Research Interests

I am now working on bioinformatics algorithms for sequence comparison, motif finding, and data management. Furthermore, I am interested in modelling and simulation of regulatory and signalling networks.

My PhD work consisted of the study parallel algorithms, parallel programming models, and algorithms for string comparison.

During my M.Sc. by research, I looked at algorithms and practicality of bulk-synchronous parallel algorithms.

You can find links to my talks and publications below.

Publications

Peter Krusche and Alexander Tiskin. New algorithms for efficient parallel string comparison. In proceedings of SPAA 2010, pp. 209-216. 2010 [doi]

Peter Krusche and Alexander Tiskin. Longest increasing subsequences in scalable time and memory. In proceedings of PPAM 2009 (1), pp. 176-185. 2009 [doi]

Peter Krusche and Alexander Tiskin. Computing Alignment Plots Efficiently. In Proceedings of ParCo 2009 // Advances in Parallel Computing, Volume 19: Parallel Computing: From Multicores and GPU's to Petascale, pp. 158-165. 2009 [preliminary version on arXiv, final version: link]

Peter Krusche and Alexander Tiskin. String comparison by transposition networks. In London Algorithmics 2008: Theory and Practice, vol. 11 of Texts in Algorithmics, College Publications, 2009. [arXiv] [Publisher’s HTML]

Peter Krusche and Alexander Tiskin. Efficient parallel string comparison. In Proceedings of ParCo, vol. 38 of NIC Series, John von Neumann Institute for Computing, pp. 193-200, 2007. [HTML+PDF]

Peter Krusche and Alexander Tiskin. Effcient Longest Common Subsequence Computation using Bulk-Synchronous Parallelism. In proceedings of ICCSA 2006, LNCS 3984, pp. 165-174, 2006. [doi]

Peter Krusche. Experimental evaluation of BSP programming libraries. Parallel Processing Letters 18(1): 7-21 (2008) [doi]

Talks

Slides for the talk at SPAA 2010 in Santorini, Greece. [PDF]

Slides for the talk at LSD/LAW 2010 at King's College London. [PDF]

Slides for the talk at PPAM 2009 in Wroclaw, Poland. [PDF]

Slides for the talk at ParCo 2009 in Lyon, France. [PDF]

Slides for the talk at the T&MC Workshop 2009. [PDF]

Slides for the talk at WPCCS'08. [PDF]

Slides for the talk at ParCo 2007 in Jülich, Germany, 4th of September 2007: [PDF].

Slides for the talk at the AFM seminar, 23rd of April 2007: [PDF].

Slides for the talk given at WPCCS'06: [PDF].

Slides for the talk given at the PDC'06 workshop at ICCSA 2006 in Glasgow: [PPT].

Slides for the talk at HLPP 2005 workshop at Warwick. [PDF].

MSc Thesis: Experimental Evaluation of BSP Algorithms

Here is the thesis in PDF format for 2-sided printing. There is also a version with hyperlinks for easier on-screen reading.

Here are some patches used in the thesis for The Oxford BSP Toolset and PUB to compile using icc on the SGI Altix machine at the Centre for Scientific Computing (this is probably of historic interest only by now...).

PhD Thesis: Parallel String Alignments: Algorithms and Applications

Here is a link to the the thesis in PDF format. The implementation of some of the algorithms from the thesis can be found here (this code is currently being developed further internally here at WSBC, but I will post new stable releases on Google code). My PhD supervisor was Dr. Alexander Tiskin.