Simon A. Berger

According to our database, Simon A. Berger authored at least 15 papers between 2009 and 2013.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2013

Phylogeny-Aware Placement and Alignment Methods for Short Reads.

Simon A. Berger

PhD thesis, 2013

libgapmis: extending short-read alignments.

Nikolaos Alachiotis, Simon A. Berger, Tomás Flouri, Solon P. Pissis, Alexandros Stamatakis

BMC Bioinform., 2013

A Generic Vectorization Scheme and a GPU Kernel for the Phylogenetic Likelihood Library.

Fernando Izquierdo-Carrasco, Nikolaos Alachiotis, Simon A. Berger, Tomás Flouri, Solon P. Pissis, Alexandros Stamatakis

Proceedings of the 2013 IEEE International Symposium on Parallel & Distributed Processing, 2013

2012

Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel.

Nikolaos Alachiotis, Simon A. Berger, Alexandros Stamatakis

BMC Bioinform., 2012

RAxML-Light: a tool for computing terabyte phylogenies.

Alexandros Stamatakis, Andre J. Aberer, Christian Goll, Stephen A. Smith, Simon A. Berger, Fernando Izquierdo-Carrasco

Bioinform., 2012

A versatile UDP/IP based PC ↔ FPGA communication platform.

Nikolaos Alachiotis, Simon A. Berger, Alexandros Stamatakis

Proceedings of the 2012 International Conference on Reconfigurable Computing and FPGAs, 2012

An Optimized Reconfigurable System for Computing the Phylogenetic Likelihood Function on DNA Data.

Simon A. Berger, Nikolaos Alachiotis, Alexandros Stamatakis

Proceedings of the 26th IEEE International Parallel and Distributed Processing Symposium Workshops & PhD Forum, 2012

Libgapmis: An ultrafast library for short-read single-gap alignment.

Nikolaos Alachiotis, Simon A. Berger, Tomás Flouri, Solon P. Pissis, Alexandros Stamatakis

Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012

2011

Aligning short reads to reference alignments and trees.

Simon A. Berger, Alexandros Stamatakis

Bioinform., 2011

Parallel Structural Graph Clustering.

Madeleine Seeland, Simon A. Berger, Alexandros Stamatakis, Stefan Kramer

Proceedings of the Machine Learning and Knowledge Discovery in Databases, 2011

Accelerating Phylogeny-Aware Short DNA Read Alignment with FPGAs.

Nikolaos Alachiotis, Simon A. Berger, Alexandros Stamatakis

Proceedings of the IEEE 19th Annual International Symposium on Field-Programmable Custom Computing Machines, 2011

2010

Evolutionary placement of short sequence reads on multi-core architectures.

Alexandros Stamatakis, Zsolt Komornik, Simon A. Berger

Proceedings of the 8th ACS/IEEE International Conference on Computer Systems and Applications, 2010

Accuracy of morphology-based phylogenetic fossil placement under Maximum Likelihood.

Simon A. Berger, Alexandros Stamatakis

Proceedings of the 8th ACS/IEEE International Conference on Computer Systems and Applications, 2010

Efficient PC-FPGA Communication over Gigabit Ethernet.

Nikolaos Alachiotis, Simon A. Berger, Alexandros Stamatakis

Proceedings of the 10th IEEE International Conference on Computer and Information Technology, 2010

2009

Accuracy and Performance of Single versus Double Precision Arithmetics for Maximum Likelihood Phylogeny Reconstruction.

Simon A. Berger, Alexandros Stamatakis

Proceedings of the Parallel Processing and Applied Mathematics, 2009