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Niko Välimäki
Niko Välimäki
Postdoctoral researcher, University of Helsinki
Verified email at cs.helsinki.fi - Homepage
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Cited by
Year
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
4122015
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
2502014
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
2262010
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), 4737, 2014
2122014
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), 12797, 2016
1912016
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
1792016
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), 6740, 2015
1362015
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
1332017
Fast scaffolding with small independent mixed integer programs
L Salmela, V Mäkinen, N Välimäki, J Ylinen, E Ukkonen
Bioinformatics 27 (23), 3259-3265, 2011
942011
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
922015
Space-efficient algorithms for document retrieval
N Välimäki, V Mäkinen
Combinatorial Pattern Matching: 18th Annual Symposium, CPM 2007, London …, 2007
902007
Run-length compressed indexes are superior for highly repetitive sequence collections
J Sirén, N Välimäki, V Mäkinen, G Navarro
String Processing and Information Retrieval: 15th International Symposium …, 2009
892009
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
642018
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
632014
Storage and retrieval of individual genomes
V Mäkinen, G Navarro, J Sirén, N Välimäki
Research in Computational Molecular Biology: 13th Annual International …, 2009
622009
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
602018
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
55*2010
Genetic and epigenetic characteristics of inflammatory bowel Disease–Associated colorectal cancer
K Rajamäki, A Taira, R Katainen, N Välimäki, A Kuosmanen, RM Plaketti, ...
Gastroenterology 161 (2), 592-607, 2021
512021
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), 4022, 2019
452019
Deficient H2A. Z deposition is associated with genesis of uterine leiomyoma
DG Berta, H Kuisma, N Välimäki, M Räisänen, M Jäntti, A Pasanen, ...
Nature 596 (7872), 398-403, 2021
422021
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