Carnegie Mellon University


Bachert C, Fimmel CJ, Linstedt AD*. Furin cleavage of cis-Golgi protein GP73 produces marker for liver disease. Traffic 8:1415-23, 2007.

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(1):92, 2007.

Ballou B, Ernst LA, Andreko S, Harper TF, Fitzpatrick JAJ, Waggoner AS*, Bruchez MP*. Sentinel Lymph Node Imaging using Quantum Dots in Mouse Tumor Models, Bioconjug Chem 2007, 18(2):389-396.

Barth AL*. Visualizing circuits and systems using transgenic reporters of neural activity. Current Opinion in Neurobiology, 2007. (epub Nov 23 2007)

Benvin AL, Creeger Y, Fisher GW, Ballou B, Waggoner AS*, Armitage BA*. Fluorescent DNA nanotags: supramolecular fluorescent labels based on intercalating dye arrays assembled on nanostructured DNA templates. J Am Chem Soc. 129(7):2025-34, 2007. Epub 2007 Jan 26.

Blankenship JR§, Mitchell AP*. The fungal frontier. Genome Biol. 8(5):305, 2007.

Cannon RC, Gewaltig MO, Gleeson P, Bhalla US, Cornelis H, Hines ML, Howell FW, Muller E, Stiles JR*, Wils S, De Schutter E. Interoperability of neuroscience modeling software: current status and future directions. Neuroinformatics. 5(2):127-38, 2007 Summer.

Castro JB, Hovis KR, Urban NN*. Recurrent dendrodendritic inhibition of accessory olfactory bulb mitral cells requires activation of group I metabotropic glutamate receptors. J. Neurosci. 27(21):5664-71, 2007.

Chakraborty SK, Fitzpatrick JAJ, Phillippi JA, Andreko S, Waggoner AS*, Bruchez MP*, Ballou, B. Cholera Toxin B Conjugated Quantum Dots for Live Cell Labeling, Nano Letters 2007, 7(9),2618-2626.

Chebira A, Barbotin Y, Jackson C, Merryman T, Srinivasa G, Murphy RF*, Kovacević J. A multiresolution approach to automated classification of protein subcellular location images. BMC Bioinformatics. 8:210, 2007 Jun 19.

Chen SC, Zhao T, Gordon GJ, Murphy RF*. Automated image analysis of protein localization in budding yeast. Bioinformatics. 23(13):i66-71, 2007 Jul 1.

Chiang LY, Sheppard DC, Bruno VM, Mitchell AP*, Edwards JE Jr, Filler SG. Candida albicans protein kinase CK2 governs virulence during oropharyngeal candidiasis. Cell Microbiol 9, 233-245, 2007.

Eagleson KL, Schlueter McFadyen-Ketchum LJ, Ahrens ET*, Mills PH, Does MD, Nickols J, Levitt P. Disruption of Foxg1 expression by knock-in of cre recombinase: effects on the development of the mouse telencephalon. Neuroscience. 148(2):385-99, 2007 Aug 24. Epub 2007 Jul 19.

Ermentrout GB, Galán RF, Urban NN*. Relating neural dynamics to neural coding. Physical Review Letters. Physical Review Letters. 99. 248103, 2007. Faculty of 1000 Must Read.

Ettensohn CA*, Kitazawa C, Cheers MS, Leonard JD and Sharma T. Gene regulatory networks and developmental plasticity in the early sea urchin embryo: alternative deployment of the skeletogenic gene regulatory network. Development, 134:3077-3087, 2007.

Feinstein T, Linstedt AD*. Mitogen-activated Protein Kinase Kinase-dependent Golgi Unlinking Occurs in G2 phase and Promotes the G2/M Cell Cycle Transition. Mol. Biol. of the Cell, 18:594-604, 2007.

Fu H, Doll B, McNelis T, Hollinger JO*. Osteoblast differentiation in vitro and in vivo promoted by Osterix. J Biomed Mater Res A. 83(3):770-8, 2007 Dec 1.

