Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

A Code for evolutionary biology

17.11.2010
Alexandros (Alexis) Stamatakis heads the new research group “Scientific Computing” at the Heidelberg Institute for Theoretical Studies (HITS) – Software and supercomputing for large-scale biological data analysis.

His own roots are international: born in Saarbrücken, Alexis Stamatakis was raised by a German mother and a Greek father and received his “Abitur” at the German school in Athens. As a computer scientist, one of his research interests is the evolutionary history of plants, which is quite unusual.

But his motivation for that interest is data-driven: He is fascinated by analyzing large trees, because of the associated grand computational challenges that entail problems from theoretical computer science as well as from parallel computing. “Evolutionary biologists are currently generating a molecular data avalanche that is even hard to analyze on the most powerful supercomputers“, says the 34 year old scientist. “The challenge for computer science is to develop programs and methods for calculating evolutionary trees and to discover knowledge in the mass of molecular data.”

As head of the new research group “Scientific Computing” (SCO) at HITS, Alexis and his students develop methods and tools to reconstruct and post-process evolutionary (phylogenetic) trees. He also works on designing dedicated computer architectures for reconstructing phylogenies. Moreover, he is responsible for the new parallel (super-) computer system that is currently being installed at HITS and shares his expert knowledge in parallel computer architectures and parallel programming with the other five HITS research groups. At present, ten scientists and system administrators form part of SCO. In 2011 additional PhD students, PostDocs, and visiting scientists will join the group to establish a strong research program in computational molecular evolution.

“Alexis is a young, ambitious scientist who stands for the goals and philosophy of HITS. Computational methods help us to cope with the current data flood in the life sciences and to extract new knowledge from this data” says the founder of HITS, Klaus Tschira.

Alexis studied computer sciences at Munich, Lyon (École Normale Supérieure), Paris, and Madrid. In 2004 he received his PhD from the Technical University of Munich. In 2007 and 2008 he declined positions as assistant professor in the US. He worked as a postdoctoral fellow in Crete and the Swiss Federal Institute of Technology at Lausanne. In 2008 Stamatakis returned to Munich where he worked at the LMU and the TU Munich as head of a junior research group under the auspices of the Emmy-Noether program of the German Science Foundation (DFG).

His primary research objective is to develop tools for reconstructing the evolution of all living beings for which molecular (genetic) data is available, with the still distant goal to reconstruct the tree of life. Most tree reconstruction methods/algorithms face a fundamental problem which computer scientists term NP-hard (non deterministic polynomial time hard). Assume trying to reconstruct the evolutionary history based on the DNA data of fifty organisms using a scoring function (optimality criterion) that tells us how well the data fits a specific evolutionary tree (an evolutionary hypothesis).

NP-hardness means that it is impossible to score all possible trees in order to find the best one, because there are simply too many trees. “Even using all the computing power in the world, we would have to wait too long to find the optimal tree”, Alexis explains. “However, recently published phylogenetic trees don’t comprise only fifty but several thousands of organisms.”

Alexis developed the program RAxML, which allows for reconstructing huge trees, of up to 120,000 organisms. By now, his software is one of the most popular applications for phylogenetic analysis and a paper describing RAxML ranks among the most frequently cited publications in computer science that were published in the last 5 years. “RAxML is publicly available as open source code. Thereby, we provide a tool that biologists around the world can use entirely free of charge to analyze their data.“ This year, RAxML was also integrated into the SPEC-Benchmark suite for parallel computing. The programs in the SPEC benchmark suite are deployed to assess the performance of supercomputer systems.

Alexis is part of the iPlant collaborative project that was initiated by the American National Science Foundation (NSF). iPlant aims to develop and make available new computational methods and cyberinfrastructure solutions to address an evolving array of grand challenges in the plant sciences. Alexandros Stamatakis is the only involved European scientist. The German Science Foundation (DFG) is funding him in conjunction with iPlant. Alexis also is the first computer scientist to be elected as member of the council of the „Society of Systematic Biologists“.

