{"id":"https://openalex.org/W7223553761","doi":"https://doi.org/10.64898/2026.10.23.761066","title":"Sequence architecture of RNA reveals key molecular signatures driving RNA phase separation","display_name":"Sequence architecture of RNA reveals key molecular signatures driving RNA phase separation","publication_year":2026,"publication_date":"2026-10-24","ids":{"openalex":"https://openalex.org/W7223553761","doi":"https://doi.org/10.64898/2026.10.23.761066"},"language":"en","primary_location":{"id":"doi:10.64898/2026.10.23.761066","doi":"https://doi.org/10.64898/2026.10.23.761066","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.23.761066","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/24/2026.10.23.761066.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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"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/2026/10/24/2026.10.23.761066.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5126361172","display_name":"Sonali Chatterjee","orcid":"https://orcid.org/0000-0002-1319-6941","observed_orcids":["https://orcid.org/0000-0002-1319-6941"]},"institutions":[{"id":"https://openalex.org/I145894827","display_name":"Indian Institute of Technology Kharagpur","ror":"https://ror.org/03w5sq511","country_code":"IN","type":"education","lineage":["https://openalex.org/I145894827"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Sonali Chatterjee","raw_affiliation_strings":["Computational Structural Biology Laboratory, Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India"],"raw_orcid":"https://orcid.org/0000-0002-1319-6941","affiliations":[{"raw_affiliation_string":"Computational Structural Biology Laboratory, Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India","institution_ids":["https://openalex.org/I145894827"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012819664","display_name":"Ranjit Prasad Bahadur","orcid":"https://orcid.org/0000-0002-6705-1713","observed_orcids":["https://orcid.org/0000-0002-6705-1713"]},"institutions":[{"id":"https://openalex.org/I145894827","display_name":"Indian Institute of Technology Kharagpur","ror":"https://ror.org/03w5sq511","country_code":"IN","type":"education","lineage":["https://openalex.org/I145894827"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Ranjit Prasad Bahadur","raw_affiliation_strings":["Bioinformatics Center, Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India","Computational Structural Biology Laboratory, Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India"],"raw_orcid":"https://orcid.org/0000-0002-6705-1713","affiliations":[{"raw_affiliation_string":"Bioinformatics Center, Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India","institution_ids":["https://openalex.org/I145894827"]},{"raw_affiliation_string":"Computational Structural Biology Laboratory, Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India","institution_ids":["https://openalex.org/I145894827"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5012819664"],"corresponding_institution_ids":["https://openalex.org/I145894827"],"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/T10604","display_name":"RNA Research and Splicing","score":0.6855000257492065,"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/T10604","display_name":"RNA Research and Splicing","score":0.6855000257492065,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.11249999701976776,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.07410000264644623,"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/biomolecular-condensates","display_name":"biomolecular condensates","score":0.9039999842643738},{"id":"https://openalex.org/keywords/liquid-liquid-phase-separation","display_name":"liquid-liquid phase separation","score":0.9369999766349792},{"id":"https://openalex.org/keywords/sequence-complexity","display_name":"sequence complexity","score":0.6690000295639038},{"id":"https://openalex.org/keywords/model-interpretability","display_name":"model interpretability","score":0.8809999823570251},{"id":"https://openalex.org/keywords/malat1","display_name":"MALAT1","score":0.7850000262260437},{"id":"https://openalex.org/keywords/tmpo-as1","display_name":"TMPO-AS1","score":0.9980000257492065}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.7421000003814697},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6115000247955322},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6072999835014343},{"id":"https://openalex.org/C33347731","wikidata":"https://www.wikidata.org/wiki/Q285210","display_name":"Stacking","level":2,"score":0.5756999850273132},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5081999897956848},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.47699999809265137},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4733999967575073},{"id":"https://openalex.org/C12713177","wikidata":"https://www.wikidata.org/wiki/Q1900281","display_name":"Perspective (graphical)","level":2,"score":0.43149998784065247},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.43140000104904175},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.3840999901294708},{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.36629998683929443},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.35679998993873596},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.3407000005245209},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3334999978542328},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.3287999927997589},{"id":"https://openalex.org/C32795469","wikidata":"https://www.wikidata.org/wiki/Q5156430","display_name":"Complementary sequences","level":2,"score":0.30250000953674316},{"id":"https://openalex.org/C29648211","wikidata":"https://www.wikidata.org/wiki/Q1995607","display_name":"Directionality","level":2,"score":0.30230000615119934},{"id":"https://openalex.org/C44280652","wikidata":"https://www.wikidata.org/wiki/Q104837","display_name":"Phase (matter)","level":2,"score":0.3005000054836273},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.2766000032424927},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.27129998803138733},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.2700999975204468},{"id":"https://openalex.org/C41282012","wikidata":"https://www.wikidata.org/wiki/Q3928341","display_name":"RNA-binding protein","level":4,"score":0.26930001378059387},{"id":"https://openalex.org/C3017666073","wikidata":"https://www.wikidata.org/wiki/Q1764062","display_name":"Base sequence","level":3,"score":0.26829999685287476},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.26739999651908875},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.2669000029563904}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.10.23.761066","doi":"https://doi.org/10.64898/2026.10.23.761066","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.23.761066","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/24/2026.10.23.761066.