{"id":"https://openalex.org/W6902634060","doi":"https://doi.org/10.6094/unifr/11472","title":"Predicting small RNA targets in prokaryotes \u2013 a challenge beyond the barriers of thermodynamic models","display_name":"Predicting small RNA targets in prokaryotes \u2013 a challenge beyond the barriers of thermodynamic models","publication_year":2016,"publication_date":"2016-01-01","ids":{"openalex":"https://openalex.org/W6902634060","doi":"https://doi.org/10.6094/unifr/11472"},"language":"en","primary_location":{"id":"pmh:oai:freidok.uni-freiburg.de:11472","is_oa":false,"landing_page_url":"https://freidok.uni-freiburg.de/data/11472","pdf_url":null,"source":{"id":"https://openalex.org/S4306401057","display_name":"FreiDok plus (Universit\u00e4tsbibliothek Freiburg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I161046081","host_organization_name":"University of Freiburg","host_organization_lineage":["https://openalex.org/I161046081"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"doctoral_thesis"},"type":"other","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.6094/unifr/11472","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Wright, Patrick R.","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Wright, Patrick R.","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"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":true,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.38089999556541443},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.2214999943971634},{"id":"https://openalex.org/keywords/limiting","display_name":"Limiting","score":0.22010000050067902},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.21539999544620514}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4618000090122223},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3903999924659729},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.38089999556541443},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3555999994277954},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.34860000014305115},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.2215999960899353},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.2214999943971634},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.22010000050067902},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.21539999544620514},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.2150000035762787}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:freidok.uni-freiburg.de:11472","is_oa":false,"landing_page_url":"https://freidok.uni-freiburg.de/data/11472","pdf_url":null,"source":{"id":"https://openalex.org/S4306401057","display_name":"FreiDok plus (Universit\u00e4tsbibliothek Freiburg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I161046081","host_organization_name":"University of Freiburg","host_organization_lineage":["https://openalex.org/I161046081"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"doctoral_thesis"},{"id":"doi:10.6094/unifr/11472","is_oa":true,"landing_page_url":"https://doi.org/10.6094/unifr/11472","pdf_url":null,"source":{"id":"https://openalex.org/S4306401057","display_name":"FreiDok plus (Universit\u00e4tsbibliothek Freiburg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I161046081","host_organization_name":"University of Freiburg","host_organization_lineage":["https://openalex.org/I161046081"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.6094/unifr/11472","is_oa":true,"landing_page_url":"https://doi.org/10.6094/unifr/11472","pdf_url":null,"source":{"id":"https://openalex.org/S4306401057","display_name":"FreiDok plus (Universit\u00e4tsbibliothek Freiburg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I161046081","host_organization_name":"University of