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Books and Theses
- 2013
[b1]Simon A. Berger:
Phylogeny-Aware Placement and Alignment Methods for Short Reads. Karlsruhe Institute of Technology, 2013
Journal Articles
- 2013
- [j4]Nikolaos Alachiotis, Simon A. Berger, Tomás Flouri
, Solon P. Pissis, Alexandros Stamatakis:
libgapmis: extending short-read alignments. BMC Bioinform. 14(S-11): S4 (2013) - 2012
- [j3]Alexandros Stamatakis, Andre J. Aberer, Christian Goll, Stephen A. Smith, Simon A. Berger, Fernando Izquierdo-Carrasco:
RAxML-Light: a tool for computing terabyte phylogenies. Bioinform. 28(15): 2064-2066 (2012) - [j2]Nikolaos Alachiotis, Simon A. Berger, Alexandros Stamatakis:
Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel. BMC Bioinform. 13: 196 (2012) - 2011
- [j1]Simon A. Berger, Alexandros Stamatakis:
Aligning short reads to reference alignments and trees. Bioinform. 27(15): 2068-2075 (2011)
Conference and Workshop Papers
- 2013
- [c10]Fernando Izquierdo-Carrasco, Nikolaos Alachiotis, Simon A. Berger, Tomás Flouri, Solon P. Pissis, Alexandros Stamatakis:
A Generic Vectorization Scheme and a GPU Kernel for the Phylogenetic Likelihood Library. IPDPS Workshops 2013: 530-538 - 2012
- [c9]Nikolaos Alachiotis, Simon A. Berger, Tomás Flouri, Solon P. Pissis, Alexandros Stamatakis:
Libgapmis: An ultrafast library for short-read single-gap alignment. BIBM Workshops 2012: 688-695 - [c8]Simon A. Berger, Nikolaos Alachiotis, Alexandros Stamatakis:
An Optimized Reconfigurable System for Computing the Phylogenetic Likelihood Function on DNA Data. IPDPS Workshops 2012: 352-359 - [c7]Nikolaos Alachiotis, Simon A. Berger, Alexandros Stamatakis:
A versatile UDP/IP based PC ↔ FPGA communication platform. ReConFig 2012: 1-6 - 2011
- [c6]Nikolaos Alachiotis, Simon A. Berger, Alexandros Stamatakis:
Accelerating Phylogeny-Aware Short DNA Read Alignment with FPGAs. FCCM 2011: 226-233 - [c5]Madeleine Seeland, Simon A. Berger, Alexandros Stamatakis, Stefan Kramer:
Parallel Structural Graph Clustering. ECML/PKDD (3) 2011: 256-272 - 2010
- [c4]Nikolaos Alachiotis, Simon A. Berger, Alexandros Stamatakis:
Efficient PC-FPGA Communication over Gigabit Ethernet. CIT 2010: 1727-1734 - [c3]Simon A. Berger, Alexandros Stamatakis:
Accuracy of morphology-based phylogenetic fossil placement under Maximum Likelihood. AICCSA 2010: 1-9 - [c2]Alexandros Stamatakis, Zsolt Komornik, Simon A. Berger:
Evolutionary placement of short sequence reads on multi-core architectures. AICCSA 2010: 1-8 - 2009
- [c1]Simon A. Berger, Alexandros Stamatakis:
Accuracy and Performance of Single versus Double Precision Arithmetics for Maximum Likelihood Phylogeny Reconstruction. PPAM (2) 2009: 270-279
Coauthor Index
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