Carnegie Mellon University


Arbour M, Epp E, Hogues H, Sellam A, Lacroix C, Rauceo J, Mitchell A*, Whiteway M, Nantel A. Widespread occurrence of chromosomal aneuploidy following the routine production of Candida albicans mutants. FEMS Yeast Res 9, 1070-1077, 2009.

Ballou B, Ernst LA, Andreko S, Fitzpatrick JA, Lagerholm BC, Waggoner AS*, Bruchez MP*. Imaging vasculature and lymphatic flow in mice using quantum dots. Methods Mol Biol. 574:63-74, 2009.

Bencherif SA, Gao H, Srinivasan A, Siegwart DJ, Hollinger JO**, Washburn NR, Matyjaszewski K. Cell-adhesive star polymers prepared by ATRP. Biomacromolecules. 10(7):1795-803, 2009 Jul 13. Epub 2009 Jun 11.

Bencherif SA, Sheehan JA, Hollinger JO*, Walker LM, Matyjaszewski K, Washburn NR. Influence of cross-linker chemistry on release kinetics of PEG-co-PGA hydrogels. J Biomed Mater Res A. 90(1):142-53, 2009 Jul.

Bencherif SA, Siegwart DJ, Srinivasan A, Horkay F, Hollinger JO*, Washburn NR, Matyjaszewski K. Nanostructured hybrid hydrogels prepared by a combination of atom transfer radical polymerization and free radical polymerization. Biomaterials. 30(29):5270-8, 2009 Oct. Epub 2009 Jul 9.

Bencherif SA, Srinivasan A, Sheehan JA, Walker LM, Gayathri C, Gil R, Hollinger JO*, Matyjaszewski K, Washburn NR. End-group effects on the properties of PEG-co-PGA hydrogels. Acta Biomater. 5(6):1872-83, 2009 Jul. Epub 2009 Feb 28.

Benedetti BL, Glazewski S, Barth AL*. Sensory plasticity improves spike timing precision and reliability in the neocortex. Journal of Neuroscience 29(38):11817-27, 2009.

Boysen JH, Fanning S§, Newberg J, Murphy RF*, Mitchell AP*. Detection of protein-protein interactions through vesicle targeting. Genetics 182:33-9, 2009.

Brinegar C, Wu YJL, Foley LM, Hitchens TK, Ye Q, Ho C*, Liang ZP. Real-Time Cardiac MRI Without Triggering, Gating, or Breath Holding. IEEE Eng Med Biol Soc 2008; pp. 3381-3384.

Buck TE, Rao A, Coelho LP, Fuhrman MH, Jarvik JW*, Berget PB*, Murphy RF*. Cell cycle dependence of protein subcellular location inferred from static, asynchronous images. Conf Proc IEEE Eng Med Biol Soc. 2009:1016-9, 2009.

Castro JB, Urban NN*. Subthreshold Glutamate Release from Mitral Cell Dendrites. J. Neurosci. 29(21):7023-30, 2009 May 27.

Chamilos G, Nobile CJ, Bruno VM, Lewis RE, Mitchell AP*, Kontoyiannis DP. Candida albicans Cas5, a regulator of cell wall integrity, is required for virulence in murine and toll mutant fly models. J Infect Dis 200:152-7, 2009.

Chang HH, Moura JM, Wu YL, Ho C*.  Automatic Detection of Regional Heart Rejection in USPIO-Enhanced MRI. IEEE Transactions on Medical Imaging 2008; 27,1095-1106.

Coelho LP, Shariff A, Murphy RF*. Nuclear Segmentation in Microscope Cell Images: A hand-segmented Dataset and Comparison of Algorithms. Proc IEEE Int Symp Biomed Imaging. 5193098:518-521, 2009.

Czech J, Dittrich M, Stiles JR*. Rapid creation, Monte Carlo simulation, and visualization of realistic 3D cell models. Methods Mol Biol. 500:237-87, 2009.

Emr S, Glick BS, Linstedt AD*, Lippincott-Schwartz J, Luini A, Malhotra V, Marsh BJ, Nakano A, Pfeffer SR, Rabouille C, Rothman JE, Warren G, Wieland FT. Journeys through the Golgi—taking stock in a new era. J. Cell Biol. 187: 449-53, 2009.

Ettensohn CA*. Lessons from a gene regulatory network: echinoderm skeletogenesis provides insights into evolution, plasticity, and morphogenesis. Development 136, 11-21, 2009.

Falco CF, Dykstra KM, Yates BP, Berget PB*. scFv-based Fluorogen Activating Proteins and Variable Domain Inhibitors as Fluorescent Biosensor Platforms. Biotechnol. J. 4 (9): 1328-1336, 2009.

Fitzpatrick JA, Andreko SK, Ernst LA, Waggoner AS*, Ballou B, Bruchez MP*. Long-term persistence and spectral blue shifting of quantum dots in vivo. Nano Lett. 9(7):2736-41, 2009.

