• PL 68 (Pietari Kalmin katu 5)

    00014

    Finland

  • Finland

  • PL 68 (Gustaf Hällströmin katu 2b)

    HELSINGIN YLIOPISTO

    Finland

20142019
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Publications 2014 2019

  • 7 Article
  • 4 Conference contribution
  • 1 Chapter
  • 1 Doctoral Thesis
2019

Hardness of Covering Alignment: Phase Transition in Post-Sequence Genomics

Rizzi, R., Cairo, M., Mäkinen, V., Tomescu, A. I. & Valenzuela, D., Feb 2019, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 16, 1, p. 23-30 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
2018

Computational pan-genomics: status, promises and challenges

The Computational Pan-Genomics Consortium, Mäkinen, V. A. T. & Valenzuela, S. D. A., Jan 2018, In : Briefings in Bioinformatics. 19, 1, p. 118-135 18 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access

Towards pan-genome read alignment to improve variation calling

Valenzuela, D., Norri, T., Välimäki, N., Pitkänen, E. & Mäkinen, V., 9 May 2018, In : BMC Genomics. 19, 8 p., 87.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
2017

Algorithms and Data Structures for Sequence Analysis in the Pan-Genomic Era

Valenzuela, S. D. A., 9 Jun 2017, Helsinki: University of Helsinki. 74 p.

Research output: ThesisDoctoral ThesisCollection of Articles

Open Access

Compressed Spaced Suffix Arrays

Gagie, T., Manzini, G. & Valenzuela, D., Jun 2017, In : Mathematics in Computer Science. 11, 2, p. 151-157 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Interval scheduling maximizing minimum coverage

Mäkinen, V., Staneva, V., Tomescu, A. I., Valenzuela, D. & Wilzbach, S., 10 Jul 2017, In : Discrete Applied Mathematics. 225, p. 130-135 6 p.

Research output: Contribution to journalArticleScientificpeer-review

2016

Analyzing Relative Lempel-Ziv Reference Construction

Gagie, T., Puglisi, S. J. & Valenzuela, D., 18 Oct 2016, String Processing and Information Retrieval: 23rd International Symposium, SPIRE 2016, Beppu, Japan, October 18-20, 2016, Proceedings. Springer, p. 160-165 6 p. (Lecture Notes in Computer Science; vol. 9954).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

CHICO: A Compressed Hybrid Index for Repetitive Collections

Valenzuela, D., 5 Jun 2016, Experimental Algorithms: 15th International Symposium, SEA 2016 St. Petersburg, Russia, June 5–8, 2016 Proceedings. Goldberg, A. V. & Kulikov, A. S. (eds.). Springer International Publishing AG, p. 326-338 13 p. (Lecture Notes in Computer Science; vol. 9685).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2015

Compressed Suffix Array

Belazzougui, D., Mäkinen, V. A. T. & Valenzuela, S. D. A., 2015, Encyclopedia of Algorithms. Kao, M-Y. (ed.). New York: Springer, 6 p.

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

Diploid Alignments and Haplotyping

Mäkinen, V. & Valenzuela, D., 2015, Bioinformatics Research and Applications: 11th International Symposium, ISBRA 2015, Norfolk, USA, June 6-9, 2015, Proceedings . Harrison, R., Li, Y. & Măndoiu, I. (eds.). Cham: Springer International Publishing AG, p. 235-246 12 p. (Lecture notes in computer science; vol. 9096)(LNCS sublibrary. SL 8, Bioinformatics).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

General Document Retrieval in Compact Space

Navarro, G., Puglisi, S. J. & Valenzuela, D., 1 Jan 2015, In : ACM Journal of Experimental Algorithmics. 19, p. 2.3:1.1-2.3:1.46

Research output: Contribution to journalArticleScientificpeer-review

2014

Compressed Spaced Suffix Arrays

Gagie, T., Manzini, G. & Valenzuela, D., 2014, ICABD 2014, 2nd International Conference on Algorithms for Big Data: Palermo, Italy, April 7-9, 2014, Proceedings. Iliopoulos, C. S. & Langui, A. (eds.). p. 37-45 9 p. (CEUR Workshop Proceedings; vol. 1146).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Recombination-aware alignment of diploid individuals

Mäkinen, V. & Valenzuela, D., 2014, In : BMC Genomics. 15, Suppl 6, p. S15 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File