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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 […]

My PLoS-ONE Academic Editor Activity Summary

I recently received an email from PLoS-ONE summarizing my editorial activity for the first half of 2014. That’s a good thing: for one, I’m terrible at keeping track of all my service activities, and this helps in keeping them straight for my own annual activities report for my university. Second, I can see how I […]

Mozilla does scientific matchmaking between programmers and researchers

Mozilla Science Labs are looking top pair programmers and scientists. If you are a scientist in need of a programmer,  read the following, and then go to the website to see how to take it further. Thanks to Miami University’s Office for Advancement of Research and Scholarship  for bringing this to my attention.   Interdisciplinary Programming is […]

The genome of nerds

What makes a nerd a nerd? The stereotype is that of someone with a high intelligence, coupled with  social awkwardness and a wardrobe that may alert the fashion police. Now scientists think they may found the genomic links to these traits. There was always a strong suspicion of a genetic component in people that are […]

Data of thousands of ALS patients made available for analysis

This came up in my inbox. An interesting and welcome initiative, making thousands of ALS patients’ medical data available for analysis. It doesn’t seem to have any sequence data (so not a bioinformatic database), but there are heaps of biomedical data in which to sink your statistical teeth. Dear All, My name is Hagit Alon […]

Top 5 in Bioinformatics

I recently applied for a Moore Foundation grant in Data Science for the biological sciences. As part of the pre-application, I was asked to choose the top 5 works in data science in my field. Not so sure about data science, so I picked what I think are the most influential works in Bioinformatics, which […]

Support Vector Machines explained well

  Found this on Reddit r/machinelearning (In related news, there’s a machine learning subreddit. Wow.) Support Vector Machines (warning: Wikipedia dense article alert in previous link!) are learning models used for classification: which individuals in a population belong where? So… how do SVM and the mysterious “kernel” work? The user curious_thoughts asked for an explanation of […]

Carnival of Evolution, February 2014 Edition

Wow, I haven’t posted anything in quite a while. Things are busy outside blogoland. But committing this blog to the February edition of the Carnival of Evolution just made me do it, so here goes. We’ll do this by scales, bottom up. Molecular Prions are the infective agents that cause transmissible spongiform encephalopathies such as […]

BOSC 2014 Guess the Keynote Competition

(From Peter Cock, via the OBF News Blog)   We’re pleased to officially confirm that one of the two keynote speakers for the 15th annual Bioinformatics Open Source Conference (BOSC 2014) will be C. Titus Brown, as he announced on Twitter recently: Titus Brown (@ctitusbrown): Excited to be a keynote speaker at BOSC 2014! My […]

PhD position in Statistical Protein Structure Prediction, Copenhagen, Denmark

One of the major unsolved problems in bioinformatics is the protein folding problem: given an amino acid sequence, predict the overall three-dimensional structure of the corresponding protein. It has been known since the seminal work of Christian B. Anfinsen in the early seventies that the sequence of a protein encodes its structure, but the exact […]

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.  […]

For Ada Lovelace Day: Florence Nightingale

Note: a repost of a 2010 post I published for Ada Lovelace day. Unfortunately, I am too busy these days to write a new one. “Ada Lovelace Day is celebrated today to “…raise the profile of women in science, technology, engineering and maths.” So without further ado: She is a ‘ministering angel’ without any exaggeration […]

Why not use the Journal Impact Factor: a Seven Point Primer

After a series of tweets and a couple of Facebook posts about the problems of the Journal Impact Factor (JIF), I was approached by a colleague who asked me: “so why are you obsessed with this”?  My answer was that it irks me that I have to use the JIF next to my publications in […]

Quit smoking, more bacteria will like you

As an ex-smoker I can attest to this: quitting is  hard.  It can also make you fat. I gained quite a few kilos when I quit, and those took a long time to lose. Happily, these days I am spending money on running marathons rather than on cigarettes. Weight gain after smoking cessation is fairly […]

Postdoctoral Position in Computational Bioengineering (Rice University)

The Kavraki group at Rice University is looking to hire an enthusiastic postdoctoral researcher to enhance their research efforts in computational structural biology, drug design, and computational bioengineering. The group has significant expertise in the development of methods for motion planning for complex systems in robotics. Their Open Motion Planning Library (OMPL, http://ompl.kavrakilab.org) is now […]