Niko Välimäki

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Veli MäkinenProfessor of Computer Science, University of HelsinkiVerified email at helsinki.fi
Jouni SirénUC Santa Cruz Genomics InstituteVerified email at ucsc.edu
Kimmo PalinCancer Researcher, Research Program in Cancer Research, Univeristy of HelsinkiVerified email at helsinki.fi
Esa PitkänenInstitute for Molecular Medicine Finland (FIMM)Verified email at helsinki.fi
Gonzalo NavarroUniversity of ChileVerified email at dcc.uchile.cl
Outi KilpivaaraUniversity of Helsinki, Memorial Sloan-Kettering Cancer CenterVerified email at helsinki.fi
Jussi TaipaleUniversity of Cambridge, Department of BiochemistryVerified email at cam.ac.uk
Antti HonkelaAssociate Professor, University of HelsinkiVerified email at helsinki.fi
Wolfgang GerlachArgonne National LaboratoryVerified email at mcs.anl.gov
Leena SalmelaUniversity of HelsinkiVerified email at cs.helsinki.fi
John A LeesEMBL-EBIVerified email at ebi.ac.uk
Johannes FischerTU DortmundVerified email at cs.tu-dortmund.de
Susana LadraUniversity of A Coruña, Centro de investigación CITICVerified email at udc.es
Kim NguyenAssistant Professor of Computer Science, Université Paris-Sud, FranceVerified email at lri.fr
Diego ArroyueloDepartamento de Informática, Universidad Técnica Federico Santa MaríaVerified email at inf.utfsm.cl
Sebastian ManethProfessor für Informatik, Universität BremenVerified email at uni-bremen.de
Sohan SethSenior Data Scientist, University of EdinburghVerified email at inf.ed.ac.uk
Lu ChengDepartment of Computer Science, Aalto University, FinlandVerified email at aalto.fi
Juha KärkkäinenDepartment of Computer scienceVerified email at cs.helsinki.fi
Simon GogKarlsruhe Institute of TechnologyVerified email at kit.edu

Niko Välimäki

Postdoctoral researcher, University of Helsinki

Verified email at cs.helsinki.fi - Homepage

compressed data structures combinatorial algorithms for sequence analysis


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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	382	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	214	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	212	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	196	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	167	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	149	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	120	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	118	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	92	2011
Space-efficient algorithms for document retrieval N Välimäki, V Mäkinen Annual Symposium on Combinatorial Pattern Matching, 205-215, 2007	91	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	90	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	83	2015
Storage and retrieval of individual genomes V Mäkinen, G Navarro, J Sirén, N Välimäki Annual International Conference on Research in Computational Molecular …, 2009	63	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	58	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	55*	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	52	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	43	2018
Approximate All-Pairs Suﬃx/Preﬁx Overlaps N Valimaki, S Ladra, V Makinen Combinatorial Pattern Matching: 21st Annual Symposium, CPM 2010, New York …, 2010	40*	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	36	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	36	2010

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