Accuracy and Performance of Single versus Double Precision Arithmetics for Maximum Likelihood Phylogeny Reconstruction. - Simon A. Berger; Alexandros Stamatakis (PPAM (2), 2009)

Efficient PC-FPGA Communication over Gigabit Ethernet. - Nikolaos Alachiotis 001; Simon A. Berger; Alexandros Stamatakis (CIT, 2010)

Accuracy of morphology-based phylogenetic fossil placement under Maximum Likelihood. - Simon A. Berger; Alexandros Stamatakis (AICCSA, 2010)

Evolutionary placement of short sequence reads on multi-core architectures. - Alexandros Stamatakis; Zsolt Komornik; Simon A. Berger (AICCSA, 2010)

Accelerating Phylogeny-Aware Short DNA Read Alignment with FPGAs. - Nikolaos Alachiotis 001; Simon A. Berger; Alexandros Stamatakis (FCCM, 2011)

Parallel Structural Graph Clustering. - Madeleine Seeland; Simon A. Berger; Alexandros Stamatakis; Stefan Kramer 001 (ECML/PKDD (3), 2011)

Aligning short reads to reference alignments and trees. - Simon A. Berger; Alexandros Stamatakis (Bioinform., 2011)

Libgapmis: An ultrafast library for short-read single-gap alignment. - Nikolaos Alachiotis 001; Simon A. Berger; Tomás Flouri; Solon P. Pissis; Alexandros Stamatakis (BIBM Workshops, 2012)

An Optimized Reconfigurable System for Computing the Phylogenetic Likelihood Function on DNA Data. - Simon A. Berger; Nikolaos Alachiotis 001; Alexandros Stamatakis (IPDPS Workshops, 2012)

A versatile UDP/IP based PC ↔ FPGA communication platform. - Nikolaos Alachiotis 001; Simon A. Berger; Alexandros Stamatakis (ReConFig, 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)

Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel. - Nikolaos Alachiotis 001; Simon A. Berger; Alexandros Stamatakis (BMC Bioinform., 2012)

A Generic Vectorization Scheme and a GPU Kernel for the Phylogenetic Likelihood Library. - Fernando Izquierdo-Carrasco; Nikolaos Alachiotis 001; Simon A. Berger; Tomás Flouri; Solon P. Pissis; Alexandros Stamatakis (IPDPS Workshops, 2013)

libgapmis: extending short-read alignments. - Nikolaos Alachiotis 001; Simon A. Berger; Tomás Flouri; Solon P. Pissis; Alexandros Stamatakis (BMC Bioinform., 2013)

Phylogeny-Aware Placement and Alignment Methods for Short Reads. - Simon A. Berger (2013)