{"id":"https://openalex.org/W3101771214","doi":"https://doi.org/10.1145/3388440.3412485","title":"Three Co-expression Pattern Types across Microbial Transcriptional Networks of Plankton in Two Oceanic Waters","display_name":"Three Co-expression Pattern Types across Microbial Transcriptional Networks of Plankton in Two Oceanic Waters","publication_year":2020,"publication_date":"2020-09-21","ids":{"openalex":"https://openalex.org/W3101771214","doi":"https://doi.org/10.1145/3388440.3412485","mag":"3101771214"},"language":"en","primary_location":{"id":"doi:10.1145/3388440.3412485","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3388440.3412485","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"type":"article","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/A5085898035","display_name":"Ruby Sharma","orcid":"https://orcid.org/0000-0002-8441-0415"},"institutions":[{"id":"https://openalex.org/I10052268","display_name":"New Mexico State University","ror":"https://ror.org/00hpz7z43","country_code":"US","type":"education","lineage":["https://openalex.org/I10052268"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ruby Sharma","raw_affiliation_strings":["Department of Computer Science, New Mexico State University, Las Cruces, New Mexico, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, New Mexico State University, Las Cruces, New Mexico, USA","institution_ids":["https://openalex.org/I10052268"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088311219","display_name":"Xuye Luo","orcid":"https://orcid.org/0000-0003-3402-269X"},"institutions":[{"id":"https://openalex.org/I10052268","display_name":"New Mexico State University","ror":"https://ror.org/00hpz7z43","country_code":"US","type":"education","lineage":["https://openalex.org/I10052268"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xuye Luo","raw_affiliation_strings":["Department of Computer Science, New Mexico State University, Las Cruces, New Mexico, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, New Mexico State University, Las Cruces, New Mexico, USA","institution_ids":["https://openalex.org/I10052268"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076579441","display_name":"Sajal Kumar","orcid":"https://orcid.org/0000-0003-0930-1582"},"institutions":[{"id":"https://openalex.org/I10052268","display_name":"New Mexico State University","ror":"https://ror.org/00hpz7z43","country_code":"US","type":"education","lineage":["https://openalex.org/I10052268"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sajal Kumar","raw_affiliation_strings":["Department of Computer Science, New Mexico State University, Las Cruces, New Mexico, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, New Mexico State University, Las Cruces, New Mexico, USA","institution_ids":["https://openalex.org/I10052268"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082897828","display_name":"Mingzhou Song","orcid":"https://orcid.org/0000-0002-6883-6547"},"institutions":[{"id":"https://openalex.org/I10052268","display_name":"New Mexico State University","ror":"https://ror.org/00hpz7z43","country_code":"US","type":"education","lineage":["https://openalex.org/I10052268"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mingzhou Song","raw_affiliation_strings":["Department of Computer Science, Molecular Biology Graduate Program, New Mexico State University, Las Cruces, New Mexico, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Molecular Biology Graduate Program, New Mexico State University, Las Cruces, New Mexico, USA","institution_ids":["https://openalex.org/I10052268"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5085898035"],"corresponding_institution_ids":["https://openalex.org/I10052268"],"apc_list":null,"apc_paid":null,"fwci":0.0829,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.45512011,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9980999827384949,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9980999827384949,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9973999857902527,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.996999979019165,"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/ocean-gyre","display_name":"Ocean gyre","score":0.6497451066970825},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5948951244354248},{"id":"https://openalex.org/keywords/trajectory","display_name":"Trajectory","score":0.563669741153717},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4625702500343323},{"id":"https://openalex.org/keywords/plankton","display_name":"Plankton","score":0.44001638889312744},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.43914172053337097},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.4298163652420044},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.4088761508464813},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3324642777442932},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3074195384979248},{"id":"https://openalex.org/keywords/subtropics","display_name":"Subtropics","score":0.23029574751853943},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.11919724941253662}],"concepts":[{"id":"https://openalex.org/C30380174","wikidata":"https://www.wikidata.org/wiki/Q1250263","display_name":"Ocean gyre","level":3,"score":0.6497451066970825},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5948951244354248},{"id":"https://openalex.org/C13662910","wikidata":"https://www.wikidata.org/wiki/Q193139","display_name":"Trajectory","level":2,"score":0.563669741153717},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4625702500343323},{"id":"https://openalex.org/C108469399","wikidata":"https://www.wikidata.org/wiki/Q25367","display_name":"Plankton","level":2,"score":0.44001638889312744},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.43914172053337097},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4298163652420044},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.4088761508464813},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3324642777442932},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3074195384979248},{"id":"https://openalex.org/C14168384","wikidata":"https://www.wikidata.org/wiki/Q16305538","display_name":"Subtropics","level":2,"score":0.23029574751853943},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.11919724941253662},{"id":"https://openalex.org/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3388440.3412485","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3388440.3412485","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.8799999952316284,"id":"https://metadata.un.org/sdg/14","display_name":"Life