{"id":"https://openalex.org/W2527844764","doi":"https://doi.org/10.1177/1094342016668567","title":"NuChart-II: The road to a fast and scalable tool for Hi-C data analysis","display_name":"NuChart-II: The road to a fast and scalable tool for Hi-C data analysis","publication_year":2016,"publication_date":"2016-10-03","ids":{"openalex":"https://openalex.org/W2527844764","doi":"https://doi.org/10.1177/1094342016668567","mag":"2527844764"},"language":"en","primary_location":{"id":"doi:10.1177/1094342016668567","is_oa":false,"landing_page_url":"https://doi.org/10.1177/1094342016668567","pdf_url":null,"source":{"id":"https://openalex.org/S60606485","display_name":"The International Journal of High Performance Computing Applications","issn_l":"1094-3420","issn":["1094-3420","1741-2846"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of High Performance Computing Applications","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/2318/1607126","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075443548","display_name":"Fabio Tordini","orcid":"https://orcid.org/0000-0001-9861-6513"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Fabio Tordini","raw_affiliation_strings":["Computer Science Department, University of Torino, Italy"],"affiliations":[{"raw_affiliation_string":"Computer Science Department, University of Torino, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015548694","display_name":"Maurizio Drocco","orcid":"https://orcid.org/0000-0001-6500-7607"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Maurizio Drocco","raw_affiliation_strings":["Computer Science Department, University of Torino, Italy"],"affiliations":[{"raw_affiliation_string":"Computer Science Department, University of Torino, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007904705","display_name":"Claudia Misale","orcid":"https://orcid.org/0000-0003-3737-7373"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Claudia Misale","raw_affiliation_strings":["Computer Science Department, University of Torino, Italy"],"affiliations":[{"raw_affiliation_string":"Computer Science Department, University of Torino, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088629765","display_name":"Luciano Milanesi","orcid":"https://orcid.org/0000-0002-1201-3939"},"institutions":[{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"funder","lineage":["https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I4210154278","display_name":"Institute of Biomedical Technologies","ror":"https://ror.org/04ehykb85","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210154278","https://openalex.org/I4210155236"]}],"countries":["GB","IT"],"is_corresponding":false,"raw_author_name":"Luciano Milanesi","raw_affiliation_strings":["Computer Laboratory, University of Cambridge, UK","Institute for Biomedical Technologies - Italian National Research Council, Segrate (Mi), Italy"],"affiliations":[{"raw_affiliation_string":"Computer Laboratory, University of Cambridge, UK","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Institute for Biomedical Technologies - Italian National Research Council, Segrate (Mi), Italy","institution_ids":["https://openalex.org/I4210154278","https://openalex.org/I4210155236"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056748708","display_name":"P\u00edetro Li\u00f3","orcid":"https://orcid.org/0000-0002-0540-5053"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Pietro Li\u00f2","raw_affiliation_strings":["Computer Laboratory, University of Cambridge, UK"],"affiliations":[{"raw_affiliation_string":"Computer Laboratory, University of Cambridge, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026770450","display_name":"Ivan Merelli","orcid":"https://orcid.org/0000-0003-3587-3680"},"institutions":[{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"funder","lineage":["https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I4210154278","display_name":"Institute of Biomedical Technologies","ror":"https://ror.org/04ehykb85","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210154278","https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Ivan Merelli","raw_affiliation_strings":["Institute for Biomedical Technologies - Italian National Research Council, Segrate (Mi), Italy"],"affiliations":[{"raw_affiliation_string":"Institute for Biomedical Technologies - Italian National Research Council, Segrate (Mi), Italy","institution_ids":["https://openalex.org/I4210154278","https://openalex.org/I4210155236"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053667707","display_name":"Massimo Torquati","orcid":"https://orcid.org/0000-0001-6323-3459"},"institutions":[{"id":"https://openalex.org/I108290504","display_name":"University of Pisa","ror":"https://ror.org/03ad39j10","country_code":"IT","type":"education","lineage":["https://openalex.org/I108290504"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Massimo