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.

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Cloning-free CRISPR by Arbab, Mandana, Srinivasan, Sharanya, Geijsen, Niels, Sherwood, Richard I., Hashimoto, Tatsunori Benjamin

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Cas9 Functionally Opens Chromatin by Barkal, Amira A., Srinivasan, Sharanya, Gifford, David K., Sherwood, Richard I., Hashimoto, Tatsunori Benjamin

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A Multiplexed Barcodelet Single-Cell RNA-Seq Approach Elucidates Combinatorial Signaling Pathways that Drive ESC Differentiation by Yeo, Grace Hui Ting, Lin, Lin, Qi, Celine Yueyue, Cha, Minsun, Gifford, David K, Sherwood, Richard I

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A Multiplexed Barcodelet Single-Cell RNA-Seq Approach Elucidates Combinatorial Signaling Pathways that Drive ESC Differentiation by Yeo, Grace Hui Ting, Lin, Lin, Qi, Celine Yueyue, Cha, Minsun, Gifford, David K, Sherwood, Richard I.

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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

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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

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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

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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

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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.

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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

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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.

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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.

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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

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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.

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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.

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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

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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

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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.

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