{"id":"https://openalex.org/W7221471669","doi":"https://doi.org/10.64898/2026.10.08.757521","title":"KEDROS: A Comparative Genomics and High-Resolution Phylogenetic Profiling Workspace","display_name":"KEDROS: A Comparative Genomics and High-Resolution Phylogenetic Profiling Workspace","publication_year":2026,"publication_date":"2026-10-11","ids":{"openalex":"https://openalex.org/W7221471669","doi":"https://doi.org/10.64898/2026.10.08.757521"},"language":"en","primary_location":{"id":"doi:10.64898/2026.10.08.757521","doi":"https://doi.org/10.64898/2026.10.08.757521","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.08.757521","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/11/2026.10.08.757521.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"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":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/11/2026.10.08.757521.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5158405198","display_name":"Athina Marougka","orcid":"https://orcid.org/0009-0000-5204-0563","observed_orcids":["https://orcid.org/0009-0000-5204-0563"]},"institutions":[{"id":"https://openalex.org/I4210105723","display_name":"FORTH Institute of Molecular Biology and Biotechnology","ror":"https://ror.org/01gzszr18","country_code":"GR","type":"facility","lineage":["https://openalex.org/I4210105723","https://openalex.org/I8901234"]},{"id":"https://openalex.org/I8901234","display_name":"Foundation for Research and Technology Hellas","ror":"https://ror.org/052rphn09","country_code":"GR","type":"facility","lineage":["https://openalex.org/I8901234"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Athina Marougka","raw_affiliation_strings":["Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece;"],"raw_orcid":"https://orcid.org/0009-0000-5204-0563","affiliations":[{"raw_affiliation_string":"Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece;","institution_ids":["https://openalex.org/I4210105723","https://openalex.org/I8901234"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050318013","display_name":"Jaime Huerta\u2010Cepas","orcid":"https://orcid.org/0000-0003-4195-5025","observed_orcids":["https://orcid.org/0000-0003-4195-5025"]},"institutions":[{"id":"https://openalex.org/I134820265","display_name":"Consejo Superior de Investigaciones Cient\u00edficas","ror":"https://ror.org/02gfc7t72","country_code":"ES","type":"government","lineage":["https://openalex.org/I134820265"]},{"id":"https://openalex.org/I4210106474","display_name":"Instituto Nacional de Investigaci\u00f3n y Tecnolog\u00eda Agraria y Alimentaria","ror":"https://ror.org/011q66e29","country_code":"ES","type":"funder","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210106474"]},{"id":"https://openalex.org/I4210162265","display_name":"Centre for Plant Biotechnology and Genomics","ror":"https://ror.org/04mfzb702","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210162265"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Jaime Huerta-Cepas","raw_affiliation_strings":["CBGP (UPM-INIA/CSIC)"],"raw_orcid":"https://orcid.org/0000-0003-4195-5025","affiliations":[{"raw_affiliation_string":"CBGP (UPM-INIA/CSIC)","institution_ids":["https://openalex.org/I134820265","https://openalex.org/I4210106474","https://openalex.org/I4210162265"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029531579","display_name":"Alexandros A. Pittis","orcid":"https://orcid.org/0000-0003-4116-9972","observed_orcids":["https://orcid.org/0000-0003-4116-9972"]},"institutions":[{"id":"https://openalex.org/I4210105723","display_name":"FORTH Institute of Molecular Biology and Biotechnology","ror":"https://ror.org/01gzszr18","country_code":"GR","type":"facility","lineage":["https://openalex.org/I4210105723","https://openalex.org/I8901234"]},{"id":"https://openalex.org/I8901234","display_name":"Foundation for Research and Technology Hellas","ror":"https://ror.org/052rphn09","country_code":"GR","type":"facility","lineage":["https://openalex.org/I8901234"]}],"countries":["GR"],"is_corresponding":true,"raw_author_name":"Alexandros A Pittis","raw_affiliation_strings":["Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece;"],"raw_orcid":"https://orcid.org/0000-0003-4116-9972","affiliations":[{"raw_affiliation_string":"Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece;","institution_ids":["https://openalex.org/I4210105723","https://openalex.org/I8901234"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5029531579"],"corresponding_institution_ids":["https://openalex.org/I4210105723","https://openalex.org/I8901234"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9945999979972839,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9945999979972839,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0017999999690800905,"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/T11879","display_name":"Protist diversity and phylogeny","score":0.0003000000142492354,"subfield":{"id":"https://openalex.org/subfields/1105","display_name":"Ecology, Evolution, Behavior and Systematics"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-profiling","display_name":"phylogenetic