Authors: Nicola Rizzo, Manuel Cáceres, Veli Mäkinen

Superior Title: Algorithms for Molecular Biology, Vol 19, Iss 1, Pp 1-17 (2024)

Subject Terms: Sequence to graph alignment, Bidirectional BWT, r-index, Suffix tree, Founder graphs, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1748-7188

Access URL: https://doaj.org/article/cc8dbf66dd9b48ef8a0824eefa03009d

Authors: Altti Ilari Maarala, Ossi Arasalo, Daniel Valenzuela, Veli Mäkinen, Keijo Heljanko

Superior Title: PLoS ONE, Vol 16, Iss 8, p e0255260 (2021)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/b60be0dcea1c4be5aa5b1e912ef8c9de

Authors: Tuukka Norri, Bastien Cazaux, Dmitry Kosolobov, Veli Mäkinen

Superior Title: Algorithms for Molecular Biology, Vol 14, Iss 1, Pp 1-15 (2019)

Subject Terms: Pan-genome indexing, Founder reconstruction, Dynamic programming, Positional Burrows–Wheeler transform, Range minimum query, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s13015-019-0147-6; https://doaj.org/toc/1748-7188

Access URL: https://doaj.org/article/f184131ea832445884b76629a936afa6

Authors: Daniel Valenzuela, Tuukka Norri, Niko Välimäki, Esa Pitkänen, Veli Mäkinen

Superior Title: BMC Genomics, Vol 19, Iss S2, Pp 123-130 (2018)

Subject Terms: Pan-genome reference, Variation calling, Read alignment, Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12864-018-4465-8; https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/c8cb363e84604f65b943f10f52007334

Authors: Nidia Obscura Acosta, Veli Mäkinen, Alexandru I. Tomescu

Superior Title: Algorithms for Molecular Biology, Vol 13, Iss 1, Pp 1-12 (2018)

Subject Terms: Genome assembly, Contig assembly, Metagenomics, Graph algorithm, Circular walk, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s13015-018-0122-7; https://doaj.org/toc/1748-7188

Access URL: https://doaj.org/article/caba839dfa7a485eb2cc83a90ad4eedd

Authors: Riku Walve, Leena Salmela, Veli Mäkinen

Superior Title: PLoS ONE, Vol 12, Iss 9, p e0184608 (2017)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC5590988?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/89ef6008664d44d8ac8a0fff9252381d

Authors: Veli Mäkinen

Superior Title: Algorithms, Vol 7, Iss 1, Pp 186-187 (2014)

Subject Terms: high-throughput sequencing, compressed index structures, pattern discovery, population simulation, dynamic programming, Industrial engineering. Management engineering, T55.4-60.8, Electronic computers. Computer science, QA75.5-76.95

File Description: electronic resource

Relation: http://www.mdpi.com/1999-4893/7/1/186; https://doaj.org/toc/1999-4893

Access URL: https://doaj.org/article/2abcc3be03264ee0a7ae95a09666e29b

Authors: Kjell Lemström, Niko Mikkilä, Veli Mäkinen

Relation: https://zenodo.org/communities/ismir; https://zenodo.org/record/1416774; https://doi.org/10.5281/zenodo.1416774; oai:zenodo.org:1416774

Availability: https://doi.org/10.5281/zenodo.1416774
https://doi.org/10.5281/zenodo.1416773
https://zenodo.org/record/1416774

Authors: Altti Ilari Maarala (11226385), Ossi Arasalo (11226388), Daniel Valenzuela (817014), Veli Mäkinen (4424200), Keijo Heljanko (8713854)

Subject Terms: Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, BLAST index, sequence alignment performance, genomic data compression, sequence alignment Computational pa., indexing methods, pan-genome-based sequence search, WGS, MB, coli sequence database, CR, 488 GB GenBank database, Bowtie 2 index, genome data compression methods, genomic data sets, 18 GB E

Relation: https://figshare.com/articles/figure/Distributed_Relative_Lempel-Ziv_compression_/15100558

