toward a gene panel for psychiatric violence

I recently developed a method for specifying a comprehensive gene list for investigating genes related to psychiatric violence, which I describe below. First though, here’s a cool picture from the analysis: Method I started by extracting a list of diseases involving violence from [1], removing epilepsy, dementia, mental retardation (is there a better word for […]

rapidly identifying potential CRISPR/Cas9 off-target sites (part one)

Before we can score segments in the genome having a small number of mismatches to a CRISPR for their off-target risk, we must first find these segments. Searching for every possible mismatch permutation proves computationally expensive, so we apply the following heuristic: We only search for mismatches in the top positions relevant to CRISPR efficiency. […]

Bayesian method for filtering out mRNA turnover rate bias from siRNA knockdown measurements

Abstract siRNA performance prediction calculations for a given siRNA may be divided into two broad categories: functions of the siRNA’s sequence, hereafter referred to as “intrinsic” properties of the siRNA, and functions of the target mRNA, hereafter referred to as “extrinsic” properties of the siRNA. When training a statistical or machine learning model to select […]

RNAfold’s and RNAcofold’s predicted dG correlates with sequence length

This seems rather obvious, but I decided to double check before building a machine learning model based on RNAfold’s and RNAcofold’s predictions involving sequences of varying length. Method I generated 30,000 random RNA sequences of random length between 15 and 30 bases. I ran RNAfold on this list; and RNAcofold on this same list where […]

how I make a living: what is bioinformatics? (part #1)

I’m constantly asked to explain what I do for a living. Here is an attempt to do so in laypersons’ terms. I’ll assume my readers are non-scientists and non-engineers, but that they’ve taken a high school biology class. “Bioinformatics” is the application of mathematics and computer science to biological data, particularly molecular biology data. By […]

the science of gender identity (part 4: summary)

To prepare for a book I intend to write on the science of gender identity, I drafted the following three blog posts to collect my thoughts. They are highly technical; I need to recast the content for the layperson. I also assembled some of my own biological data to analyze. The first blog post,, […]

the science of gender identity (part 3: psychology)

This is the third post in a multi-part series surveying the current science of gender identity, particularly with regard to the transgendered population. My first post on the subject covered proposed genetic associations and corresponding research. The second post on the matter discussed observed differences in brain anatomy between transgendered and cisgendered individuals. Here I […]

graph database for heterogeneous biological data

To assist with a project I’m working on, I recently implemented a substantial portion of DisGeNET as a graph database. Furthermore, I added MeSH, OMIM, Entrez, and GO into the database to facilitate linking of data between these sources. Here I briefly describe these data sources, describe graph databases, and then show how use of […]