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RNA Homopolymers Form Higher-Curvature Virus-like Particles Than Do Normal-Composition RNAs.

Thurm AR, Beren C, Duran-Meza AL, Knobler CM, Gelbart WM.

Biophys J. 2019 Oct 1;117(7):1331-1341. doi: 10.1016/j.bpj.2019.08.012. Epub 2019 Aug 16.


Delivery of self-amplifying RNA vaccines in in vitro reconstituted virus-like particles.

Biddlecome A, Habte HH, McGrath KM, Sambanthamoorthy S, Wurm M, Sykora MM, Knobler CM, Lorenz IC, Lasaro M, Elbers K, Gelbart WM.

PLoS One. 2019 Jun 4;14(6):e0215031. doi: 10.1371/journal.pone.0215031. eCollection 2019.


Correction for Cadena-Nava et al., "Self-Assembly of Viral Capsid Protein and RNA Molecules of Different Sizes: Requirement for a Specific High Protein/RNA Mass Ratio".

Cadena-Nava RD, Comas-Garcia M, Garmann RF, Rao ALN, Knobler CM, Gelbart WM.

J Virol. 2019 Feb 5;93(4). pii: e01939-18. doi: 10.1128/JVI.01939-18. Print 2019 Feb 15. No abstract available.


The effect of macromolecular crowding on single-round transcription by Escherichia coli RNA polymerase.

Chung S, Lerner E, Jin Y, Kim S, Alhadid Y, Grimaud LW, Zhang IX, Knobler CM, Gelbart WM, Weiss S.

Nucleic Acids Res. 2019 Feb 20;47(3):1440-1450. doi: 10.1093/nar/gky1277.


Protocol for Efficient Cell-Free Synthesis of Cowpea Chlorotic Mottle Virus-Like Particles Containing Heterologous RNAs.

Garmann RF, Knobler CM, Gelbart WM.

Methods Mol Biol. 2018;1776:249-265. doi: 10.1007/978-1-4939-7808-3_17.


The Effect of RNA Secondary Structure on the Self-Assembly of Viral Capsids.

Beren C, Dreesens LL, Liu KN, Knobler CM, Gelbart WM.

Biophys J. 2017 Jul 25;113(2):339-347. doi: 10.1016/j.bpj.2017.06.038. Epub 2017 Jul 12.


Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures.

Borodavka A, Singaram SW, Stockley PG, Gelbart WM, Ben-Shaul A, Tuma R.

Biophys J. 2016 Nov 15;111(10):2077-2085. doi: 10.1016/j.bpj.2016.10.014.


Physical Principles in the Self-Assembly of a Simple Spherical Virus.

Garmann RF, Comas-Garcia M, Knobler CM, Gelbart WM.

Acc Chem Res. 2016 Jan 19;49(1):48-55. doi: 10.1021/acs.accounts.5b00350. Epub 2015 Dec 10.


Role of RNA Branchedness in the Competition for Viral Capsid Proteins.

Singaram SW, Garmann RF, Knobler CM, Gelbart WM, Ben-Shaul A.

J Phys Chem B. 2015 Nov 5;119(44):13991-4002. doi: 10.1021/acs.jpcb.5b06445. Epub 2015 Oct 19.


Controlling the extent of viral genome release by a combination of osmotic stress and polyvalent cations.

Jin Y, Knobler CM, Gelbart WM.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Aug;92(2):022708. Epub 2015 Aug 13.


Bacteriophage P22 ejects all of its internal proteins before its genome.

Jin Y, Sdao SM, Dover JA, Porcek NB, Knobler CM, Gelbart WM, Parent KN.

Virology. 2015 Nov;485:128-34. doi: 10.1016/j.virol.2015.07.006. Epub 2015 Aug 1.


Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data.

Matthews BB, Dos Santos G, Crosby MA, Emmert DB, St Pierre SE, Gramates LS, Zhou P, Schroeder AJ, Falls K, Strelets V, Russo SM, Gelbart WM; FlyBase Consortium.

G3 (Bethesda). 2015 Jun 24;5(8):1721-36. doi: 10.1534/g3.115.018929.


Gene Model Annotations for Drosophila melanogaster: The Rule-Benders.

Crosby MA, Gramates LS, Dos Santos G, Matthews BB, St Pierre SE, Zhou P, Schroeder AJ, Falls K, Emmert DB, Russo SM, Gelbart WM; FlyBase Consortium.

