Undergraduate Publications

The following publications from 2000 to the present include undergraduate authors:


Hodor PG, Illies MR, Broadley S, Ettensohn CA. 2000. Cell-substrate interactions during sea urchin gastrulation: migrating primary mesenchyme cells interact with and align extracellular matrix fibers that contain ECM3, a molecule with NG2-like and multiple calcium-binding domains. Dev Biol 222:181-194.

McCallum SA, Hitchens TK, Torborg C, Rule GS. 2000. Ligand-induced changes in the structure and dynamics of a human class Mu glutathione S-transferase. Biochemistry 39:7343-7356.

Cao R, Venezia CF, Armitage BA. 2001. Investigation of DNA binding modes for a symmetrical cyanine dye trication: effect of DNA sequence and structure. J Biomol Struct Dyn 18:844-856.

Kushon SA, Jordan JP, Seifert JL, Nielsen H, Nielsen PE, Armitage BA. 2001. Effect of Secondary Structure on the Thermodynamics and Kinetics of PNA Hybridization to DNA Hairpins. J. Am. Chem. Soc. 123:10805-10813.

Ranganathan S, Scudiere S, Bowser R. 2001. Hyperphosphorylation of the retinoblastoma gene product and altered subcellular distribution of E2F-1 during Alzheimer's disease and amyotrophic lateral sclerosis. J Alzheimers Dis 3:377-385.

Vieta M, Vanni S. 2001. Deformation Quantification Algorithm.

Csink AK, Bounoutas A, Griffith ML, Sabl JF, Sage BT. 2002. Differential gene silencing by trans-heterochromatin in Drosophila melanogaster. Genetics 160:257-269.

Gupta SS, Stadler M, Noser CA, Ghosh A, Steinhoff B, Lenoir D, Horwitz CP, Schramm KW, Collins TJ. 2002. Rapid total destruction of chlorophenols by activated hydrogen peroxide. Science 296:326-328.

Illies MR, Peeler MT, Dechtiaruk AM, Ettensohn CA. 2002. Cloning and developmental expression of a novel, secreted frizzled-related protein from the sea urchin, Strongylocentrotus purpuratus. Mech Dev 113:61-64.

Illies MR, Peeler MT, Dechtiaruk AM, Ettensohn CA. 2002. Identification and developmental expression of new biomineralization proteins in the sea urchin Strongylocentrotus purpuratus. Dev Genes Evol 212:419-431.

Sweet HC, Gehring M, Ettensohn CA. 2002. LvDelta is a mesoderm-inducing signal in the sea urchin embryo and can endow blastomeres with organizer-like properties. Development 129:1945-1955.

Velliste M, Porreca G, Murphy RF. 2002. Numerical features for a systematics of protein subcellular location. Cytometry Supplement 11:41.

Ettensohn CA, Illies MR, Oliveri P, De Jong DL. 2003. Alx1, a member of the Cart1/Alx3/Alx4 subfamily of Paired-class homeodomain proteins, is an essential component of the gene network controlling skeletogenic fate specification in the sea urchin embryo. Development 130:2917-2928.

Murphy RF, Velliste M, Porreca G. 2003. Robust Numerical Features for Description and Classification of Subcellular Location Patterns in Fluorescence Microscope Images. The Journal of VLSI Signal Processing V35:311-321.

Pintauer T, McKenzie B, Matyjaszewski K. 2003. Towards Structural and Mechanistic Understanding of Transition Metal Catalyzed Atom Transfer Radical Processes. ACS Symp. Ser 854:130-147.

Bangal PR, Lam DMK, Peteanu LA, van der Auweraer M. 2004. Excited-State Localization in a 3-Fold-Symmetric Molecule as Probed by Electroabsorption Spectroscopy. J. Phys. Chem. B 108:16834-16840.

Barth AL, Gerkin RC, Dean KL. 2004. Alteration of neuronal firing properties after in vivo experience in a FosGFP transgenic mouse. J Neurosci 24:6466-6475.

Cackowski FC, Xu L, Hu B, Cheng SY. 2004. Identification of two novel alternatively spliced Neuropilin-1 isoforms. Genomics 84:82-94.

