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 […]

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 […]

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 […]

gene annotation database with MongoDB

After reading Datanami’s recent post “9 Must-Have Skills to Land Top Big Data Jobs in 2015” [1], I decided to round out my NoSQL knowledge by learning MongoDB. I have previously reported NoSQL work with Neo4j on this blog, where I discussed building a gene annotation graph database [2]. Here I build a similar gene […]

simulating RNA-seq read counts

The Challenge I want to explore the statistics of RNA sequencing (RNA-seq) on next-generation sequencing (NGS) platforms in greater detail, so I thought I’d start by simulating read counts to experiment with. This post details how I constructed a simulated set of read counts, examines its concordance with the expected negative binomial distribution of the […]

synthetic biology: an emerging engineering discipline

In the last decade a new engineering disciple called “synthetic biology” has emerged. It differs from the science of biology in that it applies engineering strategies to the creation of cells that perform a desired task, such as the production of drugs or biofuels. It also differs from previous genetic engineering approaches by stressing the […]

rapidly extracting a subsequence from chromosome sequence data in Java

The Challenge We have a text file containing the nucleotides of a chromosome, say human chromosome 11, and need to be able to quickly extract a subsequence from the chromosome text given a nucleotide position and number of subsequent nucleotides to include. The problem is that chromosome files are huge, e.g. 135 megabytes for chromosome […]

graph database for gene annotation

Lately I’ve been experimenting with graph databases using Neo4j and the Cypher query language. To get a feel for these tools, I created the following gene annotation network. The Cypher commands I used are discussed in this post, followed by a demonstration of querying the database. Creating the Graph Database We are creating the following […]