• Publications
  • Influence
GrGen: A Fast SPO-Based Graph Rewriting Tool
TLDR
We present GrGen, a generative programming system for graph rewriting, which applies heuristic optimizations. Expand
SWPS3 – fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and ×86/SSE2
TLDR
We present swps3, a vectorized implementation of the Smith-Waterman local alignment algorithm optimized for both the Cell/BE and ×86 architectures. Expand
Markov Models of Amino Acid Substitution to Study Proteins with Intrinsically Disordered Regions
Background Intrinsically disordered proteins (IDPs) or proteins with disordered regions (IDRs) do not have a well-defined tertiary structure, but perform a multitude of functions, often relying onExpand
The Development of Human Resources During the Process of Economic and Structural Transformation in Poland
The problem and the solution. Is it possible to speak of national differences in human resource development (HRD) when the term itself is culturally dependent? One kind of solution is exemplifiedExpand
Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts
TLDR
The current understanding of the regulation of transcription does not keep the pace with the spectacular advances in the determination of genomic sequences. Expand
Graph-based modeling of tandem repeats improves global multiple sequence alignment
Tandem repeats (TRs) are often present in proteins with crucial functions, responsible for resistance, pathogenicity and associated with infectious or neurodegenerative diseases. This motivatesExpand
Fast and robust multiple sequence alignment with phylogeny-aware gap placement
  • A. Szalkowski
  • Biology, Computer Science
  • BMC Bioinformatics
  • 13 June 2012
TLDR
This is achieved by incorporating a graph-based sequence representation combined with the advantages of the phylogeny-aware gap placement algorithm of Prank. Expand
The ethical problems of personnel management in a transition economy
The major ethical questions occuring in the process of personnel management are reviewed. These issues become particularly pronounced in the transition countries during the process of transformationExpand
SWPS 3-fast multi-threaded vectorized
Background: We present swps3, a vectorized implementation of the Smith-Waterman local alignment algorithm optimized for both the Cell/BE and ×86 architectures. The paper describes swps3 and comparesExpand
Alignment of genomic sequences with intrinsic disorder and tandem repeats
TLDR
A prerequisite to most evolutionary analyses is a reliable prediction of homologous relationships in a given set of genomic sequences. Expand
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