{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,16]],"date-time":"2025-10-16T13:52:44Z","timestamp":1760622764592},"reference-count":43,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2010,4,13]],"date-time":"2010-04-13T00:00:00Z","timestamp":1271116800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2010,12]]},"DOI":"10.1186\/1752-0509-4-44","type":"journal-article","created":{"date-parts":[[2010,4,13]],"date-time":"2010-04-13T18:13:55Z","timestamp":1271182435000},"source":"Crossref","is-referenced-by-count":19,"title":["The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression"],"prefix":"10.1186","volume":"4","author":[{"given":"Nurul","family":"Mohamad","sequence":"first","affiliation":[]},{"given":"Mikael","family":"Bod\u00e9n","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2010,4,13]]},"reference":[{"issue":"3","key":"433_CR1","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1016\/j.molcel.2006.09.013","volume":"24","author":"TH Shen","year":"2006","unstructured":"Shen TH, Lin HK, Scaglioni PP, Yung TM, Pandolfi PP: The Mechanisms of PML-Nuclear Body Formation. Molecular Cell. 2006, 24 (3): 331-339. 10.1016\/j.molcel.2006.09.013","journal-title":"Molecular Cell"},{"issue":"11","key":"433_CR2","doi-asserted-by":"publisher","first-page":"2185","DOI":"10.1016\/j.bbamcr.2008.07.002","volume":"1783","author":"E Krieghoff-Henning","year":"2008","unstructured":"Krieghoff-Henning E, Hofmann TG: Role of nuclear bodies in apoptosis signalling. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. 2008, 1783 (11): 2185-2194. 10.1016\/j.bbamcr.2008.07.002. [Functional Architecture of the Cell Nucleus],","journal-title":"Biochimica et Biophysica Acta (BBA) - Molecular Cell Research"},{"issue":"7","key":"433_CR3","doi-asserted-by":"publisher","first-page":"665","DOI":"10.1038\/ncb1147","volume":"6","author":"R Bernardi","year":"2004","unstructured":"Bernardi R, Scaglioni PP, Bergmann S, Horn HF, Vousden KH, Pandolfi PP: PML regulates p53 stability by sequestering Mdm2 to the nucleolus. Nat Cell Biol. 2004, 6 (7): 665-672. 10.1038\/ncb1147","journal-title":"Nat Cell Biol"},{"issue":"5855","key":"433_CR4","doi-asserted-by":"publisher","first-page":"1412","DOI":"10.1126\/science.1142204","volume":"318","author":"LJ Terry","year":"2007","unstructured":"Terry LJ, Shows EB, Wente SR: Crossing the Nuclear Envelope: Hierarchical Regulation of Nucleocytoplasmic Transport. Science. 2007, 318 (5855): 1412-1416. 10.1126\/science.1142204","journal-title":"Science"},{"issue":"12","key":"433_CR5","doi-asserted-by":"publisher","first-page":"4247","DOI":"10.1128\/MCB.23.12.4247-4256.2003","volume":"23","author":"ZX Xu","year":"2003","unstructured":"Xu ZX, Timanova-Atanasova A, Zhao RX, Chang KS: PML colocalizes with and stabilizes the DNA damage response protein TopBP1. Mol Cell Biol. 2003, 23 (12): 4247-4256. 10.1128\/MCB.23.12.4247-4256.2003","journal-title":"Mol Cell Biol"},{"issue":"5","key":"433_CR6","doi-asserted-by":"publisher","first-page":"e1","DOI":"10.1016\/j.cell.2006.11.026","volume":"127","author":"DL Spector","year":"2006","unstructured":"Spector DL: SnapShot: Cellular Bodies. Cell. 2006, 127 (5): e1-1071.e2. 10.1016\/j.cell.2006.11.026.","journal-title":"Cell"},{"key":"433_CR7","doi-asserted-by":"publisher","first-page":"328","DOI":"10.1093\/nar\/gkg018","volume":"31","author":"G Dellaire","year":"2003","unstructured":"Dellaire G, Farrall R, Bickmore W: The Nuclear Protein Database (NPD): sub-nuclear localisation and functional annotation of the nuclear proteome. Nucl Acids Res. 2003, 31: 328-330. 