Carnegie Mellon University


Ahrens ET*, Srinivas M, Capuano S, Simhan HN, Schatten GP. Magnetic resonance imaging of embryonic and fetal development in model systems. Methods Mol Med. 124:87-101, 2006.

Bajzek DM, Burnette JM*, Rule GS*. Constructing computer models to provide accurate visualizations and authentic online laboratory experiences in an introductory biochemistry course. In Proceedings of World Conference on E-Learning in Corporate, Government, Healthcare, and Higher Education 2006. Chesapeake, VA: AACE.

Banerjee D, Markley AL, Yano T, Ghosh A, Berget PB*, Minkley EG Jr, Khetan SK, Collins TJ. "Green" oxidation catalysis for rapid deactivation of bacterial spores. Angew Chem Int Ed Engl. 45(24):3974-7, 2006 Jun 12.

Blankenship JR, Mitchell AP*. How to build a biofilm: a fungal perspective. Current opinion in microbiology 9, 588-594, 2006.

Boysen JH, Mitchell AP*. Control of Bro1-domain protein Rim20 localization by external pH, ESCRT machinery, and the Saccharomyces cerevisiae Rim101 pathway. Mol Biol Cell. 17(3):1344-53, 2006 Mar. Epub 2006 Jan 11.

Bruno VM, Kalachikov S, Subaran R, Nobile CJ, Kyratsous C, Mitchell AP*. Control of the C. albicans cell wall damage response by transcriptional regulator Cas5. PLoS Pathog. 2(3):e21, 2006 Mar. Epub 2006 Mar 17.

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

Chang HH, Moura JM, Wu YL, Ho C*. Immune cells detection of the in vivo rejecting heart in USPIO-enhanced magnetic resonance imaging. IEEE Eng Med Biol Soc. 1:942-5, 2006.

Chattopadhyay PK, Price DA, Harper TF, Betts MR, Yu J, Gostick E, Perfetto SP, Goepfert P, Koup RA, De Rosa SC, Bruchez MP*, Roederer M. Quantum dot semiconductor nanocrystals for immunophenotyping by polychromatic flow cytometry. Nature Medicine 2006, 12:972-977.

Chen SC, Murphy RF*. A graphical model approach to automated classification of protein subcellular location patterns in multi-cell images. BMC Bioinformatics. 7:90, 2006 Feb 23.

Chen X, Murphy RF*. Automated interpretation of protein subcellular location patterns. Int Rev Cytol. 249:193-227, 2006.

Chen X, Velliste M, Murphy RF*. Automated interpretation of subcellular patterns in fluorescence microscope images for location proteomics. Cytometry A. 69(7):631-40, 2006 Jul.

Clem RL, Barth A*.  Pathway-specific trafficking of native AMPARs by in vivo experience. Neuron, 2;49 (5): 663-70, 2006.

Crawford JH, Isbell TS, Huang Z, Shiva S, Chacko BK, Schechter AN, Darley-Usmar VM,  Kerby JD, Lang JD, Kraus D, Ho C*, Gladwin MT, Patel R. Hypoxia, Red Blood Cells, and Nitrite Regulate NO-dependent Hypoxic Vasodilatation. Blood 2006; 107,566-574.

Durand D*, Hoberman R. Diagnosing duplications: can it be done? Trends in Genetics, 22(3):156-64, 2006 Mar.

Durand D*, Halldorsson BV, Vernot B. Hybrid micro-macroevolutionary approach to gene tree reconstruction. Journal of Computational Biology, 13 (2): 320-335, 2006.

Egger V, Urban NN*. Dynamic connectivity in the mitral cell-granule cell microcircuit. Semin Cell Dev Biol. 17(4):424-32, 2006 Aug. Epub 2006 May 5. Review.

Ettensohn, CA*. The emergence of pattern in embryogenesis: Regulation of beta-catenin localization during early sea urchin development. STKE Perspective, Science, 361:2006 Nov 14.

Galán RF, Fourcaud-Trocmé N, Ermentrout GB, Urban NN*. Correlation-induced synchronization of oscillations in olfactory bulb neurons. J Neurosci. 26(14):3646-55, 2006 Apr 5.

Galán RF,  Ermentrout GB, Urban NN*. Predicting synchronized neural assemblies from experimentally estimated phase-resetting curves. Neurocomputing, 69(10-12), p.1112-1115, 2006.

Gong Q§, Simplaceanu V, Lukin JA, Giovannelli JL, Ho NT, Ho C*. Quaternary Structure of Carbonmonoxyhemoglobins in Solution: Structural Changes Induced by the Allosteric Effector, Inositol Hexaphosphate. Biochemistry 45, 5140-5148, 2006.

