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DeepLigand: accurate prediction of MHC class I ligands using peptide embedding.

Zeng H, Gifford DK.

Bioinformatics. 2019 Jul 15;35(14):i278-i283. doi: 10.1093/bioinformatics/btz330.


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

Liu G, Zeng H, Gifford DK.

BMC Bioinformatics. 2019 Jul 19;20(1):401. doi: 10.1186/s12859-019-2957-4.


Quantification of Uncertainty in Peptide-MHC Binding Prediction Improves High-Affinity Peptide Selection for Therapeutic Design.

Zeng H, Gifford DK.

Cell Syst. 2019 Aug 28;9(2):159-166.e3. doi: 10.1016/j.cels.2019.05.004. Epub 2019 Jun 5.


Wnt Signaling Separates the Progenitor and Endocrine Compartments during Pancreas Development.

Sharon N, Vanderhooft J, Straubhaar J, Mueller J, Chawla R, Zhou Q, Engquist EN, Trapnell C, Gifford DK, Melton DA.

Cell Rep. 2019 May 21;27(8):2281-2291.e5. doi: 10.1016/j.celrep.2019.04.083.


High resolution discovery of chromatin interactions.

Guo Y, Krismer K, Closser M, Wichterle H, Gifford DK.

Nucleic Acids Res. 2019 Apr 8;47(6):e35. doi: 10.1093/nar/gkz051.


Author Correction: Predictable and precise template-free CRISPR editing of pathogenic variants.

Shen MW, Arbab M, Hsu JY, Worstell D, Culbertson SJ, Krabbe O, Cassa CA, Liu DR, Gifford DK, Sherwood RI.

Nature. 2019 Mar;567(7746):E1-E2. doi: 10.1038/s41586-019-0938-4.


A Peninsular Structure Coordinates Asynchronous Differentiation with Morphogenesis to Generate Pancreatic Islets.

Sharon N, Chawla R, Mueller J, Vanderhooft J, Whitehorn LJ, Rosenthal B, Gürtler M, Estanboulieh RR, Shvartsman D, Gifford DK, Trapnell C, Melton D.

Cell. 2019 Feb 7;176(4):790-804.e13. doi: 10.1016/j.cell.2018.12.003. Epub 2019 Jan 17.


Predictable and precise template-free CRISPR editing of pathogenic variants.

Shen MW, Arbab M, Hsu JY, Worstell D, Culbertson SJ, Krabbe O, Cassa CA, Liu DR, Gifford DK, Sherwood RI.

Nature. 2018 Nov;563(7733):646-651. doi: 10.1038/s41586-018-0686-x. Epub 2018 Nov 7. Erratum in: Nature. 2019 Mar;567(7746):E1-E2.


A novel k-mer set memory (KSM) motif representation improves regulatory variant prediction.

Guo Y, Tian K, Zeng H, Guo X, Gifford DK.

Genome Res. 2018 Jun;28(6):891-900. doi: 10.1101/gr.226852.117. Epub 2018 Apr 13.


Differential chromatin profiles partially determine transcription factor binding.

Chen R, Gifford DK.

PLoS One. 2017 Jul 13;12(7):e0179411. doi: 10.1371/journal.pone.0179411. eCollection 2017.


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

Zeng H, Gifford DK.

Nucleic Acids Res. 2017 Jun 20;45(11):e99. doi: 10.1093/nar/gkx177.


Accurate eQTL prioritization with an ensemble-based framework.

Zeng H, Edwards MD, Guo Y, Gifford DK.

Hum Mutat. 2017 Sep;38(9):1259-1265. doi: 10.1002/humu.23198. Epub 2017 Apr 19.


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.

Hum Mutat. 2017 Sep;38(9):1240-1250. doi: 10.1002/humu.23197. Epub 2017 Mar 9.


Modular combinatorial binding among human trans-acting factors reveals direct and indirect factor binding.

Guo Y, Gifford DK.

BMC Genomics. 2017 Jan 6;18(1):45. doi: 10.1186/s12864-016-3434-3.


Expression of Terminal Effector Genes in Mammalian Neurons Is Maintained by a Dynamic Relay of Transient Enhancers.

Rhee HS, Closser M, Guo Y, Bashkirova EV, Tan GC, Gifford DK, Wichterle H.

Neuron. 2016 Dec 21;92(6):1252-1265. doi: 10.1016/j.neuron.2016.11.037. Epub 2016 Dec 8.


Identification of new branch points and unconventional introns in Saccharomyces cerevisiae.

Gould GM, Paggi JM, Guo Y, Phizicky DV, Zinshteyn B, Wang ET, Gilbert WV, Gifford DK, Burge CB.

