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Items: 12

1.

Computational methods for analyzing and modeling genome structure and organization.

Lin D, Bonora G, Yardımcı GG, Noble WS.

Wiley Interdiscip Rev Syst Biol Med. 2018 Jul 18:e1435. doi: 10.1002/wsbm.1435. [Epub ahead of print] Review.

PMID:
30022617
2.

Unsupervised embedding of single-cell Hi-C data.

Liu J, Lin D, Yardimci GG, Noble WS.

Bioinformatics. 2018 Jul 1;34(13):i96-i104. doi: 10.1093/bioinformatics/bty285.

3.

GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs.

Ursu O, Boley N, Taranova M, Wang YXR, Yardimci GG, Stafford Noble W, Kundaje A.

Bioinformatics. 2018 Aug 15;34(16):2701-2707. doi: 10.1093/bioinformatics/bty164.

PMID:
29554289
4.

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient.

Yang T, Zhang F, Yardımcı GG, Song F, Hardison RC, Noble WS, Yue F, Li Q.

Genome Res. 2017 Nov;27(11):1939-1949. doi: 10.1101/gr.220640.117. Epub 2017 Aug 30.

5.

HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps.

Yan KK, Yardimci GG, Yan C, Noble WS, Gerstein M.

Bioinformatics. 2017 Jul 15;33(14):2199-2201. doi: 10.1093/bioinformatics/btx152.

6.

Software tools for visualizing Hi-C data.

Yardımcı GG, Noble WS.

Genome Biol. 2017 Feb 3;18(1):26. doi: 10.1186/s13059-017-1161-y. Review.

7.

Predictive model of 3D domain formation via CTCF-mediated extrusion.

Yardımcı GG, Noble WS.

Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):14404-5. doi: 10.1073/pnas.1519849112. Epub 2015 Nov 13. No abstract available.

8.

Transcriptional control of tissue formation throughout root development.

Moreno-Risueno MA, Sozzani R, Yardımcı GG, Petricka JJ, Vernoux T, Blilou I, Alonso J, Winter CM, Ohler U, Scheres B, Benfey PN.

Science. 2015 Oct 23;350(6259):426-30. doi: 10.1126/science.aad1171.

9.

Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection.

Yardımcı GG, Frank CL, Crawford GE, Ohler U.

Nucleic Acids Res. 2014 Oct 29;42(19):11865-78. doi: 10.1093/nar/gku810. Epub 2014 Oct 7.

10.

Statistical evaluation of the Rodin-Ohno hypothesis: sense/antisense coding of ancestral class I and II aminoacyl-tRNA synthetases.

Chandrasekaran SN, Yardimci GG, Erdogan O, Roach J, Carter CW Jr.

Mol Biol Evol. 2013 Jul;30(7):1588-604. doi: 10.1093/molbev/mst070. Epub 2013 Apr 10.

11.

Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity.

Tewari AK, Yardimci GG, Shibata Y, Sheffield NC, Song L, Taylor BS, Georgiev SG, Coetzee GA, Ohler U, Furey TS, Crawford GE, Febbo PG.

Genome Biol. 2012 Oct 3;13(10):R88. doi: 10.1186/gb-2012-13-10-r88.

12.

Predicting cell-type-specific gene expression from regions of open chromatin.

Natarajan A, Yardimci GG, Sheffield NC, Crawford GE, Ohler U.

Genome Res. 2012 Sep;22(9):1711-22. doi: 10.1101/gr.135129.111.

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