{"id":"https://openalex.org/W3018787322","doi":"https://doi.org/10.1007/978-3-030-45257-5_7","title":"AStarix: Fast and Optimal Sequence-to-Graph Alignment","display_name":"AStarix: Fast and Optimal Sequence-to-Graph Alignment","publication_year":2020,"publication_date":"2020-01-01","ids":{"openalex":"https://openalex.org/W3018787322","doi":"https://doi.org/10.1007/978-3-030-45257-5_7","mag":"3018787322"},"language":"en","primary_location":{"id":"doi:10.1007/978-3-030-45257-5_7","is_oa":true,"landing_page_url":"https://doi.org/10.1007/978-3-030-45257-5_7","pdf_url":"https://link.springer.com/content/pdf/10.1007%2F978-3-030-45257-5_7.pdf","source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"type":"book-chapter","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007%2F978-3-030-45257-5_7.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082350886","display_name":"Pesho Ivanov","orcid":"https://orcid.org/0000-0002-8119-3849"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Pesho Ivanov","raw_affiliation_strings":["Department of Computer Science, ETH Zurich, Zurich, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-8119-3849","affiliations":[{"raw_affiliation_string":"Department of Computer Science, ETH Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074409480","display_name":"Benjamin Bichsel","orcid":"https://orcid.org/0000-0003-3283-7908"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Benjamin Bichsel","raw_affiliation_strings":["Department of Computer Science, ETH Zurich, Zurich, Switzerland"],"raw_orcid":"https://orcid.org/0000-0003-3283-7908","affiliations":[{"raw_affiliation_string":"Department of Computer Science, ETH Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033347097","display_name":"Harun Mustafa","orcid":"https://orcid.org/0000-0002-2125-6086"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Harun Mustafa","raw_affiliation_strings":["Department of Computer Science, ETH Zurich, Zurich, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-2125-6086","affiliations":[{"raw_affiliation_string":"Department of Computer Science, ETH Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070168682","display_name":"Andr\u00e9 Kahles","orcid":"https://orcid.org/0000-0002-3411-0692"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Andr\u00e9 Kahles","raw_affiliation_strings":["Department of Computer Science, ETH Zurich, Zurich, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-3411-0692","affiliations":[{"raw_affiliation_string":"Department of Computer Science, ETH Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035416263","display_name":"Gunnar R\u00e4tsch","orcid":"https://orcid.org/0000-0001-5486-8532"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Gunnar R\u00e4tsch","raw_affiliation_strings":["Department of Computer Science, ETH Zurich, Zurich, Switzerland"],"raw_orcid":"https://orcid.org/0000-0001-5486-8532","affiliations":[{"raw_affiliation_string":"Department of Computer Science, ETH Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069901599","display_name":"Martin Vechev","orcid":"https://orcid.org/0000-0002-0054-9568"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Martin Vechev","raw_affiliation_strings":["Department of Computer Science, ETH Zurich, Zurich, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-0054-9568","affiliations":[{"raw_affiliation_string":"Department of Computer Science, ETH Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5082350886"],"corresponding_institution_ids":["https://openalex.org/I35440088"],"apc_list":{"value":5000,"currency":"EUR","value_usd":5392},"apc_paid":{"value":5000,"currency":"EUR","value_usd":5392},"fwci":3.9469,"has_fulltext":true,"cited_by_count":21,"citation_normalized_percentile":{"value":0.94220802,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"104","last_page":"119"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9984999895095825,"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"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9944000244140625,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8253433704376221},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5530816912651062},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5275347232818604},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.35136866569519043},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3418676257133484}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8253433704376221},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5530816912651062},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5275347232818604},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.35136866569519043},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3418676257133484},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1007/978-3-030-45257-5_7","is_oa":true,"landing_page_url":"https://doi.org/10.1007/978-3-030-45257-5_7","pdf_url":"https://link.springer.com/content/pdf/10.1007%2F978-3-030-45257-5_7.pdf","source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},{"id":"pmh:oai:zenodo.org:6994733","is_oa":true,"landing_page_url":"https://zenodo.org/record/6994733","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Lecture Notes in Computer Science 104-119","raw_type":"info:eu-repo/semantics/bookPart"}],"best_oa_location":{"id":"doi:10.1007/978-3-030-45257-5_7","is_oa":true,"landing_page_url":"https://doi.org/10.1007/978-3-030-45257-5_7","pdf_url":"https://link.springer.com/content/pdf/10.1007%2F978-3-030-45257-5_7.pdf","source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3018787322.pdf","grobid_xml":"https://content.openalex.org/works/W3018787322.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1562006861","https://openalex.org/W1978981589","https://openalex.org/W2004177824","https://openalex.org/W2011210839","https://openalex.org/W2042202252","https://openalex.org/W2054698853","https://openalex.org/W2055043387","https://openalex.org/W2062112417","https://openalex.org/W2093700795","https://openalex.org/W2103441770","https://openalex.org/W2110417468","https://openalex.org/W2129264270","https://openalex.org/W2134634502","https://openalex.org/W2157539385","https://openalex.org/W2160177274","https://openalex.org/W2164158485","https://openalex.org/W2169071118","https://openalex.org/W2170551349","https://openalex.org/W2179507357","https://openalex.org/W2344013120","https://openalex.org/W2474973645","https://openalex.org/W2603734366","https://openalex.org/W2767747923","https://openalex.org/W2888300707","https://openalex.org/W2891275623","https://openalex.org/W2946002370","https://openalex.org/W2950960779","https://openalex.org/W2952746707","https://openalex.org/W2953339515","https://openalex.org/W2953383174","https://openalex.org/W2964849163","https://openalex.org/W2988240595","https://openalex.org/W2999349690","https://openalex.org/W3100935868"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880"],"abstract_inverted_index":{"We":[0],"present":[1],"an":[2,28],"algorithm":[3,67],"for":[4,51],"the":[5,17,39,52,56,88],"optimal":[6,65,85],"alignment":[7,30,66],"of":[8,72,80,90],"sequences":[9],"to":[10,58,94],"genome":[11,96],"graphs.":[12,97],"It":[13],"works":[14],"by":[15],"phrasing":[16],"edit":[18],"distance":[19],"minimization":[20],"task":[21,89],"as":[22],"finding":[23],"a":[24,34,44,63],"shortest":[25,35],"path":[26],"on":[27,87],"implicit":[29],"graph.":[31],"To":[32],"find":[33],"path,":[36],"we":[37],"instantiate":[38],"A$$^\\star":[40],"$$":[41],"paradigm":[42],"with":[43],"novel":[45],"domain-specific":[46],"heuristic":[47],"function":[48],"that":[49,75],"accounts":[50],"upcoming":[53],"subsequence":[54],"in":[55,62],"query":[57],"be":[59],"aligned,":[60],"resulting":[61],"provably":[64],"called":[68],"AStarix.":[69],"Experimental":[70],"evaluation":[71],"AStarix":[73],"shows":[74],"it":[76],"is":[77],"1\u20132":[78],"orders":[79],"magnitude":[81],"faster":[82],"than":[83],"state-of-the-art":[84],"algorithms":[86],"aligning":[91],"Illumina":[92],"reads":[93],"reference":[95],"Implementations":[98],"and":[99],"evaluations":[100],"are":[101],"available":[102],"at":[103],"https://github.com/eth-sri/astarix":[104],".":[105]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