10.1093\/nar\/gkg018","journal-title":"Nucl Acids Res"},{"key":"433_CR8","doi-asserted-by":"publisher","first-page":"D190","DOI":"10.1093\/nar\/gkm895","volume":"36","author":"U Consortium","year":"2008","unstructured":"Consortium U:: The universal protein resource (UniProt). Nucleic Acids Res. 2008, D190-D195. 36 Database,","journal-title":"Nucl Acids Res"},{"key":"433_CR9","doi-asserted-by":"publisher","first-page":"D411","DOI":"10.1093\/nar\/gkj141","volume":"34","author":"GR Mishra","year":"2006","unstructured":"Mishra GR, Suresh M, Kumaran K, Kannabiran N, Suresh S, Bala P, Shivakumar K, Anuradha N, Reddy R, Raghavan TM, Menon S, Hanumanthu G, Gupta M, Upendran S, Gupta S, Mahesh M, Jacob B, Mathew P, Chatterjee P, Arun KS, Sharma S, Chandrika KN, Deshpande N, Palvankar K, Raghavnath R, Krishnakanth R, Karathia H, Rekha B, Nayak R, Vishnupriya G, Kumar HGM, Nagini M, Kumar GSS, Jose R, Deepthi P, Mohan SS, Gandhi TKB, Harsha HC, Deshpande KS, Sarker M, Prasad TSK, Pandey A: Human protein reference database-2006 update. Nucleic Acids Res. 2006, D411-D414. 34 Database,","journal-title":"Nucleic Acids Res."},{"key":"433_CR10","doi-asserted-by":"publisher","first-page":"D213","DOI":"10.1093\/nar\/gkj069","volume":"34","author":"JL Fink","year":"2006","unstructured":"Fink JL, Aturaliya RN, Davis MJ, Zhang F, Hanson K, Teasdale MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, Teasdale RD: LOCATE: a mouse protein subcellular localization database. Nucleic Acids Res. 2006, D213-D217. 34 Database,","journal-title":"Nucleic Acids Res."},{"issue":"3","key":"433_CR11","doi-asserted-by":"publisher","first-page":"521","DOI":"10.1016\/0955-0674(90)90137-4","volume":"2","author":"J Warner","year":"1990","unstructured":"Warner J: The nucleolus and ribosome formation. Current Opinion in Cell Biology. 1990, 2 (3): 521-527. 10.1016\/0955-0674(90)90137-4","journal-title":"Current Opinion in Cell Biology"},{"issue":"7","key":"433_CR12","doi-asserted-by":"publisher","first-page":"574","DOI":"10.1038\/nrm2184","volume":"8","author":"FM Boisvert","year":"2007","unstructured":"Boisvert FM, van Koningsbruggen S, Navascues J, Lamond AI: The multifunctional nucleolus. Nat Rev Mol Cell Biol. 2007, 8 (7): 574-585. 10.1038\/nrm2184","journal-title":"Nat Rev Mol Cell Biol"},{"issue":"9","key":"433_CR13","doi-asserted-by":"publisher","first-page":"963","DOI":"10.1002\/bies.20089","volume":"26","author":"G Dellaire","year":"2004","unstructured":"Dellaire G, Bazett-Jones DP: PML nuclear bodies: dynamic sensors of DNA damage and cellular stress. BioEssays. 2004, 26 (9): 963-977. 10.1002\/bies.20089","journal-title":"BioEssays"},{"issue":"12","key":"433_CR14","doi-asserted-by":"publisher","first-page":"1006","DOI":"10.1038\/nrm2277","volume":"8","author":"R Bernardi","year":"2007","unstructured":"Bernardi R, Pandolfi PP: Structure, dynamics and functions of promyelocytic leukaemia nuclear bodies. Nat Rev Mol Cell Biol. 2007, 8 (12): 1006-1016. 10.1038\/nrm2277","journal-title":"Nat Rev Mol Cell Biol"},{"issue":"8","key":"433_CR15","doi-asserted-by":"publisher","first-page":"605","DOI":"10.1038\/nrm1172","volume":"4","author":"AI Lamond","year":"2003","unstructured":"Lamond AI, Spector DL: Nuclear speckles: a model for nuclear organelles. Nat Rev Mol Cell Biol. 2003, 4 (8): 605-612. 10.1038\/nrm1172","journal-title":"Nat Rev Mol Cell Biol"},{"key":"433_CR16","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1146\/annurev.cellbio.20.010403.103738","volume":"21","author":"M Cioce","year":"2005","unstructured":"Cioce M, Lamond AI: Cajal Bodies: A Long History of Discovery. Annual Review of Cell and Developmental Biology. 2005, 21: 105-131. 