{"id":"https://openalex.org/W2129449307","doi":"https://doi.org/10.1186/1756-0381-3-4","title":"SICTIN: Rapid footprinting of massively parallel sequencing data","display_name":"SICTIN: Rapid footprinting of massively parallel sequencing data","publication_year":2010,"publication_date":"2010-08-13","ids":{"openalex":"https://openalex.org/W2129449307","doi":"https://doi.org/10.1186/1756-0381-3-4","mag":"2129449307","pmid":"https://pubmed.ncbi.nlm.nih.gov/20707885"},"language":"en","primary_location":{"id":"doi:10.1186/1756-0381-3-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1756-0381-3-4","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-3-4","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-3-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053703926","display_name":"Stefan Enroth","orcid":"https://orcid.org/0000-0002-5056-9137"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]},{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Stefan Enroth","raw_affiliation_strings":["Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, SE-75124 Uppsala, Sweden. jan.komorowski@lcb.uu.se","Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, SE-75124 Uppsala, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, SE-75124 Uppsala, Sweden. jan.komorowski@lcb.uu.se","institution_ids":["https://openalex.org/I123387679","https://openalex.org/I2800139495"]},{"raw_affiliation_string":"Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, SE-75124 Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679","https://openalex.org/I2800139495"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087439948","display_name":"Robin Andersson","orcid":"https://orcid.org/0000-0003-1516-879X"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]},{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Robin Andersson","raw_affiliation_strings":["Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, SE-75124, Uppsala, Sweden","Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, SE-75124, Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679","https://openalex.org/I2800139495"]},{"raw_affiliation_string":"Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066763304","display_name":"Claes Wadelius","orcid":"https://orcid.org/0000-0002-2033-7829"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Claes Wadelius","raw_affiliation_strings":["Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-75185, Uppsala, Sweden","Department of Genetics and Pathology Rudbeck Laboratory Uppsala University Uppsala Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-75185, Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679"]},{"raw_affiliation_string":"Department of Genetics and Pathology Rudbeck Laboratory Uppsala University Uppsala Sweden","institution_ids":["https://openalex.org/I123387679"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050406527","display_name":"Jan Komorowski","orcid":"https://orcid.org/0000-0002-0766-8789"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]},{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]},{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL","SE"],"is_corresponding":true,"raw_author_name":"Jan Komorowski","raw_affiliation_strings":["Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, SE-75124, Uppsala, Sweden","Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, PL-02-106, Warszawa, Poland","Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden","Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Warszawa, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, SE-75124, Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679","https://openalex.org/I2800139495"]},{"raw_affiliation_string":"Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, PL-02-106, Warszawa, Poland","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679"]},{"raw_affiliation_string":"Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Warszawa, Poland","institution_ids":["https://openalex.org/I4654613"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5050406527"],"corresponding_institution_ids":["https://openalex.org/I123387679","https://openalex.org/I2800139495","https://openalex.org/I4654613"],"apc_list":{"value":2490,"currency":"USD","value_usd":2490},"apc_paid":{"value":2490,"currency":"USD","value_usd":2490},"fwci":0.7471,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.69918457,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"3","issue":"1","first_page":"4","last_page":"4"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","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/T11482","display_name":"RNA modifications and cancer","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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9991000294685364,"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":0.9986000061035156,"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/footprinting","display_name":"Footprinting","score":0.9005500078201294},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7001004815101624},{"id":"https://openalex.org/keywords/massively-parallel","display_name":"Massively parallel","score":0.6779120564460754},{"id":"https://openalex.org/keywords/massive-parallel-sequencing","display_name":"Massive parallel sequencing","score":0.6249878406524658},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40645331144332886},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32990092039108276},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.29029154777526855},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.2550516724586487},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19640791416168213},{"id":"https://openalex.org/keywords/base-sequence","display_name":"Base sequence","score":0.10172215104103088},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09965348243713379},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.05183634161949158}],"concepts":[{"id":"https://openalex.org/C2778021871","wikidata":"https://www.wikidata.org/wiki/Q648006","display_name":"Footprinting","level":4,"score":0.9005500078201294},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7001004815101624},{"id":"https://openalex.org/C190475519","wikidata":"https://www.wikidata.org/wiki/Q544384","display_name":"Massively parallel","level":2,"score":0.6779120564460754},{"id":"https://openalex.org/C192800701","wikidata":"https://www.wikidata.org/wiki/Q6784807","display_name":"Massive