Genome-Scale Biology Program &
Department of Medical and Clinical Genetics
P.O. Box 63 (Haartmaninkatu 8)
FI-00014 University of Helsinki,
Postdoctoral researcher in
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).
- D. Valenzuela, T. Norri, N. Välimäki et al. Towards pan-genome read alignment to improve variation calling. BMC Genomics, May 2018.
- 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.
- 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.
- U. Hänninen et al. Exome-wide somatic mutation characterization of small bowel adenocarcinoma. PLOS Genetics, March 2018.
- 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.
- 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.
- 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.
- 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.
- Research visit to Wellcome Trust Sanger Institute, Computational Genomics & Durbin group (Dr Richard Durbin), Hinxton, Cambridge, UK, September 2015 - March 2016.
- Niko Välimäki: Insights from whole-genome sequencing of somatotropinomas. Presentation at the 4th European NeuroEndocrine Association Workshop: Acromegaly, Marseille, France, December 10-12, 2015.
- 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.
- Research visit to the Institut de Biologie Computationelle, Methods and Algorithms for Bioinformatics (CNRS Research Director Eric Rivals), Montpellier, France, January 2013.
- Niko Välimäki: Applications of Compressed Data Structures on Sequences and Structured Data. Presentation at the Institut de Biologie Computationelle, Montpellier, France, January 11, 2013.
- 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.
- 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.
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