Who am I?

Luis Pedro Coelho

I am a computational biologist. I work at the European Molecular Biology Laboratory (EMBL) in Peer Bork's group in microbial community analysis using metagenomics. I have a PhD from Carnegie Mellon University (2011), where I worked on bioimage informatics for subcellular location analysis with Bob Murphy.

I blog about science at metarabbit.wordpress.com and tweet (mostly about sciency things) as @luispedrocoelho. I co-wrote Building Machine Learning Systems with Python.

My Erdös-Bacon number is 7.

Research Interests

Technical version: I am interested in combining meta'omics (methods that obtain high-throughput information on microbial communities such as metagenomics and metatranscriptomics) analysis with bioimage informatics using machine learning approaches. In particular, in obtaining biological knowledge by exploiting large-scale datasets of mixed communities by a sequencing and imaging to be able to derive observations about the relationship between the genotypes and phenotypes. This research can answer questions such as do the measures of genomic biodiversity agree with measures of phenotypic biodiversity?

My work is a mix of of method development and applications. In methodological terms, I worry a lot about correct evaluation of methods and avoiding over-inflated measures of performance. I also work in scaling up methods to work on large-scale environments.

Not-so technical version: With modern technology, namely robotic instruments, it is easy to acquire a lot of microscopic pictures. It is also possible to acquire large sequence datasets with the DNA of many organisms. I use these two families of technologies to investigate what is happening in mixed microbial communities such as the one in our guts, the microbiome.

I work both on developing new computer methods (software) for these tasks as well as on specific biological problems.

Recent Publications

All publications...

Upcoming Travels & Talks

April 3-4 I will be at the University of Southern Denmark teaching at a software carpentry bootcamp.

July 22-29 I will be in Lisbon for the LxMLS 2014

Email me if you want to set up meetings at any of these opportunities.

Other News

(See above for papers & travels)

February 2014 I'm now a certified Software Carpentry instructor

November 2013 I'm a member of the programme committee for DILS 2014 (10th International Conference on Data Integration in the Life Sciences)

July 2013 I got a prize in the ICSB Computational Biology Wikipedia Competition for work on the Bioimage Informatics page

July 2013 My book Building Machine Learning Systems with Python is now published

older news items ...

Article filed in categories: Personal