Galán RF, Ermentrout GB, Urban NN*. Reliability and stochastic synchronization in type I vs. type II neural oscillators. Neurocomputing, 70: 2102-2106, 2007.

Galán RF, Ermentrout GB, Urban NN*. Stochastic dynamics of uncoupled neural oscillators: Fokker Planck studies with the finite element method. Physical Review E. 76(5 Pt 2):056110, 2007.

García Osuna E, Hua J, Bateman NW, Zhao T, Berget PB*, Murphy RF*. Large-scale automated analysis of location patterns in randomly tagged 3T3 cells. Ann Biomed Eng. 35(6):1081-7, 2007 Jun. Epub 2007 Feb 7.

García Osuna E, Murphy RF*. Automated, systematic determination of protein subcellular location using fluorescence microscopy. Subcell Biochem. 2007;43:263-76.

Giuliano KA, Taylor DL, Waggoner AS*. Reagents to measure and manipulate cell functions. Methods Mol Biol. 356:141-63, 2007.

Glazewski S, Benedetti BL, Barth AL*. Ipsilateral sensory deprivation enhances cortical plasticity. Journal of Neuroscience, 27 (14): 3910-20, 2007.

Glory E, Murphy RF*. Automated subcellular location determination and high-throughput microscopy. Dev Cell. 12(1):7-16, 2007 Jan. Review. No abstract available.

Hackney DD*. Jump-starting kinesin, J.Cell Biol. 176, 7-9, 2007.

Hackney DD*. Processive motor movement, Science. 316, 58-59, 2007.

Hinman VF*, Davidson EH. Evolutionary plasticity of developmental gene regulatory network architecture. Proceedings National Academy of Sciences (USA); 104(49):19404-9, 2007.

Hinman VF*, Nguyen A, Davidson EH. Caught in the evolutionary act: precise cis-regulatory basis of difference in organization of gene networks of sea stars and sea urchins. Developmental Biology; 312(2):584-95, 2007.

Jackson H, Muhammad O, Daneshvar H, Nelms J, Popescu A, Vogelbaum MA, Bruchez M*, Toms SA. Quantum dots are phagocytized by macrophages and co-localize with experimental glioma, Neurosurgery 2007, 60(3):524-529.

Kellogg RA, Chebira A, Goyal A, Cuadra PA, Zappe SF, Minden JS*, Kovacevic J. Towards an image analysis toolbox for high-throughput Drosophila embryo RNAi screens, Proc. IEEE Intl. Symp. Biomed. Imaging, Arlington, VA, Apr. 2007, 288-291.

Kou Z, Cohen WW, Murphy RF*. A stacked graphical model for associating sub-images with sub-captions. Pac Symp Biocomput. 257-68, 2007.

Lanni F*, Pane DA, Weinstein SJ, Waggoner AS*. Compact flashlamp-based fluorescence imager for use under ambient-light conditions. Rev Sci Instrum. 78(3):033702, 2007 Mar.

LeDuc P, Schwartz R*. Computational models of molecular self-organization in cellular environments. Cell Biochem Biophys. 48(1):16-31, 2007.

Leonard J, Ettensohn CA*. Analysis of dishevelled localization and function in the early sea urchin embryo. Dev. Biol., 306, 50-65, 2007.

Levitan ES, Lanni F*, Shakiryanova D. In vivo imaging of vesicle motion and release at the Drosophila neuromuscular junction. Nature Protocols 2: 1117-1125, 2007.

Li D, Manjula BN, Ho NT, Simplaceanu V, Ho C*, Acharya AS. Molecular Aspects of the High Oxygen Affinity of Non-Hypertensive Hexa Pegylated Hemoglobin, [(SP-PEG5K)6-Hb].Artificial Cells, Blood Substitutes, and Biotechnology. 35,19-29, 2007.

Macbeth MR*, Bass BL. Large-scale overexpression and purification of ADARs from Saccharomyces cerevisiae for biophysical and biochemical studies. In Methods in Enzymology, (ed. J.M. Gott) Elsevier Inc., 424:319-331, 2007.