RNA. 2016 Oct;22(10):1522-34. doi: 10.1261/rna.057216.116. Epub 2016 Jul 29.


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.

Genome Res. 2016 Oct;26(10):1430-1440. Epub 2016 Jul 25.


Convolutional neural network architectures for predicting DNA-protein binding.

Zeng H, Edwards MD, Liu G, Gifford DK.

Bioinformatics. 2016 Jun 15;32(12):i121-i127. doi: 10.1093/bioinformatics/btw255.


A distant trophoblast-specific enhancer controls HLA-G expression at the maternal-fetal interface.

Ferreira LM, Meissner TB, Mikkelsen TS, Mallard W, O'Donnell CW, Tilburgs T, Gomes HA, Camahort R, Sherwood RI, Gifford DK, Rinn JL, Cowan CA, Strominger JL.

Proc Natl Acad Sci U S A. 2016 May 10;113(19):5364-9. doi: 10.1073/pnas.1602886113. Epub 2016 Apr 13.


Cas9 Functionally Opens Chromatin.

Barkal AA, Srinivasan S, Hashimoto T, Gifford DK, Sherwood RI.

PLoS One. 2016 Mar 31;11(3):e0152683. doi: 10.1371/journal.pone.0152683. eCollection 2016.


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, β 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):171-178. 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):1191-1198. 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, Schwarzmüller 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.


Rapid haplotype inference for nuclear families.

Williams AL, Housman DE, Rinard MC, Gifford DK.

Genome Biol. 2010;11(10):R108. doi: 10.1186/gb-2010-11-10-r108. Epub 2010 Oct 29.


Discovering homotypic binding events at high spatial resolution.

Guo Y, Papachristoudis G, Altshuler RC, Gerber GK, Jaakkola TS, Gifford DK, Mahony S.

Bioinformatics. 2010 Dec 15;26(24):3028-34. doi: 10.1093/bioinformatics/btq590. Epub 2010 Oct 21.


Waveguide dispersion effects in silicon-on-insulator coupled-resonator optical waveguides.

Cooper ML, Gupta G, Schneider MA, Green WM, Assefa S, Xia F, Gifford DK, Mookherjea S.

Opt Lett. 2010 Sep 15;35(18):3030-2. doi: 10.1364/OL.35.003030.


Global control of motor neuron topography mediated by the repressive actions of a single hox gene.

Jung H, Lacombe J, Mazzoni EO, Liem KF Jr, Grinstein J, Mahony S, Mukhopadhyay D, Gifford DK, Young RA, Anderson KV, Wichterle H, Dasen JS.

Neuron. 2010 Sep 9;67(5):781-96. doi: 10.1016/j.neuron.2010.08.008.


Genotype to phenotype: a complex problem.

Dowell RD, Ryan O, Jansen A, Cheung D, Agarwala S, Danford T, Bernstein DA, Rolfe PA, Heisler LE, Chin B, Nislow C, Giaever G, Phillips PC, Fink GR, Gifford DK, Boone C.

Science. 2010 Apr 23;328(5977):469. doi: 10.1126/science.1189015.


Feed-forward regulation of a cell fate determinant by an RNA-binding protein generates asymmetry in yeast.

Wolf JJ, Dowell RD, Mahony S, Rabani M, Gifford DK, Fink GR.

Genetics. 2010 Jun;185(2):513-22. doi: 10.1534/genetics.110.113944. Epub 2010 Apr 9.


Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast.

Bumgarner SL, Dowell RD, Grisafi P, Gifford DK, Fink GR.

Proc Natl Acad Sci U S A. 2009 Oct 27;106(43):18321-6. doi: 10.1073/pnas.0909641106. Epub 2009 Sep 30.


Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET.

Mathur D, Danford TW, Boyer LA, Young RA, Gifford DK, Jaenisch R.

Genome Biol. 2008;9(8):R126. doi: 10.1186/gb-2008-9-8-r126. Epub 2008 Aug 13.


Automated discovery of functional generality of human gene expression programs.

Gerber GK, Dowell RD, Jaakkola TS, Gifford DK.

PLoS Comput Biol. 2007 Aug;3(8):e148. Epub 2007 Jun 13.


Tissue-specific transcriptional regulation has diverged significantly between human and mouse.

Odom DT, Dowell RD, Jacobsen ES, Gordon W, Danford TW, MacIsaac KD, Rolfe PA, Conboy CM, Gifford DK, Fraenkel E.

Nat Genet. 2007 Jun;39(6):730-2. Epub 2007 May 21.

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