{"id":"https://openalex.org/W2093119240","doi":"https://doi.org/10.1145/2616498.2616517","title":"Using SAGA and the Open Science Grid to Search for Aptamers","display_name":"Using SAGA and the Open Science Grid to Search for Aptamers","publication_year":2014,"publication_date":"2014-07-11","ids":{"openalex":"https://openalex.org/W2093119240","doi":"https://doi.org/10.1145/2616498.2616517","mag":"2093119240"},"language":"en","primary_location":{"id":"doi:10.1145/2616498.2616517","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2616498.2616517","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5035080151","display_name":"Kevin Shieh","orcid":"https://orcid.org/0000-0003-4339-2967"},"institutions":[{"id":"https://openalex.org/I129975664","display_name":"Albert Einstein College of Medicine","ror":"https://ror.org/05cf8a891","country_code":"US","type":"education","lineage":["https://openalex.org/I129975664","https://openalex.org/I4210112371"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kevin Shieh","raw_affiliation_strings":["Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461","Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461","institution_ids":["https://openalex.org/I129975664"]},{"raw_affiliation_string":"Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461#TAB#","institution_ids":["https://openalex.org/I129975664"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065444619","display_name":"Pilib \u00d3 Broin","orcid":"https://orcid.org/0000-0002-6702-8564"},"institutions":[{"id":"https://openalex.org/I129975664","display_name":"Albert Einstein College of Medicine","ror":"https://ror.org/05cf8a891","country_code":"US","type":"education","lineage":["https://openalex.org/I129975664","https://openalex.org/I4210112371"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pilib \u00d3. Broin","raw_affiliation_strings":["Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461","Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461","institution_ids":["https://openalex.org/I129975664"]},{"raw_affiliation_string":"Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461#TAB#","institution_ids":["https://openalex.org/I129975664"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025033669","display_name":"David B. Rhee","orcid":null},"institutions":[{"id":"https://openalex.org/I129975664","display_name":"Albert Einstein College of Medicine","ror":"https://ror.org/05cf8a891","country_code":"US","type":"education","lineage":["https://openalex.org/I129975664","https://openalex.org/I4210112371"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David Rhee","raw_affiliation_strings":["Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461","Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461","institution_ids":["https://openalex.org/I129975664"]},{"raw_affiliation_string":"Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461#TAB#","institution_ids":["https://openalex.org/I129975664"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101665630","display_name":"Matthew Levy","orcid":"https://orcid.org/0000-0002-7719-7919"},"institutions":[{"id":"https://openalex.org/I129975664","display_name":"Albert Einstein College of Medicine","ror":"https://ror.org/05cf8a891","country_code":"US","type":"education","lineage":["https://openalex.org/I129975664","https://openalex.org/I4210112371"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew Levy","raw_affiliation_strings":["Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461","Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461","institution_ids":["https://openalex.org/I129975664"]},{"raw_affiliation_string":"Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461#TAB#","institution_ids":["https://openalex.org/I129975664"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035389230","display_name":"Aaron Golden","orcid":"https://orcid.org/0000-0001-8208-4292"},"institutions":[{"id":"https://openalex.org/I129975664","display_name":"Albert Einstein College of Medicine","ror":"https://ror.org/05cf8a891","country_code":"US","type":"education","lineage":["https://openalex.org/I129975664","https://openalex.org/I4210112371"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aaron Golden","raw_affiliation_strings":["Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461","Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461","institution_ids":["https://openalex.org/I129975664"]},{"raw_affiliation_string":"Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461#TAB#","institution_ids":["https://openalex.org/I129975664"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I129975664"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.15025832,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"4"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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":0.9994000196456909,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9994000196456909,"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":0.9994000196456909,"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/aptamer","display_name":"Aptamer","score":0.9240353107452393},{"id":"https://openalex.org/keywords/systematic-evolution-of-ligands-by-exponential-enrichment","display_name":"Systematic evolution of ligands by exponential enrichment","score":0.7207261919975281},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6141980886459351},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.5943698287010193},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5465400815010071},{"id":"https://openalex.org/keywords/massively-parallel","display_name":"Massively parallel","score":0.5202130675315857},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.46120256185531616},{"id":"https://openalex.org/keywords/oligonucleotide","display_name":"Oligonucleotide","score":0.43394750356674194},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28316521644592285},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.2427251935005188},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.15170246362686157},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12605243921279907},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10312384366989136}],"concepts":[{"id":"https://openalex.org/C128972844","wikidata":"https://www.wikidata.org/wiki/Q418722","display_name":"Aptamer","level":2,"score":0.9240353107452393},{"id":"https://openalex.org/C122682173","wikidata":"https://www.wikidata.org/wiki/Q907101","display_name":"Systematic