10.1146\/annurev.cellbio.20.010403.103738","journal-title":"Annual Review of Cell and Developmental Biology"},{"key":"433_CR17","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1146\/annurev.cellbio.16.1.273","volume":"16","author":"JG Gall","year":"2000","unstructured":"Gall JG: CAJAL BODIES: The First 100 Years. Annu Rev Cell Dev Biol. 2000, 16: 273- 10.1146\/annurev.cellbio.16.1.273","journal-title":"Annu Rev Cell Dev Biol"},{"issue":"8","key":"433_CR18","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1016\/S0962-8924(99)01606-2","volume":"9","author":"AG Matera","year":"1999","unstructured":"Matera AG: Nuclear bodies: multifaceted subdomains of the interchromatin space. Trends in Cell Biology. 1999, 9 (8): 302-309. 10.1016\/S0962-8924(99)01606-2","journal-title":"Trends in Cell Biology"},{"key":"433_CR19","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1091\/mbc.E03-07-0525","volume":"15","author":"Y Zhu","year":"2004","unstructured":"Zhu Y, Tomlinson RL, Lukowiak AA, Terns RM, Terns MP: Telomerase RNA Accumulates in Cajal Bodies in Human Cancer Cells. Mol Biol Cell. 2004, 15: 81-90. 10.1091\/mbc.E03-07-0525","journal-title":"Mol Biol Cell"},{"key":"433_CR20","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1093\/nar\/gkg001","volume":"31","author":"R Nair","year":"2003","unstructured":"Nair R, Carter P, Rost B: NLSdb: database of nuclear localization signals. Nucl Acids Res. 2003, 31: 397-399. 10.1093\/nar\/gkg001","journal-title":"Nucl Acids Res"},{"key":"433_CR21","doi-asserted-by":"publisher","first-page":"1248","DOI":"10.1093\/emboj\/21.6.1248","volume":"21","author":"W Bickmore","year":"2002","unstructured":"Bickmore W, Sutherland H: NEW EMBO MEMBER'S REVIEW: Addressing protein localization within the nucleus. EMBO J. 2002, 21: 1248-1254. 10.1093\/emboj\/21.6.1248","journal-title":"EMBO J"},{"issue":"3","key":"433_CR22","doi-asserted-by":"publisher","first-page":"350","DOI":"10.1016\/j.ceb.2007.04.014","volume":"19","author":"P Heun","year":"2007","unstructured":"Heun P: SUMOrganization of the nucleus. Current Opinion in Cell Biology. 2007, 19 (3): 350-355. 10.1016\/j.ceb.2007.04.014","journal-title":"Current Opinion in Cell Biology"},{"key":"433_CR23","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1186\/1471-2105-6-291","volume":"6","author":"Z Lei","year":"2005","unstructured":"Lei Z, Dai Y: An SVM-based system for predicting protein subnuclear localizations. BMC Bioinformatics. 2005, 6: 291- 10.1186\/1471-2105-6-291","journal-title":"BMC Bioinformatics"},{"issue":"11","key":"433_CR24","doi-asserted-by":"publisher","first-page":"1682","DOI":"10.1093\/bioinformatics\/bth141","volume":"20","author":"H Saigo","year":"2004","unstructured":"Saigo H, Vert JP, Ueda N, Akutsu T: Protein homology detection using string alignment kernels. Bioinformatics. 2004, 20 (11): 1682-1689. 10.1093\/bioinformatics\/bth141","journal-title":"Bioinformatics"},{"issue":"3","key":"433_CR25","doi-asserted-by":"publisher","first-page":"410","DOI":"10.1016\/j.jsb.2006.12.008","volume":"158","author":"MT Berciano","year":"2007","unstructured":"Berciano MT, Novell M, Villagra NT, Casafont I, Bengoechea R, Val-Bernal JF, Lafarga M: Cajal body number and nucleolar size correlate with the cell body mass in human sensory ganglia neurons. Journal of Structural Biology. 2007, 158 (3): 410-420. 10.1016\/j.jsb.2006.12.008","journal-title":"Journal of Structural Biology"},{"issue":"Pt 5","key":"433_CR26","doi-asserted-by":"publisher","first-page":"847","DOI":"10.1242\/jcs.01700","volume":"118","author":"RW Ching","year":"2005","unstructured":"Ching RW, Dellaire G, Eskiw CH, Bazett-Jones DP: PML bodies: a meeting place for genomic loci?. J Cell Sci. 2005, 118 (Pt 5): 847-854. 