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John Andrew Berglund, Ph.D. - Publications

Affiliations: 
Biology University of Oregon, Eugene, OR, United States 
Area:
RNA
Website:
http://chemistry.uoregon.edu/fac.html?berglund

44 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2015 Siboni RB, Nakamori M, Wagner SD, Struck AJ, Coonrod LA, Harriott SA, Cass DM, Tanner MK, Berglund JA. Actinomycin D Specifically Reduces Expanded CUG Repeat RNA in Myotonic Dystrophy Models. Cell Reports. PMID 26686629 DOI: 10.1016/j.celrep.2015.11.028  1
2015 Almén MS, Lamichhaney S, Berglund J, Grant BR, Grant PR, Webster MT, Andersson L. Adaptive radiation of Darwin's finches revisited using whole genome sequencing. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. PMID 26606649 DOI: 10.1002/Bies.201500079  1
2015 Siboni RB, Bodner MJ, Khalifa MM, Docter AG, Choi JY, Nakamori M, Haley MM, Berglund JA. Biological Efficacy and Toxicity of Diamidines in Myotonic Dystrophy Type 1 Models. Journal of Medicinal Chemistry. PMID 26103061 DOI: 10.1021/Acs.Jmedchem.5B00356  1
2015 Khalifa MM, Bodner MJ, Berglund JA, Haley MM. Synthesis of N-substituted aryl amidines by strong base activation of amines. Tetrahedron Letters. 56: 4109-4111. PMID 26097266 DOI: 10.1016/J.Tetlet.2015.05.029  1
2015 Lamichhaney S, Berglund J, Almén MS, Maqbool K, Grabherr M, Martinez-Barrio A, Promerová M, Rubin CJ, Wang C, Zamani N, Grant BR, Grant PR, Webster MT, Andersson L. Evolution of Darwin's finches and their beaks revealed by genome sequencing. Nature. 518: 371-5. PMID 25686609 DOI: 10.1038/Nature14181  1
2015 Berglund J, Quilez J, Arndt PF, Webster MT. Germline methylation patterns determine the distribution of recombination events in the dog genome. Genome Biology and Evolution. 7: 522-30. PMID 25527838 DOI: 10.1093/gbe/evu282  1
2014 Ramirez O, Olalde I, Berglund J, Lorente-Galdos B, Hernandez-Rodriguez J, Quilez J, Webster MT, Wayne RK, Lalueza-Fox C, Vilà C, Marques-Bonet T. Analysis of structural diversity in wolf-like canids reveals post-domestication variants. Bmc Genomics. 15: 465. PMID 24923435 DOI: 10.1186/1471-2164-15-465  1
2014 Molin AM, Berglund J, Webster MT, Lindblad-Toh K. Genome-wide copy number variant discovery in dogs using the CanineHD genotyping array. Bmc Genomics. 15: 210. PMID 24640994 DOI: 10.1186/1471-2164-15-210  1
2014 Wagner SD, Berglund JA. Alternative pre-mRNA splicing. Methods in Molecular Biology (Clifton, N.J.). 1126: 45-54. PMID 24549655 DOI: 10.1007/978-1-62703-980-2_4  1
2013 Coonrod LA, Nakamori M, Wang W, Carrell S, Hilton CL, Bodner MJ, Siboni RB, Docter AG, Haley MM, Thornton CA, Berglund JA. Reducing levels of toxic RNA with small molecules. Acs Chemical Biology. 8: 2528-37. PMID 24028068 DOI: 10.1021/Cb400431F  1
2012 Lamichhaney S, Martinez Barrio A, Rafati N, Sundström G, Rubin CJ, Gilbert ER, Berglund J, Wetterbom A, Laikre L, Webster MT, Grabherr M, Ryman N, Andersson L. Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring. Proceedings of the National Academy of Sciences of the United States of America. 109: 19345-50. PMID 23134729 DOI: 10.1073/Pnas.1216128109  1
2012 Coonrod LA, Lohman JR, Berglund JA. Utilizing the GAAA tetraloop/receptor to facilitate crystal packing and determination of the structure of a CUG RNA helix. Biochemistry. 51: 8330-7. PMID 23025897 DOI: 10.1021/Bi300829W  1
2012 Berglund J, Nevalainen EM, Molin AM, Perloski M, Andre C, Zody MC, Sharpe T, Hitte C, Lindblad-Toh K, Lohi H, Webster MT. Novel origins of copy number variation in the dog genome Genome Biology. R73. PMID 22916802 DOI: 10.1186/gb-2012-13-8-r73  1
