{"id":"https://openalex.org/W2338825379","doi":"https://doi.org/10.1093/nar/gkw299","title":"GeNemo: a search engine for web-based functional genomic data","display_name":"GeNemo: a search engine for web-based functional genomic data","publication_year":2016,"publication_date":"2016-04-20","ids":{"openalex":"https://openalex.org/W2338825379","doi":"https://doi.org/10.1093/nar/gkw299","mag":"2338825379","pmid":"https://pubmed.ncbi.nlm.nih.gov/27098038"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkw299","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkw299","pdf_url":"https://academic.oup.com/nar/article-pdf/44/W1/W122/18787368/gkw299.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/44/W1/W122/18787368/gkw299.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Yongqing Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yongqing Zhang","raw_affiliation_strings":["Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043022045","display_name":"Xiaoyi Cao","orcid":"https://orcid.org/0000-0001-7222-5450"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaoyi Cao","raw_affiliation_strings":["Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047976044","display_name":"Sheng Zhong","orcid":"https://orcid.org/0000-0001-6419-7453"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I4210133661","display_name":"La Jolla Bioengineering Institute","ror":"https://ror.org/03sgbh608","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210133661"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sheng Zhong","raw_affiliation_strings":["Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA szhong@ucsd.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA szhong@ucsd.edu","institution_ids":["https://openalex.org/I4210133661","https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":1.3929,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.8170252,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"44","issue":"W1","first_page":"W122","last_page":"W127"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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":0.9994000196456909,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9984999895095825,"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":0.9965000152587891,"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/encode","display_name":"ENCODE","score":0.6813997626304626},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.588353157043457},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5411123633384705},{"id":"https://openalex.org/keywords/genome-browser","display_name":"Genome browser","score":0.5018866062164307},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4927707016468048},{"id":"https://openalex.org/keywords/genomic-dna","display_name":"genomic DNA","score":0.4877060353755951},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4796205461025238},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4686030149459839},{"id":"https://openalex.org/keywords/functional-genomics","display_name":"Functional genomics","score":0.4585847854614258},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.40059730410575867},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.33592164516448975},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2542743682861328},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.18533632159233093},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1288083791732788}],"concepts":[{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.6813997626304626},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.588353157043457},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5411123633384705},{"id":"https://openalex.org/C2781148417","wikidata":"https://www.wikidata.org/wiki/Q5533486","display_name":"Genome browser","level":5,"score":0.5018866062164307},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4927707016468048},{"id":"https://openalex.org/C17757408","wikidata":"https://www.wikidata.org/wiki/Q4135516","display_name":"genomic DNA","level":3,"score":0.4877060353755951},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4796205461025238},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4686030149459839},{"id":"https://openalex.org/C161078062","wikidata":"https://www.wikidata.org/wiki/Q1068690","display_name":"Functional genomics","level":5,"score":0.4585847854614258},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.40059730410575867},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.33592164516448975},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2542743682861328},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.18533632159233093},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1288083791732788},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057386","descriptor_name":"Search Engine","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057386","descriptor_name":"Search Engine","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057386","descriptor_name":"Search Engine","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/nar/gkw299","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkw299","pdf_url":"https://academic.oup.com/nar/article-pdf/44/W1/W122/18787368/gkw299.