{"id":"https://openalex.org/W2135645050","doi":"https://doi.org/10.1186/1751-0473-8-9","title":"Inmembrane, a bioinformatic workflow for annotation of bacterial cell-surface proteomes","display_name":"Inmembrane, a bioinformatic workflow for annotation of bacterial cell-surface proteomes","publication_year":2013,"publication_date":"2013-03-19","ids":{"openalex":"https://openalex.org/W2135645050","doi":"https://doi.org/10.1186/1751-0473-8-9","mag":"2135645050","pmid":"https://pubmed.ncbi.nlm.nih.gov/23506117"},"language":"en","primary_location":{"id":"doi:10.1186/1751-0473-8-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-8-9","pdf_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-8-9","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source Code for Biology and Medicine","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-8-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000073602","display_name":"Andrew Perry","orcid":"https://orcid.org/0000-0001-9256-6068"},"institutions":[{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Andrew J Perry","raw_affiliation_strings":["Department of Biochemistry, Monash University, Melbourne, Australia. boscoh@gmail.com","Department of Biochemistry, Monash University, Melbourne, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Monash University, Melbourne, Australia. boscoh@gmail.com","institution_ids":["https://openalex.org/I56590836"]},{"raw_affiliation_string":"Department of Biochemistry, Monash University, Melbourne, Australia","institution_ids":["https://openalex.org/I56590836"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5111880477","display_name":"Bosco Ho","orcid":null},"institutions":[{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Bosco K Ho","raw_affiliation_strings":["Department of Biochemistry, Monash University, Melbourne, Australia","Monash eResearch Centre, Monash University, Melbourne, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Monash University, Melbourne, Australia","institution_ids":["https://openalex.org/I56590836"]},{"raw_affiliation_string":"Monash eResearch Centre, Monash University, Melbourne, Australia","institution_ids":["https://openalex.org/I56590836"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5111880477"],"corresponding_institution_ids":["https://openalex.org/I56590836"],"apc_list":{"value":2040,"currency":"USD","value_usd":2040},"apc_paid":{"value":2040,"currency":"USD","value_usd":2040},"fwci":0.963,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.7503776,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"8","issue":"1","first_page":"9","last_page":"9"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.5349000096321106,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.5349000096321106,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.2797999978065491,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.0763000026345253,"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/proteome","display_name":"Proteome","score":0.7660769820213318},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7341756820678711},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.656827449798584},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6220535635948181},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.591242790222168},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.5907065868377686},{"id":"https://openalex.org/keywords/protocol","display_name":"Protocol (science)","score":0.5221027135848999},{"id":"https://openalex.org/keywords/bacterial-cell-structure","display_name":"Bacterial cell structure","score":0.4937838017940521},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4833531081676483},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.41676467657089233},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.3959224224090576},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.32635611295700073},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.29872366786003113},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2226153016090393},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.20157596468925476},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.16975653171539307},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13157781958580017}],"concepts":[{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.7660769820213318},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7341756820678711},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.656827449798584},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6220535635948181},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.591242790222168},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.5907065868377686},{"id":"https://openalex.org/C2780385302","wikidata":"https://www.wikidata.org/wiki/Q367158","display_name":"Protocol (science)","level":3,"score":0.5221027135848999},{"id":"https://openalex.org/C19655278","wikidata":"https://www.wikidata.org/wiki/Q3293735","display_name":"Bacterial cell