fshd_muscle AAV_ideo dna_strand muscle_face holoclones

1.   Daniel G Miller.  "Gene Therapy for Facioscapulohumeral Muscular Dystrophy (FSHD)", Muscle Gene Therapy : p. 509-524, 2019.  Abstract  Full text  PDF

2.   LaCroix, A.J., Stabley, D., Sahraoui, R., Adam, M.P., Mehaffey, M., Kernan, K., Myers, C.T., Fagerstrom, C., Anadiotis, G., Akkari, Y.M., Robbins, K.M., Gripp, K.W., Baratela, W.A.R., Bober, M.B., Duker, A.L., Doherty, D., Dempsey, J.C., Miller, D.G., Kircher, M., Bamshad, M.J., Nickerson, D.A., Mefford, H.C., Sol-Church, K..  "GGC Repeat Expansion and Exon 1 Methylation of XYLT1 Is a Common Pathogenic Variant in Baratela-Scott Syndrome", AJHG e-pub: p. epub, 2018.  Abstract  Full text  PDF  Supporting material

3.   Haynes, P., Bomsztyk, K., Daniel G. Miller.  "Sporadic DUX4 expression in FSHD myocytes is associated with incomplete repression by the PRC2 complex and gain of H3K9 acetylation on the contracted D4Z4 allele", Epigenetics & Chromatin 11(1): p. 13, 2018.  Abstract  Full text  PDF  Supporting material

4.   Lim J.W., Wong C.J., Yao Z., Tawil R., van der Maarel S.M., Miller D.G., Tapscott S.J., Filippova G.N..  "Small noncoding RNAs in FSHD2 muscle cells reveal both DUX4- and SMCHD1-specific signatures.", Human Molecular Genetics : p. epub, 2018.  Abstract  Full text  PDF  Supporting material

5.   Ferguson M.R., Poliachik S.L., Budech C.B., Gove N.E., Carter G.T., Wang L.H., Miller D.G., Shaw D.W.W., Friedman S.D..  "MRI change metrics of facioscapulohumeral muscular dystrophy: STIR and T1", Muscle & Nerve 57(6): p. 905, 2017.  Abstract  Full text  PDF  Supporting material

6.   Choi, M., Genereux, D.P., Goodson, J., Al-Azzawi, H., Allain, S.Q., Simon, N., Palasek, S., Ware, C.B., Cavanaugh, C., Miller, D.G., Johnson, W.C., Sinclair, K.D., Stöger, R., Laird, C.D..  "Epigenetic memory via concordant DNA methylation is inversely correlated to developmental potential of mammalian cells", PLoS Genetics 13: p. e1007060, 2017.  Abstract  Full text  PDF  Supporting material

7.   Haynes, P., Kernan, K., Zhou, S., and Daniel G.Miller.  "Expression patterns of FSHD-causing DUX4 and myogenic transcription factors PAX3 and PAX7 are spatially distinct in differentiating human stem cell cultures", Skeletal Muscle 7: p. 13, 2017.  Abstract  Full text  PDF  Supporting material

8.   Miller, D.G. and Sittig, D.F..  "Underperforming Big Ideas in Biomedical Research", JAMA 317: p. 321-22, 2017.  Abstract  Full text

Original Viewpoint here.
Response to our Letter here.

9.   Caron, L., Kher, D., Lee, L.L., McKernan, R., Dumevska, B., Hidalgo, A., Li, J., Yang, H., Main, H., Ferri, G., Petek, L.M., Poellinger, L., Miller, D.G., Gabellini, D., Schmidt, U..  "A Human Pluripotent Stem Cell Model of Facioscapulohumeral Muscular Dystrophy-Affected Skeletal Muscles. ", Stem Cells Translational Medicine 5: p. 1-17, 2016.  Abstract  Full text  PDF  Supporting material

