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Niko Välimäki
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Books and Theses
- 2012
- [b1]Niko Välimäki:
Applications of Compressed Data Structures on Sequences and Structured Data. University of Helsinki, Finland, 2012
Journal Articles
- 2018
- [j10]Daniel Valenzuela, Tuukka Norri
, Niko Välimäki, Esa Pitkänen
Towards pan-genome read alignment to improve variation calling. BMC Genom. 19(S2) (2018) - 2015
- [j9]Diego Arroyuelo, Francisco Claude, Sebastian Maneth, Veli Mäkinen
Fast in-memory XPath search using compressed indexes. Softw. Pract. Exp. 45(3): 399-434 (2015) - 2014
- [j8]Sohan Seth, Niko Välimäki, Samuel Kaski, Antti Honkela:
Exploration and retrieval of whole-metagenome sequencing samples. Bioinform. 30(17): 2471-2479 (2014) - [j7]Simon Gog, Kalle Karhu, Juha Kärkkäinen, Veli Mäkinen
Multi-pattern matching with bidirectional indexes. J. Discrete Algorithms 24: 26-39 (2014) - [j6]Veli Mäkinen
Indexing Graphs for Path Queries with Applications in Genome Research. IEEE ACM Trans. Comput. Biol. Bioinform. 11(2): 375-388 (2014) - 2012
- [j5]Niko Välimäki, Susana Ladra
Approximate all-pairs suffix/prefix overlaps. Inf. Comput. 213: 49-58 (2012) - 2011
- [j4]Leena Salmela
Fast scaffolding with small independent mixed integer programs. Bioinform. 27(23): 3259-3265 (2011) - 2010
- [j3]Veli Mäkinen
Storage and Retrieval of Highly Repetitive Sequence Collections. J. Comput. Biol. 17(3): 281-308 (2010) - 2009
- [j2]Niko Välimäki, Veli Mäkinen
Engineering a compressed suffix tree implementation. ACM J. Exp. Algorithmics 14 (2009) - 2007
- [j1]Niko Välimäki, Wolfgang Gerlach, Kashyap Dixit, Veli Mäkinen
Compressed suffix tree - a basis for genome-scale sequence analysis. Bioinform. 23(5): 629-630 (2007)
Conference and Workshop Papers
- 2014
- [c16]Sotiris K. Tasoulis, Lu Cheng
Random projection based clustering for population genomics. IEEE BigData 2014: 675-682 - 2013
- [c15]Niko Välimäki, Eric Rivals
Scalable and Versatile k-mer Indexing for High-Throughput Sequencing Data. ISBRA 2013: 237-248 - 2012
- [c14]Markus Heinonen, Niko Välimäki, Veli Mäkinen, Juho Rousu:
Efficient Path Kernels for Reaction Function Prediction. BIOINFORMATICS 2012: 202-207 - [c13]Simon Gog, Kalle Karhu, Juha Kärkkäinen, Veli Mäkinen
Multi-pattern Matching with Bidirectional Indexes. COCOON 2012: 384-395 - [c12]Niko Välimäki:
Least Random Suffix/Prefix Matches in Output-Sensitive Time. CPM 2012: 269-279 - [c11]Johannes Fischer, Travis Gagie
Forbidden Patterns. LATIN 2012: 327-337 - [c10]Niko Välimäki, Simon J. Puglisi
Distributed String Mining for High-Throughput Sequencing Data. WABI 2012: 441-452 - 2011
- [c9]Jouni Sirén, Niko Välimäki, Veli Mäkinen
Indexing Finite Language Representation of Population Genotypes. WABI 2011: 270-281 - 2010
- [c8]Veli Mäkinen
Unified View of Backward Backtracking in Short Read Mapping. Algorithms and Applications 2010: 182-195 - [c7]Niko Välimäki, Susana Ladra
Approximate All-Pairs Suffix/Prefix Overlaps. CPM 2010: 76-87 - [c6]Diego Arroyuelo, Francisco Claude, Sebastian Maneth, Veli Mäkinen
Fast in-memory XPath search using compressed indexes. ICDE 2010: 417-428 - 2009
- [c5]Veli Mäkinen
Storage and Retrieval of Individual Genomes. RECOMB 2009: 121-137 - 2008
- [c4]Johannes Fischer, Veli Mäkinen, Niko Välimäki:
Space Efficient String Mining under Frequency Constraints. ICDM 2008: 193-202 - [c3]Jouni Sirén, Niko Välimäki, Veli Mäkinen
Run-Length Compressed Indexes Are Superior for Highly Repetitive Sequence Collections. SPIRE 2008: 164-175 - 2007
- [c2]Niko Välimäki, Veli Mäkinen:
Space-Efficient Algorithms for Document Retrieval. CPM 2007: 205-215 - [c1]Niko Välimäki, Wolfgang Gerlach, Kashyap Dixit, Veli Mäkinen
Engineering a Compressed Suffix Tree Implementation. WEA 2007: 217-228
Informal and Other Publications
- 2013
- [i4]Sohan Seth, Niko Välimäki, Samuel Kaski, Antti Honkela:
Exploration and retrieval of whole-metagenome sequencing samples. CoRR abs/1308.6074 (2013) - 2010
- [i3]Jouni Sirén, Niko Välimäki, Veli Mäkinen:
Indexing Finite Language Representation of Population Genotypes. CoRR abs/1010.2656 (2010) - 2009
- [i2]Diego Arroyuelo, Francisco Claude, Sebastian Maneth, Veli Mäkinen, Gonzalo Navarro, Kim Nguyen, Jouni Sirén, Niko Välimäki:
Fast In-Memory XPath Search over Compressed Text and Tree Indexes. CoRR abs/0907.2089 (2009) - 2008
- [i1]Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, Niko Välimäki:
Storage and Retrieval of Individual Genomes. Structure-Based Compression of Complex Massive Data 2008
Coauthor Index
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