Undergraduate Publications-Department of Biological Sciences - Carnegie Mellon University

Undergraduate Publications

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


McCauley BS, Akyar E, Filliger L, Hinman VF. Expression of wnt and frizzled genes during early sea star development. Gene Expr Patterns. 2013 Jul 27. doi:pii: S1567-133X(13)00084-7. 10.1016/j.gep.2013.07.007. [Epub ahead of print]

Yankura KA, Koechlein CS, Cryan AF, Cheatle A, Hinman VF. Gene regulatory network for neurogenesis in a sea star embryo connects broad neural specification and localized patterning. Proc Natl Acad Sci U S A. 2013 May 6.

Dykstra KM, Ulengin I, Delrose N and Lee TH. Identification of discrete sites in Yip1A necessary for regulation of endoplasmic reticulum structure. PloS One 8(1):e54413. Epub 2013 Jan 14.


Stolzer M, Lai H, Xu M, Sathaye D, Vernot B, Durand D. Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees. Bioinformatics. 2012 Sep 15;28(18):i409-i415.

Fanning S, Xu W, Beaurepaire C, Suhan J, Nantel A, Mitchell A. Functional control of the Candida albicans cell wall by catalytic protein kinase A subunit Tpk1. Mol Microbiol. 2012 Aug 9. doi: 10.1111/j.1365-2958.2012.08193.x.

Kunttas-Tatli E, Zhou MN, Zimmerman S, Molinar O, Zhouzheng F, Carter K, Kapur M, Cheatle A, Decal R, McCartney BM. Destruction complex function in the Wnt signaling pathway of Drosophila requires multiple interactions between Adenomatous polyposis coli 2 and Armadillo. Genetics. 2012 Mar;190(3):1059-75. Epub 2011 Dec 14.

Hovis KR, Ramnath R, Dahlen JE, Romanova AL, Larocca G, Bier ME, Urban NN. Activity regulates functional connectivity from the vomeronasal organ to the accessory olfactory bulb. J Neurosci. 2012 Jun 6;32(23):7907-16.

Finkel JS, Xu W, Huang D, Hill EM, Desai JV, et al. (2012) Portrait of Candida albicans Adherence Regulators. PLoS Pathog 8(2): e1002525. doi:10.1371/journal.ppat.1002525


Dahlen JE, Jimenez DA, Gerkin RC, Urban NN. Morphological analysis of activity-reduced adult-born neurons in the mouse olfactory bulb. Front Neurosci. 5:66, 2011. Epub 2011 May 9.

Finkel JS, Yudanin N, Nett JE, Andes DR, Mitchell AP. Application of the systematic "DAmP" approach to create a partially defective C. albicans mutant. Fungal Genet Biol 48, 1056-1061, 2011. PMID: 21820070.

Flynn CJ, Sharma T, Ruffins SW, Guerra SL, Crowley JC, Ettensohn CA. High- resolution, three-dimensional mapping of gene expression using GeneExpressMap (GEM). Dev. Biol.,357, 532-540, 2011. PMID: 21741377.

Hitchens TK, Ye Q, Eytan DF, Janjic JM, Ahrens ET, Ho C. (19) F MRI detection of acute allograft rejection with in vivo perfluorocarbon labeling of immune cells. Magn Reson Med. 2011 65, 11-45-1154.

Truschel ST, Sengupta D, Foote A, Heroux A, Macbeth M, Linstedt AD. Structure of the membrane tethering GRASP domain reveals a unique PDZ ligand interaction that mediates Golgi biogenesis, J Biol Chem. 2011. Epub PMID: 21515684

Yuan Y, Shen T-J, Gupta P, Ho NT, Simplaceanu V, Tam TCS, Hofreiter M, Cooper A, Campbell KL, Ho C. A Biochemical-Biophysical Study of Hemoglobin from Wooly Mammoth, Asian Elephant, and Humans. Biochemistry 50, 7350-7360, 2011.

Zhou MN, Kunttas-Tatli E, Zimmerman S, Zhouzheng F, McCartney BM. Cortical localization of APC2 plays a role in actin organization but not in Wnt signaling in Drosophila. Journal of Cell Science, 124(Pt 9):1589-600, 2011 May 1.


Stamateris RE, Rafiq K, Ettensohn CA. The expression and distribution of Wnt and Wnt receptor mRNAs during early sea urchin development. Gene Expr. Patterns 10: 60-64, 2010.

Yankura KA, Martik ML, Jennings CK, Hinman VF. Uncoupling of complex regulatory patterning during evolution of larval development in echinoderms. BMC Biol. 8:143, 2010 Nov 30.

