Signatures of TSPAN8 variants associated with human metabolic regulation and diseases

Authors: De, Tisham, Goncalves, Angela, Speed, Doug, Froguel, Philippe, Gaffney, Daniel J., Johnson, Michael R., Jarvelin, Marjo-Riitta, Coin, Lachlan JM.

Source: In iScience 20 August 2021 24(8)

The contribution of genetic determinants of blood gene expression and splicing to molecular phenotypes and health outcomes

Authors: Tokolyi, Alex, Persyn, Elodie, Nath, Artika P., Burnham, Katie L., Marten, Jonathan, Vanderstichele, Thomas, Tardaguila, Manuel, Stacey, David, Farr, Ben, Iyer, Vivek, Jiang, Xilin, Lambert, Samuel A., Noell, Guillaume, Quail, Michael A., Rajan, Diana, Ritchie, Scott C., Sun, Benjamin B., Thurston, Scott A. J., Xu, Yu, Whelan, Christopher D., Runz, Heiko, Petrovski, Slavé, Gaffney, Daniel J., Roberts, David J., Di Angelantonio, Emanuele, Peters, James E., Soranzo, Nicole, Danesh, John, Butterworth, Adam S., Inouye, Michael, Davenport, Emma E., Paul, Dirk S.

Source: Nature Genetics; March 2025, Vol. 57 Issue: 3 p616-625, 10p

Niacin-mediated rejuvenation of macrophage/microglia enhances remyelination of the aging central nervous system

Authors: 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

Source: Acta neuropathologica. 139(5):893-909

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100168072383.0x000001&indx=1&recIds=ETOCvdc_100168072383.0x000001

Functional Constraints and Frequency of Deleterious Mutations in Noncoding DNA of Rodents

Authors: Keightley, Peter D., Gaffney, Daniel J.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2003 Nov 01. 100(23), 13402-13406.

Access URL: https://www.jstor.org/stable/3148152

Molecular and functional variation in iPSC-derived sensory neurons

Authors: Schwartzentruber, Jeremy, Foskolou, Stefanie, Kilpinen, Helena, Rodrigues, Julia, Alasoo, Kaur, Knights, Andrew J., Patel, Minal, Goncalves, Angela, Ferreira, Rita, Benn, Caroline Louise, Wilbrey, Anna, Bictash, Magda, Impey, Emma, Cao, Lishuang, Lainez, Sergio, Loucif, Alexandre Julien, Whiting, Paul John, Gutteridge, Alex, Gaffney, Daniel J.

Source: Nature genetics. 50(1):54-61

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100132383610.0x000001&indx=1&recIds=ETOCvdc_100132383610.0x000001

Epithelial IL-22RA1-Mediated Fucosylation Promotes Intestinal Colonization Resistance to an Opportunistic Pathogen

Authors: 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.

Source: In Cell Host & Microbe 8 October 2014 16(4):504-516

DNA Sequence-Dependent Compartmentalization and Silencing of Chromatin at the Nuclear Lamina

Authors: 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

Source: In Cell 22 June 2012 149(7):1474-1487

Author Correction: Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain

Authors: 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

Source: Nature Neuroscience; January 2025, Vol. 28 Issue: 1 p215-215, 1p

The scale of mutational variation in the murid genome.

Authors: Gaffney, Daniel J., Keightley, Peter D.

Source: Genome Research; August 2005, Vol. 15 Issue 8, p1086-1094, 9p

Robust temporal map of human in vitro myelopoiesis using single-cell genomics.

Authors: 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

Source: Nature Communications; 5/24/2022, Vol. 13 Issue 1, p1-17, 17p

Subject Terms: INDUCED pluripotent stem cells, MYELOID cells, HEMATOPOIETIC stem cells, YOLK sac, MAST cells

Locus-specific expression of transposable elements in single cells with CELLO-seq.

Authors: Berrens, Rebecca V., Yang, Andrian, Laumer, Christopher E., Lun, Aaron T. L., Bieberich, Florian, Law, Cheuk-Ting, Lan, Guocheng, Imaz, Maria, Bowness, Joseph S., Brockdorff, Neil, Gaffney, Daniel J., Marioni, John C.

