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Segway 2.0: Gaussian mixture models and minibatch training.
Chan RCW, Libbrecht MW, Roberts EG, Bilmes JA, Noble WS, Hoffman MM. Chan RCW, et al. Among authors: hoffman mm. Bioinformatics. 2018 Feb 15;34(4):669-671. doi: 10.1093/bioinformatics/btx603. Bioinformatics. 2018. PMID: 29028889 Free PMC article.
Exploratory analysis of genomic segmentations with Segtools.
Buske OJ, Hoffman MM, Ponts N, Le Roch KG, Noble WS. Buske OJ, et al. Among authors: hoffman mm. BMC Bioinformatics. 2011 Oct 26;12:415. doi: 10.1186/1471-2105-12-415. BMC Bioinformatics. 2011. PMID: 22029426 Free PMC article.
Integrative annotation of chromatin elements from ENCODE data.
Hoffman MM, Ernst J, Wilder SP, Kundaje A, Harris RS, Libbrecht M, Giardine B, Ellenbogen PM, Bilmes JA, Birney E, Hardison RC, Dunham I, Kellis M, Noble WS. Hoffman MM, et al. Nucleic Acids Res. 2013 Jan;41(2):827-41. doi: 10.1093/nar/gks1284. Epub 2012 Dec 5. Nucleic Acids Res. 2013. PMID: 23221638 Free PMC article.
Comparative analysis of metazoan chromatin organization.
Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RA, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SC, Liu XS, Lieb JD, Ahringer J, Karpen GH, Park PJ. Ho JW, et al. Among authors: hoffman mm. Nature. 2014 Aug 28;512(7515):449-52. doi: 10.1038/nature13415. Nature. 2014. PMID: 25164756 Free PMC article.
Umap and Bismap: quantifying genome and methylome mappability.
Karimzadeh M, Ernst C, Kundaje A, Hoffman MM. Karimzadeh M, et al. Among authors: hoffman mm. Nucleic Acids Res. 2018 Nov 16;46(20):e120. doi: 10.1093/nar/gky677. Nucleic Acids Res. 2018. PMID: 30169659 Free PMC article.
113 results