2012 Purcell J, Oddo JC, Wang ET, Berglund JA. Combinatorial mutagenesis of MBNL1 zinc fingers elucidates distinct classes of regulatory events. Molecular and Cellular Biology. 32: 4155-67. PMID 22890842 DOI: 10.1128/MCB.00274-12  1
2012 Voelker RB, Erkelenz S, Reynoso V, Schaal H, Berglund JA. Frequent gain and loss of intronic splicing regulatory elements during the evolution of vertebrates. Genome Biology and Evolution. 4: 659-74. PMID 22619362 DOI: 10.1093/gbe/evs051  1
2011 Gates DP, Coonrod LA, Berglund JA. Autoregulated splicing of muscleblind-like 1 (MBNL1) Pre-mRNA. The Journal of Biological Chemistry. 286: 34224-33. PMID 21832083 DOI: 10.1074/Jbc.M111.236547  1
2011 Cass D, Hotchko R, Barber P, Jones K, Gates DP, Berglund JA. The four Zn fingers of MBNL1 provide a flexible platform for recognition of its RNA binding elements. Bmc Molecular Biology. 12: 20. PMID 21548961 DOI: 10.1186/1471-2199-12-20  1
2010 Ratnakumar A, Mousset S, Glémin S, Berglund J, Galtier N, Duret L, Webster MT. Detecting positive selection within genomes: the problem of biased gene conversion. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365: 2571-80. PMID 20643747 DOI: 10.1098/Rstb.2010.0007  1
2010 Voelker RB, Berglund JA. Two ways to misregulate mRNAs in myotonic dystrophy. Nature Structural & Molecular Biology. 17: 141-2. PMID 20130573 DOI: 10.1038/nsmb0210-141  1
2010 Goers ES, Purcell J, Voelker RB, Gates DP, Berglund JA. MBNL1 binds GC motifs embedded in pyrimidines to regulate alternative splicing. Nucleic Acids Research. 38: 2467-84. PMID 20071745 DOI: 10.1093/Nar/Gkp1209  1
2010 Warf MB, Berglund JA. Role of RNA structure in regulating pre-mRNA splicing. Trends in Biochemical Sciences. 35: 169-78. PMID 19959365 DOI: 10.1016/j.tibs.2009.10.004  1
2009 Warf MB, Nakamori M, Matthys CM, Thornton CA, Berglund JA. Pentamidine reverses the splicing defects associated with myotonic dystrophy. Proceedings of the National Academy of Sciences of the United States of America. 106: 18551-6. PMID 19822739 DOI: 10.1073/pnas.0903234106  1
2009 Warf MB, Diegel JV, von Hippel PH, Berglund JA. The protein factors MBNL1 and U2AF65 bind alternative RNA structures to regulate splicing. Proceedings of the National Academy of Sciences of the United States of America. 106: 9203-8. PMID 19470458 DOI: 10.1073/pnas.0900342106  1
2009 Berglund J, Pollard KS, Webster MT. Hotspots of biased nucleotide substitutions in human genes Plos Biology. 7. PMID 19175294 DOI: 10.1371/Journal.Pbio.1000026  1
2009 Shin DS, Didonato M, Barondeau DP, Hura GL, Hitomi C, Berglund JA, Getzoff ED, Cary SC, Tainer JA. Superoxide dismutase from the eukaryotic thermophile Alvinella pompejana: structures, stability, mechanism, and insights into amyotrophic lateral sclerosis. Journal of Molecular Biology. 385: 1534-55. PMID 19063897 DOI: 10.1016/J.Jmb.2008.11.031  1
2008 Goers ES, Voelker RB, Gates DP, Berglund JA. RNA binding specificity of Drosophila muscleblind. Biochemistry. 47: 7284-94. PMID 18557632 DOI: 10.1021/Bi702252D  1
2008 Murray JI, Voelker RB, Henscheid KL, Warf MB, Berglund JA. Identification of motifs that function in the splicing of non-canonical introns. Genome Biology. 9: R97. PMID 18549497 DOI: 10.1186/gb-2008-9-6-r97  1
2008 Henscheid KL, Voelker RB, Berglund JA. Alternative modes of binding by U2AF65 at the polypyrimidine tract. Biochemistry. 47: 449-59. PMID 18067274 DOI: 10.1021/bi701240t  1
2008 Garrey SM, Cass DM, Wandler AM, Scanlan MS, Berglund JA. Transposition of two amino acids changes a promiscuous RNA binding protein into a sequence-specific RNA binding protein. Rna (New York, N.Y.). 14: 78-88. PMID 18000034 DOI: 10.1261/rna.633808  1