G3 (Bethesda). 2015 Jun 24;5(8):1737-49. doi: 10.1534/g3.115.018937.


DNA-peptide complexes: Regulation of interferon production.

Gelbart WM.

Nat Mater. 2015 Jul;14(7):661-2. doi: 10.1038/nmat4332. No abstract available.


A Simple RNA-DNA Scaffold Templates the Assembly of Monofunctional Virus-Like Particles.

Garmann RF, Sportsman R, Beren C, Manoharan VN, Knobler CM, Gelbart WM.

J Am Chem Soc. 2015 Jun 24;137(24):7584-7. doi: 10.1021/jacs.5b03770. Epub 2015 Jun 10.


Visualizing the global secondary structure of a viral RNA genome with cryo-electron microscopy.

Garmann RF, Gopal A, Athavale SS, Knobler CM, Gelbart WM, Harvey SC.

RNA. 2015 May;21(5):877-86. doi: 10.1261/rna.047506.114. Epub 2015 Mar 9.


Viral ssRNAs are indeed compact.

Ben-Shaul A, Gelbart WM.

Biophys J. 2015 Jan 6;108(1):14-6. doi: 10.1016/j.bpj.2014.11.010. No abstract available.


FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations.

dos Santos G, Schroeder AJ, Goodman JL, Strelets VB, Crosby MA, Thurmond J, Emmert DB, Gelbart WM; FlyBase Consortium.

Nucleic Acids Res. 2015 Jan;43(Database issue):D690-7. doi: 10.1093/nar/gku1099. Epub 2014 Nov 14.


Viral RNAs are unusually compact.

Gopal A, Egecioglu DE, Yoffe AM, Ben-Shaul A, Rao AL, Knobler CM, Gelbart WM.

PLoS One. 2014 Sep 4;9(9):e105875. doi: 10.1371/journal.pone.0105875. eCollection 2014.


Role of electrostatics in the assembly pathway of a single-stranded RNA virus.

Garmann RF, Comas-Garcia M, Koay MS, Cornelissen JJ, Knobler CM, Gelbart WM.

J Virol. 2014 Sep;88(18):10472-9. doi: 10.1128/JVI.01044-14. Epub 2014 Jun 25.


Characterization of Viral Capsid Protein Self-Assembly around Short Single-Stranded RNA.

Comas-Garcia M, Garmann RF, Singaram SW, Ben-Shaul A, Knobler CM, Gelbart WM.

J Phys Chem B. 2014 Jul 10;118(27):7510-7519. doi: 10.1021/jp503050z. Epub 2014 Jun 30.


Electrophoretic mobilities of a viral capsid, its capsid protein, and their relation to viral assembly.

Vega-Acosta JR, Cadena-Nava RD, Gelbart WM, Knobler CM, Ruiz-García J.

J Phys Chem B. 2014 Feb 27;118(8):1984-9. doi: 10.1021/jp407379t. Epub 2014 Feb 14.


The assembly pathway of an icosahedral single-stranded RNA virus depends on the strength of inter-subunit attractions.

Garmann RF, Comas-Garcia M, Gopal A, Knobler CM, Gelbart WM.

J Mol Biol. 2014 Mar 6;426(5):1050-60. doi: 10.1016/j.jmb.2013.10.017. Epub 2013 Oct 19.


Reconstituted plant viral capsids can release genes to mammalian cells.

Azizgolshani O, Garmann RF, Cadena-Nava R, Knobler CM, Gelbart WM.

Virology. 2013 Jun 20;441(1):12-7. doi: 10.1016/j.virol.2013.03.001. Epub 2013 Apr 19.


In vitro quantification of the relative packaging efficiencies of single-stranded RNA molecules by viral capsid protein.

Comas-Garcia M, Cadena-Nava RD, Rao AL, Knobler CM, Gelbart WM.

J Virol. 2012 Nov;86(22):12271-82. doi: 10.1128/JVI.01695-12. Epub 2012 Sep 5.


Automatic categorization of diverse experimental information in the bioscience literature.

Fang R, Schindelman G, Van Auken K, Fernandes J, Chen W, Wang X, Davis P, Tuli MA, Marygold SJ, Millburn G, Matthews B, Zhang H, Brown N, Gelbart WM, Sternberg PW.

BMC Bioinformatics. 2012 Jan 26;13:16. doi: 10.1186/1471-2105-13-16.