McManus CJ*, Schwartz M, Brow DA. A dynamic bulge in the U6 RNA internal stem-loop functions in spliceosome assembly and activation. RNA. 2007 Dec;13(12):2252-65, 2007. Epub 2007 Oct 9.

Mills PH†, Ahrens ET*. Theoretical MRI contrast model for exogenous T2 agents. Magn Reson Med. 57(2):442-7, 2007 Feb.

Minden JS*. Comparative Proteomics and Difference Gel Electrophoresis. BioTechniques 43, 739-745, 2007.

Morohashi N, Nakajima K, Kurihara D, Mukai Y, Mitchell AP*, Shimizu M. A nucleosome positioned by alpha2/Mcm1 prevents Hap1 activator binding in vivo. Biochem Biophys Res Commun 364, 583-588, 2007.

Nauman JV, Campbell PG, Lanni F*, Anderson JL. Diffusion of insulin-like growth factor-I and ribonuclease through fibrin gels. Biophys. J. 92:4444-4450, 2007.

Nobile CJ, Mitchell AP*. Microbial biofilms: e pluribus unum. Curr Biol. 17(10):R349-53, 2007 May 15.

Norice CT, Smith FJ Jr, Solis N, Filler SG, Mitchell AP*. Requirement for Candida albicans Sun41 in biofilm formation and virulence. Eukaryot Cell. 6(11):2046-55, 2007 Nov. Epub 2007 Sep 14.

Oh JK, Siegwart DJ, Lee HI, Sherwood G, Peteanu L, Hollinger JO*, Kataoka K, Matyjaszewski K. Biodegradable nanogels prepared by atom transfer radical polymerization as potential drug delivery carriers: synthesis, biodegradation, in vitro release, and bioconjugation. J Am Chem Soc. 129(18):5939-45, 2007 May 9. Epub 2007 Apr 18.

Pagliano O, Brown W, Rule G*, Bajzek D. Improving Animation Tutorials by Integrating Simulation, Assessment, and Feedback to Promote Active Learning. In G. Richards (Ed.), Proceedings of World Conference on E-Learning in Corporate, Government, Healthcare, and Higher Education 2007 (pp. 144-150). Chesapeake, VA: AACE, 2007.

Patrick MJ, Ernst LA, Waggoner AS*, Thai D, Tai D, Salama G. Enhanced Aqueous Solubility of Long Wavelength Voltage-Sensitive Dyes by Covalent Attachment of Polyethylene Glycol Org. Biomol. Chem., 5, 3347-3353, 2007.

Pennington G, Smith CA, Shackney S, Schwartz R*. Reconstructing tumor phylogenies from heterogeneous single-cell data. J Bioinform Comput Biol. 5(2a):407-27, 2007 Apr.

Pfenning AR, Schwartz R*, Barth AL*. A comparative genomics approach to identifying the plasticity transcriptome. BMC Neurosci. 8:20, 2007 Mar 13.

Puthenveedu MA*, Yudowski GA, von Zastrow M. Endocytosis of neurotransmitter receptors: location matters. Cell. 130(6):988-9, 2007.

Sahu SC§, Simplaceanu V, Gong Q§, Ho NT, Tian F, Prestegard JH, Ho C*. Insights into the Solution Structure of Human Deoxyhemoglobin in Absence and Presence of an Allostertic Effector. Biochemistry 46, 9973-9980, 2007.

Sellers KF, Miecznikowski J, Viswanathan S, Minden JS*, Eddy WF. Lights, Camera, Action! Systematic variation in 2-D difference gel electrophoresis images. Electrophoresis 28, 3324-3332, 2007.

Shaw RM, Fay AJ, Puthenveedu MA*, von Zastrow M, Jan YN, Jan LY. Microtubule plus-end-tracking proteins target gap junctions directly from the cell interior to adherens junctions. Cell. 128(3):547-60, 2007 Feb 9.

Shen T-J, Rogers H, Yu X, Lin F, Noguchi CT, Ho C*. Modification of Globin Gene Expression by RNA Targeting Strategies. Experimental Hematology 35, 1209-1218, 2007.