Fitzpatrick JA, Yan Q, Sieber JJ, Dyba M, Schwarz U, Szent-Gyorgyi C, Woolford CA, Berget PB*, Waggoner AS*, Bruchez MP*. STED nanoscopy in living cells using Fluorogen Activating Proteins. Bioconjug Chem. 20(10):1843-1847, 2009.

Fitzpatrick JAJ, Andreko SK, Ernst LA, Waggoner AS*, Ballou B, Bruchez MP*. Long term persistence and spectral blue-shifting of quantum dots in vivo. Nano Letters 2009.

Guler SD, Ghosh DD, Pan J, Mathai JC, Zeidel ML, Nagle JF*, Tristram-Nagle S. Effects of Ether Linkage on Lipid Bilayer Structure and Water Permeability. Chem Phys Lipids. 160:33-44, 2009.

Hackney DD*, Baek N, Snyder AC. Half-site inhibition of dimeric kinesin head domains by monomeric tail domains, Biochemistry. 48, 3448-3456, 2009.

Hinman VF*, Yankura KA, McCauley BS. Evolution of gene regulatory network architectures: Examples of subcircuit conservation and plasticity between classes of echinoderms. Biochim Biophys Acta.1789(4):326-32, 2009.

Huh S, Lee D, Murphy RF*. Efficient framework for automated classification of subcellular patterns in budding yeast. Cytometry A. 75(11):934-40, 2009 Nov.

Jackson C, Murphy RF*, Kovacević J. Intelligent acquisition and learning of fluorescence microscope data models. IEEE Trans Image Process. 18(9):2071-84, 2009 Sep. Epub 2009 Jun 5.

Janjic JM, Ahrens ET*. Fluorine-containing nanoemulsions for MRI cell tracking Wiley Interdiscip Rev Nanomed Nanobiotechnol. 1(5):492-501, 2009 Sep-Oct.

Joseph JM, Durand D*. Family classification without domain chaining. Bioinformatics 25(12):i45-i53, 2009.

Kaan HY, Ulaganathan V, Hackney DD*, Kozielski F. An Allosteric Transition Trapped in an Intermediate State of a New Kinesin-Inhibitor Complex. Biochem. J. 425, 55-60, 2009.

Kadri S, Hinman V*, Benos PV. HHMMiR: Efficient de novo prediction of microRNAs using hierarchical hidden Markov models. BMC Bioinformatics;10 Suppl 1:S35, 2009 Jan 30.

Kang DS, Kern RC, Puthenveedu MA*, von Zastrow M, Williams JC, Benovic JL. Structure of an arrestin2-clathrin complex reveals a novel clathrin binding domain that modulates receptor trafficking. J Biol Chem. 284(43):29860-72, 2009 Oct 23. Epub 2009 Aug 25.

Lee B, LeDuc PR*, Schwartz R*. Parameter effects on binding chemistry in crowded media using a two-dimensional stochastic off-lattice model. Physical Review E, 80:041918, 2009.

Lim JK, Tan DX, Lanni F*, Tilton RD, Majetich SA. Optical imaging and magnetophoresis of nanorods. J. Magnetism Mag. Mater. 321:1557-1562, 2009.

Manole MD, Foley LM, Hitchens TK, Kochanek PM, Hickey RW, Bayir H, Alexander H, Ho C*, Clark RSB. Magnetic Resonance Imaging Assessment of Regional Cerebral Blood Flow After Asphyxial Cardiac Arrest in Immature Rats. Journal of Cerebral Blood Flow & Metabolism. 29(1); 197-205, 2009.

Mills TT, Huang J, Feigenson GW, Nagle JF*. Effects of Cholesterol and Unsaturated DOPC Lipid on Chain Packing of Saturated Gel-Phase DPPC Bilayers. Gen. Physiol. Biophys. 28, 126-139, 2009.

Minden JS*, Dowd SR, Meyer HE, Stühler K. Difference Gel Electrophoresis. Electrophoresis 30, S156-S161, 2009.

Mittal R, Bruchez MP*. Calibration of Flow Cytometry for Quantitative Quantum Dot Measurements. Curr Protoc Cytom. Chapter 6:Unit6.26, 2009 Jul 1.

Näthke IS, McCartney BM*. APC proteins. Preface. Adv Exp Med Biol. 656:vii-x, 2009.

Newberg J, Hua J, Murphy RF*. Location proteomics: systematic determination of protein subcellular location. Methods Mol Biol. 500:313-32, 2009.

Newberg JY, Li J, Rao A, Pontén F, Uhlén M, Lundberg E, Murphy RF*. Automated Analysis of Human Protein Atlas Immunofluorescence Images. Proc IEEE Int Symp Biomed Imaging. 5193229:1023-1026, 2009.

Nobile CJ, Mitchell AP*. Large-scale gene disruption using the UAU1 cassette. Methods Mol Biol. 499:175-94, 2009.

