{"id":"https://openalex.org/W4221024268","doi":"https://doi.org/10.1093/bib/bbac071","title":"deepNEC: a novel alignment-free tool for the identification and classification of nitrogen biochemical network-related enzymes using deep learning","display_name":"deepNEC: a novel alignment-free tool for the identification and classification of nitrogen biochemical network-related enzymes using deep learning","publication_year":2022,"publication_date":"2022-03-07","ids":{"openalex":"https://openalex.org/W4221024268","doi":"https://doi.org/10.1093/bib/bbac071","pmid":"https://pubmed.ncbi.nlm.nih.gov/35325031"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac071","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac071","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"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/A5016582769","display_name":"Naveen Duhan","orcid":"https://orcid.org/0000-0003-3014-4921"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Naveen Duhan","raw_affiliation_strings":["Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, UT 84322 USA"],"affiliations":[{"raw_affiliation_string":"Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, UT 84322 USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058165268","display_name":"Jeanette M. Norton","orcid":"https://orcid.org/0000-0002-6596-8691"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jeanette M Norton","raw_affiliation_strings":["Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, UT 84322 USA"],"affiliations":[{"raw_affiliation_string":"Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, UT 84322 USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067874418","display_name":"Rakesh Kaundal","orcid":"https://orcid.org/0000-0001-8683-1240"},"institutions":[{"id":"https://openalex.org/I121980950","display_name":"Utah State University","ror":"https://ror.org/00h6set76","country_code":"US","type":"education","lineage":["https://openalex.org/I121980950"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Rakesh Kaundal","raw_affiliation_strings":["Bioinformatics Facility, Center for Integrated BioSystems, UT 84322 USA","Department of Computer Science, College of Science; Utah State University, Logan, UT 84322 USA","Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, UT 84322 USA","Department of Computer Science, College of Science"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Facility, Center for Integrated BioSystems, UT 84322 USA","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science, College of Science; Utah State University, Logan, UT 84322 USA","institution_ids":["https://openalex.org/I121980950"]},{"raw_affiliation_string":"Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, UT 84322 USA","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science, College of Science","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5067874418"],"corresponding_institution_ids":["https://openalex.org/I121980950"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.6932,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.65922911,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"23","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9993000030517578,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9993000030517578,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987000226974487,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9944000244140625,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5912575125694275},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5911931991577148},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.5313442349433899},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.5057153701782227},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.447458416223526},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.41979917883872986},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3986873924732208},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2645188271999359},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.24133867025375366},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22803428769111633},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16366896033287048}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5912575125694275},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5911931991577148},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.5313442349433899},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.5057153701782227},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.447458416223526},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.41