{"id":"https://openalex.org/W2121832832","doi":"https://doi.org/10.1093/bioinformatics/bts175","title":"GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies","display_name":"GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies","publication_year":2012,"publication_date":"2012-04-06","ids":{"openalex":"https://openalex.org/W2121832832","doi":"https://doi.org/10.1093/bioinformatics/bts175","mag":"2121832832","pmid":"https://pubmed.ncbi.nlm.nih.gov/22492642"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts175","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts175","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/11/1429/48869328/bioinformatics_28_11_1429.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/11/1429/48869328/bioinformatics_28_11_1429.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083585691","display_name":"Alexey A. Gritsenko","orcid":"https://orcid.org/0000-0003-1799-2301"},"institutions":[{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Alexey A. Gritsenko","raw_affiliation_strings":["1 The Delft Bioinformatics Lab, Department of Mediamatics, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Platform Green Synthetic Biology and 3Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, The Netherlands"],"affiliations":[{"raw_affiliation_string":"1 The Delft Bioinformatics Lab, Department of Mediamatics, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Platform Green Synthetic Biology and 3Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, The Netherlands","institution_ids":["https://openalex.org/I98358874"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055923480","display_name":"Jurgen F. Nijkamp","orcid":null},"institutions":[{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Jurgen F. Nijkamp","raw_affiliation_strings":["1 The Delft Bioinformatics Lab, Department of Mediamatics, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Platform Green Synthetic Biology and 3Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, The Netherlands"],"affiliations":[{"raw_affiliation_string":"1 The Delft Bioinformatics Lab, Department of Mediamatics, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Platform Green Synthetic Biology and 3Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, The Netherlands","institution_ids":["https://openalex.org/I98358874"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052699801","display_name":"Marcel Reinders","orcid":"https://orcid.org/0000-0002-1148-1562"},"institutions":[{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Marcel J.T. Reinders","raw_affiliation_strings":["1 The Delft Bioinformatics Lab, Department of Mediamatics, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Platform Green Synthetic Biology and 3Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, The Netherlands"],"affiliations":[{"raw_affiliation_string":"1 The Delft Bioinformatics Lab, Department of Mediamatics, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Platform Green Synthetic Biology and 3Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, The Netherlands","institution_ids":["https://openalex.org/I98358874"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080533789","display_name":"Dick de Ridder","orcid":"https://orcid.org/0000-0002-4944-4310"},"institutions":[{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Dick de Ridder","raw_affiliation_strings":["1 The Delft Bioinformatics Lab, Department of Mediamatics, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Platform Green Synthetic Biology and 3Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, The Netherlands"],"affiliations":[{"raw_affiliation_string":"1 The Delft Bioinformatics Lab, Department of Mediamatics, Delft University of Technology, Mekelweg 4, 2628 CD Delft, 2Platform Green Synthetic Biology and 3Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, The Netherlands","institution_ids":["https://openalex.org/I98358874"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5083585691"],"corresponding_institution_ids":["https://openalex.org/I98358874"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.0925,"has_fulltext":true,"cited_by_count":56,"citation_normalized_percentile":{"value":0.9231467,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"28","issue":"11","first_page":"1429","last_page":"1437"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9940999746322632,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.968500018119812,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/contig","display_name":"Contig","score":0.8688305616378784},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6778587698936462},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.6527748703956604},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5158550143241882},{"id":"https://openalex.org/keywords/scaffold","display_name":"Scaffold","score":0.5107095241546631},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4906257688999176},{"id":"https://openalex.org/keywords/binary-number","display_name":"Binary number","score":0.4502772390842438},{"id":"https://openalex.org/keywords/hybrid-genome-assembly","display_name":"Hybrid genome assembly","score":0.4466733932495117},{"id":"https://openalex.org/keywords/integer-programming","display_name":"Integer