Undergraduate Publications

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

2006

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

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

Subramanian S, Woolford CA, Drill E, Lu M, Jones EW. 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, 2006.

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

2005

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

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

Dilek I, Madrid M, Singh R, Urrea CP, Armitage BA. 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, 2005.

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

Jones EW, Berget PB, Burnette JM, Anderson C, Asafu-Adjei D, Avetisian S, Barrie F, Chen R, Chu B, Conroy S, Conroy S, Dill A, Eimer W, Garrity D, Greenwood A, Hamilton T, Hucko S, Jackson C, Livesey K, Monaco T, Onorato C, Otsuka M, Pai S, Schaeffer G, Shung S, Spath S, Stahlman J, Sweeney B, Wiltrout E, Yurovsky D, Zonneveld A. The Spectrum of Trp- Mutants Isolated as 5-Fluoroanthranilate Resistant Clones in Saccharomyces bayanus, Saccharomyces mikatae and Saccharomyces paradoxus. Yeast, 2005.

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

Subramanian S, Woolford CA, Lu M, Drill E, Jones EW. Pbn1p: An essential ER membrane glycoprotein required for protein folding and quality control in the endoplasmic reticulum of budding yeast. 2005.

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

Tomlinson A, Frezza B, Kofke M, Wang M, Armitage BA, Yaron D. A Structural Model for Cyanine Dyes Templated into the Minor Groove of DNA. Chem. Phys. 2005.

Tsarevsky NV, Cooper BM, Wojtyna OJ, Jahed NM, Gao H, Matyjaszewski K. Halogen Exchange in Atom Transfer Radical Polymerization as a Route to Well-defined Block Copolymers. ACS Polymer Preprints, 46(2):249-50, 2005.

Tsarevsky NV, Cooper BM, Matyjaszewski K, Silverstein MS, Shach-Caplan M, Bianco-Peled H. Nanoscale Structure of SAN-PEO-SAN Synthesized by ATRP. ACS Polymer Preprints, 46(2):301-2, 2005.

Tsarevsky NV, McKenzie B, Tang W, Matyjaszewski K. Tuning the Activity and Performance of the Catalyst in Atom Transfer Radical Polymerization and General Rules for Catalyst Selection. ACS Polymer Preprints, 46(2):482-3, 2005.

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

2004

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

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

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

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

Jamalyaria F, Rohlfs R, and Schwartz R. Queue-based method for efficient simulation of biological self-assembly systems. J. Computational Physics. 2004.

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

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

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

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

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

2003

Ettensohn CA, Illies MR, Oliveri P, De Jong DL. 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, 2003.

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

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

Puri S, Telfer H, Velliste M, Murphy RF, Linstedt AD. Dispersal of Golgi matrix proteins during mitotic Golgi disassembly. J. Cell Sci. 116,2003.

2002

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

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

Huang K, Lin J, Gajnak JA, and Murphy RF. Image Content-based Retrieval and Automated Interpretation of Fluorescence Microscope Images via the Protein Subcellular Location Image Database. Proceedings of the 2002 IEEE International Symposium on Biomedical Imaging (ISBI 2002):325-328, 2002.

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

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

Soto S, Velliste M, Murphy RF. Computational Modeling of Drug Effects on Protein Subcellular Location. Mol. Biol. Cell 13, 2002.

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

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

2001

Cao R, Venezia CF, Armitage BA. Investigation of DNA Binding Modes for a Symmetrical Cyanine Dye Trication: Effect of DNA Sequence and Structure. J Biomol Struct Dyn 18:844-856, 2001.

Csink AK, Bounoutas A, Griffith ML, Sabl JF, Sage BT. Differential gene silencing by trans heterochromatin in Drosophila melanogaster. Genetics. 2001.

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

Murphy RF, Velliste M, Yao J, Porreca G. Searching Online Journals for Fluorescence Microscope Images Depicting Protein Subcellular Location Patterns. Proceedings of the 2nd IEEE International Symposium on Bio-Informatics and Biomedical Engineering (BIBE 2001):119-128, 2001.

Porreca MV, Velliste M, Murphy RF. Improved Classification of Subcellular Location Patterns in Fluorescence Microscope Images using Image Resampling and Support Vector Machines. Mol. Biol. Cell 12:259a, 2001.

Ranganathan S, Scudiere S, Bowser R. 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, 2001.

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

2000

Hodor PG, Illies MR, Broadley S, Ettensohn CA. 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, 2000.

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