10.1242\/jcs.01700","journal-title":"J Cell Sci"},{"issue":"3","key":"433_CR27","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1016\/j.ceb.2006.03.002","volume":"18","author":"SA Gorski","year":"2006","unstructured":"Gorski SA, Dundr M, Misteli T: The road much traveled: trafficking in the cell nucleus. Current Opinion in Cell Biology. 2006, 18 (3): 284-290. [Nucleus and gene expression], 10.1016\/j.ceb.2006.03.002","journal-title":"Current Opinion in Cell Biology"},{"key":"433_CR28","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1186\/1741-7007-4-39","volume":"4","author":"E de Silva","year":"2006","unstructured":"de Silva E, Thorne T, Ingram P, Agrafioti I, Swire J, Wiuf C, Stumpf MPH: The effects of incomplete protein interaction data on structural and evolutionary inferences. BMC Biol. 2006, 4: 39- 10.1186\/1741-7007-4-39","journal-title":"BMC Biol"},{"key":"433_CR29","doi-asserted-by":"crossref","unstructured":"Gauthier NP, Larsen ME, Wernersson R, de Lichtenberg U, Jensen LJ, Brunak S, Jensen TS: Cyclebase.org-a comprehensive multi-organism online database of cell-cycle experiments. Nucleic Acids Res. 2008, D854-D859. 36 Database,","DOI":"10.1093\/nar\/gkm729"},{"issue":"7","key":"433_CR30","doi-asserted-by":"publisher","first-page":"1164","DOI":"10.1093\/bioinformatics\/bti093","volume":"21","author":"U de Lichtenberg","year":"2005","unstructured":"de Lichtenberg U, Jensen LJ, Fausboll A, Jensen TS, Bork P, Brunak S: Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics. 2005, 21 (7): 1164-1171. 10.1093\/bioinformatics\/bti093","journal-title":"Bioinformatics"},{"issue":"21","key":"433_CR31","doi-asserted-by":"publisher","first-page":"7718","DOI":"10.1128\/MCB.00180-07","volume":"27","author":"S Kettner","year":"2007","unstructured":"Kettner S, Kalthoff F, Graf P, Priller E, Kricek F, Lindley I, Schweighoffer T: EWI-2\/CD316 Is an Inducible Receptor of HSPA8 on Human Dendritic Cells. Mol Cell Biol. 2007, 27 (21): 7718-7726. 10.1128\/MCB.00180-07","journal-title":"Mol Cell Biol"},{"issue":"23","key":"433_CR32","doi-asserted-by":"publisher","first-page":"13153","DOI":"10.1128\/JVI.78.23.13153-13162.2004","volume":"78","author":"KS Choi","year":"2004","unstructured":"Choi KS, Mizutani A, Lai MMC: SYNCRIP, a Member of the Heterogeneous Nuclear Ribonucleoprotein Family, Is Involved in Mouse Hepatitis Virus RNA Synthesis. J Virol. 2004, 78 (23): 13153-13162. 10.1128\/JVI.78.23.13153-13162.2004","journal-title":"J Virol"},{"issue":"11","key":"433_CR33","doi-asserted-by":"publisher","first-page":"2353","DOI":"10.1016\/j.biocel.2007.08.007","volume":"40","author":"AH Mangs","year":"2008","unstructured":"Mangs AH, Morris BJ: ZRANB2: Structural and functional insights into a novel splicing protein. The International Journal of Biochemistry & Cell Biology. 2008, 40 (11): 2353-2357. 10.1016\/j.biocel.2007.08.007","journal-title":"The International Journal of Biochemistry & Cell Biology"},{"issue":"5","key":"433_CR34","doi-asserted-by":"publisher","first-page":"E85","DOI":"10.1038\/35010583","volume":"2","author":"S Zhong","year":"2000","unstructured":"Zhong S, Salomoni P, Pandolfi PP: The transcriptional role of PML and the nuclear body. Nat Cell Biol. 2000, 2 (5): E85-E90. 10.1038\/35010583","journal-title":"Nat Cell Biol"},{"key":"433_CR35","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1038\/ncb1516","volume":"9","author":"PK P","year":"2007","unstructured":"P PK, Bischof O, Purbey PK, Notani D, Urlaub H, Dejean A, Galande S: Functional interaction between PML and SATB1 regulates chromatin-loop architecture and transcription of the MHC class I locus. Nat Cell Biol. 2007, 9: 45-56. 