self-replicating RNA molecules were probably some of the first autocatalysts on Earth and likely formed the first living cells. These molecules likely served as both (1) information storage systems, enabled by complementarity, and (2) catalysts, enabled by secondary and tertiary structural elements that would let them form active and allosteric sites. The precursors to these RNAs themselves were likely more simplistic versions of RNA that retained catalytic ability and were eventually able to (1) form RNA monomers (ribonucleotides) and (2) catalyze templated polymerization reactions.

These early RNA

amulyagarimella

Anonymous feedback form: tinyurl.com/cs121-ka-feedback

Section 1: https://docs.google.com/presentation/d/1vuDm_3OsbWg0FAWSUFqzelhghoqrTBlJyregMKrnBA8/edit?usp=sharing

Section 2: https://docs.google.com/presentation/d/1CICVJCnyVl4UgSYUf58sFr9lj_oDRCtB0IYLbEtO4GM/edit?usp=sharing

Section 3: https://docs.google.com/presentation/d/1IGXY_NFLe-mWqyt9tAcccIP_VlFIelX-chwkjw0qOww/edit?usp=sharing

Section 4: https://docs.google.com/presentation/d/1giiYlYATlTBGJCEQbvxfLLqpGvY9r0s6rBHAV3K_Cko/edit?usp=sharing

amulyagarimella

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# HCS Workshop 4: Data Science\n",
    "\n",
    "Welcome to the data science workshop! "
   ]

amulyagarimella

#!/bin/sh

for f in $(ls ~/Library/Caches)
do
	if [ -d ~/Library/Caches/$f ]; then
		echo $f
		for f1 in $(ls ~/Library/Caches/$f)
		do
			if [ ~/Library/Caches/$f/$f1 ]; then
				echo $f1