Gifford DK - Search Results

1

Visualizing complex feature interactions and feature sharing in genomic deep neural networks.

Liu G, Zeng H, Gifford DK. Liu G, et al. Among authors: gifford dk. BMC Bioinformatics. 2019 Jul 19;20(1):401. doi: 10.1186/s12859-019-2957-4. BMC Bioinformatics. 2019. PMID: 31324140 Free PMC article.

2

An improved map of conserved regulatory sites for Saccharomyces cerevisiae.

MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, Fraenkel E. MacIsaac KD, et al. Among authors: gifford dk. BMC Bioinformatics. 2006 Mar 7;7:113. doi: 10.1186/1471-2105-7-113. BMC Bioinformatics. 2006. PMID: 16522208 Free PMC article.

3

ReadDB provides efficient storage for mapped short reads.

Rolfe PA, Gifford DK. Rolfe PA, et al. Among authors: gifford dk. BMC Bioinformatics. 2011 Jul 7;12:278. doi: 10.1186/1471-2105-12-278. BMC Bioinformatics. 2011. PMID: 21736741 Free PMC article.

4

High-resolution genetic mapping with pooled sequencing.

Edwards MD, Gifford DK. Edwards MD, et al. Among authors: gifford dk. BMC Bioinformatics. 2012 Apr 19;13 Suppl 6(Suppl 6):S8. doi: 10.1186/1471-2105-13-S6-S8. BMC Bioinformatics. 2012. PMID: 22537047 Free PMC article.

5

GERV: a statistical method for generative evaluation of regulatory variants for transcription factor binding.

Zeng H, Hashimoto T, Kang DD, Gifford DK. Zeng H, et al. Among authors: gifford dk. Bioinformatics. 2016 Feb 15;32(4):490-6. doi: 10.1093/bioinformatics/btv565. Epub 2015 Oct 17. Bioinformatics. 2016. PMID: 26476779 Free PMC article.

6

Convolutional neural network architectures for predicting DNA-protein binding.

Zeng H, Edwards MD, Liu G, Gifford DK. Zeng H, et al. Among authors: gifford dk. Bioinformatics. 2016 Jun 15;32(12):i121-i127. doi: 10.1093/bioinformatics/btw255. Bioinformatics. 2016. PMID: 27307608 Free PMC article.

7

A synergistic DNA logic predicts genome-wide chromatin accessibility.

Hashimoto T, Sherwood RI, Kang DD, Rajagopal N, Barkal AA, Zeng H, Emons BJ, Srinivasan S, Jaakkola T, Gifford DK. Hashimoto T, et al. Among authors: gifford dk. Genome Res. 2016 Oct;26(10):1430-1440. doi: 10.1101/gr.199778.115. Epub 2016 Jul 25. Genome Res. 2016. PMID: 27456004 Free PMC article.

8

Predicting gene expression in massively parallel reporter assays: A comparative study.

Kreimer A, Zeng H, Edwards MD, Guo Y, Tian K, Shin S, Welch R, Wainberg M, Mohan R, Sinnott-Armstrong NA, Li Y, Eraslan G, Amin TB, Tewhey R, Sabeti PC, Goke J, Mueller NS, Kellis M, Kundaje A, Beer MA, Keles S, Gifford DK, Yosef N. Kreimer A, et al. Among authors: gifford dk. Hum Mutat. 2017 Sep;38(9):1240-1250. doi: 10.1002/humu.23197. Epub 2017 Mar 9. Hum Mutat. 2017. PMID: 28220625 Free PMC article.

9

Accurate eQTL prioritization with an ensemble-based framework.

Zeng H, Edwards MD, Guo Y, Gifford DK. Zeng H, et al. Among authors: gifford dk. Hum Mutat. 2017 Sep;38(9):1259-1265. doi: 10.1002/humu.23198. Epub 2017 Apr 19. Hum Mutat. 2017. PMID: 28224684 Free PMC article.

10

Predicting the impact of non-coding variants on DNA methylation.

Zeng H, Gifford DK. Zeng H, et al. Among authors: gifford dk. Nucleic Acids Res. 2017 Jun 20;45(11):e99. doi: 10.1093/nar/gkx177. Nucleic Acids Res. 2017. PMID: 28334830 Free PMC article.

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