Carnegie Mellon University


Arevian AC, Kapoor V, Urban NN*. Dynamic Gating of Lateral inhibition in the Olfactory Bulb. Nature Neuroscience. 11(1):80-7, 2008.

Armitage BA*, Berget PB*. An Enlightening Structure-Function Relationship. Science, 319: 1195-1196, 2008.

Bajzek D, Brooks J, Jerome W, Lovett M, Rinderle J, Rule GS*, Thille C. Assessment and Instruction: Two Sides of the Same Coin. In Proceedings of World Conference on E-Learning in Corporate, Government, Healthcare, and Higher Education 2008. 2008.

Barth AL*, Wheeler ME. The barista on the bus: cellular and synaptic mechanisms for visual recognition memory. Neuron 24, 58(2):159-61, 2008.

Baughman C, Morin-Leisk J, Lee TH*. Nucleoside Diphosphate Kinase B (NDPKB) scaffolds endoplasmic reticulum membranes in vitro. Exp Cell Res, 314(14):2702-2714, 2008. Faculty of 1000 Recommended.

Bencherif SA, Srinivasan A, Horkay F, Hollinger JO*, Matyjaszewski K, Washburn NR. Influence of the degree of methacrylation on hyaluronic acid hydrogels properties. Biomaterials. 29(12):1739-49, 2008 Apr. Epub 2008 Jan 30.

Boyce M, Py BF, Ryazanov AG, Minden JS*, Long K, Ma D, Yuan J. A pharmacoproteomic approach implicates eukaryotic elongation factor 2 kinase in ER stress-induced cell death. Cell Death and Diff. 15, 589-99, 2008.

Chen S-C, Gordon GJ, Murphy RF*. Graphical Models for Structured Classification, with an Application to Interpreting Images of Protein Subcellular Location Patterns. J. Machine Learning Res. 9:651-682, 2008.

Clem RL, Celikel T, Barth AL*. Ongoing in vivo experience triggers synaptic metaplasticity in the neocortex. Science. 2008 Jan 4;319(5859):101-4.

Constantin TP, Silva GL, Robertson KL, Hamilton TP, Fague K, Waggoner AS*, Armitage BA*. Synthesis of new fluorogenic cyanine dyes and incorporation into RNA fluoromodules. Org Lett. 10(8):1561-4, 2008. Epub 2008 Mar 14.

Daneshvar H, Nelms J, Muhammad O, Jackson H, Tkach J, Davros W, Peterson T, Vogelbaum MA, Bruchez MP*, Toms SA. Imaging characteristics of zinc sulfide shell, cadmium telluride core quantum dots. Nanomedicine (Lond). 3(1):21-9, 2008 Feb.

Ermentrout GB, Galán RF, Urban NN*. Reliability, synchrony and noise. Trends Neurosci. 31(8):428-34, 2008 Aug.

Feinstein NT, Linstedt AD*. GRASP55 regulates Golgi ribbon formation. Mol. Biol. of the Cell, 19:2696–2707, 2008.

Foley LM, Hitchens TK, Melick JA, Bayir H, Ho C*, Kochanek PM. Effect of inducible nitric oxide synthase on cerebral blood flow after experimental traumatic brain injury in mice. J Neurotrauma. 25(4):299-310, 2008 Apr.

Galán RF, Ermentrout GB, Urban NN*. Optimal time scale for spike-time reliability: theory, simulations, and experiments. J Neurophysiol. 2008 Jan;99(1):277-83. Epub 2007 Oct 10.

Gibson FL, Anderson et al. Guidelines for reporting the use of gel electrophoresis in proteomics. Nat Biotech 26, 863-864, 2008.

Glory E, Newberg J, Murphy RF. Automated Comparison of Protein Subcellular Location Patterns Between Images of Normal and Cancerous Tissues. Proc IEEE Int Symp Biomed Imaging. 4540993:304-307, 2008.

Gong H, Sengupta D, Linstedt AD*, Schwartz R*. Simulated de novo assembly of Golgi compartments by selective cargo capture during vesicle budding and targeted vesicle fusion. Biophys. J., 95:1674–1688, 2008.

Greenwood AI, Pan J, Mills TT, Nagle JF*, Epand RM, Tristram-Nagle S. CRAC motif peptide of the HIV-1 gp41 protein thins SOPC membranes and interacts with cholesterol. Biochim Biophys Acta, 1778(4):1120-30, 2008 Apr. Epub 2008 Jan 16.

Guo Y, Punj V, Sengupta D, Linstedt AD*. Coat-tether interaction in Golgi organization. Mol. Biol. of the Cell, 19:2830–2843, 2008.