Greenwood AI, Tristram-Nagle S, Nagle JF*. Partial molecular volumes of lipids and cholesterol. Chem Phys Lipids. 143(1-2):1-10, 2006 Sep. Epub 2006 Apr 28.

Gu C, Zhou W, Puthenveedu MA*, Xu M, Jan YN, Jan LY. The microtubule plus-end tracking protein EB1 is required for Kv1 voltage-gated K+ channel axonal targeting. Neuron. 52(5):803-16, 2006 Dec 7.

Guo Y, Linstedt AD*. COPII-Golgi protein interactions regulate COPII coat assembly and Golgi size. J Cell Biol. 174(1):53-63, 2006 Jul 3.

Hitchens TK, Zhan Y, Richardson LV, Richardson JP, Rule GS*. Sequence-specific interactions in the RNA-binding domain of Escherichia coli transcription termination factor Rho.J Biol Chem., 281:33697-703, 2006.

Kapoor V, Urban NN*. Glomerulus-specific, long latency activity in the olfactory bulb granule-cell network. J. Neuroscience; 26(45):11709-19, 2006. Faculty of 1,00 Recommended.

Kneipp J, Balakrishnan G, Chen R, Shen TJ, Sahu SC§, Ho NT, Giovannelli JL,  Simplaceanu V, Ho C*, Spiro TG. Dynamics of Allostery in Hemoglobin:  Roles of the Penultimate Tyrosine H-Bonds. Journal of Molecular Biology. 356,335-353, 2006.

Kucerka N, Tristram-Nagle S, Nagle JF*. Closer look at structure of fully hydrated fluid phase DPPC bilayers. Biophys J. 90(11):L83-5, 2006 Jun 1. Epub 2006 Apr 14.

Livingston BT, Killian CE, Wilt F, Cameron A, Landrum MJ, Ermolaeva O, Sapojnikov V, Maglott DR, Buchanan AM, Ettensohn CA*. A genome-wide analysis of biomineralization-related proteins in the sea urchin, Strongylocentrotus purpuratus. Dev. Biol., 300, 335-348, 2006.

Larroux C, Fahey B, Liubicich D, Hinman VF*, Gauthier M, Gongora M, Green K, Wörheide G, Leys SP, Degnan BM. Developmental expression of transcription factor genes in a demosponge: insights into the origin of metazoan multicellularity.  Evol Dev. 8(2):150-73, 2006 Mar-Apr.

Lozier RH, Nagle JF*. Comment on "An apparent general solution for the kinetic models of the bacteriorhodopsin photocycles". J Phys Chem B. 110(30):15041-2; discussion 15043-4, 2006 Aug 3.

McCartney BM*, Price MH, Webb RL, Hayden MA, Holot LM, Zhou M, Bejsovec A, Peifer M. Testing hypotheses for the functions of APC family proteins using null and truncation alleles in Drosophila. Development; 133(12):2407-18, 2006 Jun.

Mitchell AP*. Cryptococcal virulence: beyond the usual suspects. J Clin Invest. 116(6):1481-3, 2006 Jun.

Morohashi N, Yamamoto Y, Kuwana S, Morita W, Shindo H, Mitchell AP*, Shimizu M. Effect of sequence-directed nucleosome disruption on cell-type-specific repression by alpha2/Mcm1 in the yeast genome. Eukaryot Cell 5, 1925-1933, 2006.

Mukherjee PK, Mohamed S, Chandra J, Kuhn D, Liu S, Antar OS, Munyon R, Mitchell AP*, Andes D, Chance MR, et al. Alcohol dehydrogenase restricts the ability of the pathogen Candida albicans to form a biofilm on catheter surfaces through an ethanol-based mechanism. Infect Immun 74, 3804-3816, 2006.

Munshi R, Coalson RD, Ermentrout GB, Madura JD, Meirovitch H, Stiles JR*, Bahar I. An introduction to simulation and visualization of biological systems at multiple scales: a summer training program for interdisciplinary research. Biotechnol Prog. 22(1):179-85, 2006 Jan-Feb.

Nobile CJ, Andes DR, Nett JE, Smith FJ, Yue F, Phan QT, Edwards JE, Filler SG, Mitchell AP*. Critical role of Bcr1-dependent adhesins in C. albicans biofilm formation in vitro and in vivo. PLoS Pathog. 2(7):e63, 2006 Jul.

Nobile CJ, Mitchell AP*. Genetics and genomics of Candida albicans biofilm formation. Cell Microbiol. 8(9):1382-91, 2006 Sep. Epub 2006 Jul 11.

Nobile CJ, Nett JE, Andes DR, Mitchell AP*. Function of Candida albicans adhesin Hwp1 in biofilm formation. Eukaryot Cell. 5(10):1604-10, 2006 Oct.