Self-assembly of viral capsid protein and RNA molecules of different sizes: requirement for a specific high protein/RNA mass ratio.

Cadena-Nava RD, Comas-Garcia M, Garmann RF, Rao AL, Knobler CM, Gelbart WM.

J Virol. 2012 Mar;86(6):3318-26. doi: 10.1128/JVI.06566-11. Epub 2011 Dec 28. Erratum in: J Virol. 2019 Feb 5;93(4):.


Visualizing large RNA molecules in solution.

Gopal A, Zhou ZH, Knobler CM, Gelbart WM.

RNA. 2012 Feb;18(2):284-99. doi: 10.1261/rna.027557.111. Epub 2011 Dec 21.


The size of RNA as an ideal branched polymer.

Fang LT, Gelbart WM, Ben-Shaul A.

J Chem Phys. 2011 Oct 21;135(15):155105. doi: 10.1063/1.3652763.


Rescue of infectious particles from preassembled alphavirus nucleocapsid cores.

Snyder JE, Azizgolshani O, Wu B, He Y, Lee AC, Jose J, Suter DM, Knobler CM, Gelbart WM, Kuhn RJ.

J Virol. 2011 Jun;85(12):5773-81. doi: 10.1128/JVI.00039-11. Epub 2011 Apr 6.


Salt-dependent DNA-DNA spacings in intact bacteriophage λ reflect relative importance of DNA self-repulsion and bending energies.

Qiu X, Rau DC, Parsegian VA, Fang LT, Knobler CM, Gelbart WM.

Phys Rev Lett. 2011 Jan 14;106(2):028102. Epub 2011 Jan 12.


A sequential folding model predicts length-independent secondary structure properties of long ssRNA.

Fang LT, Yoffe AM, Gelbart WM, Ben-Shaul A.

J Phys Chem B. 2011 Mar 31;115(12):3193-9. doi: 10.1021/jp110680e. Epub 2011 Mar 3.


Exploiting fluorescent polymers to probe the self-assembly of virus-like particles.

Cadena-Nava RD, Hu Y, Garmann RF, Ng B, Zelikin AN, Knobler CM, Gelbart WM.

J Phys Chem B. 2011 Mar 17;115(10):2386-91. doi: 10.1021/jp1094118. Epub 2011 Feb 22.


The ends of a large RNA molecule are necessarily close.

Yoffe AM, Prinsen P, Gelbart WM, Ben-Shaul A.

Nucleic Acids Res. 2011 Jan;39(1):292-9. doi: 10.1093/nar/gkq642. Epub 2010 Sep 1.


Multishell structures of virus coat proteins.

Prinsen P, van der Schoot P, Gelbart WM, Knobler CM.

J Phys Chem B. 2010 Apr 29;114(16):5522-33. doi: 10.1021/jp911040z.


Prepublication data sharing.

Toronto International Data Release Workshop Authors, Birney E, Hudson TJ, Green ED, Gunter C, Eddy S, Rogers J, Harris JR, Ehrlich SD, Apweiler R, Austin CP, Berglund L, Bobrow M, Bountra C, Brookes AJ, Cambon-Thomsen A, Carter NP, Chisholm RL, Contreras JL, Cooke RM, Crosby WL, Dewar K, Durbin R, Dyke SO, Ecker JR, El Emam K, Feuk L, Gabriel SB, Gallacher J, Gelbart WM, Granell A, Guarner F, Hubbard T, Jackson SA, Jennings JL, Joly Y, Jones SM, Kaye J, Kennedy KL, Knoppers BM, Kyrpides NC, Lowrance WW, Luo J, MacKay JJ, Martín-Rivera L, McCombie WR, McPherson JD, Miller L, Miller W, Moerman D, Mooser V, Morton CC, Ostell JM, Ouellette BF, Parkhill J, Raina PS, Rawlings C, Scherer SE, Scherer SW, Schofield PN, Sensen CW, Stodden VC, Sussman MR, Tanaka T, Thornton J, Tsunoda T, Valle D, Vuorio EI, Walker NM, Wallace S, Weinstock G, Whitman WB, Worley KC, Wu C, Wu J, Yu J.

Nature. 2009 Sep 10;461(7261):168-70. doi: 10.1038/461168a.


Phase diagram of self-assembled viral capsid protein polymorphs.

Lavelle L, Gingery M, Phillips M, Gelbart WM, Knobler CM, Cadena-Nava RD, Vega-Acosta JR, Pinedo-Torres LA, Ruiz-Garcia J.

