{"id":"https://openalex.org/W4410551341","doi":"https://doi.org/10.1093/bioinformatics/btaf315","title":"esMPRA: an easy-to-use systematic pipeline for MPRA experiment quality control and data analysis","display_name":"esMPRA: an easy-to-use systematic pipeline for MPRA experiment quality control and data analysis","publication_year":2025,"publication_date":"2025-05-21","ids":{"openalex":"https://openalex.org/W4410551341","doi":"https://doi.org/10.1093/bioinformatics/btaf315","pmid":"https://pubmed.ncbi.nlm.nih.gov/40397077"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf315","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf315","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf315/63264629/btaf315.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","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/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf315/63264629/btaf315.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Jiaqi Li","orcid":"https://orcid.org/0000-0001-9038-9010"},"institutions":[{"id":"https://openalex.org/I29955533","display_name":"Center for Information Technology","ror":"https://ror.org/03jh5a977","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I29955533"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Jiaqi Li","raw_affiliation_strings":["Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University , Beijing 100084,","Tsinghua University Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Department of Automation, , Beijing, 100084,"],"raw_orcid":"https://orcid.org/0000-0001-9038-9010","affiliations":[{"raw_affiliation_string":"Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University , Beijing 100084,","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Tsinghua University Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Department of Automation, , Beijing, 100084,","institution_ids":["https://openalex.org/I29955533","https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100365991","display_name":"Pengcheng Zhang","orcid":"https://orcid.org/0000-0003-3524-3478"},"institutions":[{"id":"https://openalex.org/I29955533","display_name":"Center for Information Technology","ror":"https://ror.org/03jh5a977","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I29955533"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Pengcheng Zhang","raw_affiliation_strings":["Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University , Beijing 100084,","Tsinghua University Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Department of Automation, , Beijing, 100084,"],"raw_orcid":"https://orcid.org/0000-0003-3524-3478","affiliations":[{"raw_affiliation_string":"Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University , Beijing 100084,","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Tsinghua University Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Department of Automation, , Beijing, 100084,","institution_ids":["https://openalex.org/I29955533","https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101915655","display_name":"Xi Xi","orcid":"https://orcid.org/0000-0002-9207-1804"},"institutions":[{"id":"https://openalex.org/I29955533","display_name":"Center for Information Technology","ror":"https://ror.org/03jh5a977","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I29955533"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Xi Xi","raw_affiliation_strings":["Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University , Beijing 100084,","Tsinghua University Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Department of Automation, , Beijing, 100084,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University , Beijing 100084,","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Tsinghua University Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Department of Automation, , Beijing, 100084,","institution_ids":["https://openalex.org/I29955533","https://openalex.org/I99065089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008093795","display_name":"Xiaowo Wang","orcid":"https://orcid.org/0000-0003-2965-8036"},"institutions":[{"id":"https://openalex.org/I29955533","display_name":"Center for Information Technology","ror":"https://ror.org/03jh5a977","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I29955533"]},{"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"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Xiaowo Wang","raw_affiliation_strings":["College of Artificial Intelligence, Tsinghua University , Beijing 100084,","Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University , Beijing 100084,","Tsinghua University College of Artificial Intelligence, , Beijing, 100084,","Tsinghua University Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Department of Automation, , Beijing, 100084,"],"raw_orcid":"https://orcid.org/0000-0003-2965-8036","affiliations":[{"raw_affiliation_string":"College of Artificial Intelligence, Tsinghua University , Beijing 100084,","institution_ids":["https://openalex.org/I4210100255"]},{"raw_affiliation_string":"Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University , Beijing 100084,","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Tsinghua University College of Artificial Intelligence, , Beijing, 100084,","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Tsinghua University Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Department of Automation, , Beijing, 100084,","institution_ids":["https://openalex.org/I29955533","https://openalex.org/I99065089"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.08825119,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.3837999999523163,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.3837999999523163,"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":0.15119999647140503,"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":0.030700000002980232,"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":0.7953193783760071},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7311854958534241},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6005043387413025},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5769067406654358},{"id":"https://openalex.org/keywords/quality-assurance","display_name":"Quality assurance","score":0.47110942006111145},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.4597042500972748},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4556598365306854},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.44549041986465454},{"id":"https://openalex.org/keywords/reliability-engineering","display_name":"Reliability engineering","score":0.42125046253204346},{"id":"https://openalex.org/keywords/data-quality","display_name":"Data