{"id":"https://openalex.org/W2071546884","doi":"https://doi.org/10.1073/pnas.1313713111","title":"Gene-centric approach to integrating environmental genomics and biogeochemical models","display_name":"Gene-centric approach to integrating environmental genomics and biogeochemical models","publication_year":2014,"publication_date":"2014-01-21","ids":{"openalex":"https://openalex.org/W2071546884","doi":"https://doi.org/10.1073/pnas.1313713111","mag":"2071546884","pmid":"https://pubmed.ncbi.nlm.nih.gov/24449851","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/3918765"},"language":"en","primary_location":{"id":"doi:10.1073/pnas.1313713111","doi":"https://doi.org/10.1073/pnas.1313713111","is_oa":false,"landing_page_url":"https://doi.org/10.1073/pnas.1313713111","pdf_url":null,"source":{"id":"https://openalex.org/S125754415","display_name":"Proceedings of the National Academy of Sciences","issn_l":"0027-8424","issn":["0027-8424","1091-6490"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","dongbi-a","doyens","erih-plus","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320052","host_organization_name":"National Academy of Sciences","host_organization_lineage":["https://openalex.org/P4310320052"],"host_organization_lineage_names":["National Academy of Sciences"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the National Academy of Sciences","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3918765","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Daniel C. Reed","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel C. Reed","raw_affiliation_strings":["Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109; and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109; and","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000924462","display_name":"Christopher Kenneth Algar","orcid":"https://orcid.org/0000-0001-9622-2182","observed_orcids":["https://orcid.org/0000-0001-9622-2182","https://orcid.org/0000-0003-2493-736X"]},"institutions":[{"id":"https://openalex.org/I1338920048","display_name":"Marine Biological Laboratory","ror":"https://ror.org/046dg4z72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1338920048"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher K. Algar","raw_affiliation_strings":["Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543","institution_ids":["https://openalex.org/I1338920048"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059991582","display_name":"Julie A. Huber","orcid":"https://orcid.org/0000-0002-4790-7633","observed_orcids":["https://orcid.org/0000-0002-4790-7633"]},"institutions":[{"id":"https://openalex.org/I1338920048","display_name":"Marine Biological Laboratory","ror":"https://ror.org/046dg4z72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1338920048"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Julie A. Huber","raw_affiliation_strings":["Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543","institution_ids":["https://openalex.org/I1338920048"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075036643","display_name":"Gregory J. Dick","orcid":"https://orcid.org/0000-0001-7666-6288","observed_orcids":["https://orcid.org/0000-0001-7666-6288"]},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gregory J. Dick","raw_affiliation_strings":["Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109; and","aDepartment of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109; and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109; and","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"aDepartment of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109; and","institution_ids":["https://openalex.org/I27837315"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":10.9147,"has_fulltext":false,"cited_by_count":176,"citation_normalized_percentile":{"value":0.99054213,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"111","issue":"5","first_page":"1879","last_page":"1884"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.8246999979019165,"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"}},"topics":[{"id":"https://openalex.org/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.8246999979019165,"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/T10564","display_name":"Wastewater Treatment and Nitrogen Removal","score":0.08479999750852585,"subfield":{"id":"https://openalex.org/subfields/2310","display_name":"Pollution"},"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/T10032","display_name":"Marine Plankton and Biogeochemistry","score":0.035599999129772186,"subfield":{"id":"https://openalex.org/subfields/1910","display_name":"Oceanography"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/metagenomics","display_name":"metagenomics","score":0.7900000214576721},{"id":"https://openalex.org/keywords/microbial-communities","display_name":"microbial communities","score":0.6269999742507935},{"id":"https://openalex.org/keywords/nitrogen-cycle","display_name":"nitrogen cycling","score":0.9010000228881836},{"id":"https://openalex.org/keywords/oxygen-minimum-zone","display_name":"oxygen minimum