fshd_muscle AAV_ideo dna_strand muscle_face holoclones

1.   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. , 2017.  Abstract  Full text  PDF  Supporting material

2.   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.

3.   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

4.   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

5.   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

6.   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

7.   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

8.   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

9.   Friedman SD, Poliachik SL, Otto RK, Carter GT, Budech CB, Bird TD, Miller DG, Shaw DW.  "Longitudinal Features of Stir Bright Signal in FSHD", Muscle Nerve 49: p. 257-60, 2013.  Abstract  Full text  PDF

10.   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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11.   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

12.   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

13.   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

14.   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

15.   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

16.   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

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

18.   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

19.   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

20.   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

21.   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

22.   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.)

23.   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

24.   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

25.   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.

26.   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

27.   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

28.   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

29.   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

30.   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

31.   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

32.   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

33.   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

34.   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

35.   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

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

37.   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

38.   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

39.   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

40.   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

41.   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

42.   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

43.   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

44.   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

45.   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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