parallel sequencing","level":4,"score":0.6249878406524658},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40645331144332886},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32990092039108276},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.29029154777526855},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.2550516724586487},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19640791416168213},{"id":"https://openalex.org/C3017666073","wikidata":"https://www.wikidata.org/wiki/Q1764062","display_name":"Base sequence","level":3,"score":0.10172215104103088},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09965348243713379},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.05183634161949158}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/1756-0381-3-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1756-0381-3-4","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-3-4","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:20707885","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20707885","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":"BioData mining","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2928217","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2928217","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Min","raw_type":"Text"},{"id":"pmh:oai:DiVA.org:uu-129177","is_oa":true,"landing_page_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-129177","pdf_url":null,"source":{"id":"https://openalex.org/S4306401559","display_name":"KTH Publication Database DiVA (KTH Royal Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I86987016","host_organization_name":"KTH Royal Institute of Technology","host_organization_lineage":["https://openalex.org/I86987016"],"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"},{"id":"pmh:oai:doaj.org/article:e8f29eb596944be49d15aba292bddf65","is_oa":true,"landing_page_url":"https://doaj.org/article/e8f29eb596944be49d15aba292bddf65","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Mining, Vol 3, Iss 1, p 4 (2010)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1756-0381-3-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1756-0381-3-4","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-3-4","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320313607","display_name":"Swedish Cancer Foundation","ror":null},{"id":"https://openalex.org/F4320320940","display_name":"Stiftelsen f\u00f6r\u00a0Strategisk Forskning","ror":"https://ror.org/044wr7g58"},{"id":"https://openalex.org/F4320322327","display_name":"Knut och Alice Wallenbergs Stiftelse","ror":"https://ror.org/004hzzk67"},{"id":"https://openalex.org/F4320322581","display_name":"Vetenskapsr\u00e5det","ror":"https://ror.org/03zttf063"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2129449307.pdf","grobid_xml":"https://content.openalex.org/works/W2129449307.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1964188377","https://openalex.org/W2004993130","https://openalex.org/W2015416439","https://openalex.org/W2017840637","https://openalex.org/W2036390512","https://openalex.org/W2042797800","https://openalex.org/W2059699217","https://openalex.org/W2072152932","https://openalex.org/W2083245183","https://openalex.org/W2098391569","https://openalex.org/W2100196653","https://openalex.org/W2102304447","https://openalex.org/W2108234281","https://openalex.org/W2114752404","https://openalex.org/W2127226151","https://openalex.org/W2127640118","https://openalex.org/W2129795133","https://openalex.org/W2143325524","https://openalex.org/W2146631202","https://openalex.org/W2150308846","https://openalex.org/W2916408032","https://openalex.org/W4210430020"],"related_works":["https://openalex.org/W1148954706","https://openalex.org/W1528913684","https://openalex.org/W4282828727","https://openalex.org/W4388367611","https://openalex.org/W958315937","https://openalex.org/W1553613240","https://openalex.org/W21615084","https://openalex.org/W1967085530","https://openalex.org/W2596828944","https://openalex.org/W2147753608"],"abstract_inverted_index":{"BACKGROUND:":[0],"Massively":[1],"parallel":[2],"sequencing":[3,134],"allows":[4,81,115],"for":[5,10,82,116,174],"genome-wide":[6],"hypothesis-free":[7],"investigation":[8,110],"of":[9,36,54,71,111,131,133,180,182,184],"instance":[11],"transcription":[12,45],"factor":[13],"binding":[14],"sites":[15,145],"or":[16,49],"histone":[17],"modifications.":[18],"Although":[19],"nucleotide":[20],"resolution":[21],"detailed":[22],"information":[23],"can":[24],"easily":[25],"be":[26],"generated,":[27],"biological":[28,117],"insight":[29],"often":[30],"requires":[31],"a":[32,59,68,89,121,156,171],"more":[33],"general":[34],"view":[35],"patterns":[37,141],"(footprints)":[38],"over":[39],"distinct":[40],"genomic":[41,161],"features":[42,162],"such":[43],"as":[44],"start":[46,144],"sites,":[47],"exons":[48],"repetitive":[50],"regions.":[51],"The":[52,64],"construction":[53],"these":[55],"footprints":[56],"is":[57,153],"however":[58],"time":[60],"consuming":[61],"task.":[62],"METHODS:":[63],"presented":[65],"software":[66],"generates":[67],"binary":[69],"representation":[70,80],"the":[72,99,104,128,178],"signals":[73],"enabling":[74],"fast":[75,175],"and":[76,103,159],"scalable":[77],"lookup.":[78],"This":[79],"footprint":[83],"generation":[84],"in":[85,148,177],"mere":[86],"minutes":[87],"on":[88,139],"desktop":[90],"computer.":[91],"Several":[92],"different":[93],"input":[94],"formats":[95],"are":[96,147,163],"accepted,":[97],"e.g.":[98],"SAM":[100],"format,":[101],"bed-files":[102],"UCSC":[105],"wiggle":[106],"track.":[107],"CONCLUSIONS:":[108],"Hypothesis-free":[109],"genome":[112],"wide":[113],"interactions":[114],"data":[118,135],"mining":[119],"at":[120],"scale":[122],"never":[123],"before":[124],"seen.":[125],"Until":[126],"recently,":[127],"main":[129],"focus":[130,152],"analysis":[132],"has":[136],"been":[137],"targeted":[138],"signal":[140],"around":[142],"transcriptional":[143],"which":[146],"manageable":[149],"numbers.":[150],"Today,":[151],"shifting":[154],"to":[155],"wider":[157],"perspective":[158],"numerous":[160],"being":[164],"studied.":[165],"To":[166],"this":[167],"end,":[168],"we":[169],"provide":[170],"system":[172],"allowing":[173],"querying":[176],"order":[179],"hundreds":[181],"thousands":[183],"features.":[185]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":3}],"updated_date":"2026-08-13T07:04:57.449891","created_date":"2016-06-24T00:00:00"}