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:27098038","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27098038","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt8xd394vd","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/8xd394vd","pdf_url":"https://escholarship.org/content/qt8xd394vd/qt8xd394vd.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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":"Nucleic Acids Research, vol 44, iss W1","raw_type":"article"},{"id":"pmh:ark:/13030/qt8xd394vd","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:europepmc.org:3952866","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4987887","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:nar:44/W1/W122","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/44/W1/W122","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/nar/gkw299","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkw299","pdf_url":"https://academic.oup.com/nar/article-pdf/44/W1/W122/18787368/gkw299.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2811043086","display_name":null,"funder_award_id":"R01 HG008135","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G6224162804","display_name":null,"funder_award_id":"DP1 HD087990","funder_id":"https://openalex.org/F4320337611","funder_display_name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development"}],"funders":[{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337364","display_name":"National Institute of Child Health and Human Development","ror":"https://ror.org/04byxyr05"},{"id":"https://openalex.org/F4320337611","display_name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","ror":"https://ror.org/04byxyr05"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2338825379.pdf"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W1964963969","https://openalex.org/W2001554877","https://openalex.org/W2008051478","https://openalex.org/W2031967690","https://openalex.org/W2076154138","https://openalex.org/W2108207895","https://openalex.org/W2127640118","https://openalex.org/W2128016314","https://openalex.org/W2129785061","https://openalex.org/W2259938310","https://openalex.org/W4255975151"],"related_works":["https://openalex.org/W2911303926","https://openalex.org/W8288889","https://openalex.org/W2521866209","https://openalex.org/W2316024100","https://openalex.org/W3177323319","https://openalex.org/W2123222904","https://openalex.org/W3206097003","https://openalex.org/W2153158720","https://openalex.org/W2413733797","https://openalex.org/W2079600570"],"abstract_inverted_index":{"A":[0],"set":[1],"of":[2,68,85,135],"new":[3,37],"data":[4,34,41,58,179],"types":[5,35],"emerged":[6],"from":[7,92,126,133],"functional":[8,28,52,61,86,106,143],"genomic":[9,29,53,62,87,107,123,188],"assays,":[10],"including":[11,64],"ChIP-seq,":[12],"DNase-seq,":[13],"FAIRE-seq":[14],"and":[15,70,184],"others.":[16],"The":[17,98],"results":[18],"are":[19,80],"typically":[20],"stored":[21],"as":[22],"genome-wide":[23],"intensities":[24],"(WIG/bigWig":[25],"files)":[26],"or":[27,94,104,116],"regions":[30],"(peak/BED":[31],"files).":[32],"These":[33],"present":[36,45],"challenges":[38],"to":[39,129,162],"big":[40],"science.":[42],"Here,":[43],"we":[44],"GeNemo,":[46],"a":[47,111,117,152,170],"web-based":[48],"search":[49,76,171],"engine":[50],"for":[51,109],"data.":[54],"GeNemo":[55,91,120,190],"searches":[56,79],"user-input":[57],"against":[59],"online":[60,137],"datasets,":[63],"the":[65,136,173,181,186],"entire":[66],"collection":[67],"ENCODE":[69,72,138],"mouse":[71],"datasets.":[73],"Unlike":[74],"text-based":[75],"engines,":[77],"GeNemo's":[78],"based":[81],"on":[82,160,169],"pattern":[83],"matching":[84],"regions.":[88,189],"This":[89,148],"distinguishes":[90],"text":[93],"DNA":[95],"sequence":[96],"searches.":[97],"user":[99,174],"can":[100,175],"input":[101],"any":[102,122,134],"complete":[103],"partial":[105],"dataset,":[108],"example,":[110],"binding":[112],"intensity":[113],"file":[114],"(bigWig)":[115],"peak":[118],"file.":[119],"reports":[121],"regions,":[124],"ranging":[125],"hundred":[127,130],"bases":[128],"thousand":[131],"bases,":[132],"datasets":[139,183],"that":[140],"share":[141],"similar":[142],"(binding,":[144],"modification,":[145],"accessibility)":[146],"patterns.":[147],"is":[149,191],"enabled":[150],"by":[151],"Markov":[153],"Chain":[154],"Monte":[155],"Carlo-based":[156],"maximization":[157],"process,":[158],"executed":[159],"up":[161],"24":[163],"parallel":[164],"computing":[165],"threads.":[166],"By":[167],"clicking":[168],"result,":[172],"visually":[176],"compare":[177],"her/his":[178],"with":[180],"found":[182],"navigate":[185],"identified":[187],"available":[192],"at":[193],"www.genemo.org.":[194]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":4},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":1}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
