| 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 | 412 | 2015 |
| 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 | 250 | 2014 |
| 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 | 226 | 2010 |
| 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 | 212 | 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), 12797, 2016 | 191 | 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 | 180 | 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), 6740, 2015 | 136 | 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 | 133 | 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 | 95 | 2011 |
| 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 | 92 | 2015 |
| Space-efficient algorithms for document retrieval N Välimäki, V Mäkinen Combinatorial Pattern Matching: 18th Annual Symposium, CPM 2007, London …, 2007 | 90 | 2007 |
| 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 | 89 | 2009 |
| 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 | 64 | 2018 |
| 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 | 63 | 2014 |
| Storage and retrieval of individual genomes V Mäkinen, G Navarro, J Sirén, N Välimäki Research in Computational Molecular Biology: 13th Annual International …, 2009 | 62 | 2009 |
| 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 | 61 | 2018 |
| 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 | 51 | 2021 |
| 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 | 45 | 2019 |
| 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 | 42 | 2021 |
Veli MäkinenProfessor of Computer Science, University of HelsinkiVerified email at helsinki.fi
