{"id":"https://openalex.org/W2749224256","doi":"https://doi.org/10.1145/3107411.3107435","title":"Inferring Microbial Interactions from Metagenomic Time-series Using Prior Biological Knowledge","display_name":"Inferring Microbial Interactions from Metagenomic Time-series Using Prior Biological Knowledge","publication_year":2017,"publication_date":"2017-08-20","ids":{"openalex":"https://openalex.org/W2749224256","doi":"https://doi.org/10.1145/3107411.3107435","mag":"2749224256"},"language":"en","primary_location":{"id":"doi:10.1145/3107411.3107435","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3107435","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th 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/A5054603014","display_name":"Chieh Lo","orcid":"https://orcid.org/0000-0002-5528-494X"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Chieh Lo","raw_affiliation_strings":["Carnegie Mellon University, Pittsburgh, PA, USA"],"affiliations":[{"raw_affiliation_string":"Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036227385","display_name":"Radu M\u0103rculescu","orcid":"https://orcid.org/0000-0003-1826-7646"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Radu Marculescu","raw_affiliation_strings":["Carnegie Mellon University, Pittsburgh, PA, USA"],"affiliations":[{"raw_affiliation_string":"Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5054603014"],"corresponding_institution_ids":["https://openalex.org/I74973139"],"apc_list":null,"apc_paid":null,"fwci":0.638,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.6752047,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"168","last_page":"177"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9995999932289124,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9995999932289124,"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/T10887","display_name":"Bioinformatics and Genomic Networks","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/T10066","display_name":"Gut microbiota and health","score":0.9977999925613403,"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/metagenomics","display_name":"Metagenomics","score":0.9388200044631958},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6607504487037659},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6360308527946472},{"id":"https://openalex.org/keywords/lasso","display_name":"Lasso (programming language)","score":0.51711106300354},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.45931604504585266},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.37905174493789673},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.34308117628097534},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3270251154899597},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2037615180015564}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.9388200044631958},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6607504487037659},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6360308527946472},{"id":"https://openalex.org/C37616216","wikidata":"https://www.wikidata.org/wiki/Q3218363","display_name":"Lasso (programming language)","level":2,"score":0.51711106300354},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.45931604504585266},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.37905174493789673},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.34308117628097534},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3270251154899597},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2037615180015564},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3107411.3107435","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3107435","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Life in Land","score":0.6399999856948853,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W2124637492","https://openalex.org/W2125156589","https://openalex.org/W2152401289","https://openalex.org/W2166325326","https://openalex.org/W3011726037","https://openalex.org/W4299542564"],"related_works":["https://openalex.org/W638577851","https://openalex.org/W2968354375","https://openalex.org/W2359440920","https://openalex.org/W2889550857","https://openalex.org/W3013372948","https://openalex.org/W3135997498","https://openalex.org/W4242417330","https://openalex.org/W3198631238","https://openalex.org/W4388282505","https://openalex.org/W4387595596"],"abstract_inverted_index":{"Due":[0],"to":[1,13,84],"the":[2,16,34,38,45,76,137,141,145],"recent":[3],"advances":[4],"in":[5,65,127,139],"modern":[6],"metagenomics":[7,57,118],"sequencing":[8,54],"methods,":[9],"it":[10],"becomes":[11],"possible":[12],"directly":[14,52],"analyze":[15,85],"microbial":[17,25,108],"communities":[18,26],"within":[19],"human":[20,35,151],"body.":[21],"To":[22,88],"understand":[23],"how":[24],"adapt,":[27],"develop,":[28],"and":[29,37,62,73,110,116,131],"interact":[30],"over":[31],"time":[32],"with":[33,107],"body":[36],"surrounding":[39],"environment,":[40],"a":[41,93],"critical":[42],"step":[43],"is":[44,59],"inference":[46],"of":[47,129],"interactions":[48,77],"among":[49,78],"different":[50],"microbes":[51],"from":[53,113,150],"data.":[55,87,119,161],"However,":[56],"data":[58,153],"both":[60],"compositional":[61],"highly":[63],"dimensional":[64],"nature.":[66],"Consequently,":[67],"new":[68],"approaches":[69],"that":[70,122],"can":[71],"accurately":[72],"robustly":[74],"estimate":[75],"various":[79],"microbe":[80],"species":[81],"are":[82],"needed":[83],"such":[86],"this":[89],"end,":[90],"we":[91,148],"propose":[92],"novel":[94],"framework":[95],"called":[96],"Microbial":[97],"Time-series":[98],"Prior":[99],"Lasso":[100],"(MTPLasso)":[101],"which":[102],"integrates":[103],"sparse":[104],"linear":[105],"regression":[106],"co-occurrences":[109],"associations":[111],"obtained":[112],"scientific":[114],"literature":[115],"cross-sectional":[117],"We":[120],"show":[121],"MTPLasso":[123],"outperforms":[124],"existing":[125],"models":[126],"terms":[128],"precision":[130],"recall":[132],"rates,":[133],"as":[134,136],"well":[135],"accuracy":[138],"inferring":[140],"interaction":[142,146],"types.":[143],"Finally,":[144],"networks":[147],"infer":[149],"gut":[152],"demonstrate":[154],"credible":[155],"results":[156],"when":[157],"compared":[158],"against":[159],"real":[160]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}