{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T16:41:16Z","timestamp":1774629676765,"version":"3.50.1"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2017,2,8]],"date-time":"2017-02-08T00:00:00Z","timestamp":1486512000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100005150","name":"Chinese Academy of Medical Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005150","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Key Plan for Scientific Research and Development of China"},{"name":"International Scientific and Technological Cooperation project of China"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Previously, we developed a computational model to identify genomic co-occurrence networks that was applied to capture the coevolution patterns within genomes of influenza viruses. To facilitate easy public use of this model, an R package \u2018cooccurNet\u2019 is presented here.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>\u2018cooccurNet\u2019 includes functionalities of construction and analysis of residues (e.g. nucleotides, amino acids and SNPs) co-occurrence network. In addition, a new method for measuring residues coevolution, defined as residue co-occurrence score (RCOS), is proposed and implemented in \u2018cooccurNet\u2019 based on the co-occurrence network.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>\u2018cooccurNet\u2019 is publicly available on CRAN repositories under the GPL-3 Open Source License (http:\/\/cran.r-project.org\/package=cooccurNet)<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx062","type":"journal-article","created":{"date-parts":[[2017,2,8]],"date-time":"2017-02-08T06:31:32Z","timestamp":1486535492000},"page":"1881-1882","source":"Crossref","is-referenced-by-count":6,"title":["cooccurNet: an R package for co-occurrence network construction and analysis"],"prefix":"10.1093","volume":"33","author":[{"given":"Yuanqiang","family":"Zou","sequence":"first","affiliation":[{"name":"College of Computer Science and Electronic Engineering, Hunan University, Changsha, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhiqiang","family":"Wu","sequence":"additional","affiliation":[{"name":"College of Computer Science and Electronic Engineering, Hunan University, Changsha, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lizong","family":"Deng","sequence":"additional","affiliation":[{"name":"Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China"},{"name":"Suzhou Institute of Systems Medicine, Suzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aiping","family":"Wu","sequence":"additional","affiliation":[{"name":"Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China"},{"name":"Suzhou Institute of Systems Medicine, Suzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fan","family":"Wu","sequence":"additional","affiliation":[{"name":"College of Computer Science and Electronic Engineering, Hunan University, Changsha, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kenli","family":"Li","sequence":"additional","affiliation":[{"name":"College of Computer Science and Electronic Engineering, Hunan University, Changsha, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Taijiao","family":"Jiang","sequence":"additional","affiliation":[{"name":"Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China"},{"name":"Suzhou Institute of Systems Medicine, Suzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yousong","family":"Peng","sequence":"additional","affiliation":[{"name":"College of Biology, Hunan University, Changsha, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,2,8]]},"reference":[{"key":"2023020205492056200_btx062-B1","author":"Bates","year":"2016"},{"key":"2023020205492056200_btx062-B2","author":"Calaway","year":"2015"},{"key":"2023020205492056200_btx062-B3","author":"Charif","year":"2016"},{"key":"2023020205492056200_btx062-B4","doi-asserted-by":"crossref","first-page":"753","DOI":"10.1038\/cr.2015.54","article-title":"Network of co-mutations in Ebola virus genome predicts the disease lethality","volume":"25","author":"Deng","year":"2015","journal-title":"Cell Res"},{"key":"2023020205492056200_btx062-B5","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1101\/gr.6969007","article-title":"Networks of genomic co-occurrence capture characteristics of human influenza A (H3N2) evolution","volume":"18","author":"Du","year":"2008","journal-title":"Genome Res"},{"key":"2023020205492056200_btx062-B6","doi-asserted-by":"crossref","first-page":"9033","DOI":"10.1073\/pnas.0402591101","article-title":"Coevolution of gene expression among interacting proteins","volume":"101","author":"Fraser","year":"2004","journal-title":"Proc. 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