Hackney DD*, Stock MF. Kinesin tail domains and Mg2+ directly inhibit release of ADP from head domains in the absence of microtubules, Biochemistry. 47, 7770-7778, 2008.

Henn A, Cao W, Hackney DD*, De La Cruz EM. The ATPase cycle mechanism of the DEAD-box rRNA helicase, DbpA, J.Mol.Biol. 377, 193-205.2, 2008.

Hinkovska-Galcheva VA, Clark S, VanWay M, Hiraoka, Abe A, Borofsky M, Kunkel RG, Huang JB, Shanley T, Shayman JA, Lanni F*, Petty HR, Boxer LA. Ceramide kinase promotes Ca+2 signaling near IgG-opsonized targets and enhances phagolysosomal fusion in COS-1 cells.  J. Lipid Res. 49: 531-542, 2008.

Hodor PG, Ettensohn CA*. Mesenchymal cell fusion in the sea urchin embryo. Meth. Mol. Biol., 475, 315-334, 2008.

Hollinger JO*, Onikepe AO, MacKrell J, Einhorn T, Bradica G, Lynch S, Hart CE. Accelerated fracture healing in the geriatric, osteoporotic rat with recombinant human platelet-derived growth factor-BB and an injectable beta-tricalcium phosphate/collagen matrix. J Orthop Res. 26(1):83-90, 2008 Jan.

Janjic JM, Srinivas M, Kadayakkara DK, Ahrens ET*. Self-delivering nanoemulsions for dual fluorine-19 MRI and fluorescence detection. J Am Chem Soc., 130(9):2832-2841, 2008 Mar 5.

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 Jan.

Kerr RA, Bartol TM, Kaminsky B, Dittrich M, Chang JC, Baden SB, Sejnowski TJ, Stiles JR*. Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces. SIAM J Sci Comput. 30(6):3126, 2008 Oct 13.

Kucerka N, Nagle JF*, Sachs JN, Feller SE, Pencer J, Jackson A, Katsaras J. Lipid bilayer structure determined by the simultaneous analysis of neutron and X-ray scattering data. Biophys J, 95(5):2356-67, 2008 Sep. Epub 2008 May 23.

Lee B, LeDuc PR*, Schwartz R*. Stochastic off-lattice modeling of molecular self-assembly in crowded environments by Greens function reaction dynamics. Physical Review E, 78:031911, 2008.

Lim JK, Eggeman A, Lanni F*, Tilton RD, Majetich SA. Synthesis and single-particle optical detection of low-polydispersity plasmonic-superparamagnetic nanoparticles. Adv. Mater. 20: 1721-1726, 2008.

Maillett DH§, Simplaceanu V, Shen T-J, Ho NT, Olson JS, Ho C*. Interfacial and Distal Pocket Mutations Exhibit Additive Effects on the Structure and Function of Hemoglobin. Biochemistry 47, 10551-10563, 2008. PMC2692483

Mathai JC, Tristram-Nagle S, Nagle JF*, Zeidel ML. Structural Determinants of Water Permeability through the Lipid Membrane. J. Gen. Physiol,131:59-68, 2008.

McCartney BM*, Näthke IS. Cell regulation by the Apc protein Apc as master regulator of epithelia. Curr Opin Cell Biol. 20(2):186-93, 2008 Apr, Epub 2008 Mar 24.

McManus CJ*, Graveley BR. Getting the message out. Mol Cell. 31(1):4-6, 2008.

Mills PH§, Wu YJ, Ho C*, Ahrens ET*. Sensitive and automated detection of iron-oxide-labeled cells using phase image cross-correlation analysis. Magn Reson Imaging. 26(5):618-28, 2008 Jun. Epub 2008 May 2.

Mills TT, Toombes GE, Tristram-Nagle S, Smilgies DM, Feigenson GW, Nagle JF*. Order parameters and areas in fluid-phase oriented lipid membranes using wide angle X-ray scattering. Biophys J, 95(2):669-81, 2008 Jul. Epub 2008 Apr 4.

Mills TT, Tristram-Nagle S, Heberle FA, Morales NF, Zhao J, Wu J, Toombes GE, Nagle JF*, Feigenson GW. Liquid-liquid domains in bilayers detected by wide angle X-ray scattering. Biophys J, 95(2):682-90, 2008 Jul. Epub 2008 Apr 4.

Minden J*. Dissection of the embryonic brain using photoactivated gene expression. Adv Exp Med Biol 628, 57-68, 2008.

