Carnegie Mellon University


Bachert C, Linstedt AD*. Dual anchoring of the GRASP membrane tether promotes trans pairing. J Biol Chem. 285: 16294-16301, 2010.

Bermejo GA, Strub MP, Ho C*. Ligand-free Open-closed Transitions of Periplasmic Binding Proteins:  The Case of Glutamine-binding Protein.  Biochemistry 2010; 49, 1893-1902. 

Blankenship JR§, Fanning S§, Hamaker JJ, Mitchell AP*. An extensive circuitry for cell wall regulation in Candida albicans. PLoS Pathog 6:e1000752, 2010.

Boysen JH, Subramanian S§, Mitchell AP*. Intervention of Bro1 in pH-responsive Rim20 localization in Saccharomyces cerevisiae. Eukaryot Cell 9:532-8, 2010.

Campbell KL, Roberts JEE, Watson LN, Stetefeld J, Sloan AM, Signore AV, Howatt JW, Tame JRH, Rohland N, Shen T-J, Austin JJ, Hofreiter M, Ho C*, Weber RE, Copper A. Substitutions in Woolly Mammoth Hemoglobin Confer Biochemical Properties Adaptive for Cold Tolerance. Nature Genetics 42, 536-540, 2010.

Castro CA, Ben-Yehudah A, Ozolek JA, Mills PH, Redinger CJ, Mich-Basso JD, McFarland DA, Oliver SL, Ahrens ET*, Schatten G. Semiquantitative histopathology and 3D magnetic resonance microscopy as collaborative platforms for tissue identification and comparison within teratomas derived from pedigreed primate embryonic stem cells. Stem Cell Res. 2010 Nov;5(3):201-11. Epub 2010 Aug 6.

Cho HY, Gao H, Srinivasan A, Hong J, Bencherif SA, Siegwart DJ, Paik HJ, Hollinger JO*, Matyjaszewski K. Rapid cellular internalization of multifunctional star polymers prepared by atom transfer radical polymerization. Biomacromolecules. 2010 Sep 13;11(9):2199-203.

Coelho LP, Ahmed A, Arnold A, Kangas J, Sheikh AS, Xing EP, Cohen WW, Murphy RF*. Structured Literature Image Finder: Extracting Information from Text and Images in Biomedical Literature. Lect Notes Comput Sci. 2010;6004:23-32.

Coelho LP, Peng T, Murphy RF*. Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing. Bioinformatics 26:i7-i12, 2010.

Cuevas Tabarés J, MacLachlan RA, Ettensohn CA*, Riviere, CN. Cell micromanipulation with an active handheld micromanipulator. Conf. Proc. IEEE Eng. Med. Biol. Soc. 4363-4366, 2010.

DeStefino NR, Pilato AA, Dittrich M, Cherry SV, Cho S, Stiles JR*, Meriney SD. (R)-roscovitine prolongs the mean open time of unitary N-type calcium channel currents. Neuroscience. 2010 May 19;167(3):838-49. Epub 2010 Feb 24.

Dykstra KM, Pokusa JE, Suhan J, Lee TH*. Yip1A structures the mammalian endoplasmic reticulum. Mol Biol Cell. 2010 May 1;21(9):1556-68. Epub 2010 Mar 17.

Fanning S§, Mitchell AP*. The Fungal Pathogen Candida albicans. In KA Borkovich & DJ Ebbole (ed.), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC, 2010.

Fisher GW, Adler SA, Fuhrman MH, Waggoner AS*, Bruchez MP*, Jarvik JW*. Detection and quantification of beta2AR internalization in living cells using FAP-based biosensor technology. J Biomol Screen. 15(6):703-9, 2010. Epub 2010 May 20.

Fishilevich E§, Fitzpatrick JAJ, Minden JS*. pHMA, a pH-sensitive GFP reporter for cell engulfment in Drosophila embryos, tissues and cells. Dev. Dyn. 238, 559-73, 2010.

Foley LM, Hitchens TK, Barbe B, Zhang F, Ho C*, Rao GR, Nemoto EM. Quantitative Temporal Profiles of Penumbra and Infarction During Permanent Middle Cerebral Artery Occlusion in Rats. Transl Stroke Res. 1(3):220-229, 2010 Sep 1.

Franke JD§. Approaches for using animal models to identify loci that genetically interact with human disease-causing point mutations. Methods Mol Biol. 634:203-13, 2010.

Fuchs BB, Eby J, Nobile CJ, El Khoury JB, Mitchell AP*, Mylonakis E. Role of filamentation in Galleria mellonella killing by Candida albicans. Microbes Infect 12, 488-496, 2010.

