{"id":"https://openalex.org/W3032995577","doi":"https://doi.org/10.1371/journal.pcbi.1007956","title":"HemoMIPs\u2014Automated analysis and result reporting pipeline for targeted sequencing data","display_name":"HemoMIPs\u2014Automated analysis and result reporting pipeline for targeted sequencing data","publication_year":2020,"publication_date":"2020-06-04","ids":{"openalex":"https://openalex.org/W3032995577","doi":"https://doi.org/10.1371/journal.pcbi.1007956","mag":"3032995577","pmid":"https://pubmed.ncbi.nlm.nih.gov/32497118"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1007956","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007956","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007956&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007956&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055901441","display_name":"Philip Kleinert","orcid":"https://orcid.org/0000-0003-3964-4877"},"institutions":[{"id":"https://openalex.org/I4210139777","display_name":"Berlin Institute of Health at Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/0493xsw21","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210139777","https://openalex.org/I7877124"]},{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I7877124"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Philip Kleinert","raw_affiliation_strings":["Berlin Institute of Health (BIH), Berlin, Germany","Charit\u00e9 -Universit\u00e4tsmedizin Berlin, Berlin, Germany","Charit\u00e9 \u2013Universit\u00e4tsmedizin Berlin, Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Berlin Institute of Health (BIH), Berlin, Germany","institution_ids":["https://openalex.org/I4210139777"]},{"raw_affiliation_string":"Charit\u00e9 -Universit\u00e4tsmedizin Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I7877124"]},{"raw_affiliation_string":"Charit\u00e9 \u2013Universit\u00e4tsmedizin Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I7877124"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015187444","display_name":"Beth Martin","orcid":"https://orcid.org/0000-0002-9661-014X"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Beth Martin","raw_affiliation_strings":["University of Washington, Department of Genome Sciences, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"University of Washington, Department of Genome Sciences, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082477584","display_name":"Martin Kircher","orcid":"https://orcid.org/0000-0001-9278-5471"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210139777","display_name":"Berlin Institute of Health at Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/0493xsw21","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210139777","https://openalex.org/I7877124"]},{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I7877124"]}],"countries":["DE","US"],"is_corresponding":true,"raw_author_name":"Martin Kircher","raw_affiliation_strings":["Berlin Institute of Health (BIH), Berlin, Germany","Charit\u00e9 -Universit\u00e4tsmedizin Berlin, Berlin, Germany","University of Washington, Department of Genome Sciences, Seattle, Washington, United States of America","Charit\u00e9 \u2013Universit\u00e4tsmedizin Berlin, Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Berlin Institute of Health (BIH), Berlin, Germany","institution_ids":["https://openalex.org/I4210139777"]},{"raw_affiliation_string":"Charit\u00e9 -Universit\u00e4tsmedizin Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I7877124"]},{"raw_affiliation_string":"University of Washington, Department of Genome Sciences, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Charit\u00e9 \u2013Universit\u00e4tsmedizin Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I7877124"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5082477584"],"corresponding_institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210139777","https://openalex.org/I7877124"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.0834,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.43945166,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"16","issue":"6","first_page":"e1007956","last_page":"e1007956"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9915000200271606,"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":0.9915000200271606,"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":0.9898999929428101,"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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.989799976348877,"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/pipeline","display_name":"Pipeline (software)","score":0.6231067776679993},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5159860253334045},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49375876784324646},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3968011140823364},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3607150912284851},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2434684932231903}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6231067776679993},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5159860253334045},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49375876784324646},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3968011140823364},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3607150912284851},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2434684932231903},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005820","descriptor_name":"Genetic Testing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005820","descriptor_name":"Genetic Testing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005820","descriptor_name":"Genetic Testing","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015331","descriptor_name":"Cohort Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015331","descriptor_name":"Cohort Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015331","descriptor_name":"Cohort Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D041322","descriptor_name":"Chromosomes, Human, Y","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D041322","descriptor_name":"Chromosomes, Human, Y","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D041322","descriptor_name":"Chromosomes, Human, Y","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1007956","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007956","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007956&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:32497118","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32497118","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1007956","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007956","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:2886bca1d9f24b8694ee30d8a7786d7d","is_oa":true,"landing_page_url":"https://doaj.org/article/2886bca1d9f24b8694ee30d8a7786d7d","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 16, Iss 6, p e1007956 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7297380","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7297380","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1007956","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007956","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007956&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3032995577.pdf","grobid_xml":"https://content.openalex.org/works/W3032995577.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W1507075706","https://openalex.org/W1511217200","https://openalex.org/W1988670106","https://openalex.org/W1996547052","https://openalex.org/W1999790790","https://openalex.org/W2103441770","https://openalex.org/W2110417468","https://openalex.org/W2119180969","https://openalex.org/W2122070307","https://openalex.org/W2149440805","https://openalex.org/W2417483443","https://openalex.org/W2554372608","https://openalex.org/W2562567311","https://openalex.org/W2614245767","https://openalex.org/W2801230589","https://openalex.org/W4247053599"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"Targeted":[0],"sequencing":[1,28],"of":[2,61],"genomic":[3],"regions":[4],"is":[5,121],"a":[6,17,78],"cost-":[7],"and":[8,19,53,70,95,101],"time-efficient":[9],"approach":[10],"for":[11],"screening":[12],"patient":[13],"cohorts.":[14],"We":[15,99],"present":[16],"fast":[18],"efficient":[20],"workflow":[21],"to":[22,65],"analyze":[23],"highly":[24],"imbalanced,":[25],"targeted":[26],"next-generation":[27],"data":[29],"generated":[30],"using":[31,74,105],"molecular":[32],"inversion":[33],"probe":[34],"(MIP)":[35],"capture.":[36],"Our":[37,117],"Snakemake":[38],"pipeline":[39,104],"performs":[40],"sample":[41],"demultiplexing,":[42],"overlap":[43],"paired-end":[44],"merging,":[45],"alignment,":[46],"MIP-arm":[47],"trimming,":[48],"variant":[49],"calling,":[50],"coverage":[51],"analysis":[52,60],"report":[54],"generation.":[55],"Further,":[56],"we":[57,82],"support":[58],"the":[59,106,114],"probes":[62],"specifically":[63],"designed":[64],"capture":[66],"certain":[67],"structural":[68],"variants":[69,94],"can":[71],"assign":[72],"sex":[73],"Y-chromosome-unique":[75],"probes.":[76],"In":[77],"user-friendly":[79],"HTML":[80],"report,":[81],"summarize":[83],"all":[84],"these":[85],"results":[86],"including":[87],"covered,":[88],"incomplete":[89],"or":[90],"missing":[91],"regions,":[92],"called":[93],"their":[96],"predicted":[97],"effects.":[98],"developed":[100],"tested":[102],"our":[103],"hemophilia":[107],"A":[108],"&":[109],"B":[110],"MIP":[111],"design":[112],"from":[113],"\"My":[115],"Life,":[116],"Future\"":[118],"initiative.":[119],"HemoMIPs":[120],"available":[122],"as":[123],"an":[124],"open-source":[125],"tool":[126],"on":[127],"GitHub":[128],"at:":[129],"https://github.com/kircherlab/hemoMIPs.":[130]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}