Niko Välimäki

Postdoctoral researcher in

• Tumor Genomics research group, and
• Finnish Center of Excellence in Tumor Genetics Research.

I obtained my Ph.D. in Computer Science from the University of Helsinki in 2012. My Ph.D. supervisor was prof. Veli Mäkinen from the Genome-Scale Algorithmics group. I have received funding from Hecse doctoral programme, ALGODAN and Academy of Finland (three-year Academy of Finland postdoctoral grant starting from Sept 2015).

Recent publications

1. D. Valenzuela, T. Norri, N. Välimäki et al. Towards pan-genome read alignment to improve variation calling. BMC Genomics, May 2018.
2. A. Cremers, F. Mobegi, C. Jongh, M. Weert, F. Opzeeland, M. Vehkala, M. Knol, H. Bootsma, N. Välimäki et al. The contribution of genetic variation of Streptococcus pneumoniae to the clinical manifestation of invasive pneumococcal disease. Clinical Infectious Diseases, Accepted, May 2018.
3. T. Tanskanen, L. van den Berg, N. Välimäki et al. Genome-wide association study and meta-analysis in Northern European populations replicate multiple colorectal cancer risk loci. International Journal of Cancer, Feb 2018.
4. U. Hänninen et al. Exome-wide somatic mutation characterization of small bowel adenocarcinoma. PLOS Genetics, March 2018.
5. S. Peacock, C. Chewapreecha, M. Holden, M. Vehkala, N. Välimäki et al. Global and regional dissemination and evolution of Burkholderia pseudomallei. Nature Microbiology, Accepted, December 8, 2016.
6. A.-K. Llarena, J. Zhang, M. Vehkala, N. Välimäki et al. Monomorphic genotypes within a generalist lineage of Campylobacter jejuni show signs of global dispersion. Microbial Genomics, Accepted, September 12, 2016.
7. A. McNally. Y. Oren, D. Kelly, B. Pascoe, S. Dunn, T. Seecharan, M. Vehkala, N. Välimäki et al. Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations. PLOS Genetics, Accepted, August 5, 2016.
8. J. Lees, M. Vehkala, N. Välimäki et al. Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes. Nature Communications, Accepted, July 28, 2016.

Full list of publications

Recent activities

1. Research visit to Wellcome Trust Sanger Institute, Computational Genomics & Durbin group (Dr Richard Durbin), Hinxton, Cambridge, UK, September 2015 - March 2016.
2. Niko Välimäki: Insights from whole-genome sequencing of somatotropinomas. Presentation at the 4th European NeuroEndocrine Association Workshop: Acromegaly, Marseille, France, December 10-12, 2015.
3. Niko Välimäki: Distributed String Mining. Presentation at Indexes and Computation over Compressed Structured Data (Dagstuhl Seminar 13232), Dagstuhl Reports, Vol. 27, No. 23, doi:10.4230/DagRep.3.6.22, pages 35-36, 2013.
4. Research visit to the Institut de Biologie Computationelle, Methods and Algorithms for Bioinformatics (CNRS Research Director Eric Rivals), Montpellier, France, January 2013.
5. Niko Välimäki: Applications of Compressed Data Structures on Sequences and Structured Data. Presentation at the Institut de Biologie Computationelle, Montpellier, France, January 11, 2013.
6. Niko Välimäki: Applications of Compressed Data Structures on Sequences and Structured Data. Ph.D. thesis, Department of Computer Science, Series of Publications A, Report A-2012-7, University of Helsinki, August 2012.

Teaching

• Algorithms for Bioinformatics, course assistant, fall 2012.
• Data compression techniques, course assistant, spring 2012.
• Algorithms for Bioinformatics, course assistant, fall 2011.
• Algorithms for Bioinformatics, course assistant, fall 2010.
• Data compression techniques, course assistant, fall 2008.
• Teacher tutor, years 2008-2012.

Previous update: 12.05.2018

firstname.lastname@helsinki.fi