Torquati","raw_affiliation_strings":["Computer Science Department, University of Pisa, Italy"],"affiliations":[{"raw_affiliation_string":"Computer Science Department, University of Pisa, Italy","institution_ids":["https://openalex.org/I108290504"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089092418","display_name":"Marco Aldinucci","orcid":"https://orcid.org/0000-0001-8788-0829"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Marco Aldinucci","raw_affiliation_strings":["Computer Science Department, University of Torino, Italy"],"affiliations":[{"raw_affiliation_string":"Computer Science Department, University of Torino, Italy","institution_ids":["https://openalex.org/I55143463"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5075443548"],"corresponding_institution_ids":["https://openalex.org/I55143463"],"apc_list":null,"apc_paid":null,"fwci":0.6073,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.73733243,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"31","issue":"3","first_page":"196","last_page":"211"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11321","display_name":"Error Correcting Code Techniques","score":0.9918000102043152,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11321","display_name":"Error Correcting Code Techniques","score":0.9918000102043152,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9878000020980835,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9876999855041504,"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/scalability","display_name":"Scalability","score":0.7409766912460327},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6751905679702759},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5503921508789062},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.49383077025413513},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4931308925151825},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4804491698741913},{"id":"https://openalex.org/keywords/external-data-representation","display_name":"External Data Representation","score":0.4629754424095154},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.43779605627059937},{"id":"https://openalex.org/keywords/big-data","display_name":"Big data","score":0.43162092566490173},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4155643582344055},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.35007327795028687},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3431949019432068},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3302127718925476},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.323594868183136},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21900340914726257},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1711558699607849},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.15375924110412598},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13736343383789062},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11052879691123962}],"concepts":[{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7409766912460327},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6751905679702759},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5503921508789062},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.49383077025413513},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4931308925151825},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4804491698741913},{"id":"https://openalex.org/C116409475","wikidata":"https://www.wikidata.org/wiki/Q1385056","display_name":"External Data Representation","level":2,"score":0.4629754424095154},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.43779605627059937},{"id":"https://openalex.org/C75684735","wikidata":"https://www.wikidata.org/wiki/Q858810","display_name":"Big data","level":2,"score":0.43162092566490173},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4155643582344055},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.35007327795028687},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3431949019432068},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3302127718925476},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.323594868183136},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21900340914726257},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1711558699607849},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.15375924110412598},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13736343383789062},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11052879691123962},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1177/1094342016668567","is_oa":false,"landing_page_url":"https://doi.org/10.1177/1094342016668567","pdf_url":null,"source":{"id":"https://openalex.org/S60606485","display_name":"The International Journal of High Performance Computing Applications","issn_l":"1094-3420","issn":["1094-3420","1741-2846"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of