{"id":"https://openalex.org/W4400116213","doi":"https://doi.org/10.1145/3665689.3665736","title":"MMF-ATAC: A User-friendly Web Server for Multiple Motifs Finding on ATAC-seq Data","display_name":"MMF-ATAC: A User-friendly Web Server for Multiple Motifs Finding on ATAC-seq Data","publication_year":2024,"publication_date":"2024-01-26","ids":{"openalex":"https://openalex.org/W4400116213","doi":"https://doi.org/10.1145/3665689.3665736"},"language":"en","primary_location":{"id":"doi:10.1145/3665689.3665736","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3665689.3665736","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2024 4th International Conference on Bioinformatics and Intelligent Computing","raw_type":"proceedings-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/A5100322699","display_name":"Yan Wang","orcid":"https://orcid.org/0000-0002-4751-0708"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yan Wang","raw_affiliation_strings":["Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, China"],"raw_orcid":"https://orcid.org/0000-0002-4751-0708","affiliations":[{"raw_affiliation_string":"Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, China","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032458772","display_name":"Xiaotian Wu","orcid":"https://orcid.org/0009-0006-1835-5725"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]},{"id":"https://openalex.org/I4210100255","display_name":"Beijing Academy of Artificial Intelligence","ror":"https://ror.org/016a74861","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210100255"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaotian Wu","raw_affiliation_strings":["School of Artificial Intelligence, Jilin University, China"],"raw_orcid":"https://orcid.org/0009-0006-1835-5725","affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence, Jilin University, China","institution_ids":["https://openalex.org/I4210100255","https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5099636428","display_name":"Haoming Da","orcid":"https://orcid.org/0009-0006-3569-3785"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]},{"id":"https://openalex.org/I4210134929","display_name":"Jilin Province Science and Technology Department","ror":"https://ror.org/049x38272","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210134929"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haoming Da","raw_affiliation_strings":["College of Computer Science and Technology, Jilin University, China"],"raw_orcid":"https://orcid.org/0009-0006-3569-3785","affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Jilin University, China","institution_ids":["https://openalex.org/I4210134929","https://openalex.org/I194450716"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004587392","display_name":"Shuangquan Zhang","orcid":"https://orcid.org/0000-0001-9245-5982"},"institutions":[{"id":"https://openalex.org/I36399199","display_name":"Nanjing University of Science and Technology","ror":"https://ror.org/00xp9wg62","country_code":"CN","type":"education","lineage":["https://openalex.org/I36399199"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuangquan Zhang","raw_affiliation_strings":["School of Cyber Science and Engineering, Nanjing University of Science and Technology, China"],"raw_orcid":"https://orcid.org/0000-0001-9245-5982","affiliations":[{"raw_affiliation_string":"School of Cyber Science and Engineering, Nanjing University of Science and Technology, China","institution_ids":["https://openalex.org/I36399199"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.2041,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.5445538,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":null,"issue":null,"first_page":"275","last_page":"279"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9991999864578247,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9991999864578247,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9979000091552734,"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":0.995199978351593,"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":0.6585120558738708},{"id":"https://openalex.org/keywords/user-friendly","display_name":"User Friendly","score":0.5792748928070068},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.514479398727417},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.41191112995147705},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.40339288115501404},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.19476431608200073},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.16530174016952515}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6585120558738708},{"id":"https://openalex.org/C61437842","wikidata":"https://www.wikidata.org/wiki/Q281291","display_name":"User Friendly","level":2,"score":0.5792748928070068},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.514479398727417},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.41191112995147705},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.40339288115501404},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.19476431608200073},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.16530174016952515}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3665689.3665736","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3665689.3665736","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2024 4th International Conference on Bioinformatics and Intelligent Computing","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W276882634","https://openalex.org/W2029426610","https://openalex.org/W2101289642","https://openalex.org/W2104594675","https://openalex.org/W2140952049","https://openalex.org/W2898601376","https://openalex.org/W2953051102","https://openalex.org/W3095189661","https://openalex.org/W3161076052","https://openalex.org/W4220872625","https://openalex.org/W4237053608","https://openalex.org/W4251346171","https://openalex.org/W4292723044","https://openalex.org/W4317436506"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052","https://openalex.org/W2382290278","https://openalex.org/W4395014643"],"abstract_inverted_index":{"Transcription":[0,10],"factors":[1],"(TFs)":[2],"bind":[3],"to":[4,156],"specific":[5],"DNA":[6],"sequences":[7],"known":[8],"as":[9,85,145],"factor":[11],"binding":[12],"sites":[13],"(TFBSs),":[14],"which":[15],"are":[16],"essential":[17,39],"for":[18,31,40,59,71,149,165],"various":[19],"biological":[20],"processes":[21],"and":[22,46,63,74,112,125,134,139,174],"disease":[23],"mechanisms.":[24,52],"The":[25],"identification":[26],"of":[27,44,136],"motifs":[28,96,158],"within":[29],"Assay":[30],"Transposase-Accessible":[32],"Chromatin":[33],"using":[34,97],"sequencing":[35],"(ATAC-seq)":[36],"data":[37,119,161],"is":[38,55,105,169],"elucidating":[41],"the":[42,163,175],"functions":[43],"TFBSs":[45,121],"their":[47],"impact":[48],"on":[49,110],"gene":[50],"regulatory":[51],"While":[53],"ATAC-seq":[54,95,118,142,160],"a":[56,68,86,98,108,146,153],"powerful":[57],"method":[58],"studying":[60],"chromatin":[61],"accessibility":[62],"predicting":[64],"TFBSs,":[65],"it":[66],"lacks":[67],"dedicated":[69],"server":[70,89,104],"motif":[72,123,131],"finding":[73,93,132],"downstream":[75,126],"analysis.":[76,127],"To":[77],"address":[78],"this":[79],"gap,":[80],"MMF-ATAC":[81,103,129,144,168],"has":[82],"been":[83],"developed":[84],"user-friendly":[87,154],"web":[88],"that":[90],"enables":[91],"efficient":[92],"multiple":[94],"graph":[99],"neural":[100],"network-based":[101],"tool.":[102],"designed":[106],"with":[107],"focus":[109],"usability":[111],"provides":[113,130],"several":[114],"key":[115],"features,":[116],"including":[117],"querying,":[120],"prediction,":[122],"finding,":[124],"Moreover,":[128],"results":[133],"visualizations":[135],"459":[137],"human":[138],"mouse":[140],"ENCODE":[141],"datasets.":[143],"valuable":[147],"resource":[148],"experimental":[150],"biologists":[151],"seeking":[152],"tool":[155],"find":[157],"from":[159],"without":[162],"need":[164],"programming":[166],"expertise.":[167],"freely":[170],"available":[171],"at":[172,181],"https://www.mmgraphws.com,":[173],"open-source":[176],"code":[177],"can":[178],"be":[179],"found":[180],"https://github.com/xiaotianr/MMF-ATAC.":[182]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
