| GrGen: A fast SPO-based graph rewriting tool R Geiß, GV Batz, D Grund, S Hack, A Szalkowski International Conference on Graph Transformation, 383-397, 2006 | 270 | 2006 |
| SWPS3–fast multi-threaded vectorized Smith-Waterman for IBM Cell/BE and× 86/SSE2 A Szalkowski, C Ledergerber, P Krähenbühl, C Dessimoz BMC research notes 1 (1), 107, 2008 | 157 | 2008 |
| Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts AM Szalkowski, CD Schmid Briefings in bioinformatics 12 (6), 626-633, 2011 | 78 | 2011 |
| Markov models of amino acid substitution to study proteins with intrinsically disordered regions AM Szalkowski, M Anisimova PloS one 6 (5), e20488, 2011 | 47 | 2011 |
| Graph-based modeling of tandem repeats improves global multiple sequence alignment AM Szalkowski, M Anisimova Nucleic acids research 41 (17), e162-e162, 2013 | 32 | 2013 |
| Fast and robust multiple sequence alignment with phylogeny-aware gap placement AM Szalkowski BMC bioinformatics 13 (1), 129, 2012 | 28 | 2012 |
| Alignment of genomic sequences with intrinsic disorder and tandem repeats AM Szalkowski ETH Zurich, 2013 | 1 | 2013 |
