Publications

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Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.
Stoltzfus A, Lapp H, Matasci N, Deus H, Sidlauskas B, Zmasek CM, Vaidya G, Pontelli E, Cranston K, Vos R, et al. 2013. Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. BMC bioinformatics 14: 158. DOI: 10.1186/1471-2105-14-158
Delineating antibody recognition in polyclonal sera from patterns of HIV-1 isolate neutralization.
Georgiev IS, Doria-Rose NA, Zhou T, Kwon YD, Staupe RP, Moquin S, Chuang GY, Louder MK, Schmidt SD, Altae-Tran HR, et al. 2013. Delineating antibody recognition in polyclonal sera from patterns of HIV-1 isolate neutralization. Science (New York, N.Y.) 340(6133): 751-6. DOI: 10.1126/science.1233989
Investigating polymer thiolation in gene delivery.
Bacalocostantis I, Mane VP, Goodley AS, Bentley WE, Muro S, Kofinas P. 2013. Investigating polymer thiolation in gene delivery. Journal of biomaterials science. Polymer edition 24(8): 912-26. DOI: 10.1080/09205063.2012.727266
Chirality-Mediated Mechanical and Structural Properties of Oligopeptide Hydrogels.
Taraban MB, Feng Y, Hammouda B, Hyland LL, Yu YB. 2012. Chirality-Mediated Mechanical and Structural Properties of Oligopeptide Hydrogels. Chemistry of materials : a publication of the American Chemical Society 24(12): 2299-2310.
A practical implementation of de-Pake-ing via weighted Fourier transformation.
Sani MA, Weber DK, Delaglio F, Separovic F, Gehman JD. 2013. A practical implementation of de-Pake-ing via weighted Fourier transformation. PeerJ 1: e30. DOI: 10.7717/peerj.30
Misplaced helix slows down ultrafast pressure-jump protein folding.
Prigozhin MB, Liu Y, Wirth AJ, Kapoor S, Winter R, Schulten K, Gruebele M. 2013. Misplaced helix slows down ultrafast pressure-jump protein folding. Proceedings of the National Academy of Sciences of the United States of America 110(20): 8087-92. DOI: 10.1073/pnas.1219163110
An interplay between electrostatic and polar interactions in peptide hydrogels.
Joyner K, Taraban MB, Feng Y, Yu YB. 2013. An interplay between electrostatic and polar interactions in peptide hydrogels. Biopolymers 100(2): 174-83. DOI: 10.1002/bip.22194
Mass spectrometry quantification revealed accumulation of C-terminal fragment of apolipoprotein E in the Alzheimer's frontal cortex.
Wang M, Turko IV. 2013. Mass spectrometry quantification revealed accumulation of C-terminal fragment of apolipoprotein E in the Alzheimer's frontal cortex. PloS one 8(4): e61498. DOI: 10.1371/journal.pone.0061498
Universal proteolysis and MS(n) for N- and O-glycan branching analysis.
Schiel JE, Smith NJ, Phinney KW. 2013. Universal proteolysis and MS(n) for N- and O-glycan branching analysis. Journal of mass spectrometry : JMS 48(4): 533-8. DOI: 10.1002/jms.3196
Rapid degradation of Streptococcus pyogenes biofilms by PlyC, a bacteriophage-encoded endolysin.
Shen Y, Köller T, Kreikemeyer B, Nelson DC. 2013. Rapid degradation of Streptococcus pyogenes biofilms by PlyC, a bacteriophage-encoded endolysin. The Journal of antimicrobial chemotherapy 68(8): 1818-24. DOI: 10.1093/jac/dkt104
Optically clear alginate hydrogels for spatially controlled cell entrapment and culture at microfluidic electrode surfaces.
Betz JF, Cheng Y, Tsao CY, Zargar A, Wu HC, Luo X, Payne GF, Bentley WE, Rubloff GW. 2013. Optically clear alginate hydrogels for spatially controlled cell entrapment and culture at microfluidic electrode surfaces. Lab on a chip 13(10): 1854-8. DOI: 10.1039/c3lc50079a
Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains.
Zhu J, Ofek G, Yang Y, Zhang B, Louder MK, Lu G, McKee K, Pancera M, Skinner J, Zhang Z, et al. 2013. Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains. Proceedings of the National Academy of Sciences of the United States of America 110(16): 6470-5. DOI: 10.1073/pnas.1219320110
Thermococcus kodakarensis has two functional PCNA homologs but only one is required for viability.
Pan M, Santangelo TJ, Čuboňová L, Li Z, Metangmo H, Ladner J, Hurwitz J, Reeve JN, Kelman Z. 2013. Thermococcus kodakarensis has two functional PCNA homologs but only one is required for viability. Extremophiles : life under extreme conditions 17(3): 453-61. DOI: 10.1007/s00792-013-0526-8
Implications of protein fold switching.
Bryan PN, Orban J. 2013. Implications of protein fold switching. Current opinion in structural biology 23(2): 314-6. DOI: 10.1016/j.sbi.2013.03.001
Archaeal DNA polymerase D but not DNA polymerase B is required for genome replication in Thermococcus kodakarensis.
Cubonová L, Richardson T, Burkhart BW, Kelman Z, Connolly BA, Reeve JN, Santangelo TJ. 2013. Archaeal DNA polymerase D but not DNA polymerase B is required for genome replication in Thermococcus kodakarensis. Journal of bacteriology 195(10): 2322-8. DOI: 10.1128/JB.02037-12