Freiburg","host_organization_lineage":["https://openalex.org/I161046081"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Advanced":[0],"high":[1,159],"throughput":[2],"sequencing":[3],"of":[4,18,21,55,70,75,87,185,204,304,343,352],"nucleic":[5],"acid":[6],"samples":[7],"coupled":[8],"with":[9,46],"sophisticated":[10],"analysis":[11,189],"algorithms":[12,100],"has":[13,80,91,311],"led":[14],"to":[15,144,158,174,239,284,318,348],"the":[16,73,85,106,135,153,167,178,183,196,208,217,240,263,274,279,293,302,329],"discovery":[17,74],"a":[19,82,115,201],"plethora":[20],"commonly":[22],"non-coding":[23],"but":[24,146,230],"functional":[25],"short":[26],"transcripts":[27,79],"present":[28],"in":[29,170,207,209,273,355],"diverse":[30],"prokaryotic":[31],"genomes.":[32],"These":[33,128],"so":[34],"called":[35],"trans-acting":[36],"small":[37,61,226,298],"RNAs":[38,62,299],"fulfill":[39],"their":[40,47,88],"regulatory":[41,89,358],"role":[42],"by":[43,328],"directly":[44],"pairing":[45],"targets":[48,90,151],"via":[49],"RNA-RNA":[50,97,247],"interaction.":[51],"Thus,":[52],"this":[53,95,165,171],"type":[54],"regulation":[56,69],"is":[57,281,324],"termed":[58],"post-transcriptional.":[59],"The":[60,309],"can":[63],"impose":[64],"both":[65],"up-":[66],"and":[67,119,176,190,253,296,323,334],"down":[68],"targets.":[71],"While":[72],"thus":[76],"far":[77],"unknown":[78],"become":[81],"standardized":[83],"procedure,":[84],"recovery":[86],"remained":[92],"challenging.":[93],"For":[94,164],"reason":[96,166],"interaction":[98,121],"prediction":[99,162,211],"that":[101,216,278,339],"attempt":[102,173],"target":[103,228,236,255],"identification":[104],"at":[105,133,148,152],"genomic":[107],"scale":[108],"have":[109],"been":[110,312],"developed.":[111],"Leading":[112],"methods":[113,129,168],"include":[114],"thermodynamic":[116,180],"energy":[117],"model":[118],"incorporate":[120],"site":[122],"accessibility":[123],"for":[124,139,195],"RNA":[125,137,141,197,227],"duplex":[126,138],"prediction.":[127,237],"are":[130],"generally":[131],"successful":[132],"predicting":[134,150],"correct":[136],"two":[140],"molecules":[142],"known":[143,246],"interact,":[145],"fail":[147],"correctly":[149],"whole":[154,191],"genome":[155,192],"level":[156],"due":[157],"false":[160,205],"positive":[161],"rates.":[163],"presented":[169],"thesis":[172],"employ":[175],"extend":[177],"purely":[179],"predictors.":[181],"Indeed,":[182],"inclusion":[184],"phylogenetic":[186],"information,":[187],"pathway":[188],"binding":[193],"data":[194],"chaperone":[198],"Hfq":[199],"allow":[200],"significant":[202],"reduction":[203],"positives":[206],"silico":[210],"lists.":[212,266],"Systematic":[213],"benchmarking":[214],"revealed":[215],"newly":[218],"developed":[219],"algorithm":[220,280,310],"CopraRNA":[221,264,305,344],"not":[222],"only":[223],"outperforms":[224],"other":[225],"predictors,":[229],"also":[231,282],"rivals":[232],"microarray":[233],"driven":[234],"experimental":[235],"Next":[238],"convincing":[241],"benchmark":[242],"performance":[243],"on":[244,292],"already":[245],"interactions,":[248],"23":[249],"novel,":[250],"previously":[251],"unreported":[252],"promising":[254],"candidates":[256],"from":[257,262],"Escherichia":[258],"coli":[259],"were":[260,270],"retrieved":[261],"predictions":[265],"Of":[267],"these,":[268],"17":[269],"experimentally":[271],"confirmed":[272],"wet-lab.":[275],"This":[276],"shows":[277],"able":[283,347],"produce":[285],"qualitatively":[286],"new":[287],"insights.":[288],"Follow":[289],"up":[290],"studies":[291],"rhizobial":[294],"AbcR1":[295],"EcpR1":[297],"furthermore":[300],"validate":[301],"applicability":[303],"beyond":[306],"enterobacterial":[307],"species.":[308],"made":[313],"available":[314],"as":[315],"an":[316,340],"easy":[317],"use":[319],"web":[320],"server":[321],"interface":[322],"being":[325],"amply":[326],"accessed":[327],"research":[330],"community.":[331],"Finally,":[332],"recent":[333],"currently":[335],"unpublished":[336],"results":[337],"indicate":[338],"extended":[341],"version":[342],"may":[345],"be":[346],"detect":[349],"hot":[350],"spots":[351],"evolutionary":[353],"diversity":[354],"post-transcriptional":[356],"gene":[357],"networks.":[359]},"counts_by_year":[],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}