Alexis will continue collaborations with several institutions such as the Dunn Lab at Brown University, Rhode Island/USA. Two of His PhD students benefit from an exchange programme with Imperial College London that is funded by the German Academic Exchange Service (DAAD). In cooperation with researchers from the European Molecular Biology Laboratory (EMBL), the European Bioinformatics Institute (EBI), and the University College London, Alexis will organize the 3rd workshop on „Computational Molecular Evolution“. It will take place from April 10-21, 2011 at Hinxton, near Cambridge/UK. This workshop introduces Biologists to the usage and underlying theory of computational tools for evolutionary data analysis.

Further information, printable pictures and press contact:
Dr. Peter Saueressig
Public Relations
HITS Heidelberg Institute for Theoretical Studies
Tel: +49-6221-533-245
Fax: +49-6221-533-198
peter.saueressig@h-its.org
www.h-its.org
Scientific contact:
Dr. Alexandros Stamatakis
HITS Heidelberg Institute for Theoretical Studies
Tel: +49-6221-533-240
Fax: +49-6221-533-298
alexandros.stamatakis@h-its.org
www.h-its.org
HITS (Heidelberg Institute for Theoretical Studies) is a private, non-for-profit research institute. It was established in 2010 as a successor to the EML Research gGmbH. It gets its base funding from the Klaus Tschira Foundation, which was established in 1995. HITS gGmbH is jointly managed by Dr. h.c. Klaus Tschira and Prof. Dr.-Ing. Andreas Reuter.

Dr. Peter Saueressig | idw
Further information:
http://www.h-its.org
http://www.h-its.org/english/research/sco/index.php

More articles from Life Sciences:

nachricht Cryo-electron microscopy achieves unprecedented resolution using new computational methods
24.03.2017 | DOE/Lawrence Berkeley National Laboratory

nachricht How cheetahs stay fit and healthy
24.03.2017 | Forschungsverbund Berlin e.V.

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Giant Magnetic Fields in the Universe

Astronomers from Bonn and Tautenburg in Thuringia (Germany) used the 100-m radio telescope at Effelsberg to observe several galaxy clusters. At the edges of these large accumulations of dark matter, stellar systems (galaxies), hot gas, and charged particles, they found magnetic fields that are exceptionally ordered over distances of many million light years. This makes them the most extended magnetic fields in the universe known so far.

The results will be published on March 22 in the journal „Astronomy & Astrophysics“.

Galaxy clusters are the largest gravitationally bound structures in the universe. With a typical extent of about 10 million light years, i.e. 100 times the...

Im Focus: Tracing down linear ubiquitination

Researchers at the Goethe University Frankfurt, together with partners from the University of Tübingen in Germany and Queen Mary University as well as Francis Crick Institute from London (UK) have developed a novel technology to decipher the secret ubiquitin code.

Ubiquitin is a small protein that can be linked to other cellular proteins, thereby controlling and modulating their functions. The attachment occurs in many...

Im Focus: Perovskite edges can be tuned for optoelectronic performance

Layered 2D material improves efficiency for solar cells and LEDs

In the eternal search for next generation high-efficiency solar cells and LEDs, scientists at Los Alamos National Laboratory and their partners are creating...

Im Focus: Polymer-coated silicon nanosheets as alternative to graphene: A perfect team for nanoelectronics

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are less stable. Now researchers at the Technical University of Munich (TUM) have, for the first time ever, produced a composite material combining silicon nanosheets and a polymer that is both UV-resistant and easy to process. This brings the scientists a significant step closer to industrial applications like flexible displays and photosensors.

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are...

Im Focus: Researchers Imitate Molecular Crowding in Cells

Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to simulate these confined natural conditions in artificial vesicles for the first time. As reported in the academic journal Small, the results are offering better insight into the development of nanoreactors and artificial organelles.

Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

International Land Use Symposium ILUS 2017: Call for Abstracts and Registration open

20.03.2017 | Event News

CONNECT 2017: International congress on connective tissue

14.03.2017 | Event News

ICTM Conference: Turbine Construction between Big Data and Additive Manufacturing

07.03.2017 | Event News

 
Latest News

Argon is not the 'dope' for metallic hydrogen

24.03.2017 | Materials Sciences

Astronomers find unexpected, dust-obscured star formation in distant galaxy

24.03.2017 | Physics and Astronomy

Gravitational wave kicks monster black hole out of galactic core

24.03.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>