Jakovljevic J, de Mayolo PA, Miles TD, Nguyen TM, Leger-Silvestre I, Gas N, Woolford JL, Jr. 2004. The carboxy-terminal extension of yeast ribosomal protein S14 is necessary for maturation of 43S preribosomes. Mol Cell 14:331-342.

Puri S, Telfer H, Velliste M, Murphy RF, Linstedt AD. 2004. Dispersal of Golgi matrix proteins during mitotic Golgi disassembly. J Cell Sci 117:451-456.

Puskar K, Apeltsin L, Ta'asan S, Schwartz R, LeDuc PR. 2004. Understanding actin organization in cell structure through lattice based Monte Carlo simulations. Mech Chem Biosyst 1:123-131.

Sarbu T, Lin KY, Ell J, Siegwart DJ, Spanswick J, Matyjaszewski K. 2004. Polystyrene with Designed Molecular Weight Distribution by Atom Transfer Radical Coupling. Macromolecules 37:3120-3127.

Sarbu T, Lin KY, Spanswick J, Gil RR, Siegwart DJ, Matyjaszewski K. 2004. Synthesis of Hydroxy-Telechelic Poly(methyl acrylate) and Polystyrene by Atom Transfer Radical Coupling. Macromolecules 37:9694-9700.

Shach-Caplan M., Bianco-Peled H, Silverstein MS, Tsarevsky NV, Cooper BM, Matyjaszewski K. 2004. Nanoscale Structure of Amorphous/Crystalline/Amorphous Triblock Copolymers. Polym. Mat. Sci. Eng 91:843.

Burnette JM, Miyamoto-Sato E, Schaub MA, Conklin J, Lopez AJ. 2005. Subdivision of large introns in Drosophila by recursive splicing at nonexonic elements. Genetics 170:661-674.

Conklin JF, Goldman A, Lopez AJ. 2005. Stabilization and analysis of intron lariats in vivo. Methods 37:368-375.

Dilek I, Madrid M, Singh R, Urrea CP, Armitage BA. 2005. Effect of PNA Backbone Modifications on Cyanine Dye Binding to PNA-DNA Duplexes Investigated by Optical Spectroscopy and Molecular Dynamics Simulations. J. Am. Chem. Soc. 127:3339-3345.

Jamalyaria F, Rohlfs R, Schwartz R. 2005. Queue-based method for efficient simulation of biological self-assembly systems. Journal of Computational Physics 204:100-120.

Shakiryanova D, Tully A, Hewes RS, Deitcher DL, Levitan ES. 2005. Activity-dependent liberation of synaptic neuropeptide vesicles. Nat Neurosci 8:173-178.

Sumerlin BS, Tsarevsky NV, Louche G, Lee RY, Matyjaszewski K. 2005. Highly Efficient "Click" Functionalization of Poly(3-azidopropyl methacrylate) Prepared by ATRP. Macromolecules 38:7540-7545.

Wiltrout ME, Giovannelli JL, Simplaceanu V, Lukin JA, Ho NT, Ho C. 2005. A biophysical investigation of recombinant hemoglobins with aromatic B10 mutations in the distal heme pockets. Biochemistry 44:7207-7217.

Greenwood AI, Tristram-Nagle S, Nagle JF. 2006. Partial molecular volumes of lipids and cholesterol. Chemistry and Physics of Lipids 143:1-10.

Shakiryanova D, Tully A, Levitan ES. 2006. Activity-dependent synaptic capture of transiting peptidergic vesicles. Nat Neurosci 9:896-900.

Subramanian S, Woolford CA, Drill E, Lu M, Jones EW. 2006. Pbn1p: an essential endoplasmic reticulum membrane protein required for protein processing in the endoplasmic reticulum of budding yeast. Proc Natl Acad Sci U S A 103:939-944.

Tomlinson A, Frezza B, Kofke M, Wang M, Armitage BA, Yaron D. 2006. A structural model for cyanine dyes templated into the minor groove of DNA. Chemical Physics 325:36-47.