10.   Petek, L.M., Rickard, A.M., Budech, C., Poliachik, S.L., Shaw, D., Ferguson, M.R., Tawil, R., Friedman, S.D., and Miller, D.G..  "A Cross Sectional Study of Two Independent Cohorts Identifies Serum Biomarkers for Facioscapulohumeral Muscular Dystrophy (FSHD)", Neuromuscular Disorders 26: p. 405-413, 2016.  Abstract  Full text  PDF  Supporting material

11.   Rickard, A.M., Petek, L.M., and Miller, D.G..  "Endogenous DUX4 Expression in FSHD Myotubes is Sufficient to Cause Cell Death and Disrupts RNA Splicing and Cell Migration Pathways ", Human Molecular Genetics 24: p. 5901-5914, 2015.  Abstract  Full text  PDF  Supporting material

12.   Hocum, J.D., Battrell, L.R., Maynard, R., Adair, J.E., Beard, B.C., Rawlings, D.J., Kiem, H.P., Miller, D.G., Trobridge G.D..  "VISA - Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing.", BMC Bioinformatics 16: p. 212, 2015.  Abstract  Full text  PDF  Supporting material

13.   Lemmers, R.J., Goeman, J.J., van der Vliet, P.J., van Nieuwenhuizen, M.P., Balog, J., Vos-Versteeg, M., Camano, P., Ramos Arroyo, M.A., Jerico, I., Rogers, M.T., Miller, D.G., Upadhyaya, M., Verschuuren, J.J., Lopez de Munain Arregui, A., van Engelen, B.G., Padberg, G.W., Sacconi, S., Tawil, R., Tapscott, S.J., Bakker, B., van der Maarel, S.M..  "Inter-individual differences in CpG methylation at D4Z4 correlate with clinical variability in FSHD1 and FSHD2", Human Molecular Genetics 24: p. 659-69, 2014.  Abstract  Full text  PDF  Supporting material

14.   Block G.J., Narayanan D., Amell A.M., Petek L.M., Davidson K.C., Bird T.D., Tawil R., Moon R.T., and Daniel G. Miller.  "Wnt/β-catenin signaling suppresses DUX4 expression and prevents apoptosis of FSHD muscle cells", Human Molecular Genetics 22: p. 4661-4672, 2013.  Abstract  Full text  PDF  Supporting material

Cover Photo for HMG was also taken from this manuscript

15.   Friedman S.D., Poliachik S.L., Otto R.K., Carter G.T., Budech C.B., Bird T.D., Miller D.G., Shaw D.W..  "Longitudinal Features of Stir Bright Signal in FSHD", Muscle & Nerve 49: p. 257-60, 2013.  Abstract  Full text  PDF

16.   Lemmers, R.J.L.F., Tawil, R., Petek, L.M., Balog, J., Block, G.J., Santen, G.W.E., Amell, A.M., van der Vliet, P.J., Almomani, R., Straasheijm, K.R., Krom, Y.D., Klooster, R., Sun, Y., den Dunnen, J.T., Helmer, Q., Donlin-Smith, C.M., Padberg, G.W., van Engelen, B.G.M., de Greef, J.C., Aartsma-Rus, A.M., Frants, R.R., de Visser, M., Desnuelle, C., Sacconi, S., Filippova, G.N., Bakker, B., Bamshad, M.J., Tapscott, S.J., Miller, D.G., van der Maarel, S.M..  "Digenic inheritance of an SMCHD1 mutation and an FSHD-permissive D4Z4 allele causes facioscapulohumeral muscular dystrophy type 2", Nature Genetics 44: p. 1370-1374, 2012.  Abstract  Full text  PDF  Supporting material

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17.   van der Maarel S.M., Miller D.G., Tawil R., Filippova G.N., Tapscott S.J..  "Facioscapulohumeral muscular dystrophy: consequences of chromatin relaxation", Current Opinion in Neurology 25: p. 614-620, 2012.  Abstract