Source: Nature Biotechnology; Apr2022, Vol. 40 Issue 4, p546-554, 9p

Unexpected conserved non-coding DNA blocks in mammals

Authors: Gaffney, Daniel J, Keightley, Peter D

Source: In Trends in Genetics 2004 20(8):332-337

Gene expression and isoform variation analysis using Affymetrix exon arrays

Authors: Kwan Tony, Benovoy David, Bemmo Amandine, Gaffney Daniel J, Jensen Roderick V, Majewski Jacek

Source: BMC Genomics, Vol 10, Iss 1, p 121 (2009)

Subject Terms: Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: http://www.biomedcentral.com/1471-2164/10/121; https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/5059ca1e8d874c77b9cdce0889377ecc

Cell reprogramming shapes the mitochondrial DNA landscape.

Authors: Wei, Wei, Gaffney, Daniel J., Chinnery, Patrick F.

Source: Nature Communications; 9/2/2021, Vol. 12 Issue 1, p1-15, 15p

Subject Terms: TRANSFER RNA, CELL morphology, MITOCHONDRIAL DNA, INDUCED pluripotent stem cells, PLURIPOTENT stem cells

Gene Expression and Isoform Variation Analysis using Affymetrix Exon Arrays

Authors: Kwan Tony, Benovoy David, Bemmo Amandine, Gaffney Daniel J, Jensen Roderick V, Majewski Jacek

Source: BMC Genomics, Vol 9, Iss 1, p 529 (2008)

Subject Terms: Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: http://www.biomedcentral.com/1471-2164/9/529; https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/a17898f9004b48fca74cf725a0868985

Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals

Authors: Keightley Peter D, Gaffney Daniel J

Source: BMC Evolutionary Biology, Vol 8, Iss 1, p 265 (2008)

Subject Terms: Evolution, QH359-425

File Description: electronic resource

Relation: http://www.biomedcentral.com/1471-2148/8/265; https://doaj.org/toc/1471-2148

Access URL: https://doaj.org/article/0681040ffcb14cfdb4feee849d68152f

Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain

Authors: 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

Source: Nature Neuroscience; March 2022, Vol. 25 Issue: 3 p306-316, 11p

Global Properties and Functional Complexity of Human Gene Regulatory Variation

Authors: Gaffney, Daniel J.¹ dg13@sanger.ac.uk

Source: PLoS Genetics. May2013, Vol. 9 Issue 5, p1-8. 8p.

Subject Terms: *GENETIC regulation, *GENOMICS, *GENE mapping research, *GENE expression, *PHENOTYPES

Controls of Nucleosome Positioning in the Human Genome.

Authors: Gaffney, Daniel J.^1,2,3 dg13@sanger.ac.uk, McVicker, Graham^1,2 gmcvicker@uchicago.edu, Pai, Athma A.¹, Fondufe-Mittendorf, Yvonne N.⁴, Lewellen, Noah^1,2, Michelini, Katelyn^1,2, Widom, Jonathan, Gilad, Yoav¹ gilad@uchicago.edu, Pritchard, Jonathan K.^1,2 pritch@uchicago.edu

Source: PLoS Genetics. Nov2012, Vol. 8 Issue 11, Special section p1-13. 13p. 6 Graphs.

Subject Terms: *CHROMATIN, *HUMAN genome, *CARRIER proteins, *NUCLEOTIDE sequence, *CHROMOSOMES, *REARRANGEMENTS (Chemistry)

Exon-Specific QTLs Skew the Inferred Distribution of Expression QTLs Detected Using Gene Expression Array Data.

Authors: Veyrieras, Jean-Baptiste^1,2 jb.veyrieras@gmail.com, Gaffney, Daniel J.^1,3, Pickrell, Joseph K.¹, Gilad, Yoav¹ gilad@uchicago.edu, Stephens, Matthew^1,4 mstephens@uchicago.edu, Pritchard, Jonathan K.^1,3 pritch@uchicago.edu

Source: PLoS ONE. Feb2012, Vol. 7 Issue 2, p1-9. 9p.

Subject Terms: *GENETIC regulation, *INTRONS, *GENE expression, *NUCLEIC acids, *IMMOBILIZED nucleic acids