J Phys Chem B. 2009 Mar 26;113(12):3813-9.


Large-scale functional annotation and expanded implementations of the P{wHy} hybrid transposon in the Drosophila melanogaster genome.

Myrick KV, Huet F, Mohr SE, Alvarez-García I, Lu JT, Smith MA, Crosby MA, Gelbart WM.

Genetics. 2009 Jul;182(3):653-60. doi: 10.1534/genetics.109.103762. Epub 2009 Apr 27.


Virology. Pressurized viruses.

Gelbart WM, Knobler CM.

Science. 2009 Mar 27;323(5922):1682-3. doi: 10.1126/science.1170645. No abstract available.


The force acting on a polymer partially confined in a tube.

Prinsen P, Fang LT, Yoffe AM, Knobler CM, Gelbart WM.

J Phys Chem B. 2009 Mar 26;113(12):3873-9. doi: 10.1021/jp808047u.


Curvature dependence of viral protein structures on encapsidated nanoemulsion droplets.

Chang CB, Knobler CM, Gelbart WM, Mason TG.

ACS Nano. 2008 Feb;2(2):281-6. doi: 10.1021/nn700385z.


Physical chemistry of DNA viruses.

Knobler CM, Gelbart WM.

Annu Rev Phys Chem. 2009;60:367-83. doi: 10.1146/annurev.physchem.59.032607.093728. Review.


VectorBase: a data resource for invertebrate vector genomics.

Lawson D, Arensburger P, Atkinson P, Besansky NJ, Bruggner RV, Butler R, Campbell KS, Christophides GK, Christley S, Dialynas E, Hammond M, Hill CA, Konopinski N, Lobo NF, MacCallum RM, Madey G, Megy K, Meyer J, Redmond S, Severson DW, Stinson EO, Topalis P, Birney E, Gelbart WM, Kafatos FC, Louis C, Collins FH.

Nucleic Acids Res. 2009 Jan;37(Database issue):D583-7. doi: 10.1093/nar/gkn857. Epub 2008 Nov 21.


Predicting the sizes of large RNA molecules.

Yoffe AM, Prinsen P, Gopal A, Knobler CM, Gelbart WM, Ben-Shaul A.

Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16153-8. doi: 10.1073/pnas.0808089105. Epub 2008 Oct 9.


Polytene chromosomal maps of 11 Drosophila species: the order of genomic scaffolds inferred from genetic and physical maps.

Schaeffer SW, Bhutkar A, McAllister BF, Matsuda M, Matzkin LM, O'Grady PM, Rohde C, Valente VL, Aguadé M, Anderson WW, Edwards K, Garcia AC, Goodman J, Hartigan J, Kataoka E, Lapoint RT, Lozovsky ER, Machado CA, Noor MA, Papaceit M, Reed LK, Richards S, Rieger TT, Russo SM, Sato H, Segarra C, Smith DR, Smith TF, Strelets V, Tobari YN, Tomimura Y, Wasserman M, Watts T, Wilson R, Yoshida K, Markow TA, Gelbart WM, Kaufman TC.

Genetics. 2008 Jul;179(3):1601-55. doi: 10.1534/genetics.107.086074. Epub 2008 Jul 13.


Chromosomal rearrangement inferred from comparisons of 12 Drosophila genomes.

Bhutkar A, Schaeffer SW, Russo SM, Xu M, Smith TF, Gelbart WM.

Genetics. 2008 Jul;179(3):1657-80. doi: 10.1534/genetics.107.086108. Epub 2008 Jul 13.


Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.

Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J; Harvard FlyBase curators; Berkeley Drosophila Genome Project, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M.

Nature. 2007 Nov 8;450(7167):219-32.


Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.

Lin MF, Carlson JW, Crosby MA, Matthews BB, Yu C, Park S, Wan KH, Schroeder AJ, Gramates LS, St Pierre SE, Roark M, Wiley KL Jr, Kulathinal RJ, Zhang P, Myrick KV, Antone JV, Celniker SE, Gelbart WM, Kellis M.

Genome Res. 2007 Dec;17(12):1823-36. Epub 2007 Nov 7.


Genome-scale analysis of positionally relocated genes.

Bhutkar A, Russo SM, Smith TF, Gelbart WM.

Genome Res. 2007 Dec;17(12):1880-7. Epub 2007 Nov 7.

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