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Data management challenges in three-dimensional EM.
Patwardhan A, Carazo JM, Carragher B, Henderson R, Heymann JB, Hill E, Jensen GJ, Lagerstedt I, Lawson CL, Ludtke SJ, Mastronarde D, Moore WJ, Roseman A, Rosenthal P, Sorzano CO, Sanz-García E, Scheres SH, Subramaniam S, Westbrook J, Winn M, Swedlow JR, Kleywegt GJ. Patwardhan A, et al. Among authors: lagerstedt i. Nat Struct Mol Biol. 2012 Dec;19(12):1203-7. doi: 10.1038/nsmb.2426. Nat Struct Mol Biol. 2012. PMID: 23211764 Free PMC article.
A 3D cellular context for the macromolecular world.
Patwardhan A, Ashton A, Brandt R, Butcher S, Carzaniga R, Chiu W, Collinson L, Doux P, Duke E, Ellisman MH, Franken E, Grünewald K, Heriche JK, Koster A, Kühlbrandt W, Lagerstedt I, Larabell C, Lawson CL, Saibil HR, Sanz-García E, Subramaniam S, Verkade P, Swedlow JR, Kleywegt GJ. Patwardhan A, et al. Among authors: lagerstedt i. Nat Struct Mol Biol. 2014 Oct;21(10):841-5. doi: 10.1038/nsmb.2897. Nat Struct Mol Biol. 2014. PMID: 25289590 Free PMC article.
Web-based volume slicer for 3D electron-microscopy data from EMDB.
Salavert-Torres J, Iudin A, Lagerstedt I, Sanz-García E, Kleywegt GJ, Patwardhan A. Salavert-Torres J, et al. Among authors: lagerstedt i. J Struct Biol. 2016 May;194(2):164-70. doi: 10.1016/j.jsb.2016.02.012. Epub 2016 Feb 10. J Struct Biol. 2016. PMID: 26876163 Free PMC article.
OMERO: flexible, model-driven data management for experimental biology.
Allan C, Burel JM, Moore J, Blackburn C, Linkert M, Loynton S, Macdonald D, Moore WJ, Neves C, Patterson A, Porter M, Tarkowska A, Loranger B, Avondo J, Lagerstedt I, Lianas L, Leo S, Hands K, Hay RT, Patwardhan A, Best C, Kleywegt GJ, Zanetti G, Swedlow JR. Allan C, et al. Among authors: lagerstedt i. Nat Methods. 2012 Feb 28;9(3):245-53. doi: 10.1038/nmeth.1896. Nat Methods. 2012. PMID: 22373911 Free PMC article.
EMDataBank unified data resource for 3DEM.
Lawson CL, Patwardhan A, Baker ML, Hryc C, Garcia ES, Hudson BP, Lagerstedt I, Ludtke SJ, Pintilie G, Sala R, Westbrook JD, Berman HM, Kleywegt GJ, Chiu W. Lawson CL, et al. Among authors: lagerstedt i. Nucleic Acids Res. 2016 Jan 4;44(D1):D396-403. doi: 10.1093/nar/gkv1126. Epub 2015 Nov 17. Nucleic Acids Res. 2016. PMID: 26578576 Free PMC article.
EMDataBank.org: unified data resource for CryoEM.
Lawson CL, Baker ML, Best C, Bi C, Dougherty M, Feng P, van Ginkel G, Devkota B, Lagerstedt I, Ludtke SJ, Newman RH, Oldfield TJ, Rees I, Sahni G, Sala R, Velankar S, Warren J, Westbrook JD, Henrick K, Kleywegt GJ, Berman HM, Chiu W. Lawson CL, et al. Among authors: lagerstedt i. Nucleic Acids Res. 2011 Jan;39(Database issue):D456-64. doi: 10.1093/nar/gkq880. Epub 2010 Oct 8. Nucleic Acids Res. 2011. PMID: 20935055 Free PMC article.
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.
Velankar S, van Ginkel G, Alhroub Y, Battle GM, Berrisford JM, Conroy MJ, Dana JM, Gore SP, Gutmanas A, Haslam P, Hendrickx PM, Lagerstedt I, Mir S, Fernandez Montecelo MA, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Sanz-García E, Sen S, Slowley RA, Wainwright ME, Deshpande MS, Iudin A, Sahni G, Salavert Torres J, Hirshberg M, Mak L, Nadzirin N, Armstrong DR, Clark AR, Smart OS, Korir PK, Kleywegt GJ. Velankar S, et al. Among authors: lagerstedt i. Nucleic Acids Res. 2016 Jan 4;44(D1):D385-95. doi: 10.1093/nar/gkv1047. Epub 2015 Oct 17. Nucleic Acids Res. 2016. PMID: 26476444 Free PMC article.
PDBe: Protein Data Bank in Europe.
Gutmanas A, Alhroub Y, Battle GM, Berrisford JM, Bochet E, Conroy MJ, Dana JM, Fernandez Montecelo MA, van Ginkel G, Gore SP, Haslam P, Hatherley R, Hendrickx PM, Hirshberg M, Lagerstedt I, Mir S, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Rinaldi L, Sahni G, Sanz-García E, Sen S, Slowley RA, Velankar S, Wainwright ME, Kleywegt GJ. Gutmanas A, et al. Among authors: lagerstedt i. Nucleic Acids Res. 2014 Jan;42(Database issue):D285-91. doi: 10.1093/nar/gkt1180. Epub 2013 Nov 27. Nucleic Acids Res. 2014. PMID: 24288376 Free PMC article.
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