Bilmes JA - Search Results

1

ChromaFold predicts the 3D contact map from single-cell chromatin accessibility.

Gao VR, Yang R, Das A, Luo R, Luo H, McNally DR, Karagiannidis I, Rivas MA, Wang ZM, Barisic D, Karbalayghareh A, Wong W, Zhan YA, Chin CR, Noble WS, Bilmes JA, Apostolou E, Kharas MG, Béguelin W, Viny AD, Huangfu D, Rudensky AY, Melnick AM, Leslie CS. Gao VR, et al. Among authors: bilmes ja. Nat Commun. 2024 Nov 1;15(1):9432. doi: 10.1038/s41467-024-53628-0. Nat Commun. 2024. PMID: 39487131 Free PMC article.

2

Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification.

Klammer AA, Reynolds SM, Bilmes JA, MacCoss MJ, Noble WS. Klammer AA, et al. Among authors: bilmes ja. Bioinformatics. 2008 Jul 1;24(13):i348-56. doi: 10.1093/bioinformatics/btn189. Bioinformatics. 2008. PMID: 18586734 Free PMC article.

3

A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data.

Chen X, Hoffman MM, Bilmes JA, Hesselberth JR, Noble WS. Chen X, et al. Among authors: bilmes ja. Bioinformatics. 2010 Jun 15;26(12):i334-42. doi: 10.1093/bioinformatics/btq175. Bioinformatics. 2010. PMID: 20529925 Free PMC article.

4

Learning a weighted sequence model of the nucleosome core and linker yields more accurate predictions in Saccharomyces cerevisiae and Homo sapiens.

Reynolds SM, Bilmes JA, Noble WS. Reynolds SM, et al. Among authors: bilmes ja. PLoS Comput Biol. 2010 Jul 8;6(7):e1000834. doi: 10.1371/journal.pcbi.1000834. PLoS Comput Biol. 2010. PMID: 20628623 Free PMC article.

5

Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure.

Aydin Z, Singh A, Bilmes J, Noble WS. Aydin Z, et al. BMC Bioinformatics. 2011 May 13;12:154. doi: 10.1186/1471-2105-12-154. BMC Bioinformatics. 2011. PMID: 21569525 Free PMC article.

6

Unsupervised pattern discovery in human chromatin structure through genomic segmentation.

Hoffman MM, Buske OJ, Wang J, Weng Z, Bilmes JA, Noble WS. Hoffman MM, et al. Among authors: bilmes ja. Nat Methods. 2012 Mar 18;9(5):473-6. doi: 10.1038/nmeth.1937. Nat Methods. 2012. PMID: 22426492 Free PMC article.

7

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. Among authors: bilmes ja. 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.

8

Learning Peptide-Spectrum Alignment Models for Tandem Mass Spectrometry.

Halloran JT, Bilmes JA, Noble WS. Halloran JT, et al. Among authors: bilmes ja. Uncertain Artif Intell. 2014;30:320-329. Uncertain Artif Intell. 2014. PMID: 25298752 Free PMC article.

9

Spectrum Identification using a Dynamic Bayesian Network Model of Tandem Mass Spectra.

Singh AP, Halloran J, Bilmes JA, Kirchoff K, Noble WS. Singh AP, et al. Among authors: bilmes ja. Uncertain Artif Intell. 2012 Aug;28:775-785. Uncertain Artif Intell. 2012. PMID: 25383048 Free PMC article.

10

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. Libbrecht MW, et al. Among authors: bilmes ja. Genome Res. 2015 Apr;25(4):544-57. doi: 10.1101/gr.184341.114. Epub 2015 Feb 12. Genome Res. 2015. PMID: 25677182 Free PMC article.

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