High Performance Computing Applications","raw_type":"journal-article"},{"id":"pmh:oai:arpi.unipi.it:11568/904305","is_oa":false,"landing_page_url":"http://hdl.handle.net/11568/904305","pdf_url":null,"source":{"id":"https://openalex.org/S4377196265","display_name":"CINECA IRIS Institutial research information system (University of Pisa)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I108290504","host_organization_name":"University of Pisa","host_organization_lineage":["https://openalex.org/I108290504"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:iris.unito.it:2318/1607126","is_oa":true,"landing_page_url":"http://hdl.handle.net/2318/1607126","pdf_url":null,"source":{"id":"https://openalex.org/S4306400637","display_name":"Institutional Research Information System University of Turin (University of Turin)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I55143463","host_organization_name":"University of Turin","host_organization_lineage":["https://openalex.org/I55143463"],"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":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:oai:iris.unito.it:2318/1607126","is_oa":true,"landing_page_url":"http://hdl.handle.net/2318/1607126","pdf_url":null,"source":{"id":"https://openalex.org/S4306400637","display_name":"Institutional Research Information System University of Turin (University of Turin)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I55143463","host_organization_name":"University of Turin","host_organization_lineage":["https://openalex.org/I55143463"],"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":"","raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W1579108863","https://openalex.org/W1945579058","https://openalex.org/W1988888548","https://openalex.org/W2001576815","https://openalex.org/W2012811541","https://openalex.org/W2024704296","https://openalex.org/W2039417226","https://openalex.org/W2045158825","https://openalex.org/W2055497547","https://openalex.org/W2070021921","https://openalex.org/W2073026107","https://openalex.org/W2076202384","https://openalex.org/W2090037139","https://openalex.org/W2105778988","https://openalex.org/W2123596692","https://openalex.org/W2131004167","https://openalex.org/W2142270559","https://openalex.org/W2160694821","https://openalex.org/W2167602547","https://openalex.org/W2801490189","https://openalex.org/W4249327473"],"related_works":["https://openalex.org/W4247566972","https://openalex.org/W2960264696","https://openalex.org/W3090563135","https://openalex.org/W2497432351","https://openalex.org/W4206777497","https://openalex.org/W4233347783","https://openalex.org/W2910064364","https://openalex.org/W4255224757","https://openalex.org/W2499527417","https://openalex.org/W3209527236"],"abstract_inverted_index":{"Recent":[0],"advances":[1],"in":[2,22,79,166],"molecular":[3,29],"biology":[4,30],"and":[5,71,84,106,120,131,148],"bioinformatic":[6],"techniques":[7,31],"have":[8],"brought":[9],"about":[10,15],"an":[11,129,151],"explosion":[12],"of":[13,19,25,36,40,68,82,89,111,115,145,169],"information":[14,61,147],"the":[16,20,23,37,66,90,167],"spatial":[17,38],"organisation":[18,39],"DNA":[21],"nucleus":[24],"a":[26,33,57,80,141],"cell.":[27],"High-throughput":[28],"provide":[32],"genome-wide":[34],"capture":[35],"chromosomes":[41],"at":[42],"unprecedented":[43],"scales,":[44],"which":[45,149],"permit":[46],"one":[47],"to":[48],"identify":[49],"physical":[50],"interactions":[51],"between":[52],"genetic":[53],"elements":[54],"located":[55],"throughout":[56],"genome.":[58],"This":[59],"important":[60],"is,":[62],"however,":[63],"hampered":[64],"by":[65],"lack":[67],"biologist-friendly":[69],"analysis":[70,138],"visualisation":[72],"software:":[73],"these":[74],"disciplines":[75],"are":[76,85],"literally":[77],"caught":[78],"flood":[81],"data":[83,121,137],"now":[86],"facing":[87],"many":[88],"scale-out":[91],"issues":[92,165],"that":[93,139],"high-performance":[94],"computing":[95],"has":[96],"been":[97],"addressing":[98],"for":[99,135,155,172],"years.":[100],"Data":[101],"must":[102],"be":[103],"managed,":[104],"analysed":[105],"integrated,":[107],"with":[108],"substantial":[109],"requirements":[110],"speed":[112],"(in":[113],"terms":[114],"execution":[116],"time),":[117],"application":[118],"scalability":[119],"representation.":[122],"In":[123],"this":[124],"work,":[125],"we":[126,161],"present":[127],"NuChart-II,":[128,160],"efficient":[130],"highly":[132],"optimised":[133],"tool":[134],"genomic":[136,146],"provides":[140],"gene-centric,":[142],"graph-based":[143],"representation":[144],"proposes":[150],"ex-post":[152],"normalisation":[153],"technique":[154],"Hi-C":[156],"data.":[157],"While":[158],"designing":[159],"addressed":[162],"several":[163],"common":[164],"parallelisation":[168],"memory-bound":[170],"algorithms":[171],"shared-memory":[173],"systems.":[174]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