Availability: https://doi.org/10.1371/journal.pone.0255260.g001

Authors: Altti Ilari Maarala (11226385), Ossi Arasalo (11226388), Daniel Valenzuela (817014), Veli Mäkinen (4424200), Keijo Heljanko (8713854)

Subject Terms: Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, BLAST index, sequence alignment performance, genomic data compression, sequence alignment Computational pa., indexing methods, pan-genome-based sequence search, WGS, MB, coli sequence database, CR, 488 GB GenBank database, Bowtie 2 index, genome data compression methods, genomic data sets, 18 GB E

Relation: https://figshare.com/articles/figure/Distributed_hybrid-indexing_with_BLAST_/15100564

Availability: https://doi.org/10.1371/journal.pone.0255260.g003

Authors: Altti Ilari Maarala (11226385), Ossi Arasalo (11226388), Daniel Valenzuela (817014), Veli Mäkinen (4424200), Keijo Heljanko (8713854)

Subject Terms: Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, BLAST index, sequence alignment performance, genomic data compression, sequence alignment Computational pa., indexing methods, pan-genome-based sequence search, WGS, MB, coli sequence database, CR, 488 GB GenBank database, Bowtie 2 index, genome data compression methods, genomic data sets, 18 GB E

Relation: https://figshare.com/articles/figure/Distributed_compression_pipeline_for_hybrid-index_/15100561

Availability: https://doi.org/10.1371/journal.pone.0255260.g002

Authors: Altti Ilari Maarala (11226385), Ossi Arasalo (11226388), Daniel Valenzuela (817014), Veli Mäkinen (4424200), Keijo Heljanko (8713854)

Subject Terms: Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, BLAST index, sequence alignment performance, genomic data compression, sequence alignment Computational pa., indexing methods, pan-genome-based sequence search, WGS, MB, coli sequence database, CR, 488 GB GenBank database, Bowtie 2 index, genome data compression methods, genomic data sets, 18 GB E

Relation: https://figshare.com/articles/figure/Sequence_alignment_with_hybrid-index_/15100567

Availability: https://doi.org/10.1371/journal.pone.0255260.g004

Authors: Altti Ilari Maarala (11226385), Ossi Arasalo (11226388), Daniel Valenzuela (817014), Veli Mäkinen (4424200), Keijo Heljanko (8713854)

Subject Terms: Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, BLAST index, sequence alignment performance, genomic data compression, sequence alignment Computational pa., indexing methods, pan-genome-based sequence search, WGS, MB, coli sequence database, CR, 488 GB GenBank database, Bowtie 2 index, genome data compression methods, genomic data sets, 18 GB E

Relation: https://figshare.com/articles/figure/Summary_of_compressing_and_indexing_complete_human_pan-genomes_with_distributed_and_non-distributed_methods_/15100570

Availability: https://doi.org/10.1371/journal.pone.0255260.g005

Authors: Altti Ilari Maarala (11226385), Ossi Arasalo (11226388), Daniel Valenzuela (817014), Veli Mäkinen (4424200), Keijo Heljanko (8713854)

Subject Terms: Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, BLAST index, sequence alignment performance, genomic data compression, sequence alignment Computational pa., indexing methods, pan-genome-based sequence search, WGS, MB, coli sequence database, CR, 488 GB GenBank database, Bowtie 2 index, genome data compression methods, genomic data sets, 18 GB E

Relation: https://figshare.com/articles/dataset/Compressing_a_human_pan-genome_n_250_with_increasing_RLZ_dictionary_length_of_pan-genome_length_/15100573

Availability: https://doi.org/10.1371/journal.pone.0255260.t001

Authors: Altti Ilari Maarala (11226385), Ossi Arasalo (11226388), Daniel Valenzuela (817014), Veli Mäkinen (4424200), Keijo Heljanko (8713854)

Subject Terms: Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, BLAST index, sequence alignment performance, genomic data compression, sequence alignment Computational pa., indexing methods, pan-genome-based sequence search, WGS, MB, coli sequence database, CR, 488 GB GenBank database, Bowtie 2 index, genome data compression methods, genomic data sets, 18 GB E

