{"id":"https://openalex.org/W4396572216","doi":"https://doi.org/10.1093/bioinformatics/btae299","title":"PlasCAT: Plasmid Cloud Assembly Tool","display_name":"PlasCAT: Plasmid Cloud Assembly Tool","publication_year":2024,"publication_date":"2024-05-01","ids":{"openalex":"https://openalex.org/W4396572216","doi":"https://doi.org/10.1093/bioinformatics/btae299","pmid":"https://pubmed.ncbi.nlm.nih.gov/38696761"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae299","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae299","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae299/57390668/btae299.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae299/57390668/btae299.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084973074","display_name":"Samuel Peccoud","orcid":"https://orcid.org/0009-0006-2930-7526"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Samuel Peccoud","raw_affiliation_strings":["GenoFAB, Inc. , Fort Collins, CO 80528, United States"],"affiliations":[{"raw_affiliation_string":"GenoFAB, Inc. , Fort Collins, CO 80528, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063451704","display_name":"Casey-Tyler Berezin","orcid":"https://orcid.org/0000-0001-7201-8929"},"institutions":[{"id":"https://openalex.org/I92446798","display_name":"Colorado State University","ror":"https://ror.org/03k1gpj17","country_code":"US","type":"education","lineage":["https://openalex.org/I92446798"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Casey-Tyler Berezin","raw_affiliation_strings":["Department of Chemical and Biological Engineering, Colorado State University , Fort Collins, CO 80523, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Colorado State University , Fort Collins, CO 80523, United States","institution_ids":["https://openalex.org/I92446798"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026573204","display_name":"Sarah Hern\u00e1ndez","orcid":"https://orcid.org/0000-0002-1217-234X"},"institutions":[{"id":"https://openalex.org/I92446798","display_name":"Colorado State University","ror":"https://ror.org/03k1gpj17","country_code":"US","type":"education","lineage":["https://openalex.org/I92446798"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sarah I Hernandez","raw_affiliation_strings":["Department of Chemical and Biological Engineering, Colorado State University , Fort Collins, CO 80523, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Colorado State University , Fort Collins, CO 80523, United States","institution_ids":["https://openalex.org/I92446798"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086336387","display_name":"Jean Peccoud","orcid":"https://orcid.org/0000-0001-7649-6127"},"institutions":[{"id":"https://openalex.org/I92446798","display_name":"Colorado State University","ror":"https://ror.org/03k1gpj17","country_code":"US","type":"education","lineage":["https://openalex.org/I92446798"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jean Peccoud","raw_affiliation_strings":["Department of Chemical and Biological Engineering, Colorado State University , Fort Collins, CO 80523, United States","GenoFAB, Inc. , Fort Collins, CO 80528, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Colorado State University , Fort Collins, CO 80523, United States","institution_ids":["https://openalex.org/I92446798"]},{"raw_affiliation_string":"GenoFAB, Inc. , Fort Collins, CO 80528, United States","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5086336387"],"corresponding_institution_ids":["https://openalex.org/I92446798"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.2568,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.92604355,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":97},"biblio":{"volume":"40","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11614","display_name":"Cloud Data Security Solutions","score":0.978600025177002,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11614","display_name":"Cloud Data Security Solutions","score":0.978600025177002,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10192","display_name":"Catalytic Processes in Materials Science","score":0.9527000188827515,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11181","display_name":"Advanced Data Storage Technologies","score":0.9523000121116638,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/cloud-computing","display_name":"Cloud computing","score":0.7444237470626831},{"id":"https://openalex.org/keywords/plasmid","display_name":"Plasmid","score":0.6896106600761414},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6011964678764343},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23958119750022888},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.17508184909820557},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1674019992351532},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.05789652466773987}],"concepts":[{"id":"https://openalex.org/C79974875","wikidata":"https://www.wikidata.org/wiki/Q483639","display_name":"Cloud computing","level":2,"score":0.7444237470626831},{"id":"https://openalex.org/C22744801","wikidata":"https://www.wikidata.org/wiki/Q172778","display_name":"Plasmid","level":3,"score":0.6896106600761414},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6011964678764343},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23958119750022888},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.17508184909820557},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1674019992351532},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.05789652466773987}],"mesh":[{"descriptor_ui":"D000067917","descriptor_name":"Cloud Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000067917","descriptor_name":"Cloud Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000067917","descriptor_name":"Cloud Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000067917","descriptor_name":"Cloud Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000067917","descriptor_name":"Cloud Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000067917","descriptor_name":"Cloud Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000067917","descriptor_name":"Cloud Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000067917","descriptor_name":"Cloud Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000067917","descriptor_name":"Cloud Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010957","descriptor_name":"Plasmids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010957","descriptor_name":"Plasmids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010957","descriptor_name":"Plasmids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010957","descriptor_name":"Plasmids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010957","descriptor_name":"Plasmids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010957","descriptor_name":"Plasmids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010957","descriptor_name":"Plasmids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010957","descriptor_name":"Plasmids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010957","descriptor_name":"Plasmids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae299","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae299","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae299/57390668/btae299.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38696761","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38696761","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:11101281","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11101281","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11101281/pdf/btae299.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae299","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae299","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae299/57390668/btae299.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","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","score":0.5699999928474426,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G1068219154","display_name":null,"funder_award_id":"R21AI168482","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2769792809","display_name":null,"funder_award_id":"R01GM147816","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6756162696","display_name":null,"funder_award_id":"#MCB-2123367","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4396572216.pdf"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1997939758","https://openalex.org/W2118464978","https://openalex.org/W2131271579","https://openalex.org/W2139701562","https://openalex.org/W2153325555","https://openalex.org/W2911251965","https://openalex.org/W2941874147","https://openalex.org/W2942757983","https://openalex.org/W2951325968","https://openalex.org/W2951563276","https://openalex.org/W2952167528","https://openalex.org/W2969831762","https://openalex.org/W2994969834","https://openalex.org/W3083399670","https://openalex.org/W3114199289","https://openalex.org/W3120923229","https://openalex.org/W3125215968","https://openalex.org/W3141815669","https://openalex.org/W3173711206","https://openalex.org/W4214845870","https://openalex.org/W4225908493","https://openalex.org/W4244292587","https://openalex.org/W4289518197","https://openalex.org/W4295973404","https://openalex.org/W4313471730","https://openalex.org/W4313824304","https://openalex.org/W4378071169","https://openalex.org/W4382198793","https://openalex.org/W4388734930","https://openalex.org/W6786379927","https://openalex.org/W6852695532"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4391250611","https://openalex.org/W4388965752","https://openalex.org/W2429129060","https://openalex.org/W2908588478","https://openalex.org/W2114870167","https://openalex.org/W2409844362","https://openalex.org/W2890718724"],"abstract_inverted_index":{"PlasCAT":[0],"is":[1],"freely":[2],"available":[3,18],"on":[4],"the":[5,24,29],"web":[6],"at":[7,21],"https://sequencing.genofab.com.":[8],"The":[9],"assembly":[10],"pipeline":[11],"source":[12,30],"code":[13,16,31],"and":[14,39],"server":[15],"are":[17],"for":[19],"download":[20],"https://bitbucket.org/genofabinc/workspace/projects/PLASCAT.":[22],"Click":[23],"Cancel":[25],"button":[26],"to":[27],"access":[28],"without":[32],"authenticating.":[33],"Web":[34],"servers":[35],"implemented":[36],"in":[37],"React.js":[38],"Python,":[40],"with":[41],"all":[42],"major":[43],"browsers":[44],"supported.":[45]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
