Niko Välimäki
Niko Välimäki
Postdoctoral researcher, University of Helsinki
Verified email at - Homepage
Cited by
Cited by
CTCF/cohesin-binding sites are frequently mutated in cancer
R Katainen, K Dave, E Pitkänen, K Palin, T Kivioja, N Välimäki, AE Gylfe, ...
Nature genetics 47 (7), 818-821, 2015
Storage and retrieval of highly repetitive sequence collections
V Mäkinen, G Navarro, J Sirén, N Välimäki
Journal of Computational Biology 17 (3), 281-308, 2010
Indexing graphs for path queries with applications in genome research
J Sirén, N Välimäki, V Mäkinen
IEEE/ACM Transactions on Computational Biology and Bioinformatics 11 (2 …, 2014
The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera
V Ahola, R Lehtonen, P Somervuo, L Salmela, P Koskinen, P Rastas, ...
Nature communications 5 (1), 1-9, 2014
Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes
JA Lees, M Vehkala, N Välimäki, SR Harris, C Chewapreecha, ...
Nature communications 7 (1), 1-8, 2016
Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations
A McNally, Y Oren, D Kelly, B Pascoe, S Dunn, T Sreecharan, M Vehkala, ...
PLoS genetics 12 (9), e1006280, 2016
Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis
LA Weinert, RR Chaudhuri, J Wang, SE Peters, J Corander, T Jombart, ...
Nature communications 6 (1), 1-10, 2015
Global and regional dissemination and evolution of Burkholderia pseudomallei
C Chewapreecha, MTG Holden, M Vehkala, N Välimäki, Z Yang, ...
Nature microbiology 2 (4), 1-8, 2017
Fast scaffolding with small independent mixed integer programs
L Salmela, V Mäkinen, N Välimäki, J Ylinen, E Ukkonen
Bioinformatics 27 (23), 3259-3265, 2011
Space-efficient algorithms for document retrieval
N Välimäki, V Mäkinen
Annual Symposium on Combinatorial Pattern Matching, 205-215, 2007
Run-length compressed indexes are superior for highly repetitive sequence collections
J Sirén, N Välimäki, V Mäkinen, G Navarro
International Symposium on String Processing and Information Retrieval, 164-175, 2008
Whole-genome sequencing of growth hormone (GH)-secreting pituitary adenomas
N Välimäki, H Demir, E Pitkänen, E Kaasinen, A Karppinen, L Kivipelto, ...
The Journal of Clinical Endocrinology & Metabolism 100 (10), 3918-3927, 2015
Storage and retrieval of individual genomes
V Mäkinen, G Navarro, J Sirén, N Välimäki
Annual International Conference on Research in Computational Molecular …, 2009
Frequent L1 retrotranspositions originating from TTC28 in colorectal cancer
E Pitkänen, T Cajuso, R Katainen, E Kaasinen, N Välimäki, K Palin, ...
Oncotarget 5 (3), 853, 2014
Fast in-memory XPath search using compressed indexes
D Arroyuelo, F Claude, S Maneth, V Maakinen, G Navarro, K Nguyên, ...
Data Engineering (ICDE), 2010 IEEE 26th International Conference on, 417-428, 2010
Exome-wide somatic mutation characterization of small bowel adenocarcinoma
UA Hänninen, R Katainen, T Tanskanen, RM Plaketti, R Laine, ...
PLoS genetics 14 (3), e1007200, 2018
Genetic predisposition to uterine leiomyoma is determined by loci for genitourinary development and genome stability
N Välimäki, H Kuisma, A Pasanen, O Heikinheimo, J Sjöberg, R Bützow, ...
Elife 7, e37110, 2018
Approximate All-Pairs Suffix/Prefix Overlaps
N Valimaki, S Ladra, V Makinen
Combinatorial Pattern Matching: 21st Annual Symposium, CPM 2010, New York …, 2010
Retrotransposon insertions can initiate colorectal cancer and are associated with poor survival
T Cajuso, P Sulo, T Tanskanen, R Katainen, A Taira, UA Hänninen, ...
Nature communications 10 (1), 1-9, 2019
Engineering a compressed suffix tree implementation
N Välimäki, V Mäkinen, W Gerlach, K Dixit
Journal of Experimental Algorithmics (JEA) 14, 4.2-4.23, 2010
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