Gerkin RC§, Clem RL, Shruti S, Kass RE, Barth AL*. Cortical up state activity is enhanced after seizures: a quantitative analysis. J Clin Neurophysiol. 27(6): 425-32, 2010 Dec.

Glory-Afshar E, Osuna-Highley E, Granger B, Murphy RF*. A Graphical Model to Determine the Subcellular Protein Location in Artificial Tissues. Proc IEEE Int Symp Biomed Imaging. 2010:1037-1040, 2010 Apr.

Gong H, Guo Y, Linstedt AD*, Schwartz R*. Discrete, continuous, and stochastic models of protein sorting in the Golgi. Physical Review E, 81(1):011914, 2010.

Goodman A, Bajzek D, Rule G*. Advantages and Challenges in Adopting Open Learning Initiative (OLI) materials to Supplement a Lecture Course in Biochemistry: Instructor’s Perspective. In Proceedings of World Conference on Educational Multimedia, Hypermedia and Telecommunications 2010 (pp. 1705-1708), 2010. Chesapeake, VA: AACE.

Goodman A, Bajzek D, Rule G*. Using Online Materials to Supplement a Lecture Course in Biochemistry: Student Attitudes and Student Success. In Proceedings of World Conference on Educational Multimedia, Hypermedia and Telecommunications 2010 (pp. 1709-1712), 2010. Chesapeake, VA: AACE.

Hackney DD*. When is weaker better? Design of an ADP sensor with weak ADP affinity, but still selective against ATP. ACS Chem Biol. 5(4):353-4, 2010 Apr 16.

Helfer BM, Nelson AD, Janjic JM, Gil RR, Kalinski P, de Vries J, Ahrens ET*, Mailliard RB. Functional assessment of human dendritic cells labeled for in vivo 19F magnetic resonance imaging cell tracking. Cytotherapy 12(2): 238-250, 2010.

Henn A, Cao W, Licciardello N, Heitkamp SE, Hackney DD*, De La Cruz EM. Pathway of ATP Utilization and Duplex RRNA Unwinding by the DEAD-Box Helicase, DbpA. Proc. Natl. Acad. Sci. U. S. A. 107, 4046-4050, 2010.

Ho C*,Yue Y. Haemoglobin: Cooperativity in Protein-Ligand Interactions. (version 2.0) in Encyclopedia of Life Sciences, John Wiley & Sons, Ltd., Chichester http://www/, April 2010.

Ho C*, Yuan Y, Simplaceanu V. NMR Provides a New Structural and Dynamic View of Hemoglobin Allostery in Solution, in Hemoglobin:  Recent Developments and Topics, edited by Masako Nagai, Research Signpost, Kerala, India, 17-36, 2010.

Holleran J, Brown D, Fuhrman MH, Adler SA, Fisher GW, Jarvik JW*. Fluorogen-activating proteins as biosensors of cell-surface proteins in living cells. Cytometry A. 77(8):776-82, 2010 Aug.

Hovis KR, Padmanabhan K§, Urban NN*. A simple method of in vitro electroporation allows visualization, recording, and calcium imaging of local neuronal circuits. J Neurosci Methods;191(1):1-10, 2010 Aug 15.

Hu Y, Garcia Osuna E, Hua J, Nowicki TS, Stolz R, McKayle C, Murphy RF*. Automated Analysis of Protein Subcellular Locations in Time Series Images. Bioinformatics 26:1630-1636, 2010.

Iordanova B, Robison CS, Goins WF, Ahrens ET*. Single chain ferritin chimera as an improved MRI gene reporter. Prilozi. 31(2):151-5, 2010 Dec.

Iordanova B, Robison CS, Ahrens ET*. Design and characterization of a chimeric ferritin with enhanced iron loading and transverse NMR relaxation rate. J. Biol. Inorg. Chem. 15(6): 957-965, 2010.

Kadayakkara DK, Beatty PL, Turner M, Janjic JM, Ahrens ET*, Finn OJ. Inflammation driven by overexpression of the hypoglycosylated abnormal mucin 1 (MUC1) links inflammatory bowel disease and pancreatitis. Pancreas 39(4): 510-515, 2010.

Kadayakkara DKK, Janjic JM, Pusateri LB, Young WB, Ahrens ET*. In vivo observation of intracellular oximetry in perfluorocarbon-labeled glioma cells and chemotherapeutic response in the CNS using fluorine-19 MRI. Magn. Reson. Med. 64(5): 1252-1259, 2010.

Kucerka N, Katsaras J, Nagle JF*. Comparing Membrane Simulations to Scattering Experiment: Introducing SIMtoEXP Software. J. Memb. Biol. 235, 43-50, 2010.

Kumar MS, Schwartz R*. A parameter estimation technique for stochastic self-assembly systems and its application to human papillomavirus self-assembly. Phys Biol. 2010 Dec 9;7(4):045005.

