{"id":"https://openalex.org/W4385156656","doi":"https://doi.org/10.1093/bioinformatics/btad448","title":"ReCo: automated NGS <u> <i>re</i> </u>ad-<u> <i>co</i> </u>unting of single and combinatorial CRISPR gRNAs","display_name":"ReCo: automated NGS <u> <i>re</i> </u>ad-<u> <i>co</i> </u>unting of single and combinatorial CRISPR gRNAs","publication_year":2023,"publication_date":"2023-07-22","ids":{"openalex":"https://openalex.org/W4385156656","doi":"https://doi.org/10.1093/bioinformatics/btad448","pmid":"https://pubmed.ncbi.nlm.nih.gov/37481709"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad448","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad448","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/8/btad448/51035797/btad448.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/article-pdf/39/8/btad448/51035797/btad448.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061010822","display_name":"Martin Wegner","orcid":"https://orcid.org/0000-0001-6403-3926"},"institutions":[{"id":"https://openalex.org/I114090438","display_name":"Goethe University Frankfurt","ror":"https://ror.org/04cvxnb49","country_code":"DE","type":"education","lineage":["https://openalex.org/I114090438"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Martin Wegner","raw_affiliation_strings":["Goethe University Frankfurt, University Hospital, Institute of Biochemistry II , 60590, Frankfurt am Main, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Goethe University Frankfurt, University Hospital, Institute of Biochemistry II , 60590, Frankfurt am Main, Germany","institution_ids":["https://openalex.org/I114090438"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050030738","display_name":"Manuel Kaulich","orcid":"https://orcid.org/0000-0002-9528-8822"},"institutions":[{"id":"https://openalex.org/I114090438","display_name":"Goethe University Frankfurt","ror":"https://ror.org/04cvxnb49","country_code":"DE","type":"education","lineage":["https://openalex.org/I114090438"]},{"id":"https://openalex.org/I4210154233","display_name":"Cardio-Pulmonary Institute","ror":"https://ror.org/04ckbty56","country_code":"DE","type":"facility","lineage":["https://openalex.org/I114090438","https://openalex.org/I149899117","https://openalex.org/I200763008","https://openalex.org/I4210102801","https://openalex.org/I4210154233"]},{"id":"https://openalex.org/I4210161239","display_name":"Frankfurt Cancer Institute","ror":"https://ror.org/05bx21r34","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I4210161239"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Manuel Kaulich","raw_affiliation_strings":["Cardio-Pulmonary Institute , Frankfurt am Main, Germany","Frankfurt Cancer Institute , Frankfurt am Main, Germany","Goethe University Frankfurt, University Hospital, Institute of Biochemistry II , 60590, Frankfurt am Main, Germany"],"raw_orcid":"https://orcid.org/0000-0002-9528-8822","affiliations":[{"raw_affiliation_string":"Cardio-Pulmonary Institute , Frankfurt am Main, Germany","institution_ids":["https://openalex.org/I4210154233"]},{"raw_affiliation_string":"Frankfurt Cancer Institute , Frankfurt am Main, Germany","institution_ids":["https://openalex.org/I4210161239"]},{"raw_affiliation_string":"Goethe University Frankfurt, University Hospital, Institute of Biochemistry II , 60590, Frankfurt am Main, Germany","institution_ids":["https://openalex.org/I114090438"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5050030738"],"corresponding_institution_ids":["https://openalex.org/I114090438","https://openalex.org/I4210154233","https://openalex.org/I4210161239"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.9929,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.76403936,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"39","issue":"8","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.8495000004768372,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.8495000004768372,"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":0.04490000009536743,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.023099999874830246,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/crispr","display_name":"CRISPR","score":0.8201735019683838},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6788658499717712},{"id":"https://openalex.org/keywords/guide-rna","display_name":"Guide RNA","score":0.45612066984176636},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.4373679459095001},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.43048542737960815},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.42300617694854736},{"id":"https://openalex.org/keywords/analytics","display_name":"Analytics","score":0.4206632971763611},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.32582592964172363},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.2984682321548462},{"id":"https://openalex.org/keywords/cas9","display_name":"Cas9","score":0.2775370478630066},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.20251789689064026},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1935763955116272},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17793133854866028},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14370152354240417}],"concepts":[{"id":"https://openalex.org/C98108389","wikidata":"https://www.wikidata.org/wiki/Q412563","display_name":"CRISPR","level":3,"score":0.8201735019683838},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6788658499717712},{"id":"https://openalex.org/C97702854","wikidata":"https://www.wikidata.org/wiki/Q4039747","display_name":"Guide