evolution of ligands by exponential enrichment","level":4,"score":0.7207261919975281},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6141980886459351},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.5943698287010193},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5465400815010071},{"id":"https://openalex.org/C190475519","wikidata":"https://www.wikidata.org/wiki/Q544384","display_name":"Massively parallel","level":2,"score":0.5202130675315857},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.46120256185531616},{"id":"https://openalex.org/C129312508","wikidata":"https://www.wikidata.org/wiki/Q133686","display_name":"Oligonucleotide","level":3,"score":0.43394750356674194},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28316521644592285},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.2427251935005188},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.15170246362686157},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12605243921279907},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10312384366989136},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2616498.2616517","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2616498.2616517","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1964591062","https://openalex.org/W1970773045","https://openalex.org/W2011368877","https://openalex.org/W2023206235","https://openalex.org/W2034837534","https://openalex.org/W2057382350","https://openalex.org/W2062949048","https://openalex.org/W2079321730","https://openalex.org/W2103311193","https://openalex.org/W2104525153","https://openalex.org/W2121918723","https://openalex.org/W2124088880","https://openalex.org/W2129099356","https://openalex.org/W2139244298","https://openalex.org/W2148317584","https://openalex.org/W2156113162","https://openalex.org/W3011856351"],"related_works":["https://openalex.org/W2146864995","https://openalex.org/W4313237059","https://openalex.org/W2077323385","https://openalex.org/W2392306680","https://openalex.org/W2918405227","https://openalex.org/W2095052940","https://openalex.org/W4283324873","https://openalex.org/W4307216241","https://openalex.org/W3093450845","https://openalex.org/W3108749156"],"abstract_inverted_index":{"RNA":[0,136,173,177],"aptamers":[1,35],"are":[2,36,142],"small":[3],"oligonucleotide":[4],"molecules":[5],"whose":[6],"composition":[7],"and":[8,19,25,68,179,191,209,213,249,272,276,294,308],"resulting":[9],"folded":[10],"structure":[11],"enable":[12],"them":[13],"to":[14,22,94,153,224,238,255,268,311,316],"bind":[15],"with":[16,89,270,297],"high":[17,20],"affinity":[18,93],"selectivity":[21],"target":[23,73],"ligands":[24,53],"therefore":[26],"hold":[27],"great":[28],"promise":[29],"as":[30,48,201],"potential":[31,222],"therapeutic":[32],"drugs.":[33],"Functional":[34],"selected":[37],"from":[38],"a":[39,45,71,126,169,182,193,221,286],"large,":[40],"randomized":[41],"initial":[42],"library":[43,106],"in":[44,125,147,167,185,218,251,281,313],"process":[46,61],"known":[47],"SELEX":[49],"(systematic":[50],"evolution":[51],"of":[52,65,81,120,128,133,242,306],"by":[54,245,291],"exponential":[55],"enrichment).":[56],"This":[57],"is":[58,137,192,205],"an":[59,103],"iterative":[60],"involving":[62],"numerous":[63],"rounds":[64],"binding,":[66],"elution,":[67],"amplification":[69],"against":[70],"specific":[72],"substrate.":[74],"During":[75],"each":[76,131,161,202],"iteration":[77],"--":[78,83],"or":[79],"round":[80,132],"selection":[82],"we":[84,100,230],"enrich":[85],"for":[86,108,130,144,197,264],"the":[87,90,95,118,233,240,261,304,309],"species":[88],"highest":[91],"binding":[92],"target.":[96],"After":[97],"multiple":[98],"rounds,":[99],"ideally":[101],"have":[102,164],"enriched":[104],"aptamer":[105,158,243],"suitable":[107],"subsequent":[109],"investigation.":[110],"Modern":[111],"techniques":[112],"employ":[113],"massively":[114],"parallel":[115,219,252],"sequencing,":[116],"enabling":[117],"generation":[119],"large":[121],"libraries":[122],"(~106":[123],"sequences)":[124],"matter":[127],"hours":[129,190],"selection.":[134],"As":[135],"single-stranded,":[138],"covariance":[139],"models":[140],"(CMs)":[141],"ideal":[143],"representing":[145],"motifs":[146,244],"their":[148,216],"secondary":[149],"structures,":[150],"allowing":[151],"us":[152],"discover":[154],"patterns":[155],"within":[156],"functional":[157],"populations":[159],"following":[160],"round.":[162],"CMs":[163],"been":[165],"implemented":[166],"Infernal,":[168],"program":[170],"that":[171],"infers":[172],"alignments":[174],"based":[175],"on":[176],"sequence":[178],"structure.":[180],"Calibrating":[181],"single":[183],"CM":[184,203,247],"Infernal":[186],"can":[187],"take":[188],"several":[189],"significant":[194,287],"performance":[195],"bottleneck":[196],"our":[198,283],"work.":[199],"However,":[200],"calculation":[204],"itself":[206],"independently":[207],"determined":[208],"requires":[210],"defined":[211],"processing":[212],"memory":[214],"resources,":[215],"computation":[217],"offers":[220],"solution":[223],"this":[225,228],"problem.":[226],"In":[227],"paper,":[229],"describe":[231],"using":[232],"Open":[234],"Science":[235],"Grid":[236,265],"(OSG)":[237],"facilitate":[239],"identification":[241],"running":[246],"calibrations":[248],"refinements":[250],"across":[253],"up":[254],"ten":[256],"OSG":[257,271,299,310],"clients.":[258],"We":[259],"use":[260],"Simple":[262],"API":[263],"Applications":[266],"(SAGA)":[267],"interface":[269],"manage":[273],"job":[274],"submissions":[275],"file":[277],"transfers.":[278],"When":[279],"run":[280],"parallel,":[282],"results":[284],"show":[285],"speed":[288],"up,":[289],"constrained":[290],"typical":[292],"latencies":[293],"QoS":[295],"associated":[296],"nominal":[298],"usage.":[300],"Our":[301],"work":[302],"demonstrates":[303],"ability":[305],"SAGA":[307],"assist":[312],"parallelizing":[314],"solutions":[315],"complex":[317],"sequencing-based":[318],"biomedical":[319],"challenges.":[320]},"counts_by_year":[],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}