979917883872986},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3986873924732208},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2645188271999359},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.24133867025375366},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22803428769111633},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16366896033287048}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009584","descriptor_name":"Nitrogen","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009584","descriptor_name":"Nitrogen","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009584","descriptor_name":"Nitrogen","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbac071","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac071","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35325031","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35325031","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Clean water and sanitation","id":"https://metadata.un.org/sdg/6","score":0.8500000238418579}],"awards":[{"id":"https://openalex.org/G1312215613","display_name":null,"funder_award_id":"A45112","funder_id":"https://openalex.org/F4320327947","funder_display_name":"Universitas Sumatera Utara"}],"funders":[{"id":"https://openalex.org/F4320327947","display_name":"Universitas Sumatera Utara","ror":"https://ror.org/01kknrc90"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":84,"referenced_works":["https://openalex.org/W94122642","https://openalex.org/W1494484168","https://openalex.org/W1511002280","https://openalex.org/W1965373464","https://openalex.org/W1968416380","https://openalex.org/W1970898136","https://openalex.org/W1973429093","https://openalex.org/W1976656799","https://openalex.org/W1980256262","https://openalex.org/W1981977817","https://openalex.org/W1984794455","https://openalex.org/W1987134040","https://openalex.org/W1990748933","https://openalex.org/W1991310235","https://openalex.org/W1994787881","https://openalex.org/W1998263233","https://openalex.org/W2007828112","https://openalex.org/W2018228674","https://openalex.org/W2018459257","https://openalex.org/W2026666393","https://openalex.org/W2028222272","https://openalex.org/W2033054377","https://openalex.org/W2038873127","https://openalex.org/W2040500459","https://openalex.org/W2048322438","https://openalex.org/W2049381178","https://openalex.org/W2049617155","https://openalex.org/W2055903902","https://openalex.org/W2064146062","https://openalex.org/W2071546884","https://openalex.org/W2072762503","https://openalex.org/W2085176241","https://openalex.org/W2085836460","https://openalex.org/W2095132285","https://openalex.org/W2096294058","https://openalex.org/W2101234009","https://openalex.org/W2103182909","https://openalex.org/W2104812418","https://openalex.org/W2104960492","https://openalex.org/W2113475314","https://openalex.org/W2114690198","https://openalex.org/W2114915599","https://openalex.org/W2119988314","https://openalex.org/W2125546020","https://openalex.org/W2129368756","https://openalex.org/W2131366108","https://openalex.org/W2132292391","https://openalex.org/W2133215312","https://openalex.org/W2137639237","https://openalex.org/W2142075090","https://openalex.org/W2142529984","https://openalex.org/W2149352713","https://openalex.org/W2155704095","https://openalex.org/W2159482845","https://openalex.org/W2159628188","https://openalex.org/W2165163979","https://openalex.org/W2166575747","https://openalex.org/W2170747616","https://openalex.org/W2172210212","https://openalex.org/W2179653678","https://openalex.org/W2340861812","https://openalex.org/W2346975780","https://openalex.org/W2490378810","https://openalex.org/W2518034873","https://openalex.org/W2559588208","https://openalex.org/W2570075946","https://openalex.org/W2611792444","https://openalex.org/W2620760558","https://openalex.org/W2765734056","https://openalex.org/W2766352633","https://openalex.org/W2786671949","https://openalex.org/W2892210937","https://openalex.org/W2937720853","https://openalex.org/W2941112903","https://openalex.org/W2953321375","https://openalex.org/W3016202688","https://openalex.org/W3097021932","https://openalex.org/W3112376646","https://openalex.org/W4213149192","https://openalex.org/W6603825087","https://openalex.org/W6648129645","https://openalex.org/W6668807014","https://openalex.org/W6675354045","https://openalex.org/W6745213239"],"related_works":["https://openalex.org/W2947496432","https://openalex.org/W4312200629","https://openalex.org/W4223943233","https://openalex.org/W4360585206","https://openalex.org/W4364306694","https://openalex.org/W4309045103","https://openalex.org/