High-resolution genetic mapping of putative causal interactions between regions of open chromatin von Kumasaka, Natsuhiko, Knights, Andrew J., Gaffney, Daniel J.

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Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer’s disease risk genes von Schwartzentruber, Jeremy, Cooper, Sarah, Liu, Jimmy Z., Barrio-Hernandez, Inigo, Bello, Erica, Kumasaka, Natsuhiko, Young, Adam M. H., Franklin, Robin J. M., Johnson, Toby, Estrada, Karol, Gaffney, Daniel J., Beltrao, Pedro, Bassett, Andrew

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Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response von Alasoo, Kaur, Rodrigues, Julia, Mukhopadhyay, Subhankar, Knights, Andrew J., Mann, Alice L., Kundu, Kousik, Hale, Christine, Dougan, Gordon, Gaffney, Daniel J.

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Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation von Jerber, Julie, Seaton, Daniel D., Cuomo, Anna S. E., Kumasaka, Natsuhiko, Haldane, James, Steer, Juliette, Patel, Minal, Pearce, Daniel, Andersson, Malin, Bonder, Marc Jan, Mountjoy, Ed, Ghoussaini, Maya, Lancaster, Madeline A., Marioni, John C., Merkle, Florian T., Gaffney, Daniel J., Stegle, Oliver

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Controls of nucleosome positioning in the human genome von Gaffney, Daniel J, McVicker, Graham, Pai, Athma A, Fondufe-Mittendorf, Yvonne N, Lewellen, Noah, Michelini, Katelyn, Widom, Jonathan, Gilad, Yoav, Pritchard, Jonathan K

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DNA Sequence-Dependent Compartmentalization and Silencing of Chromatin at the Nuclear Lamina von Zullo, Joseph M., Demarco, Ignacio A., Piqué-Regi, Roger, Gaffney, Daniel J., Epstein, Charles B., Spooner, Chauncey J., Luperchio, Teresa R., Bernstein, Bradley E., Pritchard, Jonathan K., Reddy, Karen L., Singh, Harinder

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Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain von Marsh, Samuel E., Walker, Alec J., Kamath, Tushar, Dissing-Olesen, Lasse, Hammond, Timothy R., de Soysa, T. Yvanka, Young, Adam M. H., Murphy, Sarah, Abdulraouf, Abdulraouf, Nadaf, Naeem, Dufort, Connor, Walker, Alicia C., Lucca, Liliana E., Kozareva, Velina, Vanderburg, Charles, Hong, Soyon, Bulstrode, Harry, Hutchinson, Peter J., Gaffney, Daniel J., Hafler, David A., Franklin, Robin J. M., Macosko, Evan Z., Stevens, Beth

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Epithelial IL-22RA1-Mediated Fucosylation Promotes Intestinal Colonization Resistance to an Opportunistic Pathogen von Pham, Tu Anh N., Clare, Simon, Goulding, David, Arasteh, Julia M., Stares, Mark D., Browne, Hilary P., Keane, Jacqueline A., Page, Andrew J., Kumasaka, Natsuhiko, Kane, Leanne, Mottram, Lynda, Harcourt, Katherine, Hale, Christine, Arends, Mark J., Gaffney, Daniel J., Dougan, Gordon, Lawley, Trevor D.

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A map of transcriptional heterogeneity and regulatory variation in human microglia von Young, Adam M. H., Kumasaka, Natsuhiko, Calvert, Fiona, Hammond, Timothy R., Knights, Andrew, Panousis, Nikolaos, Park, Jun Sung, Schwartzentruber, Jeremy, Liu, Jimmy, Kundu, Kousik, Segel, Michael, Murphy, Natalia A., McMurran, Christopher E., Bulstrode, Harry, Correia, Jason, Budohoski, Karol P., Joannides, Alexis, Guilfoyle, Mathew R., Trivedi, Rikin, Kirollos, Ramez, Morris, Robert, Garnett, Matthew R., Timofeev, Ivan, Jalloh, Ibrahim, Holland, Katherine, Mannion, Richard, Mair, Richard, Watts, Colin, Price, Stephen J., Kirkpatrick, Peter J., Santarius, Thomas, Mountjoy, Edward, Ghoussaini, Maya, Soranzo, Nicole, Bayraktar, Omer A., Stevens, Beth, Hutchinson, Peter J., Franklin, Robin J. M., Gaffney, Daniel J.

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Cell reprogramming shapes the mitochondrial DNA landscape von Wei, Wei, Gaffney, Daniel J., Chinnery, Patrick F.

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Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data von Pique-Regi, Roger, Degner, Jacob F, Pai, Athma A, Gaffney, Daniel J, Gilad, Yoav, Pritchard, Jonathan K

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Global properties and functional complexity of human gene regulatory variation von Gaffney, Daniel J

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Niacin-mediated rejuvenation of macrophage/microglia enhances remyelination of the aging central nervous system von Rawji, Khalil S., Young, Adam M.H., Ghosh, Tanay, Michaels, Nathan J., Mirzaei, Reza, Kappen, Janson, Kolehmainen, Kathleen L., Alaeiilkhchi, Nima, Lozinski, Brian, Mishra, Manoj K., Pu, Annie, Tang, Weiwen, Zein, Salma, Kaushik, Deepak K., Keough, Michael B., Plemel, Jason R., Calvert, Fiona, Knights, Andrew J., Gaffney, Daniel J., Tetzlaff, Wolfram, Franklin, Robin J. M., Yong, V. Wee

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Genetic effects on promoter usage are highly context-specific and contribute to complex traits von Alasoo, Kaur, Rodrigues, Julia, Danesh, John, Freitag, Daniel F, Paul, Dirk S, Gaffney, Daniel J

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The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels von Pai, Athma A, Cain, Carolyn E, Mizrahi-Man, Orna, De Leon, Sherryl, Lewellen, Noah, Veyrieras, Jean-Baptiste, Degner, Jacob F, Gaffney, Daniel J, Pickrell, Joseph K, Stephens, Matthew, Pritchard, Jonathan K, Gilad, Yoav

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Robust temporal map of human in vitro myelopoiesis using single-cell genomics von Alsinet, Clara, Primo, Maria Nascimento, Lorenzi, Valentina, Bello, Erica, Kelava, Iva, Jones, Carla P., Vilarrasa-Blasi, Roser, Sancho-Serra, Carmen, Knights, Andrew J., Park, Jong-Eun, Wyspianska, Beata S., Trynka, Gosia, Tough, David F., Bassett, Andrew, Gaffney, Daniel J., Alvarez-Errico, Damiana, Vento-Tormo, Roser

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Fine-mapping cellular QTLs with RASQUAL and ATAC-seq von Kumasaka, Natsuhiko, Knights, Andrew J, Gaffney, Daniel J

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False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions von Pickrell, Joseph K., Gaffney, Daniel J., Gilad, Yoav, Pritchard, Jonathan K.

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Mapping and predicting gene–enhancer interactions von Gaffney, Daniel J.

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A survey of best practices for RNA-seq data analysis von Conesa, Ana, Madrigal, Pedro, Tarazona, Sonia, Gomez-Cabrero, David, Cervera, Alejandra, McPherson, Andrew, Szcześniak, Michał Wojciech, Gaffney, Daniel J, Elo, Laura L, Zhang, Xuegong, Mortazavi, Ali

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