18.   Lemmers R.J.L.F., Miller D.G., van der Maarel S.M..  "Facioscapulohumeral Muscular Dystrophy", GeneReviews at GeneTests Medical Genetics Information Resource: p. [database online], 2012.  Abstract  Full text

19.   Block G.J., Petek L.M., Narayanan D., Amell A.M., Moore J.M., Rabaia N.A., Tyler A., van der Maarel S.M., Tawil R., Filippova G.N., and Daniel G. Miller.  "Asymmetric Bidirectional Transcription from the FSHD-Causing D4Z4 Array Modulates DUX4 Production", PLoS ONE 7: p. e35532, 2012.  Abstract  Full text  PDF  Supporting material

20.   Vêncio E.F., Nelson A.M., Cavanaugh C., Ware C.B., Milller D.G., Garcia J.C., Vêncio R.Z., Loprieno M.A., Liu A.Y..  "Reprogramming of prostate cancer-associated stromal cells to embryonic stem-like", Prostate 72: p. 1453-1463, 2012.  Abstract  Full text  PDF

21.   van Rensburg R., Beyer I., Yao X.Y., Wang H., Denisenko O., Li Z.Y., Russell D.W., Miller D.G., Gregory P., Holmes M., Bomsztyk K., Lieber A..  "Chromatin structure of two genomic sites for targeted transgene integration in induced pluripotent stem cells and hematopoietic stem cells.", Gene Ther 20: p. 201-214, 2012.  Abstract  Full text  PDF

22.   Balog J., Miller D.G., Sanchez-Curtailles E., Carbo-Marques J., Block G., Potman M., de Knijff P., Lemmers R.J., Tapscott S.J., van der Maarel S.M. .  "Epigenetic regulation of the X-chromosomal macrosatellite repeat encoding for the cancer/testis gene CT47", Eur. J. Hum. Genet. 20: p. 185-191, 2011.  Abstract  Full text  PDF  Supporting material

23.   Daniel G. Miller.  "AAV-mediated Gene Targeting", Methods in Molecular Biology, Adeno-Associated Virus 807: p. 301-315, 2011.  Abstract  PDF

24.   Petek L.M., Russell D.W., Miller D.G..  "Frequent Endonuclease Cleavage at Off-target Locations In Vivo", Molecular Therapy 18: p. 983-986, 2010.  Abstract  Full text  PDF

25.   Stadler B.M., Ivanovska I., Mehta K., Song S., Nelson A., Tan Y., Mathieu J., Darby G.C., Blau C.A., Ware C., Peters G., Miller D.G., Shen L., Cleary M., Ruohola-Baker H..  "Characterization of microRNAs Involved in Embryonic Stem Cell States.", Stem Cells and Development 19: p. 935-950, 2010.  Abstract  PDF  Supporting material

26.   Petek L.M., Fleckman P., Miller D.G..  "Efficient KRT14 Targeting and Functional Characterization of Transplanted Human Keratinocytes for the Treatment of Epidermolysis Bullosa Simplex.", Molecular Therapy 18: p. 1624-1632, 2010.  Abstract  Full text  PDF  Supporting material

27.   Snider L., Geng L.N., Lemmers R.J.L.F., Kyba M., Ware C.B., Nelson A.M., Tawil R., Filippova G.N., van der Maarel S.M., Tapscott S.J., Miller D.G..  "Facioscapulohumeral Dystrophy: Incomplete Suppression of a Retrotransposed Gene", Plos Genetics 6: p. e1001181, 2010.  Abstract  Full text  PDF

(See also the perspective by Christopher E. Pearson). "FSHD: A Repeat Contraction Disease Finally Ready to Expand (Our Understanding of Its Pathogenesis)", PLOS Genetics; 6: p.e1001180, 2010 Full text PDF

28.   Lemmers, R.J.L.F., van der Vliet, P.J., Klooster, R., Sacconi, S., Camano, P., Dauwerse, J.G., Snider, L., Straasheijm, K.R., van Ommen, G.J., Padberg, G.W., Miller, D.G., Tapscott, S.J., Tawil, R., Frants, R.R., van der Maarel, S.M..  "A Unifying Genetic Model for Facioscapulohumeral Muscular Dystrophy", Science 329: p. 1650-53, 2010.  Abstract  Full text  PDF  Supporting material

(See also "Perspectives" by Mani S. Mahadevan) "Exposing the DUX Tale", Science; 329: p.1607, 2010.)