10.1038\/ncb1516","journal-title":"Nat Cell Biol"},{"issue":"21","key":"433_CR36","doi-asserted-by":"publisher","first-page":"16044","DOI":"10.1074\/jbc.275.21.16044","volume":"275","author":"P Karhumaa","year":"2000","unstructured":"Karhumaa P, Parkkila S, Waheed A, Parkkila AK, Kaunisto K, Tucker PW, Huang CJ, Sly WS, Rajaniemi H: Nuclear NonO\/p54nrb Protein Is a Nonclassical Carbonic Anhydrase. J Biol Chem. 2000, 275 (21): 16044-16049. 10.1074\/jbc.275.21.16044","journal-title":"J Biol Chem"},{"key":"433_CR37","doi-asserted-by":"publisher","first-page":"D218","DOI":"10.1093\/nar\/gkj004","volume":"34","author":"AKL Leung","year":"2006","unstructured":"Leung AKL, Trinkle-Mulcahy L, Lam YW, Andersen JS, Mann M, Lamond AI: NOPdb: Nucleolar Proteome Database. Nucleic Acids Res. 2006, D218-D220. 34 Database,","journal-title":"Nucleic Acids Res."},{"key":"433_CR38","doi-asserted-by":"publisher","first-page":"D724","DOI":"10.1093\/nar\/gkm961","volume":"36","author":"CJ Bult","year":"2008","unstructured":"Bult CJ, Eppig JT, Kadin JA, Richardson JE, Blake JA, Group MGD: The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Res. 2008, D724-D728. 36 Database,","journal-title":"Nucleic Acids Res."},{"key":"433_CR39","doi-asserted-by":"publisher","first-page":"R15","DOI":"10.1186\/gb-2008-9-1-r15","volume":"9","author":"JL Fink","year":"2008","unstructured":"Fink JL, Karunaratne S, Mittal A, Gardiner D, Hamilton N, Mahony D, Kai C, Suzuki H, Hayashizaki Y, Teasdale R: Towards defining the nuclear proteome. Genome Biology. 2008, 9: R15- 10.1186\/gb-2008-9-1-r15","journal-title":"Genome Biology"},{"key":"433_CR40","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/S0960-9822(01)00650-9","volume":"12","author":"JS Andersen","year":"2002","unstructured":"Andersen JS, Lyon CE, Fox AH, Leung AK, Lam YW, Steen H, Mann M, Lamond AI: Directed Proteomic Analysis of the Human Nucleolus. Current Biology. 2002, 12: 1-11. 10.1016\/S0960-9822(01)00650-9","journal-title":"Current Biology"},{"key":"433_CR41","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1016\/S0960-9822(01)00632-7","volume":"12","author":"AH Fox","year":"2002","unstructured":"Fox AH, Lam YW, Leung AK, Lyon CE, Andersen J, Mann M, Lamond AI: Paraspeckles: A Novel Nuclear Domain. Current Biology. 2002, 12: 13-25. 10.1016\/S0960-9822(01)00632-7","journal-title":"Current Biology"},{"issue":"5","key":"433_CR42","doi-asserted-by":"publisher","first-page":"915","DOI":"10.1083\/jcb.200206106","volume":"158","author":"JM Cronshaw","year":"2002","unstructured":"Cronshaw JM, Krutchinsky AN, Zhang W, Chait BT, Matunis MJ: Proteomic analysis of the mammalian nuclear pore complex. J Cell Biol. 2002, 158 (5): 915-927. 10.1083\/jcb.200206106","journal-title":"J Cell Biol"},{"key":"433_CR43","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1093\/bioinformatics\/btg431","volume":"20","author":"C Leslie","year":"2004","unstructured":"Leslie C, Eskin E, Cohen A, Weston J, Noble W: Mismatch string kernels for discriminative protein classification. Bioinformatics. 2004, 20: 467-476. 10.1093\/bioinformatics\/btg431","journal-title":"Bioinformatics"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-4-44.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1752-0509-4-44\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-4-44.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,28]],"date-time":"2019-05-28T07:38:54Z","timestamp":1559029134000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-4-44"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,4,13]]},"references-count":43,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2010,12]]}},"alternative-id":["433"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-4-44","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,4,13]]},"article-number":"44"}}