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The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.
Katayama T, Wilkinson MD, Micklem G, Kawashima S, Yamaguchi A, Nakao M, Yamamoto Y, Okamoto S, Oouchida K, Chun HW, Aerts J, Afzal H, Antezana E, Arakawa K, Aranda B, Belleau F, Bolleman J, Bonnal RJ, Chapman B, Cock PJ, Eriksson T, Gordon PM, Goto N, Hayashi K, Horn H, Ishiwata R, Kaminuma E, Kasprzyk A, Kawaji H, Kido N, Kim YJ, Kinjo AR, Konishi F, Kwon KH, Labarga A, Lamprecht AL, Lin Y, Lindenbaum P, McCarthy L, Morita H, Murakami K, Nagao K, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Ono K, Oshita K, Park KJ, Prins P, Saito TL, Samwald M, Satagopam VP, Shigemoto Y, Smith R, Splendiani A, Sugawara H, Taylor J, Vos RA, Withers D, Yamasaki C, Zmasek CM, Kawamoto S, Okubo K, Asai K, Takagi T. Katayama T, et al. Among authors: withers d. J Biomed Semantics. 2013 Feb 11;4(1):6. doi: 10.1186/2041-1480-4-6. J Biomed Semantics. 2013. PMID: 23398680 Free PMC article.
SADI, SHARE, and the in silico scientific method.
Wilkinson MD, McCarthy L, Vandervalk B, Withers D, Kawas E, Samadian S. Wilkinson MD, et al. Among authors: withers d. BMC Bioinformatics. 2010 Dec 21;11 Suppl 12(Suppl 12):S7. doi: 10.1186/1471-2105-11-S12-S7. BMC Bioinformatics. 2010. PMID: 21210986 Free PMC article.
Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data.
Li P, Castrillo JI, Velarde G, Wassink I, Soiland-Reyes S, Owen S, Withers D, Oinn T, Pocock MR, Goble CA, Oliver SG, Kell DB. Li P, et al. Among authors: withers d. BMC Bioinformatics. 2008 Aug 7;9:334. doi: 10.1186/1471-2105-9-334. BMC Bioinformatics. 2008. PMID: 18687127 Free PMC article.
The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud.
Wolstencroft K, Haines R, Fellows D, Williams A, Withers D, Owen S, Soiland-Reyes S, Dunlop I, Nenadic A, Fisher P, Bhagat J, Belhajjame K, Bacall F, Hardisty A, Nieva de la Hidalga A, Balcazar Vargas MP, Sufi S, Goble C. Wolstencroft K, et al. Among authors: withers d. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W557-61. doi: 10.1093/nar/gkt328. Epub 2013 May 2. Nucleic Acids Res. 2013. PMID: 23640334 Free PMC article.
Author Correction: mTOR regulates MAPKAPK2 translation to control the senescence-associated secretory phenotype.
Herranz N, Gallage S, Mellone M, Wuestefeld T, Klotz S, Hanley CJ, Raguz S, Acosta JC, Innes AJ, Banito A, Georgilis A, Montoya A, Wolter K, Dharmalingam G, Faull P, Carroll T, Martínez-Barbera JP, Cutillas P, Reisinger F, Heikenwalder M, Miller RA, Withers D, Zender L, Thomas GJ, Gil J. Herranz N, et al. Among authors: withers d. Nat Cell Biol. 2024 May 22. doi: 10.1038/s41556-024-01443-6. Online ahead of print. Nat Cell Biol. 2024. PMID: 38778130 No abstract available.
Protein restriction during pregnancy alters Cdkn1c silencing, dopamine circuitry and offspring behaviour without changing expression of key neuronal marker genes.
Prodani C, Irvine EE, Sardini A, Gleneadie HJ, Dimond A, Van de Pette M, John R, Kokkinou M, Howes O, Withers DJ, Ungless MA, Merkenschlager M, Fisher AG. Prodani C, et al. Among authors: withers dj. Sci Rep. 2024 Apr 12;14(1):8528. doi: 10.1038/s41598-024-59083-7. Sci Rep. 2024. PMID: 38609446 Free PMC article.
Correction: Sub-Chronic Ketamine Administration Increases Dopamine Synthesis Capacity in the Mouse Midbrain: a Preclinical In Vivo PET Study.
Petty A, Garcia-Hidalgo A, Halff EF, Natesan S, Withers DJ, Irvine EE, Kokkinou M, Wells LA, Bonsall DR, Tang SP, Veronese M, Howes OD. Petty A, et al. Among authors: withers dj. Mol Imaging Biol. 2024 Apr 3. doi: 10.1007/s11307-024-01916-y. Online ahead of print. Mol Imaging Biol. 2024. PMID: 38570447 No abstract available.
Differential CpG methylation at Nnat in the early establishment of beta cell heterogeneity.
Yu V, Yong F, Marta A, Khadayate S, Osakwe A, Bhattacharya S, Varghese SS, Chabosseau P, Tabibi SM, Chen K, Georgiadou E, Parveen N, Suleiman M, Stamoulis Z, Marselli L, De Luca C, Tesi M, Ostinelli G, Delgadillo-Silva L, Wu X, Hatanaka Y, Montoya A, Elliott J, Patel B, Demchenko N, Whilding C, Hajkova P, Shliaha P, Kramer H, Ali Y, Marchetti P, Sladek R, Dhawan S, Withers DJ, Rutter GA, Millership SJ. Yu V, et al. Among authors: withers dj. Diabetologia. 2024 Jun;67(6):1079-1094. doi: 10.1007/s00125-024-06123-6. Epub 2024 Mar 21. Diabetologia. 2024. PMID: 38512414 Free PMC article.
Detection of senescence using machine learning algorithms based on nuclear features.
Duran I, Pombo J, Sun B, Gallage S, Kudo H, McHugh D, Bousset L, Barragan Avila JE, Forlano R, Manousou P, Heikenwalder M, Withers DJ, Vernia S, Goldin RD, Gil J. Duran I, et al. Among authors: withers dj. Nat Commun. 2024 Feb 3;15(1):1041. doi: 10.1038/s41467-024-45421-w. Nat Commun. 2024. PMID: 38310113 Free PMC article.
286 results