structure","level":3,"score":0.4937838017940521},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4833531081676483},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.41676467657089233},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.3959224224090576},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32635611295700073},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.29872366786003113},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2226153016090393},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.20157596468925476},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.16975653171539307},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13157781958580017},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C204787440","wikidata":"https://www.wikidata.org/wiki/Q188504","display_name":"Alternative medicine","level":2,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/1751-0473-8-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-8-9","pdf_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-8-9","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source Code for Biology and Medicine","raw_type":"journal-article"},{"id":"pmid:23506117","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23506117","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":"Source code for biology and medicine","raw_type":null},{"id":"pmh:oai:europepmc.org:2668335","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3668253","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3668253","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3668253","pdf_url":null,"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":"Source Code Biol Med","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1751-0473-8-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-8-9","pdf_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-8-9","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source Code for Biology and Medicine","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2135645050.pdf","grobid_xml":"https://content.openalex.org/works/W2135645050.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1821139715","https://openalex.org/W1972475361","https://openalex.org/W1973253766","https://openalex.org/W1974165330","https://openalex.org/W1975588116","https://openalex.org/W1981604960","https://openalex.org/W1991608395","https://openalex.org/W2035728933","https://openalex.org/W2042133316","https://openalex.org/W2065215967","https://openalex.org/W2076573583","https://openalex.org/W2094201044","https://openalex.org/W2101466114","https://openalex.org/W2105986552","https://openalex.org/W2107986672","https://openalex.org/W2108632205","https://openalex.org/W2127648442","https://openalex.org/W2130248239","https://openalex.org/W2131778683","https://openalex.org/W2137382456","https://openalex.org/W2149818637","https://openalex.org/W2150044256","https://openalex.org/W2151408783","https://openalex.org/W2152770371","https://openalex.org/W2154633062","https://openalex.org/W2161481967","https://openalex.org/W2162792752","https://openalex.org/W2169654753"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2046765700","https://openalex.org/W2625833328","https://openalex.org/W1533177136","https://openalex.org/W4380994516"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,151],"annotation":[2,123],"of":[3,17,34,62,66,92,102,142],"surface":[4,26,144],"exposed":[5,32,145],"bacterial":[6,67,77,149],"membrane":[7,35,57,96],"proteins":[8,22,36,58],"is":[9,51,116,153],"an":[10,109,140],"important":[11],"step":[12],"in":[13,46,64,147],"interpretation":[14],"and":[15,79,95,112,134],"validation":[16],"proteomic":[18],"experiments.":[19],"In":[20],"particular,":[21],"detected":[23],"by":[24],"cell":[25],"protease":[27],"shaving":[28],"experiments":[29],"can":[30],"indicate":[31],"regions":[33,61],"that":[37,115],"may":[38],"contain":[39],"antigenic":[40],"determinants":[41],"or":[42],"constitute":[43],"vaccine":[44],"targets":[45],"pathogenic":[47],"bacteria.":[48],"RESULTS:":[49],"Inmembrane":[50,126],"a":[52,73,81,103,148],"tool":[53],"to":[54,118,137],"predict":[55],"the":[56,100,156],"with":[59,89],"surface-exposed":[60],"polypeptide":[63],"sets":[65],"protein":[68,97,146],"sequences.":[69],"We":[70],"have":[71],"re-implemented":[72],"protocol":[74,83],"for":[75,84,120],"Gram-positive":[76],"proteomes,":[78],"developed":[80],"new":[82],"Gram-negative":[85],"bacteria,":[86],"which":[87],"interface":[88],"multiple":[90],"predictors":[91],"subcellular":[93],"localization":[94],"topology.":[98],"Through":[99],"use":[101],"modern":[104],"scripting":[105],"language,":[106],"inmembrane":[107],"provides":[108],"accessible":[110],"code-base":[111],"extensible":[113],"architecture":[114],"amenable":[117],"modification":[119],"related":[121],"sequence":[122],"tasks.":[124],"CONCLUSIONS:":[125],"easily":[127],"integrates":[128],"predictions":[129],"from":[130],"both":[131],"local":[132],"binaries":[133],"web-based":[135],"queries":[136],"help":[138],"gain":[139],"overview":[141],"likely":[143],"proteome.":[150],"program":[152],"hosted":[154],"on":[155],"Github":[157],"repository":[158],"http://github.com/boscoh/inmembrane.":[159]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":2}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}