Category: Genetics & Computational Biology
-
Genome Wide Association Study & Manhattan Plot Tutorial
Using Gemma to calculate association between phenotypes and genetic variants. Manhattan plots in Python as well.
-
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…
-
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…
-
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.
-
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.
-
Population STRUCTURE of Arctic Dogs & Wolves – How Similar Are They?
Overview Arctic dogs are now lovable pets, but were once bred for their ability to pull a sled around. What’s more interesting, at least to me, is that they share a high degree of genetic similarity with wolves. Here, I’m going to be looking at the Arctic Dog clade to understand the relationships between the…
-
Using Coalescent Analysis to Map the 2016 Zika Virus Outbreak
In this write-up, I’ll retrieve and process Zika genome data, use Bayesian software to generate a Zika gene tree, and propose a route that Zika took to get from Africa to the Americas.
Piper Writes 