Nobile CJ, Nett JE, Hernday AD, Homann OR, Deneault JS, Nantel A, Andes DR, Johnson AD, Mitchell AP*. Biofilm matrix regulation by Candida albicans Zap1. PLoS Biol 7:e1000133, 2009.

Pan J, Tieleman DP, Nagle JF*, Kucerka N, Tristram-Nagle S. Alamethicin in Lipid Bilayers: Combined Use of X-ray Scattering and MD Simulations. Biochim. Biophys. Acta 1788, 1387-1397, 2009.

Pan J, Tristram-Nagle S, Nagle JF*. Alamethicin aggregation in lipid membranes. J. Membrane Biol. 231, 11-27, 2009.

Pan J, Tristram-Nagle S, Nagle JF*. Effect of cholesterol on structural and mechanical properties of membranes depends on lipid chain saturation. Phys. Rev. E. 80, 021931(1-12), 2009.

Park H, Liu Y, Solis N, Spotkov J, Hamaker J, Blankenship JR§, Yeaman MR, Mitchell AP*, Liu H, Filler SG. Transcriptional responses of candida albicans to epithelial and endothelial cells. Eukaryot Cell 8:1498-510, 2009.

Park Y, Shackney S, Schwartz R*. Network-based inference of cancer progression from microarray data .IEEE/ACM Trans Comput Biol Bioinform. 6(2):200-12, 2009 Apr-Jun.

Peng T, Wang W, Rohde GK, Murphy RF*. Instance-Based Generative Biological Shape Modeling. Proc IEEE Int Symp Biomed Imaging. 2009;5193141:690-693.

Poll G, Braun T, Jakovljevic J, Neueder A, Jakob S, Woolford Jr JL*, Tschochner H, Milkereit P. rRNA maturation in yeast cells depleted of large ribosomal subunit proteins. PLOS One 4: e8249, 2009.

Raghupathy N, Durand D*. Gene cluster statistics with gene families. Molecular Biology and Evolution, 26:957-968, 2009.

Rule GS*, Bajzek D. Building an Online Biochemistry Course with Assessment and Feedback Embedded Into All Online Instructional Activities. In Proceedings of World Conference on E-Learning in Corporate, Government, Healthcare, and Higher Education 2009. Chesapeake, VA: AACE.

Sengupta D, Truschel S§, Bachert C, Linstedt AD*. Organelle tethering by a homotypic PDZ interaction underlies formation of the Golgi membrane network.  J. Cell Biol. 186:51-55, 2009.

Shank NI, Zanotti KJ, Lanni F*, Berget PB*, Armitage BA*. Enhanced photostability of genetically encodable fluoromodules based on fluorogenic cyanine dyes and a promiscuous protein partner. J Am Chem Soc. 131(36):12960-9, 2009 Sep 16.

Sheehan JS, Benedetti BL, Barth AL*. Anticonvulsant effects of the BK channel antagonist paxilline. Epilepsia Apr; 50(4):711-20, 2009.

Siegwart DJ, Srinivasan A, Bencherif SA, Karunanidhi A, Oh JK, Vaidya S, Jin R, Hollinger JO*, Matyjaszewski K. Cellular uptake of functional nanogels prepared by inverse miniemulsion ATRP with encapsulated proteins, carbohydrates, and gold nanoparticles. Biomacromolecules. 10(8):2300-9, 2009 Aug 10.

Srinivas M, Turner MS, Janjic JM, Morel PA, Laidlaw DH, Ahrens ET*. In vivo cytometry of antigen specific T-cells using 19F MRI. Magn. Reson. Med. 62: 747-753, 2009.

Srinivasa G, Fickus MC, Guo Y, Linstedt AD*, Kovačević J. Active mask segmentation of fluorescence microscope images. IEEE Trans Image Process. 18(8):1817-29, 2009.

Staley J, Woolford Jr JL*. Assembly of ribosomes and spliceosomes:complex ribonucleoprotein machines.Current Opinion in Cell Biology 21:109-118, 2009.

Talkish J†,Woolford Jr JL*. The Rea1 tadpole loses its tail. Cell 138: 832-834, 2009.

Urban NN*, Arevian AC. Computing with dendrodendritic synapses in the olfactory bulb. Ann N Y Acad Sci. 1170:264-9, 2009 Jul. Review.

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

Webb RL, Zhou MN, McCartney BM*. A novel role for an APC2-Diaphanous complex in regulating actin organization in Drosophila. Development; 136(8):1283-93, 2009 Apr. Epub 2009 Mar 11.

Yadav S, Puri S, Linstedt AD*. A Primary Role for Golgi Positioning in Directed Secretion, Cell Polarity and Wound Healing. Mol. Biol. of the Cell 20:1728-1736, 2009.

Yudowski GA, Puthenveedu MA*, Henry AG, von Zastrow M. Cargo-mediated regulation of a rapid Rab4-dependent recycling pathway. Mol Biol Cell. 20(11):2774-84, 2009 Jun.