below water"}],"awards":[{"id":"https://openalex.org/G1167651922","display_name":null,"funder_award_id":"2016-51181-25408","funder_id":"https://openalex.org/F4320306114","funder_display_name":"U.S. Department of Agriculture"},{"id":"https://openalex.org/G5042958073","display_name":null,"funder_award_id":"1661331","funder_id":"https://openalex.org/F4320309085","funder_display_name":"Center for Selective C-H Functionalization, National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306114","display_name":"U.S. Department of Agriculture","ror":"https://ror.org/01na82s61"},{"id":"https://openalex.org/F4320309085","display_name":"Center for Selective C-H Functionalization, National Science Foundation","ror":"https://ror.org/02h8v7m77"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W1525754348","https://openalex.org/W1605141624","https://openalex.org/W1761036082","https://openalex.org/W1844186501","https://openalex.org/W1866307014","https://openalex.org/W1960046401","https://openalex.org/W1965055200","https://openalex.org/W1978355786","https://openalex.org/W1982713507","https://openalex.org/W1999455283","https://openalex.org/W2014939628","https://openalex.org/W2031648200","https://openalex.org/W2099123062","https://openalex.org/W2101694541","https://openalex.org/W2110065044","https://openalex.org/W2114104545","https://openalex.org/W2121154910","https://openalex.org/W2130322476","https://openalex.org/W2131925745","https://openalex.org/W2147029889","https://openalex.org/W2149491227","https://openalex.org/W2159482845","https://openalex.org/W2182189596","https://openalex.org/W2341548809","https://openalex.org/W2412095308","https://openalex.org/W2554705260","https://openalex.org/W2594201657","https://openalex.org/W2787994442","https://openalex.org/W2791559636","https://openalex.org/W2804722511","https://openalex.org/W2883273193","https://openalex.org/W2891123370","https://openalex.org/W2949084500","https://openalex.org/W2966268928","https://openalex.org/W3040182561","https://openalex.org/W3093463983","https://openalex.org/W4210702584","https://openalex.org/W4229954146","https://openalex.org/W4294216483","https://openalex.org/W4302791744"],"related_works":["https://openalex.org/W2901533710","https://openalex.org/W271696883","https://openalex.org/W4220916127","https://openalex.org/W2052374367","https://openalex.org/W2186223391","https://openalex.org/W2402052586","https://openalex.org/W2013650479","https://openalex.org/W1965084365","https://openalex.org/W2490221126","https://openalex.org/W2149789347"],"abstract_inverted_index":{"Patterns":[0],"of":[1,26,82,109,119,132,139,147,206,240],"two":[2,110],"molecules":[3],"across":[4,28,85,112],"biological":[5,222],"systems":[6],"are":[7,157,173,226,244],"often":[8],"labeled":[9],"as":[10,193],"conserved":[11,37,41,47,159],"or":[12,183],"differential.":[13],"We":[14,62,99,114],"argue":[15],"that":[16,153],"this":[17],"classification":[18],"is":[19,46,56,142,217],"insufficient.":[20],"Here,":[21],"we":[22],"introduce":[23,101],"three":[24],"types":[25],"relationships":[27],"systems.":[29,113,223],"Upon":[30],"stimuli,":[31],"a":[32,43,53,64,102,201],"type-0":[33,150,185],"pattern":[34,45,55],"arises":[35],"from":[36],"circuitry":[38,48,58,162],"with":[39,49,59,175],"active":[40,50,60],"trajectory;":[42,52],"type-1":[44,140],"differential":[51],"type-2":[54,148],"rewired":[57],"trajectory.":[61],"present":[63],"1st-order":[65,94],"marginal":[66],"change":[67],"test,":[68],"prove":[69],"its":[70,74],"optimality,":[71],"and":[72,149,170,195,238],"establish":[73],"asymptotic":[75],"chi-squared":[76],"distribution":[77],"under":[78],"the":[79,129,154,207,229],"null":[80],"hypothesis":[81],"identical":[83],"marginals":[84],"conditions.":[86],"The":[87,137,215],"test":[88,105],"outperformed":[89],"other":[90,221],"methods":[91],"in":[92,96,123,160,212,228],"detecting":[93],"difference":[95],"simulation":[97],"studies.":[98],"also":[100],"zeroth-order":[103],"strength":[104],"to":[106,166,178,180,204,220],"assess":[107],"association":[108],"variables":[111],"compared":[115],"gene":[116,210,242],"co-expression":[117],"networks":[118],"planktonic":[120],"microbial":[121,155,213],"communities":[122,156],"cold":[124],"California":[125],"coastal":[126],"water":[127,131],"against":[128],"warm":[130],"North":[133],"Pacific":[134],"Subtropical":[135],"Gyre.":[136],"frequency":[138],"patterns":[141,172,186,243],"much":[143],"higher":[144],"than":[145],"those":[146],"patterns,":[151],"revealing":[152],"mostly":[158],"molecular":[161],"but":[163],"responded":[164],"differentially":[165],"ocean":[167],"habitats.":[168],"Type-1":[169],"2":[171],"enriched":[174],"genes":[176,188],"known":[177],"respond":[179],"environmental":[181],"changes":[182],"stress;":[184],"involve":[187],"having":[189],"essential":[190],"function":[191],"such":[192],"photosynthesis":[194],"general":[196],"transcription.":[197],"Our":[198],"work":[199],"provides":[200],"deep":[202],"understanding":[203],"effects":[205],"environment":[208],"on":[209],"regulation":[211],"communities.":[214],"method":[216],"generally":[218],"applicable":[219],"All":[224],"tests":[225],"provided":[227],"R":[230],"package":[231],"'DiffXTables'":[232],"at":[233,246],"https://cran.r-project.org/package=DiffXTables.":[234],"Other":[235],"source":[236],"code":[237],"lists":[239],"significant":[241],"available":[245],"https://www.cs.nmsu.edu/~joemsong/ACM-BCB-2020/Plankton":[247]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}