Relation: https://figshare.com/articles/dataset/Compressing_human_pan-genomes_using_reference_sequence_size_of_30_/15100576

Availability: https://doi.org/10.1371/journal.pone.0255260.t002

Authors: Altti Ilari Maarala (11226385), Ossi Arasalo (11226388), Daniel Valenzuela (817014), Veli Mäkinen (4424200), Keijo Heljanko (8713854)

Subject Terms: Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, BLAST index, sequence alignment performance, genomic data compression, sequence alignment Computational pa., indexing methods, pan-genome-based sequence search, WGS, MB, coli sequence database, CR, 488 GB GenBank database, Bowtie 2 index, genome data compression methods, genomic data sets, 18 GB E

Relation: https://figshare.com/articles/dataset/DRLZ_compression_and_indexing_of_bacterial_pan-genomes_with_BLAST_/15100585

Availability: https://doi.org/10.1371/journal.pone.0255260.t004

Authors: Altti Ilari Maarala (11226385), Ossi Arasalo (11226388), Daniel Valenzuela (817014), Veli Mäkinen (4424200), Keijo Heljanko (8713854)

Subject Terms: Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, BLAST index, sequence alignment performance, genomic data compression, sequence alignment Computational pa., indexing methods, pan-genome-based sequence search, WGS, MB, coli sequence database, CR, 488 GB GenBank database, Bowtie 2 index, genome data compression methods, genomic data sets, 18 GB E

Relation: https://figshare.com/articles/dataset/Building_a_complete_hybrid-index_for_a_human_pan-genome_using_distributed_indexing_/15100582

Availability: https://doi.org/10.1371/journal.pone.0255260.t003

Authors: Altti Ilari Maarala (11226385), Ossi Arasalo (11226388), Daniel Valenzuela (817014), Veli Mäkinen (4424200), Keijo Heljanko (8713854)

Subject Terms: Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, BLAST index, sequence alignment performance, genomic data compression, sequence alignment Computational pa., indexing methods, pan-genome-based sequence search, WGS, MB, coli sequence database, CR, 488 GB GenBank database, Bowtie 2 index, genome data compression methods, genomic data sets, 18 GB E

Relation: https://figshare.com/articles/dataset/Aligning_sequences_to_compressed_human_pan-genome_index_of_size_n_genomes_/15100588

Availability: https://doi.org/10.1371/journal.pone.0255260.t005

Authors: Altti Ilari Maarala (11226385), Ossi Arasalo (11226388), Daniel Valenzuela (817014), Veli Mäkinen (4424200), Keijo Heljanko (8713854)

Subject Terms: Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, BLAST index, sequence alignment performance, genomic data compression, sequence alignment Computational pa., indexing methods, pan-genome-based sequence search, WGS, MB, coli sequence database, CR, 488 GB GenBank database, Bowtie 2 index, genome data compression methods, genomic data sets, 18 GB E

Relation: https://figshare.com/articles/dataset/Aligning_next-generation_sequencing_reads_to_a_compressed_index_with_Bowtie2_/15100600

Availability: https://doi.org/10.1371/journal.pone.0255260.t008

Authors: Altti Ilari Maarala (11226385), Ossi Arasalo (11226388), Daniel Valenzuela (817014), Veli Mäkinen (4424200), Keijo Heljanko (8713854)

Subject Terms: Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, BLAST index, sequence alignment performance, genomic data compression, sequence alignment Computational pa., indexing methods, pan-genome-based sequence search, WGS, MB, coli sequence database, CR, 488 GB GenBank database, Bowtie 2 index, genome data compression methods, genomic data sets, 18 GB E

Relation: https://figshare.com/articles/dataset/The_effect_of_CHIC_aligner_parameters_to_the_number_of_pan-genome_mapped_reads_n_10_/15100591

Availability: https://doi.org/10.1371/journal.pone.0255260.t006