W4225161397","https://openalex.org/W3171187312","https://openalex.org/W3014300295","https://openalex.org/W1501213224"],"abstract_inverted_index":{"Nitrogen":[0],"is":[1,145,405],"essential":[2,19],"for":[3,109,168,227,291],"life":[4],"and":[5,35,37,40,74,104,152,178,199,205,212,251,276,313,325,340,354,368],"its":[6,38,48],"transformations":[7],"are":[8],"an":[9,18,80,148,319],"important":[10],"part":[11],"of":[12,26,54,67,124,174,288,308,335,349,363],"the":[13,55,58,86,93,137,184,230,244,264,278,283,296,303,373,377,393],"global":[14],"biogeochemical":[15],"cycle.":[16],"Being":[17],"nutrient,":[20],"nitrogen":[21,60,88,110,255,273,292],"exists":[22],"in":[23,69,229,243,263,277,310,315,329,337,342,351,356,365,370],"a":[24,64,99,122,224,236,385,399],"range":[25,66],"oxidation":[27,39],"states":[28],"from":[29,92,136,155],"+5":[30],"(nitrate)":[31],"to":[32,84,132,182,217,388],"-3":[33],"(ammonium":[34],"amino-nitrogen),":[36],"reduction":[41],"reactions":[42],"catalyzed":[43],"by":[44],"microbial":[45],"enzymes":[46,62,91,177,253,258,270],"determine":[47,85],"environmental":[49],"fate.":[50],"The":[51,115,141,209],"functional":[52],"annotation":[53],"genes":[56],"encoding":[57],"core":[59],"network":[61],"has":[63],"broad":[65],"applications":[68],"metagenomics,":[70],"agriculture,":[71],"wastewater":[72],"treatment":[73],"industrial":[75],"biotechnology.":[76],"This":[77],"study":[78],"developed":[79,118],"alignment-free":[81],"computational":[82],"approach":[83,108,226],"predicted":[87,269],"biochemical":[89,111,256],"network-related":[90,112,257],"sequence":[94,144,188,238],"itself.":[95],"We":[96,381],"propose":[97],"deepNEC,":[98],"novel":[100],"end-to-end":[101],"feature":[102,301,375],"selection":[103],"classification":[105,162],"model":[106,220],"training":[107,312,324,339,353,367],"enzyme":[113,169,240,284],"prediction.":[114,170],"algorithm":[116],"was":[117],"using":[119],"Deep":[120],"Learning,":[121],"class":[123],"machine":[125],"learning":[126],"algorithms":[127],"that":[128],"uses":[129,223],"multiple":[130],"layers":[131],"extract":[133],"higher-level":[134],"features":[135,154,189],"raw":[138,156],"input":[139],"data.":[140],"derived":[142],"protein":[143,158,175,187],"used":[146,181],"as":[147,239],"input,":[149],"extracting":[150],"sequential":[151],"convolutional":[153],"encoded":[157],"sequences":[159],"based":[160],"on":[161,398],"rather":[163],"than":[164],"traditional":[165],"alignment-based":[166],"methods":[167],"Two":[171],"large":[172],"datasets":[173],"sequences,":[176],"non-enzymes":[179],"were":[180,215],"train":[183],"models":[185,394],"with":[186,318],"like":[190],"amino":[191],"acid":[192],"composition,":[193],"dipeptide":[194],"composition":[195],"(DPC),":[196],"conformation":[197],"transition":[198],"distribution,":[200],"normalized":[201],"Moreau-Broto":[202],"(NMBroto),":[203],"conjoint":[204],"quasi":[206],"order,":[207],"etc.":[208],"k-fold":[210,311,338,352,366],"cross-validation":[211],"independent":[213,316,327,343,357,371],"testing":[214],"performed":[216],"validate":[218],"our":[219],"training.":[221],"deepNEC":[222],"four-tier":[225],"prediction;":[228],"first":[231],"phase,":[232,246,266,280],"it":[233,247,267,281],"will":[234,248],"predict":[235,250],"query":[237],"or":[241,259],"non-enzyme;":[242],"second":[245],"further":[249],"classify":[252],"into":[254,271],"non-nitrogen":[260],"metabolism":[261,274],"enzymes;":[262],"third":[265],"classifies":[268],"nine":[272],"classes;":[275],"fourth":[279],"predicts":[282],"commission":[285],"number":[286],"out":[287],"20":[289],"classes":[290],"metabolism.":[293],"Among":[294],"all,":[295],"DPC":[297,374],"+":[298],"NMBroto":[299],"hybrid":[300],"gave":[302,376],"best":[304,378],"prediction":[305,379],"performance":[306],"(accuracy":[307,334],"96.15%":[309],"93.43%":[314],"testing)":[317,328],"Matthews":[320],"correlation":[321],"coefficient":[322],"(0.92":[323],"0.87":[326],"phase":[330,332,345,359],"I;":[331],"II":[333],"99.71%":[336],"98.30%":[341],"testing);":[344,358],"III":[346],"(overall":[347,361],"accuracy":[348,362],"99.03%":[350],"98.98%":[355],"IV":[360],"99.05%":[364],"98.18%":[369],"testing),":[372],"performance.":[380],"have":[382,395],"also":[383],"implemented":[384,397],"homology-based":[386],"method":[387],"remove":[389],"false":[390],"negatives.":[391],"All":[392],"been":[396],"web":[400],"server":[401],"(prediction":[402],"tool),":[403],"which":[404],"freely":[406],"available":[407],"at":[408],"http://bioinfo.usu.edu/deepNEC/.":[409]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-03-31T07:56:22.981413","created_date":"2025-10-10T00:00:00"}