Computational pan-genomics: status, promises and challenges Computational Pan-Genomics Consortium Briefings in Bioinformatics, bbw089, 2016 | 341 | 2016 |
Improved compressed indexes for full-text document retrieval D Belazzougui, G Navarro, D Valenzuela Journal of Discrete Algorithms 18, 3-13, 2013 | 58 | 2013 |
Towards pan-genome read alignment to improve variation calling D Valenzuela, T Norri, N Välimäki, E Pitkänen, V Mäkinen BMC genomics 19 (2), 123-130, 2018 | 55* | 2018 |
Practical compressed document retrieval G Navarro, SJ Puglisi, D Valenzuela International Symposium on Experimental Algorithms, 193-205, 2011 | 41 | 2011 |
Space-efficient top-k document retrieval G Navarro, D Valenzuela International Symposium on Experimental Algorithms, 307-319, 2012 | 28 | 2012 |
General document retrieval in compact space G Navarro, SJ Puglisi, D Valenzuela Journal of Experimental Algorithmics (JEA) 19, 1-46, 2015 | 25 | 2015 |
CHICO: A compressed hybrid index for repetitive collections D Valenzuela International Symposium on Experimental Algorithms, 326-338, 2016 | 22 | 2016 |
Lempel–ziv‑like parsing in small space D Kosolobov, D Valenzuela, G Navarro, SJ Puglisi Springer, 2020 | 16* | 2020 |
Analyzing Relative Lempel-Ziv Reference Construction T Gagie, SJ Puglisi, D Valenzuela International Symposium on String Processing and Information Retrieval, 160-165, 2016 | 14 | 2016 |
CHIC: a short read aligner for pan-genomic references D Valenzuela, V Mäkinen bioRxiv, 178129, 2017 | 13 | 2017 |
Founder reconstruction enables scalable and seamless pangenomic analysis T Norri, B Cazaux, S Dönges, D Valenzuela, V Mäkinen Bioinformatics 37 (24), 4611-4619, 2021 | 10 | 2021 |
Compressed spaced suffix arrays T Gagie, G Manzini, D Valenzuela Mathematics in Computer Science 11 (2), 151-157, 2017 | 10 | 2017 |
Interval scheduling maximizing minimum coverage V Mäkinen, V Staneva, AI Tomescu, D Valenzuela, S Wilzbach Discrete Applied Mathematics, 2017 | 8 | 2017 |
Hardness of Covering Alignment: Phase Transition in Post-Sequence Genomics R Rizzi, M Cairo, V Makinen, AI Tomescu, D Valenzuela IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018 | 7* | 2018 |
Recombination-aware alignment of diploid individuals V Mäkinen, D Valenzuela BMC genomics 15 (6), 1-9, 2014 | 7 | 2014 |
Scalable Reference Genome Assembly from Compressed Pan-Genome Index with Spark AI Maarala, O Arasalo, D Valenzuela, K Heljanko, V Mäkinen International Conference on Big Data, 68-84, 2020 | 6 | 2020 |
Distributed hybrid-indexing of compressed pan-genomes for scalable and fast sequence alignment AI Maarala, O Arasalo, D Valenzuela, V Mäkinen, K Heljanko Plos one 16 (8), e0255260, 2021 | 5 | 2021 |
Compressed Suffix Array. D Belazzougui, V Mäkinen, D Valenzuela Encyclopedia of Algorithms, 386-390, 2016 | 5 | 2016 |
Algorithms and Data Structures for Sequence Analysis in the Pan-Genomic Era D Valenzuela Ph. D. Dissertation. University of Helsinki, Finland, 2017 | 3 | 2017 |
Diploid Alignments and Haplotyping V Mäkinen, D Valenzuela International Symposium on Bioinformatics Research and Applications, 235-246, 2015 | 2 | 2015 |