Displaying posts tagged with

“protein function prediction”

Predicting protein function: what’s new?

(New: the paper was recently published in Genome Biology!) Long time readers of this blog (hi mom!) know that I am working with many other people in an effort called CAFA: the Critical Assessment of protein Function Annotation. This is a challenge that many research groups participate in, and its goal is to determine how […]

Estimating how much we don’t know

Or: “Estimating how much we don’t know, and how much it can hurt us”. This post is about a paper I published recently with Predrag Radivojac’s group at Indiana University, who lead the study. One of the main activities I’m involved with is CAFA,* the critical assessment of function annotations.   The general idea of CAFA […]

The 2014 International Biocuration Conference

Hi all, I’m happy to say that the 2014 International Biocuration Conference is off to a good start. I have attended this excellent meeting twice before, and this year I am honored to be on the organizing committee. There was a lot of work behind the scenes, and we have agreed on five session topics.  […]

The Second Critical Assessment of protein Function Annotations

Announcing CAFA 2: The Second Critical Assessment of protein Function Annotations Friends and Colleagues, We are pleased to announce the Second Critical Assessment of protein Function Annotation (CAFA) challenge. In CAFA 2, we would like to evaluate the performance of protein function prediction tools/methods (in old and new scenarios) and also expand the challenge to […]

Automated Function Prediction: Submit your abstracts by Saturday

You have until Friday Saturday, April 20th to submit your abstracts to the Automated Function Prediction meeting, an ISMB 2013 Special Interest Group and CAFA: Critical Assessment of Function Annotations. Keynote speakers: Patricia Babbitt, University of California, San Francisco. Protein similarity networks: Identification of functional trends from the context of sequence similarity Alex Bateman, European Bioinformatics […]

Annotating Proteins in the Uncanny Valley

The Uncanny Valley Every day, software appears to do more things that we thought were exclusively in the human realm. Like beating a grandmaster in chess,  or carrying out a conversation. I say “appears” because there is obviously no self-aware intelligence involved, as this rather bizarre conversation between  Cleverbots demonstrates. For humans, playing chess  and carrying […]

Biocuration 2012

  Great meeting:  Biocuration 2012, Georgetown University, DC.  When I leave a meeting with my head exploding with new ideas and a need to try them all out at once, I know I got my money’s worth, and then some. Even a three hour flight delay followed by discovering my car with a dead battery […]