29.   Snider L., Asawachaicharn A., Tyler A.E., Geng L.N., Petek L.M., Maves L., Miller D.G., Lemmers R.J.L.F., Winokur S.T., Tawil R., van der Maarel S.M., Filippova G.N., Tapscott S.J..  "RNA Transcripts, miRNA-sized fragments and proteins produced from D4Z4 units: new candidates for the pathophysiology of facioscapulohumeral dystrophy.", Human Molecular Genetics 18: p. 2414-2430, 2008.  Abstract  Full text  PDF  Supporting material

30.   Beard B.C., Keyser K.A., Trobridge G.D., Peterson L.J., Miller D.G., Jacobs M., Kaul R., Kiem H. .  "Unique Integration Profiles in a Canine Model of Long-Term Repopulating Cells Transduced with Gammaretrovirus, Lentivirus, or Foamy Virus", Human Gene Therapy 18: p. 423-434, 2007.  Abstract  PDF

31.   Donsante A., Miller D.G., Li Y., Vogler C., Brunt E.M., Russell D.W., Sands M.S..  "AAV Vector Integration Sites in Mouse Hepatocellular Carcinoma", Science 317: p. 477, 2007.  Abstract  PDF  Supporting material

Miller and Donsante listed as equal contribution.

32.   Beard B.C., Dickerson D., Beebe K., Gooch C., Fletcher J., Okbinoglu T., Miller D.G., Jacobs M.A., Kaul R., Kiem H., Trobridge G.D..  "Comparison of HIV-derived Lentiviral and MLV-based Gammaretroviral Vector Integration Sites in Primate Repopulating Cells", Molecular Therapy 15: p. 1356-1365, 2007.  Abstract  Full text  PDF  Supporting material

33.   Aker M., Tubb J., Miller D.G., Stamatoyannopoulos G., Emery D.W..  "Integration Bias of Gammaretrovirus Vectors following Transduction and Growth of Primary Mouse Hematopoietic Progenitor Cells with and without Selection", Molecular Therapy 14: p. 226-235, 2006.  Abstract  Full text  PDF  Supporting material

34.   Trobridge G.D., Miller D.G., Jacobs M.A., Allen J.M., Kiem H., Kaul R., Russell D.W..  "Foamy virus vector integration sites in normal human cells", Proceedings of the National Academy of Sciences 103: p. 1498-1503, 2006.  Abstract  Full text  PDF  Supporting material

35.   Miller, D.G., Wang, P., Petek, L.M., Hirata, R.K., Sands, M.S., Russell, D.W. .  "Gene targeting in vivo by adeno-associated virus vectors", Nature Biotechnology 24: p. 1022-1026, 2006.  Abstract  Full text  PDF  Supporting material

(See also Commentary by John F. Engelhardt), "AAV hits the genomic bulls eye", Nature Biotechnology; 24: p.949-950, 2006. Full text pdf

36.   Miller D.G., Trobridge G.D., Petek L.M., Jacobs M.A., Kaul R., Russell D.W..  "Large-Scale Analysis of Adeno-Associated Virus Vector Integration Sites in Normal Human Cells", Journal of Virology 79: p. 11434-11442, 2005.  Abstract  Full text  PDF  Supporting material

37.   Miller D.G., Petek L.M., Russell D.W..  "Adeno-associated virus vectors integrate at chromosome breakage sites", Nature Genetics 36: p. 767-773, 2004.  Abstract  Full text  PDF