McCauley BS, Weideman E, Hinman VF. A conserved gene regulatory network subcircuit drives different developmental fates in the vegetal pole of highly divergent echinoderm embryos. Developmental Biology. 340(2):200-208, 2010.

Shruti S, Remmers CL, Vaidya AK, Fitzpatrick JA, Bruchez MP, Barth AL. Activity-regulated expression of the brain-specific β4 subunit controls BK channel fate (submitted).

Tristram-Nagle S, Kim DJ, Akhunzada N, Kučerka N, Mathai JC, Katsaras J, Zeidel M, Nagle JF. Structure and water permeability of fully hydrated diphytanoyl PC. Chem Phys Lipids. 2010.

Zimmerman SG, Thorpe LM, Medrano VR, Mallozzi CA, McCartney BM. Apical constriction and invagination downstream of the canonical Wnt signaling pathway requires Rho1 and Myosin II. Developmental Biology. 340(1): 54-66, 2010.


Hackney DD, Baek N, Snyder AC. Half-site inhibition of dimeric kinesin head domains by monomeric tail domains. Biochemistry. 48(15):3448-56, 2009.   

Webb RL, Rozov O, Watkins S, McCartney BM. Using Total Internal Reflection Fluorescence (TIRF) microscopy to visualize cortical microtubules in the Drosophila syncytial embryo. Developmental Dynamics. 238(10): 2622-2632, 2009.


Jones EW, Berget PB, Burnette JM 3rd, 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, S. mikatae and S. paradoxus. Yeast. 25(1):41-6, 2008.

Nain AS, Phillippi JA, Sitti M, MacKrell J, Campbell PG, Amon C. Control of cell behavior by aligned micro/nanofibrous biomaterial scaffolds fabricated by spinneret-based tunable engineered parameters (STEP) technique. Small. 4: 1153-1159, 2008.

Nisha P, Plank JL, Csink AK. Analysis of chromatin structure of genes silenced by heterochromatin in trans. Genetics. 179:359–373, 2008.

Sage BT, Wu MD, Csink AK. Interplay of developmentally regulated gene expression and heterochromatic silencing in trans in Drosophila. Genetics. 178 749–759, 2008.

Sweeney B, Zhang T, Schwartz R. Exploring the parameter space of complex self-assembly through virus capsid models. Biophys J. 94(3): 772-783, 2008.

Tang L, Sahasranaman A, Jakovljevic J, Schleifman E, Woolford JL., Jr. Interactions among Ytm1, Erb1, and Nop7 required for assembly of the Nop7-subcomplex in yeast preribosomes. Mol Biol Cell. 19:2844–2856, 2008.

Tang W, Kwak Y, Braunecker W, Tsarevsky NV, Coote ML, Matyjaszewski K. Understanding atom transfer radical polymerization: effect of ligand and initiator structures on the equilibrium constants. J Am Chem Soc. 130(32):10702-13, 2008.

Ye Q, Wu YL, Foley LM, Hitchens TK, Eytan DF, Shirwan H, Ho C. Longitudinal tracking of recipient macrophages in a rat chronic cardiac allograft rejection model with noninvasive magnetic resonance imaging using micrometer-sized paramagnetic iron oxide particles. Circulation. 118:149–156, 2008.


Bagley J, LaRocca G, Jimenez DA, Urban NN. Adult neurogenesis and specific replacement of interneuron subtypes in the mouse main olfactory bulb. BMC neuroscience. 8:92, 2007.

Pennington G, Smith CA, Shackney S, Schwartz R. Reconstructing tumor phylogenies from heterogeneous single-cell data. J Bioinform Comput Biol. 5(2a):407-427, 2007.

Pfenning AR, Schwartz R, Barth AL. A comparative genomics approach to identifying the plasticity transcriptome. BMC Neurosci. 8:20, 2007.


Castellana N, Dhamdhere K, Sridhar S, Schwartz R. Relaxing haplotype block models for association testing. Pac Symp Biocomput. 454-66, 2006.

Dragulescu-Andrasi A, Rapireddy S, Frezza BM, Gayathri C, Gil RR, Ly DH. J Am Chem Soc. 128:10258–10267, 2006.

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

Matyjaszewski K, Jakubowski W, Min K, Tang W, Huang J, Braunecker WA, Tsarevsky NV. Diminishing catalyst concentration in atom transfer radical polymerization with reducing agents. Proc Natl Acad Sci USA. 103:15309–15314, 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.


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.

Sage BT, Jones JL, Holmes AL, Wu MD, Csink AK. Sequence elements in cis influence heterochromatic silencing in trans. Mol. Cell. Biol. 25 377–388, 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.


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.


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.


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.


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.


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.