zone","score":0.8289999961853027},{"id":"https://openalex.org/keywords/arabian-sea","display_name":"Arabian Sea","score":0.9800000190734863},{"id":"https://openalex.org/keywords/denitrification","display_name":"denitrification","score":0.9240000247955322},{"id":"https://openalex.org/keywords/anammox","display_name":"anammox","score":0.9980000257492065},{"id":"https://openalex.org/keywords/chemolithoautotrophs","display_name":"chemolithoautotrophic bacteria","score":0.8840000033378601},{"id":"https://openalex.org/keywords/dinitrogen-production","display_name":"dinitrogen production","score":0.7409999966621399},{"id":"https://openalex.org/keywords/functional-genes","display_name":"functional genes","score":0.3799999952316284}],"concepts":[{"id":"https://openalex.org/C71915725","wikidata":"https://www.wikidata.org/wiki/Q846303","display_name":"Biogeochemical cycle","level":2,"score":0.9361479878425598},{"id":"https://openalex.org/C130309983","wikidata":"https://www.wikidata.org/wiki/Q864379","display_name":"Biogeochemistry","level":2,"score":0.7374787926673889},{"id":"https://openalex.org/C49045045","wikidata":"https://www.wikidata.org/wiki/Q82551","display_name":"Nitrogen cycle","level":3,"score":0.5918266773223877},{"id":"https://openalex.org/C550995028","wikidata":"https://www.wikidata.org/wiki/Q10872","display_name":"Archaea","level":3,"score":0.5844178199768066},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.5312711000442505},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.5271541476249695},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5066617131233215},{"id":"https://openalex.org/C69562835","wikidata":"https://www.wikidata.org/wiki/Q3054637","display_name":"Microbial ecology","level":3,"score":0.4879609942436218},{"id":"https://openalex.org/C81407943","wikidata":"https://www.wikidata.org/wiki/Q17149178","display_name":"Microbial population biology","level":3,"score":0.46059927344322205},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.44137296080589294},{"id":"https://openalex.org/C1965285","wikidata":"https://www.wikidata.org/wiki/Q8008","display_name":"Earth science","level":1,"score":0.33011531829833984},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.324613094329834},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1469842791557312},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.13536664843559265},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.119778573513031},{"id":"https://openalex.org/C537208039","wikidata":"https://www.wikidata.org/wiki/Q627","display_name":"Nitrogen","level":2,"score":0.11294373869895935},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.10925167798995972},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10619568824768066},{"id":"https://openalex.org/C127313418","wikidata":"https://www.wikidata.org/wiki/Q1069","display_name":"Geology","level":0,"score":0.08898815512657166},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D006862","descriptor_name":"Hydrogen Sulfide","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009566","descriptor_name":"Nitrates","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009792","descriptor_name":"Oceans and Seas","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010084","descriptor_name":"Oxidation-Reduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010100","descriptor_name":"Oxygen","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058458","descriptor_name":"Nitrogen Cycle","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1073/pnas.1313713111","doi":"https://doi.org/10.1073/pnas.1313713111","is_oa":false,"landing_page_url":"https://doi.org/10.1073/pnas.1313713111","pdf_url":null,"source":{"id":"https://openalex.org/S125754415","display_name":"Proceedings of the National Academy of Sciences","issn_l":"0027-8424","issn":["0027-8424","1091-6490"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","dongbi-a","doyens","erih-plus","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320052","host_organization_name":"National Academy of Sciences","host_organization_lineage":["https://openalex.org/P4310320052"],"host_organization_lineage_names":["National Academy of Sciences"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the National Academy of Sciences","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:3089425","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3918765","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3918765","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3918765","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"Proc Natl Acad Sci U S A","raw_type":"Text"},{"id":"pmid:24449851","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24449851","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,"listed_in":[],"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":"Proceedings of the National Academy of Sciences of the United States of America","raw_type":"Journal Article"}],"best_oa_location":{"id":"pmh:oai:europepmc.org:3089425","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3918765","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},"sustainable_development_goals":[{"score":1.0,"id":"https://metadata.un.org/sdg/14","display_name":"Life