Smith JD, Chen A, Ernst LA, Waggoner AS*, Campbell PG*. Immobilization of aprotinin to fibrinogen as a novel method for controlling degradation of fibrin gels. Bioconjug Chem. 18(3):695-701, 2007 May-Jun. Epub 2007 Apr 14.

Smith JD, Fisher GW, Waggoner AS*, Campbell PG*. The use of quantum dots for analysis of chick CAM vasculature. Microvasc Res. 73(2):75-83, 2007 Mar. Epub 2006 Oct 27.

Smith JD, Melhem ME, Magge KT, Waggoner AS*, Campbell PG*. Improved growth factor directed vascularization into fibrin constructs through inclusion of additional extracellular molecules. Microvasc Res. 73(2):84-94, 2007 Mar. Epub 2007 Jan 16.

Song N, Sedgewick RD, Durand D*. Domain architecture comparison for multidomain homology identification. Journal of Computational Biology, 14(4): 496-516, 2007.

Song XJ§, Yuan Y, Simplaceanu V, Sahu SC§, Ho NT, Ho C*. A comparative NMR study of the polypeptide backbone dynamics of hemoglobin in the deoxy and carbonmonoxy forms. Biochemistry. 46(23):6795-803, 2007 Jun 12. Epub 2007 May 12.

Sridhar S, Dhamdhere K, Blelloch G, Halperin E, Ravi R, Schwartz R*. Algorithms for efficient near-perfect phylogenetic tree reconstruction in theory and practice. IEEE/ACM Trans Comput Biol Bioinform. 4(4):561-71, 2007 Oct-Dec.

Sridhar S, Lam F, Blelloch GE, Ravi R, Schwartz R*. Direct maximum parsimony phylogeny reconstruction from genotype data. BMC Bioinformatics. 8:472, 2007 Dec 5.

Srinivas M, Morel PA, Ernst LA, Laidlaw DH, Ahrens ET*. Fluorine-19 MRI for visualization and quantification of cell migration in a diabetes model. Magn Reson Med, 58(4):725-734, 2007 Oct.

Tristram-Nagle S, Nagle JF*. HIV-1 fusion peptide decreases bending energy and promotes curved fusion intermediates. Biophys J. 93(6):2048-55, 2007 Sep 15. Epub 2007 May 25.

Villar CC, Kashleva H, Nobile CJ, Mitchell AP*, Dongari-Bagtzoglou, A. Mucosal tissue invasion by Candida albicans is associated with E-cadherin degradation, mediated by transcription factor Rim101p and protease Sap5p. Infect Immun 75, 2126-2135, 2007.

Williams JB§, Ye Q, Hitchens TK, Kaufman CL, Ho C*. MRI detection of macrophages labeled using micrometer-sized iron oxide particles. J Magn Reson Imaging. 25(6):1210-8, 2007 Jun.

Wilt FH, Ettensohn CA*. Morphogenesis of biomineralized structures. In: "Handbook of Biomineralization" (E. Bauerlein, Ed.), Wiley-VCH Press, pp. 183-210, 2007.

Yudowski GA, Puthenveedu MA*, Leonoudakis D, Panicker S, Thorn KS, Beattie EC, von Zastrow M. Real-time imaging of discrete exocytic events mediating surface delivery of AMPA receptors. J Neurosci. 2007 Oct 10;27(41):11112-21.

Zhang T, Kim WT, Schwartz R*. Investigating scaling effects on virus capsid-like self-assembly using discrete event simulations. IEEE Trans Nanobioscience. 6(3):235-41, 2007 Sep.

Zhang J, Harnpicharnchai P, Jakovljevic J, Tang L, Guo Y, Oeffinger M, Rout MP, Hiley SL, Hughes T, Woolford JL Jr*. Assembly factors Rpf2 and Rrs1 recruit 5S rRNA and ribosomal proteins rpL5 and rpL11 into nascent ribosomes. Genes Dev. 21(20):2580-92, 2007 Oct 15.

Zhao T, Murphy RF*. Automated Learning of Generative Models for Subcellular Location: Building Blocks for Systems Biology. Cytometry 71A:978-990, 2007.