quality","score":0.4121403098106384},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39501383900642395},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.3301526606082916},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.324518620967865},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.3168630599975586}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7953193783760071},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7311854958534241},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6005043387413025},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5769067406654358},{"id":"https://openalex.org/C106436119","wikidata":"https://www.wikidata.org/wiki/Q836575","display_name":"Quality assurance","level":3,"score":0.47110942006111145},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.4597042500972748},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4556598365306854},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.44549041986465454},{"id":"https://openalex.org/C200601418","wikidata":"https://www.wikidata.org/wiki/Q2193887","display_name":"Reliability engineering","level":1,"score":0.42125046253204346},{"id":"https://openalex.org/C24756922","wikidata":"https://www.wikidata.org/wiki/Q1757694","display_name":"Data quality","level":3,"score":0.4121403098106384},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39501383900642395},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.3301526606082916},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.324518620967865},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.3168630599975586},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C2780378061","wikidata":"https://www.wikidata.org/wiki/Q25351891","display_name":"Service (business)","level":2,"score":0.0},{"id":"https://openalex.org/C136264566","wikidata":"https://www.wikidata.org/wiki/Q159810","display_name":"Economy","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","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":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf315","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf315","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf315/63264629/btaf315.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40397077","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40397077","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:10946766","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12133320","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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf315","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf315","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf315/63264629/btaf315.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.550000011920929,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G5022137638","display_name":null,"funder_award_id":"2023YFF1204500","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G8025262204","display_name":null,"funder_award_id":"62225307","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410551341.pdf","grobid_xml":"https://content.openalex.org/works/W4410551341.grobid-xml"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W2145674897","https://openalex.org/W2157107905","https://openalex.org/W2412481123","https://openalex.org/W2970956693","https://openalex.org/W2981751257","https://openalex.org/W3041065315","https://openalex.org/W4400729643","https://openalex.org/W4403680549","https://openalex.org/W4407269017"],"related_works":["https://openalex.org/W1981780420","https://openalex.org/W2182707996","https://openalex.org/W45233828","https://openalex.org/W2964988449","https://openalex.org/W2397952901","https://openalex.org/W2029380707","https://openalex.org/W188202134","https://openalex.org/W4255934811","https://openalex.org/W2465382974","https://openalex.org/W2010229520"],"abstract_inverted_index":{"MOTIVATION:":[0],"Massively":[1],"Parallel":[2],"Reporter":[3],"Assays":[4],"(MPRAs)":[5],"have":[6],"emerged":[7],"as":[8,185,217],"pivotal":[9],"tools":[10],"for":[11,88,139,176,196,207,220],"systematically":[12],"profiling":[13],"cis-regulatory":[14],"element":[15,28],"activity,":[16],"playing":[17],"critical":[18],"roles":[19],"in":[20,95],"deciphering":[21],"gene":[22],"regulation":[23],"mechanisms":[24],"and":[25,54,59,70,84,97,115,127,148,165,204,210,212,222],"synthetic":[26],"regulatory":[27],"engineering.":[29],"However,":[30],"MPRA":[31,89,96,107,177],"experiments":[32],"involve":[33],"multi-step":[34],"library":[35],"processing":[36],"procedures":[37],"coupled":[38,101],"with":[39,102,169],"high-throughput":[40],"sequencing.":[41],"Operational":[42],"errors":[43],"during":[44],"these":[45],"complex":[46],"workflows":[47],"can":[48],"lead":[49],"to":[50,66,131],"substantial":[51],"resource":[52],"depletion":[53],"experimental":[55,68,129],"delays.":[56],"Thus":[57],"robust":[58],"user-friendly":[60],"quality":[61,82,112,119,154],"control":[62,83,113],"methods":[63],"are":[64],"essential":[65],"minimize":[67],"failures":[69],"ensure":[71],"reproducibility":[72],"between":[73],"replicates.":[74],"RESULTS:":[75],"Here,":[76],"we":[77,109],"present":[78],"esMPRA,":[79],"an":[80,173,186],"integrated":[81],"analysis":[85,104,163],"pipeline":[86,157],"designed":[87],"experiments.":[90],"Building":[91],"on":[92,200],"our":[93],"experience":[94],"its":[98],"derivative":[99],"techniques,":[100],"systematic":[103],"of":[105],"public":[106],"datasets,":[108],"established":[110],"standardized":[111],"metrics":[114],"developed":[116],"a":[117,144],"stepwise":[118],"monitoring":[120],"framework.":[121],"esMPRA":[122,142,182,197],"generates":[123],"stage-specific":[124],"diagnostic":[125],"reports":[126],"provides":[128],"recommendations":[130],"avoid":[132],"potential":[133],"risks":[134],"throughout":[135],"the":[136,156,190],"workflow.":[137],"Designed":[138],"maximal":[140],"accessibility,":[141],"features":[143],"one-line":[145],"command-line":[146],"interface":[147,166],"requires":[149],"minimal":[150],"bioinformatics":[151],"expertise.":[152],"Beyond":[153],"assessment,":[155],"delivers":[158],"processed":[159],"data":[160],"outputs,":[161],"comprehensive":[162],"reports,":[164],"files":[167],"compatible":[168],"downstream":[170],"analyses,":[171],"establishing":[172],"end-to-end":[174],"solution":[175],"experimentation.":[178],"AVAILABILITY":[179],"AND":[180],"IMPLEMENTATION:":[181],"is":[183,198,213,224],"released":[184],"open-source":[187],"software":[188],"under":[189],"MIT":[191],"license.":[192],"The":[193],"source":[194],"code":[195],"available":[199,214,225],"Zenodo":[201,227],"(DOI:":[202],"10.5281/zenodo.15362711)":[203],"GitHub":[205],"(https://github.com/WangLabTHU/esMPRA/)":[206],"Linux,":[208],"macOS,":[209],"Windows":[211],"via":[215,226],"PyPI":[216],"esMPRA.":[218],"Data":[219],"testing":[221],"reference":[223],"repository":[228],"at":[229],"https://zenodo.org/records/15034449.":[230]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