below water"},{"score":0.54830002784729,"id":"https://metadata.un.org/sdg/6","display_name":"Clean water and sanitation"},{"score":0.46149998903274536,"id":"https://metadata.un.org/sdg/13","display_name":"Climate action"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W168236623","https://openalex.org/W1605383624","https://openalex.org/W1885254586","https://openalex.org/W1965849849","https://openalex.org/W1974766384","https://openalex.org/W1991173854","https://openalex.org/W2002973793","https://openalex.org/W2010009661","https://openalex.org/W2016896717","https://openalex.org/W2022584152","https://openalex.org/W2022946794","https://openalex.org/W2048829317","https://openalex.org/W2054300247","https://openalex.org/W2054607874","https://openalex.org/W2055375681","https://openalex.org/W2064334669","https://openalex.org/W2067790594","https://openalex.org/W2071965166","https://openalex.org/W2079980893","https://openalex.org/W2087814760","https://openalex.org/W2100088878","https://openalex.org/W2113601822","https://openalex.org/W2115078611","https://openalex.org/W2122286557","https://openalex.org/W2122571325","https://openalex.org/W2135374774","https://openalex.org/W2138465606","https://openalex.org/W2142620138","https://openalex.org/W2145096130","https://openalex.org/W2145649717","https://openalex.org/W2147783737","https://openalex.org/W2161164464","https://openalex.org/W2164514888"],"related_works":["https://openalex.org/W2522918942","https://openalex.org/W6990463042","https://openalex.org/W4416168887","https://openalex.org/W7096441862","https://openalex.org/W96446417","https://openalex.org/W4408166189","https://openalex.org/W2096198048","https://openalex.org/W2889548154","https://openalex.org/W2569619938","https://openalex.org/W2110149841"],"abstract_inverted_index":{"Rapid":[0],"advances":[1],"in":[2,33,74,92,96,118,129,161,166,239],"molecular":[3],"microbial":[4,21,72,205],"ecology":[5],"have":[6],"yielded":[7],"an":[8,225],"unprecedented":[9],"amount":[10],"of":[11,20,36,48,141,169,204,221,233],"data":[12,80],"about":[13,110],"the":[14,34,37,90,97,130,139,145,155,167,170,179,191,201,207,234],"evolutionary":[15],"relationships":[16],"and":[17,41,50,114,173,218],"functional":[18,67],"traits":[19],"communities":[22,73],"that":[23,84,124],"regulate":[24],"global":[25],"geochemical":[26,198],"cycles.":[27],"Biogeochemical":[28],"models,":[29],"however,":[30],"are":[31,53,85],"trailing":[32],"wake":[35],"environmental":[38],"genomics":[39,79],"revolution,":[40],"such":[42],"models":[43,76,187],"rarely":[44],"incorporate":[45],"explicit":[46],"representations":[47],"bacteria":[49],"archaea,":[51],"nor":[52],"they":[54,193],"compatible":[55],"with":[56],"nucleic":[57],"acid":[58],"or":[59],"protein":[60],"sequence":[61],"data.":[62],"Here,":[63],"we":[64],"present":[65],"a":[66,210],"gene-based":[68],"framework":[69,211],"for":[70,138,212,229],"describing":[71],"biogeochemical":[75,186,219],"by":[77],"incorporating":[78],"to":[81,106,153,164,181,200],"provide":[82],"predictions":[83],"readily":[86],"testable.":[87],"To":[88],"demonstrate":[89],"approach":[91,226],"practice,":[93],"nitrogen":[94,143],"cycling":[95,113,150],"Arabian":[98,132],"Sea":[99],"oxygen":[100],"minimum":[101],"zone":[102],"(OMZ)":[103],"was":[104,151],"modeled":[105],"examine":[107],"key":[108,235],"questions":[109],"cryptic":[111,148],"sulfur":[112,149],"dinitrogen":[115],"production":[116],"pathways":[117],"OMZs.":[119],"Simulations":[120],"support":[121],"previous":[122],"assertions":[123],"denitrification":[125],"dominates":[126],"over":[127],"anammox":[128],"central":[131],"Sea,":[133],"which":[134],"has":[135],"important":[136],"implications":[137],"loss":[140],"fixed":[142],"from":[144],"oceans.":[146],"Furthermore,":[147],"shown":[152],"attenuate":[154],"secondary":[156],"nitrite":[157],"maximum":[158],"often":[159],"observed":[160],"OMZs":[162],"owing":[163],"changes":[165],"composition":[168,203],"chemolithoautotrophic":[171],"community":[172],"dominant":[174],"metabolic":[175],"pathways.":[176],"Results":[177],"underscore":[178],"need":[180],"explicitly":[182],"integrate":[183],"microbes":[184,237],"into":[185,216],"rather":[188],"than":[189],"just":[190],"metabolisms":[192],"mediate.":[194],"By":[195],"directly":[196],"linking":[197],"dynamics":[199],"genetic":[202],"communities,":[206],"method":[208],"provides":[209],"achieving":[213],"mechanistic":[214],"insights":[215],"patterns":[217],"consequences":[220],"marine":[222],"microbes.":[223],"Such":[224],"is":[227],"critical":[228],"informing":[230],"our":[231],"understanding":[232],"role":[236],"play":[238],"modulating":[240],"Earth's":[241],"biogeochemistry.":[242]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":19},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":15},{"year":2021,"cited_by_count":26},{"year":2020,"cited_by_count":14},{"year":2019,"cited_by_count":18},{"year":2018,"cited_by_count":16},{"year":2017,"cited_by_count":13},{"year":2016,"cited_by_count":15},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":4}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}