ReadDB Provides Efficient Storage for Mapped Short Reads

by Rolfe, P Alexander, Gifford, David K
Published 2011

High-resolution genetic mapping with pooled sequencing

by Edwards, Matthew D, Gifford, David K
Published 2012

High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints

by Guo, Yuchun, Mahony, Shaun, Gifford, David K.
Published 2012

Universal Count Correction for High-Throughput Sequencing

by Hashimoto, Tatsunori B., Edwards, Matthew D., Gifford, David K.
Published 2014

Convolutional neural network architectures for predicting DNA–protein binding

by Zeng, Haoyang, Edwards, Matthew D., Liu, Ge, Gifford, David K.
Published 2016

Rapid haplotype inference for nuclear families

by Williams, Amy L, Housman, David E, Rinard, Martin C, Gifford, David K
Published 2010

Automated Discovery of Functional Generality of Human Gene Expression Programs

by Gerber, Georg K, Dowell, Robin D, Jaakkola, Tommi S, Gifford, David K
Published 2007

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

by Mahony, Shaun, Mazzoni, Esteban O, McCuine, Scott, Young, Richard A, Wichterle, Hynek, Gifford, David K
Published 2011

Ruler Arrays Reveal Haploid Genomic Structural Variation

by Rolfe, P. Alexander, Bernstein, Douglas A., Grisafi, Paula, Fink, Gerald R., Gifford, David K.
Published 2012

MARIS: Method for Analyzing RNA following Intracellular Sorting

by Hrvatin, Siniša, Deng, Francis, O'Donnell, Charles W., Gifford, David K., Melton, Douglas A.
Published 2014

Cas9 Functionally Opens Chromatin

by Barkal, Amira A., Srinivasan, Sharanya, Hashimoto, Tatsunori, Gifford, David K., Sherwood, Richard I.
Published 2016

An improved map of conserved regulatory sites for Saccharomyces cerevisiae

by MacIsaac, Kenzie D, Wang, Ting, Gordon, D Benjamin, Gifford, David K, Stormo, Gary D, Fraenkel, Ernest
Published 2006

Embryonic stem cell-based system for mapping developmental transcriptional programs

by Mazzoni, Esteban O., Mahony, Shaun, Iacovino, Michelina, Morrison, Carolyn A., Mountoufaris, George, Closser, Michael, Whyte, Warren A., Young, Richard A., Kyba, Michael, Gifford, David K., Wichterle, Hynek
Published 2011

Core transcriptional regulatory circuitry in human hepatocytes

by Odom, Duncan T, Dowell, Robin D, Jacobsen, Elizabeth S, Nekludova, Lena, Rolfe, P Alexander, Danford, Timothy W, Gifford, David K, Fraenkel, Ernest, Bell, Graeme I, Young, Richard A
Published 2006

Saltatory remodeling of Hox chromatin in response to rostro-caudal patterning signals

by Mazzoni, Esteban O., Mahony, Shaun, Peljto, Mirza, Patel, Tulsi, Thornton, Seraphim R., McCuine, Scott, Reeder, Christopher, Boyer, Laurie A., Young, Richard A., Gifford, David K., Wichterle, Hynek
Published 2013

Discovery of non-directional and directional pioneer transcription factors by modeling DNase profile magnitude and shape

by Sherwood, Richard I, Hashimoto, Tatsunori, O'Donnell, Charles W, Lewis, Sophia, Barkal, Amira A, van Hoff, John Peter, Karun, Vivek, Jaakkola, Tommi, Gifford, David K
Published 2014

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding

by Mahony, Shaun, Edwards, Matthew D., Mazzoni, Esteban O., Sherwood, Richard I., Kakumanu, Akshay, Morrison, Carolyn A., Wichterle, Hynek, Gifford, David K.
Published 2014

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

by Arbab, Mandana, Mahony, Shaun, Cho, Hyunjii, Chick, Joel M., Rolfe, P. Alexander, van Hoff, John Peter, Morris, Viveca W.S., Gygi, Steven P., Maas, Richard L., Gifford, David K., Sherwood, Richard I.
Published 2013