profiling","score":0.972000002861023},{"id":"https://openalex.org/keywords/gene-function-prediction","display_name":"gene function prediction","score":0.5389999747276306},{"id":"https://openalex.org/keywords/paralogous-gene-families","display_name":"paralogous gene families","score":0.6079999804496765},{"id":"https://openalex.org/keywords/gene-duplication","display_name":"gene duplication","score":0.6330000162124634},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"comparative genomics","score":0.7009999752044678},{"id":"https://openalex.org/keywords/lineage-specific-genes","display_name":"lineage-specific genes","score":0.6539999842643738},{"id":"https://openalex.org/keywords/functional-divergence","display_name":"functional divergence","score":0.8600000143051147},{"id":"https://openalex.org/keywords/trypanothione-reductase","display_name":"trypanothione reductase","score":0.7919999957084656},{"id":"https://openalex.org/keywords/trypanosomatids","display_name":"trypanosomatids","score":0.9210000038146973},{"id":"https://openalex.org/keywords/firmicutes","display_name":"Firmicutes","score":0.878000020980835},{"id":"https://openalex.org/keywords/sporulation","display_name":"sporulation","score":0.7710000276565552},{"id":"https://openalex.org/keywords/orthogroups","display_name":"orthogroups","score":0.46000000834465027},{"id":"https://openalex.org/keywords/web-based-platform","display_name":"web platform","score":0.492000013589859}],"concepts":[{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.6503000259399414},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6315000057220459},{"id":"https://openalex.org/C50929876","wikidata":"https://www.wikidata.org/wiki/Q164280","display_name":"Subfamily","level":3,"score":0.6312000155448914},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6019999980926514},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.5515000224113464},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5034999847412109},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.47380000352859497},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4180000126361847},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.41780000925064087},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.4108999967575073},{"id":"https://openalex.org/C105176652","wikidata":"https://www.wikidata.org/wiki/Q1147112","display_name":"Comparative genomics","level":5,"score":0.40630000829696655},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4025000035762787},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3698999881744385},{"id":"https://openalex.org/C65603577","wikidata":"https://www.wikidata.org/wiki/Q3427877","display_name":"Web resource","level":2,"score":0.3691999912261963},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.35249999165534973},{"id":"https://openalex.org/C70343354","wikidata":"https://www.wikidata.org/wiki/Q3381973","display_name":"Phylogenomics","level":5,"score":0.3474000096321106},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.3418000042438507},{"id":"https://openalex.org/C58581272","wikidata":"https://www.wikidata.org/wiki/Q12741163","display_name":"Workspace","level":3,"score":0.3125999867916107},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31200000643730164},{"id":"https://openalex.org/C5911399","wikidata":"https://www.wikidata.org/wiki/Q2278983","display_name":"Gene family","level":4,"score":0.3100000023841858},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.3086000084877014},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.3068000078201294},{"id":"https://openalex.org/C171897839","wikidata":"https://www.wikidata.org/wiki/Q417841","display_name":"Protein family","level":3,"score":0.30480000376701355},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.2904999852180481},{"id":"https://openalex.org/C178180057","wikidata":"https://www.wikidata.org/wiki/Q7251477","display_name":"Protein superfamily","level":3,"score":0.289900004863739},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.2897999882698059},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.2777999937534332},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.2773999869823456},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.2696000039577484},{"id":"https://openalex.org/C66882249","wikidata":"https://www.wikidata.org/wiki/Q169336","display_name":"Homogeneous","level":2,"score":0.2612999975681305},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.26100000739097595},{"id":"https://openalex.org/C62177273","wikidata":"https://www.wikidata.org/wiki/Q5531556","display_name":"Gene nomenclature","level":4,"score":0.25859999656677246},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.25859999656677246},{"id":"https://openalex.org/C2909108991","wikidata":"https://www.wikidata.org/wiki/Q414601","display_name":"Orthologous Gene","level":4,"score":0.2563000023365021},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2547999918460846}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.10.08.757521","doi":"https://doi.org/10.64898/2026.10.08.757521","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.08.757521","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/11/2026.10.08.757521.