{"id":"https://openalex.org/W3037864229","doi":"https://doi.org/10.1093/bioinformatics/btaa587","title":"HaDeX: an R package and web-server for analysis of data from hydrogen\u2013deuterium exchange mass spectrometry experiments","display_name":"HaDeX: an R package and web-server for analysis of data from hydrogen\u2013deuterium exchange mass spectrometry experiments","publication_year":2020,"publication_date":"2020-06-16","ids":{"openalex":"https://openalex.org/W3037864229","doi":"https://doi.org/10.1093/bioinformatics/btaa587","mag":"3037864229","pmid":"https://pubmed.ncbi.nlm.nih.gov/32579220"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa587","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa587","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/16/4516/33965582/btaa587.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/16/4516/33965582/btaa587.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020630771","display_name":"Weronika Pucha\u0142a","orcid":"https://orcid.org/0000-0003-2163-1429"},"institutions":[{"id":"https://openalex.org/I4210128244","display_name":"Institute of Biochemistry and Biophysics, Polish Academy of Sciences","ror":"https://ror.org/034tvp782","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210128244","https://openalex.org/I99542240"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Weronika Pucha\u0142a","raw_affiliation_strings":["Institute of Biochemistry and Biophysics, Polish Academy of Sciences , Warsaw 02-106, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biochemistry and Biophysics, Polish Academy of Sciences , Warsaw 02-106, Poland","institution_ids":["https://openalex.org/I4210128244"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015968787","display_name":"Micha\u0142 Burdukiewicz","orcid":"https://orcid.org/0000-0001-8926-582X"},"institutions":[{"id":"https://openalex.org/I108403487","display_name":"Warsaw University of Technology","ror":"https://ror.org/00y0xnp53","country_code":"PL","type":"education","lineage":["https://openalex.org/I108403487"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Micha\u0142 Burdukiewicz","raw_affiliation_strings":["Faculty of Mathematics and Information Science, Warsaw University of Technology , Warsaw 00-662, Poland"],"raw_orcid":"https://orcid.org/0000-0001-8926-582X","affiliations":[{"raw_affiliation_string":"Faculty of Mathematics and Information Science, Warsaw University of Technology , Warsaw 00-662, Poland","institution_ids":["https://openalex.org/I108403487"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052340990","display_name":"Micha\u0142 Kistowski","orcid":"https://orcid.org/0000-0001-5167-4011"},"institutions":[{"id":"https://openalex.org/I4210128244","display_name":"Institute of Biochemistry and Biophysics, Polish Academy of Sciences","ror":"https://ror.org/034tvp782","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210128244","https://openalex.org/I99542240"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Micha\u0142 Kistowski","raw_affiliation_strings":["Institute of Biochemistry and Biophysics, Polish Academy of Sciences , Warsaw 02-106, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biochemistry and Biophysics, Polish Academy of Sciences , Warsaw 02-106, Poland","institution_ids":["https://openalex.org/I4210128244"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079656899","display_name":"Katarzyna D\u0105browska","orcid":"https://orcid.org/0000-0001-7833-0374"},"institutions":[{"id":"https://openalex.org/I4210128244","display_name":"Institute of Biochemistry and Biophysics, Polish Academy of Sciences","ror":"https://ror.org/034tvp782","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210128244","https://openalex.org/I99542240"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Katarzyna A D\u0105browska","raw_affiliation_strings":["Institute of Biochemistry and Biophysics, Polish Academy of Sciences , Warsaw 02-106, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biochemistry and Biophysics, Polish Academy of Sciences , Warsaw 02-106, Poland","institution_ids":["https://openalex.org/I4210128244"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036112045","display_name":"Aleksandra E. Badaczewska-Dawid","orcid":"https://orcid.org/0000-0003-1832-4364"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Aleksandra E Badaczewska-Dawid","raw_affiliation_strings":["Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw , Warsaw 02-093, Poland"],"raw_orcid":"https://orcid.org/0000-0003-1832-4364","affiliations":[{"raw_affiliation_string":"Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw , Warsaw 02-093, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006164198","display_name":"Dominik Cysewski","orcid":"https://orcid.org/0000-0001-6206-0672"},"institutions":[{"id":"https://openalex.org/I4210128244","display_name":"Institute of Biochemistry and Biophysics, Polish Academy of Sciences","ror":"https://ror.org/034tvp782","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210128244","https://openalex.org/I99542240"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Dominik Cysewski","raw_affiliation_strings":["Institute of Biochemistry and Biophysics, Polish Academy of Sciences , Warsaw 02-106, Poland"],"raw_orcid":"https://orcid.org/0000-0001-6206-0672","affiliations":[{"raw_affiliation_string":"Institute of Biochemistry and Biophysics, Polish Academy of Sciences , Warsaw 02-106, Poland","institution_ids":["https://openalex.org/I4210128244"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008996018","display_name":"Micha\u0142 Dadlez","orcid":"https://orcid.org/0000-0001-8811-5176"},"institutions":[{"id":"https://openalex.org/I4210128244","display_name":"Institute of Biochemistry and Biophysics, Polish Academy of Sciences","ror":"https://ror.org/034tvp782","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210128244","https://openalex.org/I99542240"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Micha\u0142 Dadlez","raw_affiliation_strings":["Institute of Biochemistry and Biophysics, Polish Academy of Sciences , Warsaw 02-106, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biochemistry and Biophysics, Polish Academy of Sciences , Warsaw 