Olivares AO, Chang W, Mooseker MS, Hackney DD*, De La Cruz EM. The tail domain of myosin Va modulates actin binding to one head, J.Biol.Chem. 281, 31326-31336, 2006.

Pennington G, Smith CA, Shackney S, Schwartz R*. Expectation-maximization method for reconstructing tumor phylogenies from single-cell data. Comput Syst Bioinformatics Conf. 2006:371-80.

Przytycka T, Davis GB, Song N, Durand D*. Graph theoretical insights into evolution of multidomain proteins. Journal of Computational Biology, 13 (2): 351-363, 2006.

Puskar K, Ta 'asan S, Schwartz R*, LeDuc PR*. Evaluating spatial constraints in cellular assembly processes using a monte carlo approach. Cell Biochem Biophys. 45(2):195-201, 2006.

Puthenveedu MA*, von Zastrow M. Cargo regulates clathrin-coated pit dynamics. Cell. 127(1):113-24, 2006.

Puthenveedu MA, Bachert C, Puri S, Lanni F*, Linstedt AD*. GM130 and GRASP65-dependent lateral cisternal fusion allows uniform Golgi-enzyme distribution. Nat Cell Biol. 8(3):238-48, 2006 Mar. Epub 2006 Feb 19.

Robertson KL, Yu L, Armitage BA*, Lopez AJ*, Peteanu LA. Fluorescent PNA probes as hybridization labels for biological RNA. Biochemistry, 45(19):6066-6074, 2006.

Roux MM, Townley IK, Raisch M, Reade A, Bradham C, Humphreys G, Gunaratne HJ, Killian CE, Moy G, Su YH, Ettensohn CA*, Wilt F, Vacquier VD, Burke RD, Wessel G, Foltz KR. A functional genomic and proteomic perspective of sea urchin calcium signaling and egg activation. Dev. Biol. 300, 416-33, 2006.

Sahu SC§, Simplaceanu V, Gong Q§, Ho NT, Glushka JG, Prestegard JH, Ho C*. Orientation of deoxyhemoglobin at high magnetic fields: structural insights from RDCs in solution. J Am Chem Soc. 128(19):6290-1, 2006 May 17.

Sahu SC§, Simplaceanu V, Ho NT, Giovannelli JL, Ho C*. Backbone resonance assignment of human adult hemoglobin in the deoxy form. J Biomol NMR. 36 Suppl 1:1, 2006.

Schwartz R*, King J. Frequencies of hydrophobic and hydrophilic runs and alternations in proteins of known structure. Protein Sci.15(1):102-12, 2006 Jan.

Sea Urchin Genome Sequencing Consortium. The genome of the sea urchin Strongylocentrotus purpuratus. Science, 341, 941-952, 2006.

Skoufias DA, De Bonis S, Lebeau L, Crevel I, Cross R, Wade RH, Hackney DD*, Kozielski F. S-Trityl-L-Cysteine Is a Reversible, Tight-Binding Inhibitor of the Human Kinesin Eg5 That Specifically Blocks Mitotic Progression. J. Biol. Chem. 2006.

Sridhar S, Blelloch GE, Ravi R, Schwartz R*. Optimal imperfect phylogeny reconstruction and haplotyping (IPPH). Comput Syst Bioinformatics Conf. 199-210, 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(4):939-44, 2006 Jan 24. Epub 2006 Jan 17.

Vasseur-Godbillon C, Sahu SC§, Domingues E, Fable C, Giovannelli JL, Tam TC, Ho NT, Ho C*, Marden MC, Baudin-Creuza V. Recombinant Hemoglobin βG83C-F41Y An Octameric Protein. FEBS Journal 2006; 273,230-241.

Viswanathan S, Ünlü M, Minden JS*. Two-dimensional difference gel electrophoresis. Nature Protocols, 1, 1351-1358, 2006.

Wu YL, Ye Q, Foley LM, Hitchens TK, Sato K, Williams JB§, Ho C*. In Situ Labeling of Immune Cells with Iron Oxide Particles: An Approach to Detect Organ Rejection by Cellular MRI. Proceedings of National Academy Sciences USA 103:1852-1857, 2006.

Yudowski GA, Puthenveedu MA*, von Zastrow M. Distinct modes of regulated receptor insertion to the somatodendritic plasma membrane. Nature Neuroscience. 9(5):622-7, 2006.

Zhang T†, Schwartz R*. Simulation study of the contribution of oligomer/oligomer binding to capsid assembly kinetics. Biophys J. 2006 Jan 1;90(1):57-64. Epub 2005 Oct 7.