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"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":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.10.08.757521","doi":"https://doi.org/10.64898/2026.10.08.757521","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.08.757521","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/11/2026.10.08.757521.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"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":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7221471669.pdf","grobid_xml":"https://content.openalex.org/works/W7221471669.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2032506253","https://openalex.org/W7096320253","https://openalex.org/W7098709454","https://openalex.org/W7096113005","https://openalex.org/W2795814231","https://openalex.org/W2136180457","https://openalex.org/W4415659933","https://openalex.org/W3115830369","https://openalex.org/W1748819278","https://openalex.org/W2181511771"],"abstract_inverted_index":{"Phylogenetic":[0],"profiling":[1],"infers":[2],"gene":[3,78,95],"function":[4],"from":[5,177,287,301,327],"the":[6,104,107,119,122,178,249,259,268,279,284,292,298,314,318],"presence":[7],"and":[8,57,67,97,106,142,147,153,166,175,184,204,209,278,308,336],"absence":[9],"of":[10,33,138,228,251,272,317],"genes":[11,183,335],"across":[12,84,305],"genomes,":[13],"but":[14,236],"it":[15,168,194,274,296],"loses":[16],"resolution":[17],"in":[18,172,218,232],"eukaryotes,":[19],"where":[20],"many":[21],"protein":[22,82],"families":[23,105,165],"contain":[24],"several":[25],"functionally":[26],"distinct":[27],"paralogs.":[28],"Existing":[29],"resources":[30],"address":[31],"parts":[32],"this":[34],"problem":[35],"separately:":[36],"web":[37,74,220],"services":[38],"build":[39],"trees":[40,66,79,112],"for":[41,53,80],"one":[42,173],"family":[43,83,271,312],"at":[44,93,110,161,248,342],"a":[45,73,133,140,145,155,188,219,323,328],"time,":[46],"orthology":[47],"databases":[48],"provide":[49],"precomputed":[50],"orthologous":[51],"groups":[52],"predefined":[54],"species":[55],"sets,":[56,193],"tree-profiling":[58],"tools":[59],"require":[60],"users":[61],"to":[62,181,237,246,331],"supply":[63],"their":[64],"own":[65],"groupings.":[68],"Here,":[69],"we":[70],"present":[71,171],"KEDROS,":[72],"platform":[75],"that":[76,128,199,282],"builds":[77],"any":[81,126],"UniProt":[85],"reference":[86],"proteomes,":[87,253,307],"splits":[88],"each":[89,99],"tree":[90],"into":[91],"subfamilies":[92,277],"inferred":[94],"duplications,":[96],"profiles":[98],"subfamily":[100,189],"separately.":[101],"The":[102],"organisms,":[103],"taxonomic":[108],"depth":[109],"which":[111],"are":[113,115],"split":[114],"all":[116],"chosen":[117],"by":[118,191,258],"user,":[120],"so":[121],"same":[123],"workflow":[124],"serves":[125],"question":[127,330],"can":[129],"be":[130],"posed":[131],"as":[132],"contrast":[134],"between":[135,202],"two":[136,162,265],"sets":[137,256],"organisms:":[139],"pathogen":[141],"its":[143],"host,":[144],"pest":[146],"non-target":[148],"species,":[149],"or":[150,225],"lineages":[151],"with":[152,222,264],"without":[154],"trait.":[156,319],"KEDROS":[157,263,320,338],"answers":[158],"such":[159],"contrasts":[160],"levels.":[163],"Across":[164],"subfamilies,":[167],"ranks":[169,309],"those":[170],"set":[174],"absent":[176],"other,":[179],"pointing":[180],"lineage-specific":[182],"candidate":[185],"targets.":[186],"Within":[187],"shared":[190],"both":[192],"identifies":[195],"amino":[196],"acid":[197],"positions":[198],"differ":[200],"consistently":[201],"them":[203,211,244],"may":[205],"underlie":[206],"functional":[207],"divergence,":[208],"displays":[210],"on":[212,254],"AlphaFold":[213],"structures.":[214],"All":[215],"analyses":[216],"run":[217],"browser,":[221],"no":[223,240],"installation":[224],"programming.":[226],"Each":[227],"these":[229],"steps":[230],"exists":[231],"some":[233],"form":[234],"elsewhere,":[235],"our":[238],"knowledge":[239],"other":[241],"resource":[242],"runs":[243],"end":[245],"end,":[247],"scale":[250],"whole":[252],"organism":[255],"defined":[257],"user.":[260],"We":[261],"illustrate":[262],"cases.":[266],"In":[267,291],"trypanothione":[269],"reductase":[270],"trypanosomatids,":[273],"recovers":[275,297],"parasite-specific":[276],"substrate-binding":[280],"substitutions":[281],"separate":[283],"parasite":[285],"enzyme":[286],"human":[288],"glutathione":[289],"reductase.":[290],"bacterial":[293],"phylum":[294],"Bacillota,":[295],"sporulation":[299],"machinery":[300],"phenotype":[302],"labels":[303],"alone":[304],"1,218":[306],"an":[310],"uncharacterized":[311],"among":[313],"strongest":[315],"markers":[316],"thus":[321],"offers":[322],"general,":[324],"code-free":[325],"route":[326],"comparative":[329],"testable":[332],"hypotheses":[333],"about":[334],"residues.":[337],"is":[339],"freely":[340],"available":[341],"https://kedros.cgenomicslab.org.":[343]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-10-12T00:00:00"}