Misra N, Lees D, Zhang T, Schwartz R*. Pathway complexity of model virus capsid assembly systems. Computational and Mathematical Methods in Medicine, 9(3):277-293, 2008.

Misra N, Schwartz R*. Efficient stochastic sampling of first-passage times with applications to self-assembly simulations. Journal of Chemical Physics, 129:204109, 2008.

Mitchell AP*. A VAST staging area for regulatory proteins. Proc Natl Acad Sci U S A. 2008 May 20;105(20):7111-2. Epub 2008 May 12.

Morin-Leisk J, Lee TH*. Nucleotide dependent self-assembly of Nucleoside Diphosphate Kinase (NDPK) in vitro. Biochimica et Biophysica Acta, 1784(12):2045-2051, 2008.

Murphy RF*. Automated Proteome-Wide Determination of Subcellular Location Using High Throughput Microscopy. Proc IEEE Int Symp Biomed Imaging. 2008 May 14;2008:308-311.

N'Diaye EN, Hanyaloglu AC, Kajihara KK, Puthenveedu MA*, Wu P, von Zastrow M, Brown EJ. The ubiquitin-like protein PLIC-2 is a negative regulator of G protein-coupled receptor endocytosis. Mol Biol Cell. 19(3):1252-60, 2008 Mar.

Nagle JF*, Mathai JC, Zeidel ML, Tristram-Nagle S. Theory of passive permeability through lipid bilayers. J Gen Physiol. 131(1):77-85, 2008 Jan.

Newberg J, Murphy RF*. A Framework for the Automated Analysis of Subcellular Patterns in Human Protein Atlas Images. J. Proteome Res. 7: 2300-2308, 2008.

Nobile CJ, Schneider HA, Nett JE, Sheppard DC, Filler SG, Andes DR, Mitchell AP*. Complementary adhesin function in C. albicans biofilm formation. Curr Biol 18:1017-24, 2008.

Nobile CJ, Solis N, Myers CL, Fay AJ, Deneault JS, Nantel A, Mitchell AP*, Filler SG. Candida albicans transcription factor Rim101 mediates pathogenic interactions through cell wall functions. Cell Microbiol 10:2180-96, 2008.

Ozhalici-Unal H, Pow CL, Marks SA, Jesper LD, Silva GL, Shank NI, Jones EW*, Burnette JM 3rd*, Berget PB*, Armitage BA*. A rainbow of fluoromodules: a promiscuous scFv protein binds to and activates a diverse set of fluorogenic cyanine dyes. J Am Chem Soc. 130(38):12620-1, 2008 Sep 24. Epub 2008 Aug 30.

Pan J, Mills TT, Tristram-Nagle S, Nagle JF*. Cholesterol perturbs lipid bilayers nonuniversally. Phys Rev Lett, 100(19):198103, 2008 May 16. Epub 2008 May 15.

Pan J, Tristram-Nagle S, Kucerka N, Nagle JF*. Temperature dependence of structure, bending rigidity, and bilayer interactions of dioleoylphosphatidylcholine bilayers. Biophys J. 94(1):117-24, 2008 Jan 1. Epub 2007 Sep 7.

Phillippi JA, Miller E, Weiss L, Huard J, Waggoner A*, Campbell P*. Microenvironments engineered by inkjet bioprinting spatially direct adult stem cells toward muscle- and bone-like subpopulations. Stem Cells 26(1):127-34, 2008.

Puri M, Goyal A, Senutovich N, Dowd SR, Minden JS*. Building proteomic pathways using Drosophila ventral furrow formation as a model. Mol. Biosystems 4, 1126-35, 2008.

Qian Y, Murphy RF*. Improved recognition of figures containing fluorescence microscope images in online journal articles using graphical models. Bioinformatics. 24(4):569-76, 2008 Feb 15. Epub 2007 Nov 22.

Qui H, Eifert J, Wacheul L, Thiry M, Berger A, Jakovljevic J, Woolford Jr JL*, Corbett A, Lafontaine DLJ, Terns RM, Terns MP. Identification of Genes That Function In the Biogenesis and Localization of Small Nucleolar RNAs in Saccharomyces cerevisiae. Molecular and Cellular Biology, 28:3686-3699, 2008.

Raghupathy N, Hoberman R, Durand D*. Two plus two does not equal three: Statistical tests for multiple genome comparison. Journal of Bioinformatics and Computational Biology, 6(1): 1-22, 2008.

Rauceo JM, Blankenship JR§, Fanning S§, Hamaker JJ, Deneault JS, Smith FJ, Nantel A, Mitchell AP*. Regulation of the Candida albicans cell wall damage response by transcription factor Sko1 and PAS kinase Psk1. Mol Biol Cell 19:2741-51, 2008.