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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.10.23.761066","doi":"https://doi.org/10.64898/2026.10.23.761066","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.23.761066","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/24/2026.10.23.761066.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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7223553761.pdf","grobid_xml":"https://content.openalex.org/works/W7223553761.grobid-xml"},"referenced_works_count":61,"referenced_works":["https://openalex.org/W28412257","https://openalex.org/W1498436455","https://openalex.org/W1678356000","https://openalex.org/W1972978214","https://openalex.org/W1976526581","https://openalex.org/W1978813754","https://openalex.org/W1988790447","https://openalex.org/W2001619934","https://openalex.org/W2025495726","https://openalex.org/W2039385533","https://openalex.org/W2056132907","https://openalex.org/W2079712877","https://openalex.org/W2086561953","https://openalex.org/W2109553965","https://openalex.org/W2110065044","https://openalex.org/W2117897510","https://openalex.org/W2122111042","https://openalex.org/W2139066576","https://openalex.org/W2139995722","https://openalex.org/W2140921549","https://openalex.org/W2156125289","https://openalex.org/W2158698691","https://openalex.org/W2160838724","https://openalex.org/W2170747616","https://openalex.org/W2295598076","https://openalex.org/W2590568317","https://openalex.org/W2596417560","https://openalex.org/W2617594926","https://openalex.org/W2756821926","https://openalex.org/W2784401093","https://openalex.org/W2786469974","https://openalex.org/W2887292446","https://openalex.org/W2890778381","https://openalex.org/W2903950532","https://openalex.org/W2911964244","https://openalex.org/W2922474405","https://openalex.org/W2939777553","https://openalex.org/W2967960129","https://openalex.org/W2999615587","https://openalex.org/W3022721113","https://openalex.org/W3038184119","https://openalex.org/W3123015207","https://openalex.org/W3134163647","https://openalex.org/W3143253488","https://openalex.org/W3172035218","https://openalex.org/W3190135694","https://openalex.org/W3212488072","https://openalex.org/W4212848381","https://openalex.org/W4234698323","https://openalex.org/W4239510810","https://openalex.org/W4281490610","https://openalex.org/W4283576022","https://openalex.org/W4290546063","https://openalex.org/W4292933682","https://openalex.org/W4323352445","https://openalex.org/W4362460273","https://openalex.org/W4388615740","https://openalex.org/W4402622749","https://openalex.org/W4403781819","https://openalex.org/W4404595545","https://openalex.org/W6969706136"],"related_works":["https://openalex.org/W7214220548","https://openalex.org/W4407364690","https://openalex.org/W7155696702","https://openalex.org/W4407435718","https://openalex.org/W3038184119","https://openalex.org/W4319916462","https://openalex.org/W3093704839","https://openalex.org/W4319930116","https://openalex.org/W2899928186","https://openalex.org/W3126441452"],"abstract_inverted_index":{"Abstract":[0],"Biomolecular":[1],"condensates":[2,24],"are":[3,105],"dynamic":[4],"membraneless":[5],"assemblies":[6],"that":[7,192],"organize":[8],"various":[9],"cellular":[10],"processes":[11],"through":[12,29,107],"liquid\u2013liquid":[13],"phase":[14],"separation":[15],"(LLPS).":[16],"RNA":[17,78],"is":[18,79],"an":[19,53,116],"active":[20],"regulator":[21],"of":[22,118,121,125,172],"biomolecular":[23],"and":[25,93,123,131,153,162],"influence":[26],"their":[27],"formation":[28],"sequence-encoded":[30],"features.":[31],"Despite":[32],"its":[33],"established":[34],"role":[35],"in":[36],"condensate":[37,75],"formation,":[38],"no":[39],"computational":[40],"framework":[41,56,114],"exists":[42],"to":[43,47,57,188],"identify":[44,189],"underlying":[45],"signatures":[46],"predict":[48],"LLPS-associated":[49,62],"RNAs.":[50,66],"We":[51,67],"develop":[52],"interpretable":[54,181],"hybrid":[55],"distinguish":[58],"reviewed,":[59],"experimentally":[60,169],"supported":[61],"RNAs":[63],"from":[64,101,148],"background":[65],"uncover":[68],"biologically":[69],"meaningful":[70],"sequence":[71,89,137,190],"properties":[72],"associated":[73],"with":[74,97,110,145,168],"participation.":[76],"Each":[77],"represented":[80],"by":[81,140],"167":[82],"handcrafted":[83],"descriptors":[84],"capturing":[85],"composition,":[86],"k-mer":[87,143],"usage,":[88],"complexity,":[90],"repeat":[91],"organization":[92,152],"dinucleotide":[94,155],"autocorrelation":[95],"together":[96],"640-dimensional":[98],"contextual":[99],"embeddings":[100],"RNA-FM.":[102],"These":[103],"representations":[104],"integrated":[106],"cross-validated":[108],"stacking":[109],"neural-network":[111],"meta-learner.":[112],"The":[113],"achieves":[115],"AUC-ROC":[117],"0.935,":[119],"AUC-PR":[120],"0.944":[122],"MCC":[124],"0.782.":[126],"Feature":[127],"statistics,":[128],"ablation":[129],"analysis":[130],"SHAP":[132],"interpretation":[133],"reveal":[134],"a":[135],"distributed":[136],"architecture":[138],"dominated":[139],"altered":[141],"local":[142],"usage":[144],"additional":[146],"contributions":[147],"low-complexity":[149],"burden,":[150],"repeat-associated":[151],"long-range":[154],"pattern.":[156],"Biological":[157],"case":[158],"studies":[159],"including":[160],"MALAT1":[161],"TMPO-AS1":[163],"further":[164],"connect":[165],"these":[166],"patterns":[167],"characterized":[170],"modes":[171],"multivalent":[173],"RNA\u2013protein":[174],"assembly.":[175],"Together,":[176],"the":[177],"results":[178],"show":[179],"how":[180],"machine":[182],"learning":[183],"can":[184],"move":[185],"beyond":[186],"prediction":[187],"features":[191],"generate":[193],"mechanistic":[194],"hypotheses":[195],"for":[196],"RNA-mediated":[197],"condensation.":[198]},"counts_by_year":[],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2026-10-26T00:00:00"}