About me

Felipe Fernandes Albrecht, also know as Π, or simply, Pí

I am a PhD candidate at Max Planck Institut für Informatk in the Computational Biology and Applied Algorithmics department, in the beaufiful city of Saarbrücken, Germany.

Now, I am doing a researching visit in the Professor Suyama Laboratory in the Medical Institue of Bioregulation, Kyushu University, Fukuoka, Japan.

Please, check my LinkedIn profile for a complete list and description of my professional experiences or access my Curriculum vitae.

Current work

DeepBlue - The idea behind DeepBlue is to provide a central access hub for large collections of epigenomic data and organize this data using controlled vocabularies. The data are kept in a central server, where they can be accessed, operated, and transfered as needed.

Albrecht,F., List,M., Bock,C. and Lengauer,T. (2016) DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets. Nucleic Acids Research, doi:10.1093/nar/gkw211

EpiExplorer - Originally developed by Konstantin Halachev, EpiExplorer is a web tool that allows you to use large reference epigenome datasets for your own analysis without complex scripting or laborous preprocessing. EpiExplorer was developed in the Computational Epigenetics Group at the Max-Planck Institute for Informatics. EpiExplorer was published at Genome Biology http://genomebiology.com/2012/13/10/R96.

Previous work

Genoogle - Genoogle aims to be a fast and sensible similar sequences searching software, which it uses parallelization and indexing techiniques. It was my masters thesis and a personal project. It is a free software (GPL 3) and it is write in Java language, working at Linux, Windows and Mac platforms. As I am not working on it anymore, I made the source code available at github. You can find more information in my notes about genoogle and also in its ArXiv.org paper: http://arxiv.org/abs/1507.02987


Publications & related work

DeepBlueR: large-scale epigenomic analysis in R. Albrecht, M List, C Bock, T Lengauer - Bioinformatics, 2017 - https://academic.oup.com/bioinformatics/article/3045024/DeepBlueR

Ten Simple Rules for Developing Usable Software in Computational Biology. M List, P Ebert, F Albrecht - PLOS Computational Biology, 2017 - http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005265

DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets. F Albrecht, M List, C Bock, T Lengauer - Nucleic acids research, 2016 - http://nar.oxfordjournals.org/content/44/W1/W581.short

Genoogle: an indexed and parallelized search engine for similar DNA sequences. F Albrecht - arXiv preprint arXiv:1507.02987, 2015 - https://arxiv.org/abs/1507.02987

EpiExplorer: live exploration and global analysis of large epigenomic datasets. K Halachev, H Bast, F Albrecht, T Lengauer, C Bock - Genome biology, 2012 - http://genomebiology.com/2012/13/10/R96

Algoritmo otimizado para comparação de sequências e busca em base de dados - My Master thesis (2009). Unfortunately in portuguese.

Numerical methods for inferring phylogenies - Presented by Professor Nelson Borges at the ICIAM07 about our work on distance methods for inferring phylogenies.

Parallel numerical methods for inferring Phylogenies and its poster - Abstract for X-Meeting 2007 (English, 2007). (Missing...)

A Distributed Algorithm for Phylogenetics Inference and its poster - Extended abstract for Brazilian Symposium on Bioinformatics (English, 2007).

Reconstrução filogenética em ambiente distribuido - My graduation final work (Portuguese, 2006). The Source code.

Técnicas para Comparação e Visualização de Similaridades entre Seqüências Genéticas - A good introduction on sequences comparison. (Portuguese, 2005).


"The same stream of life that runs through my veins night and day runs through the world and dances in rhythmic measures" - Rabindranath Tagore, Gitanjali (the most beautiful book ever)

"Hate is baggage. Life's too short to be pissed off all the time. It's just not worth it." - Danny Vinyard, American History X

"For whom does not has nothing, half is twice" (Para quem não tem nada, metade é dobro)

"No eternal reward will forgive us now for wasting the dawn" - Jim Morrison

"There is no dark side of the moon really. Matter of fact its all dark." - Pink Floyd

"They're taking the Hobbits to Isengard." - Legolas in The Lord of the Rings, The Two Towers



"Sentado quietamente,
Nada fazendo,
A primavera vem,
A grama cresce por si."

"Sitting quietly,
doing nothing,
the spring comes,
the grass grows by itself."