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Items: 1 to 20 of 60


High-throughput mapping of regulatory DNA.

Rajagopal N, Srinivasan S, Kooshesh K, Guo Y, Edwards MD, Banerjee B, Syed T, Emons BJ, Gifford DK, Sherwood RI.

Nat Biotechnol. 2016 Feb;34(2):167-74. doi: 10.1038/nbt.3468. Epub 2016 Jan 25.


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

Zeng H, Hashimoto T, Kang DD, Gifford DK.

Bioinformatics. 2016 Feb 15;32(4):490-6. doi: 10.1093/bioinformatics/btv565. Epub 2015 Oct 17.


Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons.

Lodato S, Molyneaux BJ, Zuccaro E, Goff LA, Chen HH, Yuan W, Meleski A, Takahashi E, Mahony S, Rinn JL, Gifford DK, Arlotta P.

Nat Neurosci. 2014 Aug;17(8):1046-54. doi: 10.1038/nn.3757. Epub 2014 Jul 6.


Interactions between chromosomal and nonchromosomal elements reveal missing heritability.

Edwards MD, Symbor-Nagrabska A, Dollard L, Gifford DK, Fink GR.

Proc Natl Acad Sci U S A. 2014 May 27;111(21):7719-22. doi: 10.1073/pnas.1407126111. Epub 2014 May 13.


An integrated model of multiple-condition ChIP-Seq data reveals predeterminants of Cdx2 binding.

Mahony S, Edwards MD, Mazzoni EO, Sherwood RI, Kakumanu A, Morrison CA, Wichterle H, Gifford DK.

PLoS Comput Biol. 2014 Mar 27;10(3):e1003501. doi: 10.1371/journal.pcbi.1003501. eCollection 2014 Mar.


Universal count correction for high-throughput sequencing.

Hashimoto TB, Edwards MD, Gifford DK.

PLoS Comput Biol. 2014 Mar 6;10(3):e1003494. doi: 10.1371/journal.pcbi.1003494. eCollection 2014 Mar.


MARIS: method for analyzing RNA following intracellular sorting.

Hrvatin S, Deng F, O'Donnell CW, Gifford DK, Melton DA.

PLoS One. 2014 Mar 3;9(3):e89459. doi: 10.1371/journal.pone.0089459. eCollection 2014.


Differentiated human stem cells resemble fetal, not adult, ╬▓ cells.

Hrvatin S, O'Donnell CW, Deng F, Millman JR, Pagliuca FW, DiIorio P, Rezania A, Gifford DK, Melton DA.

Proc Natl Acad Sci U S A. 2014 Feb 25;111(8):3038-43. doi: 10.1073/pnas.1400709111. Epub 2014 Feb 10.


Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape.

Sherwood RI, Hashimoto T, O'Donnell CW, Lewis S, Barkal AA, van Hoff JP, Karun V, Jaakkola T, Gifford DK.

Nat Biotechnol. 2014 Feb;32(2):171-8. doi: 10.1038/nbt.2798. Epub 2014 Jan 19.


Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals.

Mazzoni EO, Mahony S, Peljto M, Patel T, Thornton SR, McCuine S, Reeder C, Boyer LA, Young RA, Gifford DK, Wichterle H.

Nat Neurosci. 2013 Sep;16(9):1191-8. doi: 10.1038/nn.3490. Epub 2013 Aug 18.


Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity.

Mazzoni EO, Mahony S, Closser M, Morrison CA, Nedelec S, Williams DJ, An D, Gifford DK, Wichterle H.

Nat Neurosci. 2013 Sep;16(9):1219-27. doi: 10.1038/nn.3467. Epub 2013 Jul 21.


A multi-parametric flow cytometric assay to analyze DNA-protein interactions.

Arbab M, Mahony S, Cho H, Chick JM, Rolfe PA, van Hoff JP, Morris VW, Gygi SP, Maas RL, Gifford DK, Sherwood RI.

Nucleic Acids Res. 2013 Jan;41(2):e38. doi: 10.1093/nar/gks1034. Epub 2012 Nov 11.


Global gene deletion analysis exploring yeast filamentous growth.

Ryan O, Shapiro RS, Kurat CF, Mayhew D, Baryshnikova A, Chin B, Lin ZY, Cox MJ, Vizeacoumar F, Cheung D, Bahr S, Tsui K, Tebbji F, Sellam A, Istel F, Schwarzm├╝ller T, Reynolds TB, Kuchler K, Gifford DK, Whiteway M, Giaever G, Nislow C, Costanzo M, Gingras AC, Mitra RD, Andrews B, Fink GR, Cowen LE, Boone C.

Science. 2012 Sep 14;337(6100):1353-6. doi: 10.1126/science.1224339.


Ruler arrays reveal haploid genomic structural variation.

Rolfe PA, Bernstein DA, Grisafi P, Fink GR, Gifford DK.

PLoS One. 2012;7(8):e43210. doi: 10.1371/journal.pone.0043210. Epub 2012 Aug 27.


High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints.

Guo Y, Mahony S, Gifford DK.

PLoS Comput Biol. 2012;8(8):e1002638. doi: 10.1371/journal.pcbi.1002638. Epub 2012 Aug 9.


High-resolution genetic mapping with pooled sequencing.

Edwards MD, Gifford DK.

BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S8. doi: 10.1186/1471-2105-13-S6-S8.


Embryonic stem cell-based mapping of developmental transcriptional programs.

Mazzoni EO, Mahony S, Iacovino M, Morrison CA, Mountoufaris G, Closser M, Whyte WA, Young RA, Kyba M, Gifford DK, Wichterle H.

Nat Methods. 2011 Nov 13;8(12):1056-8. doi: 10.1038/nmeth.1775.


ReadDB provides efficient storage for mapped short reads.

Rolfe PA, Gifford DK.

BMC Bioinformatics. 2011 Jul 7;12:278. doi: 10.1186/1471-2105-12-278.


Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis.

Mahony S, Mazzoni EO, McCuine S, Young RA, Wichterle H, Gifford DK.

Genome Biol. 2011;12(1):R2. doi: 10.1186/gb-2011-12-1-r2. Epub 2011 Jan 13.


Control of transcription by cell size.

Wu CY, Rolfe PA, Gifford DK, Fink GR.

PLoS Biol. 2010 Nov 2;8(11):e1000523. doi: 10.1371/journal.pbio.1000523.

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