Publications #
AI/ML/drug development, work done while at Novartis #
2024 #
Monod, Mélodie, et al. TorchSurv: A Lightweight Package for Deep Survival Analysis. arXiv:2404.10761, arXiv, 17 Apr. 2024. doi:10.48550/arXiv.2404.10761.
(contributed to Python package development & publication, see also https://github.com/Novartis/torchsurv)
2023 #
Coroller, Thibaud et al. Multi-Omics Investigation on the Prognostic and Predictive Factors in Metastatic Breast Cancer Using Data from Phase III Ribociclib Clinical Trials: A Statistical and Machine Learning Analysis Plan. Oncology, 2023. http://medrxiv.org/lookup/doi/10.1101/2023.08.30.23294367.
(contributed some notes on technical good data science practices)
2022 #
J. D. Ziegler, S. Subramaniam, M. Azzarito, O. Doyle, P. Krusche, T. Coroller. Multi-Modal Conditional GAN: Data Synthesis in the Medical Domain. NeurIPS 2022 Workshop on Synthetic Data for Empowering ML Research. 2022. on OpenReview
2021 #
Mallon, Ann-Marie et al. Advancing Data Science in Drug Development through an Innovative Computational Framework for Data Sharing and Statistical Analysis. BMC Medical Research Methodology 21.1 (2021): 250. BioMed Central. Web. 4 Nov. 2023. doi.org/10.1186/s12874-021-01409-4
(helped with some technical input)
Genomics, work done while at Illumina #
2019 #
S. Chen, P. Krusche, E. Dolzhenko, R.M. Sherman, R. Petrovski, F. Schlesinger, M. Kirsche, D.R. Bentley, M.C. Schatz, F. J. Sedlazeck, M.A. Eberle. Paragraph: A graph-based structural variant genotyper for short-read sequence data. pre-print on bioRxiv doi.org/10.1101/635011, github.com/illumina/paragraph, 2019.
E. Dolzhenko, V. Deshpande, F. Schlesinger, P. Krusche, R. Petrovski, S. Chen, D. Emig-Agius, A. Gross, G. Narzisi, B. Bowman, K. Scheffler, J. J.F.A. van Vugt, C. French, A. Sanchis-Juan, K. Ibáñez, A. Tucci, B. Lajoie, J. H. Veldink, L Raymond, R. J. Taft, D. R. Bentley, M. A. Eberle. ExpansionHunter: A sequence-graph based tool to analyze variation in short tandem repeat regions. Bioinformatics, btz431, doi:10.1093/bioinformatics/btz431, 2019. github.com/illumina/expansionhunter
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, Nature Biotechnology 37, 555–560 (2019), 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 (during my Postdoc) #
2015 #
N. J. Davies, P. Krusche, E. Tauber and S. Ott. 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, 2015. Available at: 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 #
C. Feillet, P. Krusche, F. Tamanini, R. C. Janssens, M. J. Downey, P. Martin, M. Teboul, S. Saito, F. A. Levi, T. Bretschneider, G. T. J. van der Horst, F. Delaunay, D. A. Rand, Phase locking and multiple oscillating attractors for the coupled mammalian clock and cell cycle. PNAS 111 (27) 9828-9833, 2014. doi:10.1073/pnas.1320474111
Contribution: Data analysis and visualisation, mathematical modelling.
2013 #
R. Laranjeiro, T. K. Tamai, E. Peyric, P. Krusche, S. Ott, D. Whitmore. Cyclin-dependent kinase inhibitor p20 controls circadian cell-cycle timing. PNAS 110 (17) 6835-6840; doi:10.1073/pnas.1217912110, 2013.
Contribution: Bioinformatic sequence analysis and phylogenetic tree construction.
2012 #
L. Baxter, A. Jironkin, R. Hickman, J. Moore, C. Barrington, P. Krusche, N. P. Dyer, V. Buchanan-Wollaston, A. Tiskin, J. Beynon, K. Denby, S. Ott. 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, 2012.
Contribution: Code and documentation to the APPLES promoter sequence analysis software package.
2010 #
E. Picot, P. Krusche, A. Tiskin, I. Carré, S. Ott. Evolutionary analysis of regulatory sequences (EARS) in plants. The Plant journal for cell and molecular biology, 64(1), pp.165–176; doi:10.1111/j.1365-313X.2010.04314.x. Available via: http://www.ncbi.nlm.nih.gov/pubmed/20659275, 2010.
Contribution: Fast alignment-plot code in C++/Assembler for EARS Web Tool.
Code available at github.com/pkrusche/seaweeds
Parallel Algorithms (during my PhD and MSc work) #
2010 #
P. Krusche, A. Tiskin. New algorithms for efficient parallel string comparison. SPAA '10: Proceedings of the twenty-second annual ACM symposium on Parallelism in algorithms and architectures, pp. 209–216; [doi:10.1145/1810479.1810521]{https://doi.org/10.1145/1810479.1810521}, 2010.
P. Krusche, A. Tiskin. Computing alignment plots efficiently. Parallel Computing: From Multicores and GPU's to Petascale, pp. 158-165, [http://www.booksonline.iospress.nl/Content/View.aspx?piid=16553]{http://www.booksonline.iospress.nl/Content/View.aspx?piid=16553}, 2010.
Slides for the talk at LSD/LAW 2010 at King's College London.
P. Krusche, A. Tiskin. Parallel longest increasing subsequences in scalable time and memory. Parallel Processing and Applied Mathematics, Lecture Notes in Computer Science vol. 6067 pp. 176-185; [doi:10.1007/978-3-642-14390-8_19]{https://doi.org/10.1007/978-3-642-14390-8_19}, 2010.
Slides for the talk at the T&MC Workshop 2009.
2009 #
P. Krusche, A. Tiskin. String comparison by transposition networks. Texts in Algorithmics, vol. 11 of London Algorithmics 2008: Theory and Practice, [http://www.collegepublications.co.uk/algorithmics/?00011]{http://www.collegepublications.co.uk/algorithmics/?00011} and [http://arxiv.org/abs/0903.3579]{http://arxiv.org/abs/0903.3579}, 2009.
Slides for the talk at WPCCS'08.
2007 #
P. Krusche, A. Tiskin. Efficient parallel string comparison. Proceedings of ParCo 2007, vol. 38 of NIC Series, pp. 193-200, John von Neumann Institute for Computing, ISBN: 978-3-9810843-4-4; [http://www.fz-juelich.de/nic-series/volume38/volume38.html]{http://www.fz-juelich.de/nic-series/volume38/volume38.html} 2007.
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 #
P. Krusche, A. Tiskin. Efficient Longest Common Subsequence Computation Using Bulk-Synchronous Parallelism. Proceedings of ICCSA 2006, Lecture Notes in Computer Science vol. 3984, pp. 165-174; [doi:10.1007/11751649_18]{https://doi.org/10.1007/11751649_18}, 2006.
Slides for the talk given at the PDC'06 workshop at ICCSA 2006 in Glasgow
2005 #
P. Krusche, Experimental Evalution of BSP Programming Libraries. Parallel Processing Letters vol. 18:1 pp. 7-21 [doi:10.1142/S0129626408003193]{https://doi.org/10.1142/S0129626408003193}