{"id":"https://openalex.org/W3122471673","doi":"https://doi.org/10.1109/tit.2022.3152392","title":"Improved Rank-Modulation Codes for DNA Storage With Shotgun Sequencing","display_name":"Improved Rank-Modulation Codes for DNA Storage With Shotgun Sequencing","publication_year":2022,"publication_date":"2022-02-16","ids":{"openalex":"https://openalex.org/W3122471673","doi":"https://doi.org/10.1109/tit.2022.3152392","mag":"3122471673"},"language":"en","primary_location":{"id":"doi:10.1109/tit.2022.3152392","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tit.2022.3152392","pdf_url":null,"source":{"id":"https://openalex.org/S4502562","display_name":"IEEE Transactions on Information Theory","issn_l":"0018-9448","issn":["0018-9448","1557-9654"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Information Theory","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049176441","display_name":"Niv Beeri","orcid":null},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Niv Beeri","raw_affiliation_strings":["School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel","institution_ids":["https://openalex.org/I124227911"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054043026","display_name":"Moshe Schwartz","orcid":"https://orcid.org/0000-0002-1449-0026"},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Moshe Schwartz","raw_affiliation_strings":["School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel"],"raw_orcid":"https://orcid.org/0000-0002-1449-0026","affiliations":[{"raw_affiliation_string":"School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel","institution_ids":["https://openalex.org/I124227911"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5049176441"],"corresponding_institution_ids":["https://openalex.org/I124227911"],"apc_list":null,"apc_paid":null,"fwci":0.3472,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.53721456,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"68","issue":"6","first_page":"3719","last_page":"3730"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12029","display_name":"DNA and Biological Computing","score":1.0,"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/T12029","display_name":"DNA and Biological Computing","score":1.0,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9995999932289124,"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":0.9866999983787537,"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/substring","display_name":"Substring","score":0.8572039604187012},{"id":"https://openalex.org/keywords/rank","display_name":"Rank (graph theory)","score":0.5155284404754639},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4628009498119354},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.42271220684051514},{"id":"https://openalex.org/keywords/hamming-distance","display_name":"Hamming distance","score":0.4130144417285919},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.3899511992931366},{"id":"https://openalex.org/keywords/discrete-mathematics","display_name":"Discrete mathematics","score":0.3431605100631714},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.33274033665657043},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.30911701917648315}],"concepts":[{"id":"https://openalex.org/C182407805","wikidata":"https://www.wikidata.org/wiki/Q2626534","display_name":"Substring","level":3,"score":0.8572039604187012},{"id":"https://openalex.org/C164226766","wikidata":"https://www.wikidata.org/wiki/Q7293202","display_name":"Rank (graph theory)","level":2,"score":0.5155284404754639},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4628009498119354},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.42271220684051514},{"id":"https://openalex.org/C193319292","wikidata":"https://www.wikidata.org/wiki/Q272172","display_name":"Hamming distance","level":2,"score":0.4130144417285919},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.3899511992931366},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.3431605100631714},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.33274033665657043},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.30911701917648315},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/tit.2022.3152392","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tit.2022.3152392","pdf_url":null,"source":{"id":"https://openalex.org/S4502562","display_name":"IEEE Transactions on Information Theory","issn_l":"0018-9448","issn":["0018-9448","1557-9654"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Information Theory","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","score":0.8700000047683716,"display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G3732991021","display_name":null,"funder_award_id":"270/18","funder_id":"https://openalex.org/F4320322252","funder_display_name":"Israel Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320322252","display_name":"Israel