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Items: 9

1.

A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types.

Libbrecht MW, Rodriguez OL, Weng Z, Bilmes JA, Hoffman MM, Noble WS.

Genome Biol. 2019 Aug 28;20(1):180. doi: 10.1186/s13059-019-1784-2.

2.

PREDICTD PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition.

Durham TJ, Libbrecht MW, Howbert JJ, Bilmes J, Noble WS.

Nat Commun. 2018 Apr 11;9(1):1402. doi: 10.1038/s41467-018-03635-9.

3.

Choosing non-redundant representative subsets of protein sequence data sets using submodular optimization.

Libbrecht MW, Bilmes JA, Noble WS.

Proteins. 2018 Apr;86(4):454-466. doi: 10.1002/prot.25461. Epub 2018 Feb 1.

4.

Segway 2.0: Gaussian mixture models and minibatch training.

Chan RCW, Libbrecht MW, Roberts EG, Bilmes JA, Noble WS, Hoffman MM.

Bioinformatics. 2018 Feb 15;34(4):669-671. doi: 10.1093/bioinformatics/btx603.

5.

Choosing panels of genomics assays using submodular optimization.

Wei K, Libbrecht MW, Bilmes JA, Noble WS.

Genome Biol. 2016 Nov 15;17(1):229.

6.

Distinct epigenetic features of differentiation-regulated replication origins.

Smith OK, Kim R, Fu H, Martin MM, Lin CM, Utani K, Zhang Y, Marks AB, Lalande M, Chamberlain S, Libbrecht MW, Bouhassira EE, Ryan MC, Noble WS, Aladjem MI.

Epigenetics Chromatin. 2016 May 10;9:18. doi: 10.1186/s13072-016-0067-3. eCollection 2016.

7.

Machine learning applications in genetics and genomics.

Libbrecht MW, Noble WS.

Nat Rev Genet. 2015 Jun;16(6):321-32. doi: 10.1038/nrg3920. Epub 2015 May 7. Review.

8.

Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression.

Libbrecht MW, Ay F, Hoffman MM, Gilbert DM, Bilmes JA, Noble WS.

Genome Res. 2015 Apr;25(4):544-57. doi: 10.1101/gr.184341.114. Epub 2015 Feb 12.

9.

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.

Nature. 2014 Aug 28;512(7515):449-52. doi: 10.1038/nature13415.

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