2007 Warf MB, Berglund JA. MBNL binds similar RNA structures in the CUG repeats of myotonic dystrophy and its pre-mRNA substrate cardiac troponin T. Rna (New York, N.Y.). 13: 2238-51. PMID 17942744 DOI: 10.1261/rna.610607  1
2007 Voelker RB, Berglund JA. A comprehensive computational characterization of conserved mammalian intronic sequences reveals conserved motifs associated with constitutive and alternative splicing. Genome Research. 17: 1023-33. PMID 17525134 DOI: 10.1101/gr.6017807  1
2006 Cass DM, Berglund JA. The SF3b155 N-terminal domain is a scaffold important for splicing. Biochemistry. 45: 10092-101. PMID 16906767 DOI: 10.1021/bi060429o  1
2006 Garrey SM, Voelker R, Berglund JA. An extended RNA binding site for the yeast branch point-binding protein and the role of its zinc knuckle domains in RNA binding. The Journal of Biological Chemistry. 281: 27443-53. PMID 16861232 DOI: 10.1074/jbc.M603137200  1
2005 Mooers BH, Logue JS, Berglund JA. The structural basis of myotonic dystrophy from the crystal structure of CUG repeats. Proceedings of the National Academy of Sciences of the United States of America. 102: 16626-31. PMID 16269545 DOI: 10.1073/pnas.0505873102  1
2005 Henscheid KL, Shin DS, Cary SC, Berglund JA. The splicing factor U2AF65 is functionally conserved in the thermotolerant deep-sea worm Alvinella pompejana. Biochimica Et Biophysica Acta. 1727: 197-207. PMID 15777616 DOI: 10.1016/j.bbaexp.2005.01.008  1
2003 Berglund JA. Expanding the structural repertoire of g-quadruplexes. Structure (London, England : 1993). 11: 1315-6. PMID 14604520 DOI: 10.1016/j.str.2003.10.008  1
2003 Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, FitzHugh W, Ma LJ, Smirnov S, Purcell S, Rehman B, Elkins T, Engels R, Wang S, Nielsen CB, ... ... Berglund JA, et al. The genome sequence of the filamentous fungus Neurospora crassa. Nature. 422: 859-68. PMID 12712197 DOI: 10.1038/Nature01554  1
2001 Peled-Zehavi H, Berglund JA, Rosbash M, Frankel AD. Recognition of RNA branch point sequences by the KH domain of splicing factor 1 (mammalian branch point binding protein) in a splicing factor complex. Molecular and Cellular Biology. 21: 5232-41. PMID 11438677 DOI: 10.1128/Mcb.21.15.5232-5241.2001  1
2001 Berglund JA, Rosbash M, Schultz SC. Crystal structure of a model branchpoint-U2 snRNA duplex containing bulged adenosines. Rna (New York, N.Y.). 7: 682-91. PMID 11350032 DOI: 10.1017/S1355838201002187  1
1998 Berglund JA, Fleming ML, Rosbash M. The KH domain of the branchpoint sequence binding protein determines specificity for the pre-mRNA branchpoint sequence. Rna (New York, N.Y.). 4: 998-1006. PMID 9701290 DOI: 10.1017/S1355838298980499  1
1998 Berglund JA, Abovich N, Rosbash M. A cooperative interaction between U2AF65 and mBBP/SF1 facilitates branchpoint region recognition. Genes & Development. 12: 858-67. PMID 9512519  1
1997 Berglund JA, Chua K, Abovich N, Reed R, Rosbash M. The splicing factor BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC. Cell. 89: 781-7. PMID 9182766 DOI: 10.1016/S0092-8674(00)80261-5  1
1997 Berglund JA, Charpentier B, Rosbash M. A high affinity binding site for the HIV-1 nucleocapsid protein. Nucleic Acids Research. 25: 1042-9. PMID 9023116 DOI: 10.1093/Nar/25.5.1042  1
1996 Lietzke SE, Barnes CL, Berglund JA, Kundrot CE. The structure of an RNA dodecamer shows how tandem U-U base pairs increase the range of stable RNA structures and the diversity of recognition sites. Structure (London, England : 1993). 4: 917-30. PMID 8805576 DOI: 10.1016/S0969-2126(96)00099-8  1
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