Science Foundation","ror":"https://ror.org/04sazxf24"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W1946587648","https://openalex.org/W1972924519","https://openalex.org/W1991296248","https://openalex.org/W2002410252","https://openalex.org/W2005913625","https://openalex.org/W2025383314","https://openalex.org/W2025829207","https://openalex.org/W2076639947","https://openalex.org/W2085621845","https://openalex.org/W2087464200","https://openalex.org/W2087888940","https://openalex.org/W2110233418","https://openalex.org/W2115370421","https://openalex.org/W2128970384","https://openalex.org/W2141215384","https://openalex.org/W2141731854","https://openalex.org/W2143726250","https://openalex.org/W2144030381","https://openalex.org/W2156683452","https://openalex.org/W2162980030","https://openalex.org/W2293169577","https://openalex.org/W2294759895","https://openalex.org/W2329095262","https://openalex.org/W2333320475","https://openalex.org/W2336019055","https://openalex.org/W2468845102","https://openalex.org/W2592122940","https://openalex.org/W2800700497","https://openalex.org/W2963304363","https://openalex.org/W2963412269","https://openalex.org/W2963635273","https://openalex.org/W2969308577","https://openalex.org/W3006320382","https://openalex.org/W3020856174","https://openalex.org/W3081324042","https://openalex.org/W3104543179","https://openalex.org/W4234461109"],"related_works":["https://openalex.org/W1674453943","https://openalex.org/W1540916738","https://openalex.org/W3127593639","https://openalex.org/W2062696773","https://openalex.org/W2122887143","https://openalex.org/W4287814113","https://openalex.org/W3016364484","https://openalex.org/W2999485669","https://openalex.org/W2020935936","https://openalex.org/W2064153048"],"abstract_inverted_index":{"A":[0],"common":[1],"method":[2,14],"for":[3,67,87,167],"reading":[4],"information":[5,48,230],"stored":[6],"in":[7,49,188,214,231,252],"DNA":[8,125,189,239],"molecules":[9,240],"is":[10,94,129],"shotgun":[11,68,88],"sequencing.":[12,89],"This":[13],"outputs":[15],"a":[16,27,105,117,124,196,215],"histogram":[17],"of":[18,21,26,53,58,84,104,108,140,146,169,171,184],"the":[19,23,43,47,50,54,63,97,102,109,112,134,138,144,150,210,228,248,256],"frequencies":[20,103,139],"all":[22,260],"molecules\u2019":[24],"substrings":[25,170],"given":[28],"length":[29,172],"<inline-formula":[30,173,200,219],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[31,174,201,220],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">":[32,175,202,221],"<tex-math":[33,176,203,222],"notation=\"LaTeX\">$\\ell":[34,177],"$":[35],"</tex-math></inline-formula>":[36,179,206,225],".":[37,226],"To":[38],"protect":[39],"against":[40],"noisy":[41],"readings,":[42],"rank-modulation":[44,65,85],"scheme":[45],"encodes":[46],"relative":[51],"ranking":[52],"substring":[55],"frequencies,":[56],"instead":[57],"their":[59],"absolute":[60],"values.":[61],"However,":[62],"best":[64,211],"codes":[66,86,154,250],"sequencing":[69],"have":[70,155],"low":[71],"rates":[72],"which":[73,111],"are":[74,192,255],"asymptotically":[75],"vanishing.":[76],"In":[77],"this":[78,253],"paper":[79,254],"we":[80,191],"propose":[81],"new":[82],"constructions":[83],"The":[90,127,152],"first":[91],"code":[92,197,216],"construction":[93,128,212,233],"systematic,":[95],"allowing":[96,133],"user":[98,135],"to":[99,116,136,194,237],"arbitrarily":[100],"set":[101,137],"large":[106],"subset":[107],"substrings,":[110,142],"encoder":[113],"then":[114,130],"completes":[115],"permutation":[118],"that":[119,247],"may":[120,234],"be":[121,235],"realized":[122],"by":[123,132],"molecule.":[126],"improved":[131],"additional":[141],"at":[143],"cost":[145],"imposing":[147],"constraints":[148],"on":[149],"frequencies.":[151],"resulting":[153],"higher,":[156],"non-vanishing":[157],"rates,":[158],"compared":[159],"with":[160,198,217],"previously":[161],"known":[162],"codes.":[163,262],"As":[164],"an":[165,182],"example,":[166],"histograms":[168],"=2$":[178],",":[180,207],"and":[181],"alphabet":[183],"size":[185],"4":[186],"(as":[187],"molecules),":[190],"able":[193],"construct":[195],"rate":[199,218],"notation=\"LaTeX\">$\\approx":[204,223],"0.909$":[205],"whereas":[208],"previously,":[209],"resulted":[213],"0.654$":[224],"Additionally,":[227],"encoded":[229],"our":[232],"written":[236],"shorter":[238],"than":[241],"possible":[242,258],"before.":[243],"We":[244],"also":[245],"prove":[246],"systematic":[249,261],"constructed":[251],"largest":[257],"among":[259]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2021,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