RNA","level":5,"score":0.45612066984176636},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.4373679459095001},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.43048542737960815},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42300617694854736},{"id":"https://openalex.org/C79158427","wikidata":"https://www.wikidata.org/wiki/Q485396","display_name":"Analytics","level":2,"score":0.4206632971763611},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.32582592964172363},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.2984682321548462},{"id":"https://openalex.org/C132455925","wikidata":"https://www.wikidata.org/wiki/Q16965677","display_name":"Cas9","level":4,"score":0.2775370478630066},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.20251789689064026},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1935763955116272},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17793133854866028},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14370152354240417},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0}],"mesh":[{"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":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064112","descriptor_name":"Clustered Regularly Interspaced Short Palindromic Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064112","descriptor_name":"Clustered Regularly Interspaced Short Palindromic Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064112","descriptor_name":"Clustered Regularly Interspaced Short Palindromic Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad448","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad448","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/8/btad448/51035797/btad448.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:37481709","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37481709","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:pubmedcentral.nih.gov:10400375","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10400375","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10400375/pdf/btad448.pdf","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad448","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad448","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/8/btad448/51035797/btad448.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":[{"id":"https://metadata.un.org/sdg/9","score":0.4300000071525574,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G2192196445","display_name":null,"funder_award_id":"CPI-EXC 2026","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G5290293035","display_name":null,"funder_award_id":"SFB 1177","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G590706412","display_name":null,"funder_award_id":"EXC 2026","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8253053231","display_name":null,"funder_award_id":"259130777","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8859224315","display_name":null,"funder_award_id":"259130777-SFB 1177","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4385156656.pdf"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1973260880","https://openalex.org/W1982846895","https://openalex.org/W2036897871","https://openalex.org/W2045435533","https://openalex.org/W2064815984","https://openalex.org/W2152505144","https://openalex.org/W2170551349","https://openalex.org/W2252568502","https://openalex.org/W2770300757","https://openalex.org/W2811037407","https://openalex.org/W2919380816","https://openalex.org/W3035764705","https://openalex.org/W3042582592","https://openalex.org/W3157276932","https://openalex.org/W4200424290","https://openalex.org/W4211123163","https://openalex.org/W4211219428","https://openalex.org/W4317437864"],"related_works":["https://openalex.org/W3110102429","https://openalex.org/W2951741674","https://openalex.org/W2989961838","https://openalex.org/W4221016141","https://openalex.org/W4320033130","https://openalex.org/W4281940004","https://openalex.org/W2921720530","https://openalex.org/W2667943050","https://openalex.org/W2374359118","https://openalex.org/W2117924928"],"abstract_inverted_index":{"SUMMARY:":[0],"CRISPR":[1,51],"screens":[2],"are":[3],"increasingly":[4],"performed":[5],"to":[6,20],"associate":[7],"genotypes":[8],"with":[9,58],"genotypes.":[10],"So":[11],"far,":[12],"however,":[13],"their":[14],"analysis":[15],"required":[16],"specialized":[17],"computational":[18],"knowledge":[19],"transform":[21],"high-throughput":[22],"next-generation":[23],"sequencing":[24],"(NGS)":[25],"data":[26],"into":[27],"sequence":[28,64],"formats":[29],"amenable":[30],"for":[31,43,62,81],"downstream":[32,83],"analysis.":[33],"We":[34],"developed":[35],"ReCo,":[36],"a":[37],"stand-alone":[38],"and":[39,49,53,60,66,98],"user-friendly":[40],"analytics":[41],"tool":[42],"generating":[44],"read-count":[45],"tables":[46,76],"of":[47,73,85],"single":[48],"combinatorial":[50],"library":[52],"screen-based":[54],"NGS":[55,79],"data.":[56],"Together":[57],"cutadapt":[59],"bowtie2":[61],"rapid":[63],"trimming":[65],"alignment,":[67],"ReCo":[68,91],"enables":[69],"the":[70,82,95],"automated":[71],"generation":[72],"read":[74],"count":[75],"from":[77],"staggered":[78],"reads":[80],"identification":[84],"gRNA-induced":[86],"phenotypes.":[87],"AVAILABILITY":[88],"AND":[89],"IMPLEMENTATION:":[90],"is":[92],"published":[93],"under":[94],"MIT":[96],"license":[97],"available":[99],"at:":[100],"https://github.com/KaulichLab/ReCo.":[101]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2023-07-24T00:00:00"}