Piper Writes – Writings in the Biological and Data Sciences

Iterative Knockout for Feature Importance in Neural Networks [Python] [Keras]

Python package/scripts for determining feature importance and high order interactions in a recurrent neural network in Keras.

May 2, 2018
Genome Wide Association Study & Manhattan Plot Tutorial

Using Gemma to calculate association between phenotypes and genetic variants. Manhattan plots in Python as well.

April 4, 2018
Competing Endogenous RNA: A Mechanism for Cancer to Regulate Gene Expression

Competing endogenous RNA (ceRNA) is a post-transcriptional regulatory mechanism that is an emerging focal point in the field of molecular biology. As our knowledge on ceRNA grows, we also uncover tumorigenic exploitations of this mechanism. In this write-up, I’ll explain ceRNA and its role in cancer.

March 29, 2018
Linkage Disequilibrium, Human Population Diversity, and the Hemoglobin Gene

Introduction Linkage disequilibrium is a somewhat rudimentary, but effective way to measure of the evolution of a population. It is, essentially, a quantification of the association between alleles (which, in this case, includes single nucleotide variants) as they exist in a population. In a fixed, non-evolving population, there should, theoretically be no association, and all…

March 24, 2018
Environmental DNA Detection: New Method for Monitoring Manatees

Researchers use new wildlife sampling technique to identify site occupancy of Manatees in a more accurate, less intrusive, cheaper manner. Listed by the IUCN as a vulnerable species, the West Indian Manatee is a prime candidate for conservation efforts[1]. However, designating protected areas for manatees can be difficult if you don’t know where they are.…

March 21, 2018
How Genetic Similarity is Calculated and a Little on What the NASA Twin Study Really Means

You’ve probably heard statistics claiming that DNA between humans and chimpanzees are over 99% similar, or that humans share 50% of there DNA with a banana, or whatever-the-case. More recently, you might have heard news articles from sources such as CNN[1] or Time[2] claim that an astronaut’s (Scott Kelly), DNA changed 7% compared to his…

March 17, 2018
Tracking the Flu with Twitter & Machine Learning

Scraping, geolocating, and classifying tweets to survey cases of the flu.

March 14, 2018
Environment vs Inheritance – Air Pollutants Account for More Variation in Gene Expression than Ancestry, Transcriptome Analysis Reveals

Researchers at the Ontario Institute for Cancer Research use RNA-sequence methods to generate transcription profiles of over 1000 French Canadians and find correlations between a number of environmental factors, chiefly air composition.

March 12, 2018
Cancer Cells Send MicroRNA In Exosomes to Macrophages, Rewiring Them for Tumorigenesis

Researchers at the National Cancer Institute in Maryland pinpoint miR-1246, a micro RNA, as a potential therapeutic target in mutant p53 colorectal cancers.

March 10, 2018
An Endangered Animal For Every State

Fun little infographic I made. Full disclosure, apart from being listed as threatened/endangered, these choices were fairly arbitrary. I tried to get a good mix of phyla (obviously biased towards mammals lol).

March 9, 2018