I collaborate with several investigators on gene expression projects using both microarray and RNA-seq. After I show a collaborator which genes are dysregulated in a particular condition or tissue, the most common question I get is "what are the transc...
Since the near beginning of genome-wide association studies, the PLINK software package (developed by Shaun Purcell’s group at the Broad Institute and MGH) has been the standard for manipulating the large-scale data produced by these studies.&...
Automatically Archiving Twitter Results Ever since Twitter gamed its own API and killed off great services like IFTTT triggers, I've been looking for a way to automatically archive tweets containing certain search terms of interest to me. Twitter's bu...
A handful of good metagenomics papers have come out over the last few months. Below I've linked to and copied my evaluation of each of these articles from F1000. ... 1. Willner, Dana, and Philip Hugenholtz. "From deep sequencing to viral tagging...
I frequently get asked to recommend workshops or online learning resources for bioinformatics, genomics, statistics, and programming. I compiled a list of both online learning resources and in-person workshops (preferentially highlighting those where w...
For over 15 years, members of the computer science, machine learning, and data mining communities have gathered in a beautiful European location each spring to share ideas about biologically-inspired computation. Stemming from the work of John Ho...
Metagenomics is the study of DNA collected from environmental samples (e.g., seawater, soil, acid mine drainage, the human gut, sputum, pus, etc.). While traditional microbial genomics typically means sequencing a pure cultured isolate, metagenomics in...
Editor’s note: With the sequestration deadline hours away, the career of many young US scientists is on the line. In this guest post, our colleague Steven Salzberg , an avid defender of NIH and its peer review process, tells us why now more … Continue reading →
If you ever write code for scientific computing (chances are you do if you're here), stop what you're doing and spend 8 minutes reading this open-access paper: Wilson et al. Best Practices for Scientific Computing. arXiv:1210.0530 (2012). (Direct li...
Two of the most common questions at the beginning of an RNA-seq experiments are "how many reads do I need?" and "how many replicates do I need?". This paper describes a web application for designing RNA-seq applications that calculates an appropriate s...