02-106, Poland","institution_ids":["https://openalex.org/I4210128244"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5006164198","https://openalex.org/A5008996018"],"corresponding_institution_ids":["https://openalex.org/I4210128244"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.467,"has_fulltext":true,"cited_by_count":30,"citation_normalized_percentile":{"value":0.79985342,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"36","issue":"16","first_page":"4516","last_page":"4518"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9023000001907349,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9023000001907349,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.02449999935925007,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.006500000134110451,"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":0.7109850645065308},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6042417883872986},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5975342988967896},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4826560616493225},{"id":"https://openalex.org/keywords/hydrogen\u2013deuterium-exchange","display_name":"Hydrogen\u2013deuterium exchange","score":0.45036008954048157},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.4400753676891327},{"id":"https://openalex.org/keywords/mass-spectrometry","display_name":"Mass spectrometry","score":0.40411490201950073},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.38859719038009644},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.341043084859848},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2961232662200928},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.24539342522621155}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7109850645065308},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6042417883872986},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5975342988967896},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4826560616493225},{"id":"https://openalex.org/C167569220","wikidata":"https://www.wikidata.org/wiki/Q5954985","display_name":"Hydrogen\u2013deuterium exchange","level":3,"score":0.45036008954048157},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.4400753676891327},{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.40411490201950073},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.38859719038009644},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.341043084859848},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2961232662200928},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.24539342522621155},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000080307","descriptor_name":"Hydrogen Deuterium Exchange-Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000080307","descriptor_name":"Hydrogen Deuterium Exchange-Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000080307","descriptor_name":"Hydrogen Deuterium Exchange-Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003903","descriptor_name":"Deuterium","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003903","descriptor_name":"Deuterium","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003903","descriptor_name":"Deuterium","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006859","descriptor_name":"Hydrogen","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006859","descriptor_name":"Hydrogen","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006859","descriptor_name":"Hydrogen","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D041961","descriptor_name":"Deuterium Exchange Measurement","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D041961","descriptor_name":"Deuterium Exchange Measurement","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D041961","descriptor_name":"Deuterium Exchange Measurement","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa587","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa587","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/16/4516/33965582/btaa587.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32579220","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32579220","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:7575049","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7575049","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa587","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa587","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/16/4516/33965582/btaa587.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.6200000047683716}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321042","display_name":"Fundacja na rzecz Nauki Polskiej","ror":"https://ror.org/048zd9m77"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3037864229.pdf","grobid_xml":"https://content.openalex.org/works/W3037864229.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1996334859","https://openalex.org/W1997095359","https://openalex.org/W2070278191","https://openalex.org/W2084692275","https://openalex.org/W2135287247","https://openalex.org/W2170036411","https://openalex.org/W2474169383","https://openalex.org/W2519464604","https://openalex.org/W2626622682","https://openalex.org/W2951230445","https://openalex.org/W2955168413","https://openalex.org/W2959745021","https://openalex.org/W2979422598"],"related_works":["https://openalex.org/W4380887824","https://openalex.org/W2068608913","https://openalex.org/W3124914020","https://openalex.org/W2141033859","https://openalex.org/W2077542787","https://openalex.org/W1517177013","https://openalex.org/W2156434174","https://openalex.org/W2071701083","https://openalex.org/W2383687187","https://openalex.org/W1909926609"],"abstract_inverted_index":{"MOTIVATION:":[0],"Hydrogen-deuterium":[1],"mass":[2],"spectrometry":[3],"(HDX-MS)":[4],"is":[5,71],"a":[6,40,53,75],"rapidly":[7],"developing":[8],"technique":[9],"for":[10,43],"monitoring":[11],"dynamics":[12],"and":[13,46,62,90],"interactions":[14],"of":[15,19,48,64],"proteins.":[16],"The":[17],"development":[18],"new":[20,27],"devices":[21],"has":[22],"to":[23],"be":[24],"followed":[25],"with":[26],"software":[28,92],"suites":[29],"addressing":[30],"emerging":[31],"standards":[32],"in":[33],"data":[34,58,97],"analysis.":[35],"RESULTS:":[36],"We":[37],"propose":[38],"HaDeX,":[39],"novel":[41],"tool":[42],"processing,":[44],"analysis":[45],"visualization":[47],"HDX-MS":[49],"experiments.":[50],"HaDeX":[51,70],"supports":[52],"reproducible":[54],"analytical":[55],"process,":[56],"including":[57],"exploration,":[59],"quality":[60],"control":[61],"generation":[63],"publication-quality":[65],"figures.":[66],"AVAILABILITY":[67],"AND":[68],"IMPLEMENTATION:":[69],"available":[72,99],"primarily":[73],"as":[74,85],"web-server":[76],"(http://mslab-ibb.pl/shiny/HaDeX/),":[77],"but":[78],"its":[79],"all":[80],"functionalities":[81],"are":[82,98],"also":[83],"accessible":[84],"the":[86],"R":[87],"package":[88],"(https://CRAN.R-project.org/package=HaDeX)":[89],"standalone":[91],"(https://sourceforge.net/projects/HaDeX/).":[93],"SUPPLEMENTARY":[94],"INFORMATION:":[95],"Supplementary":[96],"at":[100],"Bioinformatics":[101],"online.":[102]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":1}],"updated_date":"2026-06-06T09:05:17.133730","created_date":"2025-10-10T00:00:00"}