Rohde GK, Ribeiro A, Dahl KN*, Murphy RF*. Deformation-based nuclear morphometry: capturing nuclear shape variation in HeLa Cells. Cytometry, 73A:341-350, 2008.

Shruti S, Clem RL, Barth AL*. A seizure-induced gain-of-function in BK channel is associated with elevated firing activity in neocortical pyramidal neurons. Neurobiology of Disease, 30(3):323-30, 2008.

Siegwart DJ, Bencherif SA, Srinivasan A, Hollinger JO*, Matyjaszewski K. Synthesis, characterization, and in vitro cell culture viability of degradable poly(N-isopropylacrylamide-co-5,6-benzo-2-methylene-1,3-dioxepane)-based polymers and crosslinked gels. J Biomed Mater Res A. 87(2):345-58, 2008 Nov.

Song N, Joseph JM, Davis GB, Durand D*. Sequence similarity network reveals common ancestry of multidomain proteins. PLOS Computational Biology, 4(5): e1000063, 2008.

Song XJ§, Simplaceanu V, Ho NT, Ho C*. Effector-Induced Structure Fluctuation Regulates the Ligand Affinity of an Allosteric Protein: Binding of Inositol Hexaphosphate Has Distinct Dynamic Consequences for the T and R States of Hemoglobin. Biochemistry 47:4907-4915, 2008.

Sridhar S, Lam F, Blelloch GE, Ravi R, Schwartz R*. Mixed integer linear programming for maximum-parsimony phylogeny inference. IEEE/ACM Trans Comput Biol Bioinform. 5(3):323-31, 2008 Jul-Sep.

Sridhar S, Schwartz R*. A human genome-wide library of local phylogeny predictions for whole-genome inference problems. BMC Genomics. 2008 Aug 18;9:389.

Srinivasa G, Fickus M, Gonzalez-Rivero, Hsieh S, Guo Y, Linstedt AD*, Kovacevic J. Active-mask segmentation for the cell-volume computation and Golgi-body segmentation of HeLa cell images. Proc. IEEE Intl. Symp. Biomed. Imaging, Paris, France, pp. 348-351, 2008.

Sweeney B, Zhang T, Schwartz R*. Exploring the parameter space of complex self-assembly through virus capsid models. Biophysical Journal, 94:772-783 2008.

Szent-Gyorgyi C, Schmidt BA, Creeger Y, Fisher GW, Zakel KL, Adler S, Fitzpatrick JA, Woolford CA, Yan Q, Vasilev KV, Berget PB*, Bruchez MP*, Jarvik JW*, Waggoner A*. Fluorogen-activating single-chain antibodies for imaging cell surface proteins. Nature biotechnology, 26: 235-240, 2008.

Tang L, Sahasranaman A, Jakovljevic J, Schleifman E, Woolford Jr JL*. Interactions among Ytm1, Erb1, and Nop7 Required for Assembly of the Nop7-Subcomplex in Yeast Preribosomes. Molecular Biology of the Cell, 19:2844-2856, 2008.

Toppings M, Castro C, Mills PH†, Reinhart B, Schatten G, Ahrens ET*, Chaillet JR, Trasler JM. Profound phenotypic variation among mice deficient in the maintenance of genomic imprints. Hum Reprod. 23(4):807-18, 2008 Apr. Epub 2008 Feb 13.

Vernot B, Stolzer M, Goldman A, Durand D*. Reconciliation with non-binary species trees. Journal of Computational Biology, 15(8): 981-1006, 2008.

Weinstein S, Pane D, Ernst LA, Warren-Rhodes K, Dohm JM, Hock AN, Piatek JL, Emani S, Lanni F*, Wagner M, Fisher GW, Minkley E, Dansey LE, Smith T, Grin EA, Stubbs K, Thomas G, Cockell CS, Marinangeli L, Ori GG, Heys S, Teza JP, Moersch JE, Coppin P, Chong Diaz G, Wettergreen DS, Cabrol NA, Waggoner AS*.  Application of pulsed-excitation fluorescence imager for daylight detection of sparse life in tests in the Atacama Desert.  J. Geophys. Res. 113, 2008.

Witzberger MM, Fitzpatrick JA, Crowley JC*, Minden JS*. End-on imaging: a new perspective on dorsoventral development in Drosophila embryos. Dev Dyn. 237(11):3252-9, 2008 Nov.

Ye Q, Wu Y-JL, 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.