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Bioinformatics

Category archives for Bioinformatics

In our series on why $1000 genomes cost $2000, I raised the issue that the $1000 genome is a value based on simplistic calculations that do not account for the costs of confirming the results. Next, I discussed how errors are a natural occurrence of the many processing steps required to sequence DNA and why…

Bio Databases 2014

By @finchtalk (Todd Smith) In 2014 and beyond Finchtalk will be contributing to Digitalbio’s blog at this site. We kick off 2014 with Finchtalk’s traditional post on the annual database issue from Nucleic Acids Research (NAR). Biological data and databases are ever expanding. This year was no exception as the number of databases tracked by…

I had the good fortune on Thursday to hear a fascinating talk on deep transcriptome analysis by Chris Mason, Assistant Professor, at the Institute for Computational Biomedicine at Cornell University.  Several intriguing observations were presented during the talk.  I’ll present the key points first and then discuss the data. These data concern the human transcriptome,…

One of my hobbies lately has been to get either RNA seq or microarray data from GEO and do quick analyses. Not only is this fun, I can find good examples to use for teaching biology. One of these fun examples comes from some Arabidopsis data. In this experiment, some poor little seedlings were taken…

Is there a place for citizen scientists in the world of digital biology? Many of the citizen science projects that I’ve been reading about have a common structure. There’s a University lab at the top, outreach educators in the middle, and a group of citizens out in the field collecting data. After the data are…

These days, DNA sequencing happens in one of three ways. In the early days of DNA sequencing (like the 80′s), labs prepared their own samples, sequenced those samples, and analyzed their results. Some labs still do this. Then, in the 90′s, genome centers came along. Genome centers are like giant factories that manufacture sequence data.…

What do you call a biologist who uses bioinformatics tools to do research, but doesn’t program? You don’t know? Neither does anyone else.

I often get questions about bioinformatics, bioinformatics jobs and career paths. Most of the questions reflect a general sense of confusion between creating bioinformatics resources and using them. Bioinformatics is unique in this sense. No one confuses writing a package like Photoshop with being a photographer, yet for some odd reason, people seem to expect…

For many years, I’ve been perfectly content to work with small numbers of things. Working with one gene or one protein is great. Even small groups of genes are okay. I’m fine with alternatively spliced genes with multiple transcripts, or multiple polymorphisms, or genes in multi-gene families, or groups of genes in operons. But I…

For those of you who may have been wondering where I’ve been, these past few weeks have seen me grading final projects, writing a chapter on analyzing Next Gen DNA sequencing data for the Current Protocols series, and flying back and forth between Seattle and various meetings elsewhere in the U.S. It will probably take…