38.   Gregorevic P., Blankinship M.J., Allen J.M., Crawford R.W., Meuse L., Miller D.G., Russell D.W., Chamberlain J.S. .  "Systemic delivery of genes to striated muscles using adeno-associated viral vectors", Nature Medicine 10: p. 828-834, 2004.  Abstract  Full text  PDF  Supporting material

39.   Hirata R.K., Xu C., Dong R., Miller D.G., Russell D.W..  "Efficient PRNP Gene Targeting in Bovine Embryo Fibroblasts by Adeno-Associated Virus Vectors.", Cloning and Stem Cells 6: p. 31-36, 2004.  Abstract  PDF

40.   Miller D.G., Petek L.M., Russell D.W..  "Human Gene Targeting by Adeno-Associated Virus Vectors Is Enhanced by DNA Double-Strand Breaks", Molecular and Cellular Biology 23: p. 3550-3557, 2003.  Abstract  Full text  PDF

41.   Miller D.G., Rutledge E.A., Russell D.W..  "Chromosomal effects of adeno-associated virus vector integration", Nature Genetics 30: p. 147-148, 2002.  Abstract  PDF

42.   Miller D.G., and Stamatoyannopoulos G..  "Gene Therapy for Hemophilia", New England Journal of Medicine 344: p. 1782-1784, 2001.  Abstract  Full text

43.   Miller D.G..  "Clinical Genetics in an Age of Molecular Diagnosis", Archives of Pediatrics and Adolescent Medicine 156: p. 411, 2001.  Abstract  Full text  PDF

44.   Miller D.G., Miller A.D..  "A Family of Retroviruses That Utilize Related Phosphate Transporters for Cell Entry", Journal of Virology 68: p. 8270-8276, 1994.  Abstract  PDF

45.   Miller D.G., Edwards R.H., Miller A.D..  "Cloning of the cellular receptor for amphotropic murine retroviruses reveals homology to that for gibbon ape leukemia virus", Proceedings of the National Academy of Sciences 91: p. 78-82, 1994.  Abstract  PDF

46.   Clowes M.M., Lynch C.M., Miller A.D., Miller D.G., Osborne W.R.A., Clowes A. W..  "Long-Term Biological Response of Injured Rat Carotid Artery Seeded with Smooth Muscle Cells Expressing Retrovirally Introduced Human Genes", Journal of Clinical Investigation 93: p. 644-651, 1994.  Abstract  Full text  PDF

47.   Kavanaugh M.P., Miller D.G., Zhang W., Law W., Kozak S.L., Kabat D., Miller A.D..  "Cell-surface receptors for gibbon ape leukemia virus and amphotropic murine retrovirus are inducible sodium-dependent phosphate symporters", Proceedings of the National Academy of Sciences 91: p. 7071-7975, 1994.  Abstract  Full text  PDF

48.   Miller D.G., Miller A.D. .  "Inhibitors of Retrovirus Infection Are Secreted by Several Hamster Cell Lines and Are Also Present in Hamster Sera", Journal of Virology 67: p. 5346-5352, 1993.  Abstract  PDF

49.   Miller A. D., Miller D. G., Garcia J. V. and C. M. Lynch..  "Use of retroviral vectors for gene transfer and expression.", Methods in Enzymology 217: p. 581-599, 1993.  Abstract

50.   Miller D.G., Miller A.D..  "Tunicamycin Treatment of CHO Cells Abrogates Multiple Blocks to Retrovirus Infection, One of Which Is Due to a Secreted Inhibitor", Journal of Virology 66: p. 78-74, 1992.  Abstract  PDF

51.   Miller D.G., Adam M.A., Miller A.D..  "Gene Transfer by Retrovirus Vectors Occurs Only in Cells That Are Actively Replicating at the Time of Infection", Molecular and Cellular Biology 10: p. 4239-4242, 1990.  Abstract  Full text  PDF



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