Carles Fenollosa

Abstract

I'm a research engineer, specialized in bioinformatics and with a background in artificial intelligence and data mining.

Currently I'm working on a technology transfer project, re-engineering published methods into an integrated platform for drug design and personalized medicine. This is a very challenging but interesting software engineering project with a lot of R+D and huge computing and data requirements.

As a research technician, I have contributed to several projects on DNA and protein structure, genomics and drug design.

Keywords: biology, biomedicine, bioinformatics, molecular biology, modeling, DNA, proteins, molecular dynamics, promoters, gene regulation, molecular similarity, drug design, chemoinformatics, statistics, databases, phylogenetics, genetics, genomics, nucleosomes, protein flexibility, data mining, physical properties, H-NS, artificial intelligence, data mining, personalized medicine, unix, linux, programming, startups

Publications

Most recent first. If you need a copy of a paper for research purposes, please send me an e-mail. Please keep in mind that I am not pursuing an academic career, so my scientific output is low.

• Hospital M, Andrio P, Fenollosa C, Cicin-Sain D, Orozco M, Gelpí JL.
  MDWeb and MDMoby: An integrated web-based platform for molecular dynamics simulations
  Bioinformatics (2012) 28(9): 1278-1279. doi:10.1093/bioinformatics/bts139
• Meyer T, D'Abramo M, Hospital A, Rueda M, Ferrer-Costa C, Pérez A, Carrillo O, Camps J, Fenollosa C, Repchevsky D, Gelpí JL, Orozco M.
  MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories.
  Structure 2010 Nov 10;18(11):1399-1409. doi:10.1016/j.str.2010.07.013
• Goñi JR, Fenollosa C, Pérez A, Torrents D, Orozco M.
  DNAlive: a tool for the physical analysis of DNA at the genomic scale.
  Bioinformatics 2008 Aug 1;24(15):1731-2. Epub 2008 Jun 9. doi:10.1093/bioinformatics/btn259

Education

• MSc in Artificial Intelligence, UPC - Barcelona Tech (2008)
  • Thesis: Using AI techniques to determine promoter location based on DNA structure calculations.
  • Directors: Javier Vázquez-Salceda and Ramon Goñi
• Computer Engineering, UPC - Barcelona Tech (2008)

Software

Some software and projects I've contributed to

• ProStar, a promoter detector based on physical properties.
• DNAlive, an online tool to compute and visualize DNA physical properties.
• PCAsuite, a suite to compress Molecular Dynamics trajectories.
• MoDEL, a Molecular Dynamics library.
• MDWeb, a web site to prepare and run protein Molecular Dynamics
• [coming soon] a drug discovery platform

Programming

I love GUIs but spend many time on the command line when I really need to be productive. Here are some interesting tutorials, cheat sheets and random links which can speed your productivity up.

Blog

I have a simple blog named Waiting for the jobs to finish which I use to develop some tips regarding my research.

As a curiosity, the blog is managed by a single homemade bash script which parses the entries and generates all the pages.

I also have a favorite articles list with links to long, insightful walls of text covering topics like computing, startups and the internet. I curate content from sources like Reddit or Hacker news. You can also subscribe to its RSS feed, I promise not to overload you with references.

Funny papers

This is a collection of papers I find weird, funny, or just caught my attention. I don't mean to bash other people's work; I believe in the scientific process. Referees of the field are the most able people to decide if something is worth publishing.

But you know, some are really funny.

Congresses

I keep this record mostly for reference purposes. If you need a copy of the presentation or any further information, please send me an e-mail.

• ICREA Conference on Network Medicine Approaches to Human Disease: From computer to the Clinics, 2011. Attendance.
• Exascale Challenges in Computational Biology, 2010. Attendance.
• X Jornadas de Bioinformática, 2010. Attendance.
• Expanding the frontiers of molecular dynamics simulations in biology, 2009. Attendance.
• VII Reunión de Ácidos Nucleicos y Nucleósidos, 2009. Using DNA Physical Properties to Determine Biological Markers. Oral contribution.
• International Workshop in Memoriam of Ángel Ramírez Ortiz, 2009. Attendance.
• Grand Challenges in Computational Biology, 2008. Attendance
• VIII Jornadas Nacionales de Bioinformática, 2008. DNAlive: a tool for a realistic representation of the DNA at a genomic scale. Written contribution.

Resources

Links to the institutions which help me with my research

• The Spanish Ministry of Science and Innovation for the PTA grants.
• The Catalan Government for the VALOR grants.
• The BSC-CNS hosts me and provides computing power and resources.
• MMB, my research group.
• Also thanks to the INB, the IRB Barcelona and the PCB.

About me

In my free time: music, journalism, sports, art, the internet, beer and good company.

• My personal page, with links to some of the online stuff I use/produce.
• Linkedin profile with my resume.
• Facebook for friends.
• Twitter, mostly politics, with a hint of computing.
• Spotify with my favorite music.