Research Overview

parallel computing, bioinformatics, systems biology, statistics

Research Interests

I am interested in computation, statistics and data visualisation. I work as a consultant for statistical/computational methods at Novartis.

Note that this is my personal page. Content here is my own responsibility and not connected to/endorsed by my employer.

Until June 2018, I worked at Illumina as a bioinformatics scientist. I worked on variant calling / genotyping on human whole-genome sequencing data, and among other things worked on tools like hap.py for comparing variant calls to gold standard data, truth datasets (Platinum Genomes, Polaris), and a structural variant genotyper named paragraph.

I also did a post-doc in systems biology at the University of Warwick, where I worked on sequence conservation and Motif finding for regulatory sequences (see here for a video we made about some of this work), and on imaging timeseries analysis and theoretical modelling of the circadian clock and of the cell cycle in single cells.

Before this, I did a Ph.D. and an M.Sc. by research in Computer Science at the Dept. of Computer Science, also at Warwick. I worked on parallel algorithms and string comparison.

Before that, I studied computer science at the University of Chemnitz.

Publications

Genomics

2018

P. Krusche, L. Trigg, P. C. Boutros, C. E. Mason, F. M. De La Vega, B. L. Moore, M. Gonzalez-Porta, M. A. Eberle, Z. Tezak, S. Labadibi, R. Truty, G. Asimenos, B. Funke, M. Fleharty, M. Salit, J. M. Zook, The Global Alliance for Genomics and Health Benchmarking Team. Best Practices for Benchmarking Germline Small Variant Calls in Human Genomes, pre-print on bioRxiv doi.org/10.1101/270157, github.com/ga4gh/benchmarking-tools / github.com/illumina/hap.py.

P. Krusche, E. Dolzhenko, N. Johnson, M.A. Bekritsky, A. Gross, B.R. Lajoie, V. Rajan, Z. Kingsbury, S.J. Humphray, S.S. Ajay, R.J. Taft, D.R. Bentley, M.A. Eberle. A graph method for population genotyping of structural variants. Poster at ASHG 2017, github.com/illumina/paragraph.

2017

P. Krusche, E. Dolzhenko, N. Johnson, M.A. Bekritsky, A. Gross, B.R. Lajoie, V. Rajan, N. Gonzaludo, Z. Kingsbury, S.J. Humphray, S.S. Ajay, R.J. Taft, D.R. Bentley, M.A. Eberle. Polaris: A collection of 220 publicly available whole genomes for sharing validated structural variants. Poster at ASHG 2017, github.com/illumina/polaris.

S. Kim, K. Scheffler, A. L. Halpern, M. A. Bekritsky, E. Noh, M. Källberg, X. Chen, D. Beyter, P. Krusche, C. T. Saunders. Strelka2: Fast and accurate variant calling for clinical sequencing applications. BioArxiv: doi:10.1101/192872, Poster at WABI 2017, github.com/illumina/strelka2.

M.A. Eberle, E. Fritzilas, P. Krusche, M. Källberg, B. Moore, M.A. Bekritsky, Z. Iqbal, H. Chuang, S.J. Humphray, A. Halpern, S. Kruglyak, E.H. Margulies, G. McVean and D.R. Bentley. A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree. Genome Research, 27:157-164. doi:10.1101/gr.210500.116, 2017.

Systems Biology

 2015

Davies, N.J. et al., 2015. Analysis of 5’ gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals. BMC Evolutionary Biology, 15(1), p.426. Available at: http://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-015-0499-6.

Contribution: Some of the analysis in this paper is based on the APPLES promoter sequence analysis software package.

 2014

Feillet, C. et al., 2014. Phase locking and multiple oscillating attractors for the coupled mammalian clock and cell cycle. Proceedings of the National Academy of Sciences. Available at: http://pnas.org/content/early/2014/06/18/1320474111.

Contribution: Data analysis and visualisation, mathematical modelling.

 2013

Laranjeiro, R. et al., 2013. Cyclin-dependent kinase inhibitor p20 controls circadian cell-cycle timing. PNAS 2013, published ahead of print April 8. Available at: http://www.ncbi.nlm.nih.gov/pubmed/23569261.

Contribution: Bioinformatic sequence analysis and phylogenetic tree construction.

 2012

Baxter, L. et al., 2012. Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants. The Plant Cell, 24(10), pp.3949–3965. Available at: http://www.ncbi.nlm.nih.gov/pubmed/23110901.

Contribution: Code and documentation to the APPLES promoter sequence analysis software package.

2010

Picot, E. et al., 2010. Evolutionary analysis of regulatory sequences (EARS) in plants. The Plant journal : for cell and molecular biology, 64(1), pp.165–176. Available at: http://www.ncbi.nlm.nih.gov/pubmed/20659275.

Contribution: Fast alignment-plot code in C++/Assembler for EARS Web Tool.

Parallel Algorithms

2010

Krusche, P. & Tiskin, A., 2010. New algorithms for efficient parallel string comparison. In the 22nd ACM symposium. New York, New York, USA: ACM Press, pp. 209–216. Available at: http://portal.acm.org/citation.cfm?doid=1810479.1810521.

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

Krusche, P. & Tiskin, A., 2010. Computing alignment plots efficiently. In B. Chapman et al., eds. Parallel Computing: From Multicores and GPU’s to Petascale. pp. 158–165. Available at: http://www.booksonline.iospress.nl/Content/View.aspx?piid=16553.

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

Slides for the talk at LSD/LAW 2010 at King’s College London.

Krusche, P. & Tiskin, A., 2010. Parallel longest increasing subsequences in scalable time and memory. Parallel Processing and Applied Mathematics, 6067, pp.176–185. Available at: http://link.springer.com/chapter/10.1007%2F978-3-642-14390-8_19.

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

Slides for the talk at the T&MC Workshop 2009.

2009

Krusche, P. & Tiskin, A., 2009. String comparison by transposition networks. Texts in Algorithmics, Vol. 11 of London Algorithmics 2008: Theory and Practice. Available at: http://www.collegepublications.co.uk/algorithmics/?00011 and http://arxiv.org/abs/0903.3579.

Slides for the talk at WPCCS’08.

2007

Krusche, P. & Tiskin, A., 2007. Efficient parallel string comparison. In Proceedings of ParCo 2007, vol. 38 of NIC Series. John von Neumann Institute for Computing, pp. 193–200. Available at: http://www.fz-juelich.de/nic-series/volume38/volume38.html.

Slides for the talk at ParCo 2007 in Jülich, Germany, 4th of September 2007

Slides for the talk at the AFM seminar at Warwick, 23rd of April 2007

2006

Krusche, P. & Tiskin, A., 2006. Efficient Longest Common Subsequence Computation Using Bulk-Synchronous Parallelism. In Proceedings of ICCSA 2006, LNCS 3984. pp. 165–174.

Slides for the talk given at the PDC’06 workshop at ICCSA 2006 in Glasgow

Slides for the talk given at WPCCS’06

2005

Krusche, P., 2005. Experimental Evalution of BSP Programming Libraries. Parallel Processing Letters, 18(1), pp.7–21.

Slides from the HLPP 2005 workshop at Warwick