Search Results - "Gifford, David K."

Convolutional neural network architectures for predicting DNA-protein binding by Zeng, Haoyang, Edwards, Matthew D, Liu, Ge, Gifford, David K

“…Convolutional neural networks (CNN) have outperformed conventional methods in modeling the sequence specificity of DNA-protein binding. Yet inappropriate CNN…”
Get full text

Predictable and precise template-free CRISPR editing of pathogenic variants by Shen, Max W., Arbab, Mandana, Hsu, Jonathan Y., Worstell, Daniel, Culbertson, Sannie J., Krabbe, Olga, Cassa, Christopher A., Liu, David R., Gifford, David K., Sherwood, Richard I.

“…Following Cas9 cleavage, DNA repair without a donor template is generally considered stochastic, heterogeneous and impractical beyond gene disruption. Here, we…”
Get full text

Antibody complementarity determining region design using high-capacity machine learning by Liu, Ge, Zeng, Haoyang, Mueller, Jonas, Carter, Brandon, Wang, Ziheng, Schilz, Jonas, Horny, Geraldine, Birnbaum, Michael E, Ewert, Stefan, Gifford, David K

“…Abstract Motivation The precise targeting of antibodies and other protein therapeutics is required for their proper function and the elimination of deleterious…”
Get full text

Discovery of directional and nondirectional 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

“…A new algorithm learns features of chromatin profiles left by transcription factors, shedding light on when DNA sequence motifs are bound. We describe protein…”
Get full text

Discovering differential genome sequence activity with interpretable and efficient deep learning by Hammelman, Jennifer, Gifford, David K

“…Discovering sequence features that differentially direct cells to alternate fates is key to understanding both cellular development and the consequences of…”
Get full text

Differentiated human stem cells resemble fetal, not adult, β cells by Hrvatin, Siniša, O'Donnell, Charles W., Deng, Francis, Millman, Jeffrey R., Pagliuca, Felicia Walton, Dilorio, Philip, Rezania, Alireza, Gifford, David K., Melton, Douglas A.

“…Human pluripotent stem cells (hPSCs) have the potential to generate any human cell type, and one widely recognized goal is to make pancreatic β cells. To this…”
Get full text

Generative modeling of single-cell time series with PRESCIENT enables prediction of cell trajectories with interventions by Yeo, Grace Hui Ting, Saksena, Sachit D., Gifford, David K.

“…Existing computational methods that use single-cell RNA-sequencing (scRNA-seq) for cell fate prediction do not model how cells evolve stochastically and in…”
Get full text

Visualizing complex feature interactions and feature sharing in genomic deep neural networks by Liu, Ge, Zeng, Haoyang, Gifford, David K

“…Visualization tools for deep learning models typically focus on discovering key input features without considering how such low level features are combined in…”
Get full text

IDR2D identifies reproducible genomic interactions by Krismer, Konstantin, Guo, Yuchun, Gifford, David K

“…Abstract Chromatin interaction data from protocols such as ChIA-PET, HiChIP and Hi-C provide valuable insights into genome organization and gene regulation,…”
Get full text

Wnt Signaling Separates the Progenitor and Endocrine Compartments during Pancreas Development by Sharon, Nadav, Vanderhooft, Jordan, Straubhaar, Juerg, Mueller, Jonas, Chawla, Raghav, Zhou, Quan, Engquist, Elise N., Trapnell, Cole, Gifford, David K., Melton, Douglas A.

“…In vitro differentiation of pluripotent cells into β cells is a promising alternative to cadaveric-islet transplantation as a cure for type 1 diabetes (T1D)…”
Get full text

Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity by Mazzoni, Esteban O, Mahony, Shaun, Closser, Michael, Morrison, Carolyn A, Nedelec, Stephane, Williams, Damian J, An, Disi, Gifford, David K, Wichterle, Hynek

“…In this study, Mazzoni et al . describe the mechanism behind the combinatorial action of transcription factors in cell type specification. Specifically, the…”
Get full text

MARIS: method for analyzing RNA following intracellular sorting by Hrvatin, Siniša, Deng, Francis, O'Donnell, Charles W, Gifford, David K, Melton, Douglas A

“…Transcriptional profiling is a key technique in the study of cell biology that is limited by the availability of reagents to uniquely identify specific cell…”
Get full text

Transcriptional dynamics of murine motor neuron maturation in vivo and in vitro by Patel, Tulsi, Hammelman, Jennifer, Aziz, Siaresh, Jang, Sumin, Closser, Michael, Michaels, Theodore L., Blum, Jacob A., Gifford, David K., Wichterle, Hynek

“…Neurons born in the embryo can undergo a protracted period of maturation lasting well into postnatal life. How gene expression changes are regulated during…”
Get full text

A high-throughput yeast display approach to profile pathogen proteomes for MHC-II binding by Huisman, Brooke D, Dai, Zheng, Gifford, David K, Birnbaum, Michael E

“…T cells play a critical role in the adaptive immune response, recognizing peptide antigens presented on the cell surface by major histocompatibility complex…”
Get full text

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

“…The regulatory map of a genome consists of the binding sites for proteins that determine the transcription of nearby genes. An initial regulatory map for S…”
Get full text

Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast by Bumgarner, Stacie L, Dowell, Robin D, Grisafi, Paula, Gifford, David K, Fink, Gerald R

“…The identification of specific functional roles for the numerous long noncoding (nc)RNAs found in eukaryotic transcriptomes is currently a matter of intense…”
Get full text

Genotype to Phenotype: A Complex Problem by Dowell, Robin D, Ryan, Owen, Jansen, An, Cheung, Doris, Agarwala, Sudeep, Danford, Timothy, Bernstein, Douglas A, Rolfe, P. Alexander, Heisler, Lawrence E, Chin, Brian, Nislow, Corey, Giaever, Guri, Phillips, Patrick C, Fink, Gerald R, Gifford, David K, Boone, Charles

“…We generated a high-resolution whole-genome sequence and individually deleted 5100 genes in Σ1278b, a Saccharomyces cerevisiae strain closely related to…”
Get full text

Small molecule inhibition of ATM kinase increases CRISPR-Cas9 1-bp insertion frequency by Bermudez-Cabrera, Heysol C., Culbertson, Sannie, Barkal, Sammy, Holmes, Benjamin, Shen, Max W., Zhang, Sophia, Gifford, David K., Sherwood, Richard I.

“…Mutational outcomes following CRISPR-Cas9-nuclease cutting in mammalian cells have recently been shown to be predictable and, in certain cases, skewed toward…”
Get full text

Saltatory remodeling of Hox chromatin in response to rostrocaudal 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

“…In this study, the authors show that chromatin of Hox genes is arranged in discrete domains. Patterning signals trigger recruitment of transcription factors to…”
Get full text

Differential chromatin profiles partially determine transcription factor binding by Chen, Rujian, Gifford, David K

“…We characterize how genomic variants that alter chromatin accessibility influence regulatory factor binding with a new method called DeltaBind that predicts…”
Get full text