Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay

by Hammelman, Jennifer, Krismer, Konstantin, Gifford, David K, Sherwood, Richard I.
Published 2021

Cloning-free CRISPR

by Arbab, Mandana, Srinivasan, Sharanya, Geijsen, Niels, Sherwood, Richard I, Hashimoto, Tatsunori Benjamin
Published 2016

Cas9 Functionally Opens Chromatin

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

Lineage-based identification of cellular states and expression programs

by Hashimoto, Tatsunori Benjamin, Jaakkola, Tommi S., Sherwood, Richard, Mazzoni, Esteban O., Wichterle, Hynek, Gifford, David K.
Published 2012

DNase-capture reveals differential transcription factor binding modalities

by Sherwood, Richard, Barkal, Amira, Kang, Daniel D, Hashimoto, Tatsunori Benjamin, Engstrom, Logan G., Gifford, David K
Published 2018

Machine learning based CRISPR gRNA design for therapeutic exon skipping

by Louie, Wilson, Shen, Max W, Tahiry, Zakir, Zhang, Sophia, Worstell, Daniel, Cassa, Christopher A, Sherwood, Richard I, Gifford, David K
Published 2022

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

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

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
Published 2022

Detection of gene cis-regulatory element perturbations in single-cell transcriptomes

by Yeo, Grace Hui Ting, Juez, Oscar, Chen, Qing, Banerjee, Budhaditya, Chu, Lendy, Shen, Max Walt, Sabry, May, Logister, Ive, Sherwood, Richard I., Gifford, David K
Published 2021

High-throughput mapping of regulatory DNA

by Kooshesh, Kameron, Banerjee, Budhaditya, Emons, Bart J M, Sherwood, Richard I, Rajagopal, Nisha, Srinivasan, Sharanya, Guo, Yuchun, Edwards, Matthew D, Syed, Tahin Fahmid, Gifford, David K
Published 2017

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

by Lewis, Sophia, van Hoff, John Peter, Karun, Vivek, Hashimoto, Tatsunori Benjamin, Sherwood, Richard I., O'Donnell, Charles William, Barkal, Amira A., Jaakkola, Tommi S., Gifford, David K.
Published 2015

A synergistic DNA logic predicts genome-wide chromatin accessibility

by Sherwood, Richard I., Emons, Bart J.M, Hashimoto, Tatsunori Benjamin, Kang, Daniel D., Rajagopal, Nisha, Barkal, Amira, Zeng, Haoyang, Srinivasan, Sharanya, Jaakkola, Tommi S., Gifford, David K.
Published 2017

Predictable and precise template-free CRISPR editing of pathogenic variants

by Shen, Max Walt, Arbab, Mandana, Hsu, Jonathan Yee-Ting, Worstell, Daniel, Culbertson, Sannie J., Krabbe, Olga, Cassa, Christopher A., Liu, David R., Gifford, David K., Sherwood, Richard I.
Published 2020

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

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

Chemogenetic System Demonstrates That Cas9 Longevity Impacts Genome Editing Outcomes

by Sreekanth, Vedagopuram, Zhou, Qingxuan, Kokkonda, Praveen, Bermudez-Cabrera, Heysol C., Lim, Donghyun, Law, Benjamin K., Holmes, Benjamin Ray, Chaudhary, Santosh K., Pergu, Rajaiah, Leger, Brittany S., Walker, James A., Gifford, David K, Sherwood, Richard I., Choudhary, Amit
Published 2020

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

by Ferreira, Leonardo M. R., Meissner, Torsten B., Mikkelsen, Tarjei S., Mallard, William, O'Donnell, Charles W., Tilburgs, Tamara, Gomes, Hannah A. B., Camahort, Raymond, Sherwood, Richard I., Rinn, John L., Cowan, Chad A., Strominger, Jack L., Gifford, David K
Published 2017

A CD47-associated super-enhancer links pro-inflammatory signalling to CD47 upregulation in breast cancer

by Betancur, Paola A., Abraham, Brian J., Yiu, Ying Y., Willingham, Stephen B., Khameneh, Farnaz, Zarnegar, Mark, Kuo, Angera H., McKenna, Kelly, Kojima, Yoko, Leeper, Nicholas J., Ho, Po, Gip, Phung, Swigut, Tomek, Sherwood, Richard I., Clarke, Michael F., Somlo, George, Weissman, Irving L., Young, Richard A.
Published 2017