programming","score":0.4391050934791565},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4287509322166443},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.18605747818946838},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17858722805976868},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11193335056304932},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10501837730407715},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08113229274749756}],"concepts":[{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.8688305616378784},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6778587698936462},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.6527748703956604},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5158550143241882},{"id":"https://openalex.org/C89429830","wikidata":"https://www.wikidata.org/wiki/Q735710","display_name":"Scaffold","level":2,"score":0.5107095241546631},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4906257688999176},{"id":"https://openalex.org/C48372109","wikidata":"https://www.wikidata.org/wiki/Q3913","display_name":"Binary number","level":2,"score":0.4502772390842438},{"id":"https://openalex.org/C113425843","wikidata":"https://www.wikidata.org/wiki/Q5953213","display_name":"Hybrid genome assembly","level":5,"score":0.4466733932495117},{"id":"https://openalex.org/C56086750","wikidata":"https://www.wikidata.org/wiki/Q6042592","display_name":"Integer programming","level":2,"score":0.4391050934791565},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4287509322166443},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.18605747818946838},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17858722805976868},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11193335056304932},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10501837730407715},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08113229274749756},{"id":"https://openalex.org/C94375191","wikidata":"https://www.wikidata.org/wiki/Q11205","display_name":"Arithmetic","level":1,"score":0.0},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044166","descriptor_name":"Xanthomonadaceae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D044166","descriptor_name":"Xanthomonadaceae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D044166","descriptor_name":"Xanthomonadaceae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D044224","descriptor_name":"Pseudomonas syringae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D044224","descriptor_name":"Pseudomonas syringae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D044224","descriptor_name":"Pseudomonas syringae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bts175","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts175","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/11/1429/48869328/bioinformatics_28_11_1429.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22492642","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22492642","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:tud:oai:tudelft.nl:uuid:d7c93283-3de2-4c3d-9320-2bac198bb7a4","is_oa":true,"landing_page_url":"http://resolver.tudelft.nl/uuid:d7c93283-3de2-4c3d-9320-2bac198bb7a4","pdf_url":"http://resolver.tudelft.nl/uuid:d7c93283-3de2-4c3d-9320-2bac198bb7a4","source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 6 April 2012","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.470.2343","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.470.2343","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.pgsb.nl/wordpress/wp-content/uploads/Gritsenk_etal_Bioinformatics.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts175","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts175","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/11/1429/48869328/bioinformatics_28_11_1429.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2121832832.pdf","grobid_xml":"https://content.openalex.org/works/W2121832832.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W135055223","https://openalex.org/W241716011","https://openalex.org/W1598134722","https://openalex.org/W1635391495","https://openalex.org/W1968143987","https://openalex.org/W1970995855","https://openalex.org/W1984236772","https://openalex.org/W2040678023","https://openalex.org/W2044055478","https://openalex.org/W2055298722","https://openalex.org/W2083215220","https://openalex.org/W2090382945","https://openalex.org/W2095685450","https://openalex.org/W2096634299","https://openalex.org/W2102619694","https://openalex.org/W2103441770","https://openalex.org/W2108234281","https://openalex.org/W2114795390","https://openalex.org/W2124985265","https://openalex.org/W2127470768","https://openalex.org/W2129744420","https://openalex.org/W2131852975","https://openalex.org/W2145186656","https://openalex.org/W2147841875","https://openalex.org/W2149017136","https://openalex.org/W2160969485","https://openalex.org/W2165654401","https://openalex.org/W2169399056","https://openalex.org/W2171531867","https://openalex.org/W2505968561","https://openalex.org/W2553975995","https://openalex.org/W2905576637","https://openalex.org/W2993222596","https://openalex.org/W6605513013","https://openalex.org/W6635722443","https://openalex.org/W6684978482"],"related_works":["https://openalex.org/W4381279187","https://openalex.org/W2530885695","https://openalex.org/W4280563008","https://openalex.org/W4281620341","https://openalex.org/W2150081252","https://openalex.org/W2142749416","https://openalex.org/W1992950355","https://openalex.org/W1968613135","https://openalex.org/W4226176616","https://openalex.org/W2119121014"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":12},{"year":2013,"cited_by_count":2}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}