Lancia G, Rizzi R, Schwartz R*. Tiling Binary Matrices in Haplotyping: Complexity, Models and Algorithms. Proceedings of the Prague Stringology Conference (PSC 2010), pp. 89-102, 2010.

Lin T, Murphy RF*, Bar-Joseph Z*. Discriminative Motif Finding for Predicting Protein Subcellular Localization. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2010, in press.

Luo G, Ibrahim AS, Spellberg B, Nobile CJ, Mitchell AP*, Fu Y. Candida albicans Hyr1p confers resistance to neutrophil killing and is a potential vaccine target. J Infect Dis 201:1718-28, 2010.

McCauley BS, Weideman EP, Hinman VF*. A conserved gene regulatory network subcircuit drives different developmental fates in the vegetal pole of highly divergent echinoderm embryos. Dev Biol. 340(2):200-8, 2010 Apr 15. Epub 2009 Nov 23.

McManus CJ*, Coolon JD, Duff MO, Eipper-Mains J, Graveley BR, Wittkopp PJ. Regulatory Divergence in Drosophila revealed by mRNA-seq. Genome Res 20(6):816-825, 2010.

McManus CJ*, Duff MO, Eipper-Mains J, Graveley BR. Global analysis of trans-splicing in Drosophila. Proc Natl Acad Sci USA 107(29):12975-12979, 2010.

Monzo K, Dowd SR, Minden JS*, Sisson JS. Proteomic analysis reveals CCT is a target of Fragile X mental retardation protein regulation in Drosophila. Dev. Biol. 16, 2891-902, 2010.

Mukhopadhyay S§, Bachert C, Smith D, Linstedt AD*. Manganese-induced trafficking and turnover of the cis Golgi glycoprotein GPP130. Mol. Biol. of the Cell, 21: 1282-1292, 2010.

Murphy RF*. Communicating Subcellular Distributions. Cytometry Part A 77A:686-692, 2010.

Padmanabhan K§, Eddy WF*, Crowley JC*. A novel algorithm for optimal image thresholding of biological data. J Neurosci Methods. 2010 Nov 30;193(2):380-4. Epub 2010 Sep 15.

Padmanabhan K§, Urban NN*. Intrinsic biophysical diversity decorrelates neuronal firing while increasing information content. Nat Neurosci. 13(10):1276-82, 2010 Oct. Epub 2010 Aug 29.

Park S, Cho HY, Yoon JA, Kwak Y, Srinivasan A, Hollinger JO*, Paik HJ, Matyjaszewski K. Photo-cross-linkable thermoresponsive star polymers designed for control of cell-surface interactions. Biomacromolecules. 11(10):2647-52, 2010 Oct 11.

Peng T, Bonamy GMC, Glory-Afshar E, Rines DR, Chanda SK, Murphy RF*. Determining the distribution of probes between different subcellular locations through automated unmixing of subcellular patterns. Proc. Natl. Acad. Sci. U.S.A. 107:2944-2949, 2010.

Puthenveedu MA*, Lauffer B, Temkin P, Vistein R, Carlton P, Thorn K, Taunton J, Weiner OD, Parton RG, von Zastrow M. Sequence-dependent sorting of recycling proteins by actin-stabilized endosomal microdomains. Cell. 143(5):761-73, 2010 Nov 24.

Ribeiro AS, Dahl KN. The nucleus as a central structure in defining the mechanical properties of stem cells. Conf Proc IEEE Eng Med Biol Soc. 2010;1:831-4.

Rule GS*, Kessler A, Bajzek D. Molecular Visualization in STEM Education: Leveraging Jmol in an Integrated Assessment Platform. In Proceedings of World Conference on E-Learning in Corporate, Government, Healthcare, and Higher Education 2010. Chesapeake, VA: AACE.

Schwartz R*, Shackney S. Applying unmixing to gene expression data for tumor phylogeny inference. BMC Bioinformatics, 11:42, 2010.

Sengupta D, Linstedt AD*. Mitotic inhibition of GRASP65 organelle tethering involves Polo-like kinase 1 (PLK1) phosphorylation proximate to an internal PDZ ligand. J Biol Chem. 285: 39994-40003, 2010. PMID: 20937827.

Shariff A, Kangas J, Coelho LP, Quinn S, Murphy RF*. Automated image analysis for high-content screening and analysis. J Biomol Screen. 726-34, 2010 Aug;15(7). Epub 2010 May 20.

Shariff A, Murphy RF*, Rohde GK. A generative model of microtubule distributions, and indirect estimation of its parameters from fluorescence microscopy images. Cytometry A. 77(5):457-66, 2010 May.

Shariff A, Rohde GK, Murphy RF*. A Generative Model of Microtubule Distributions, and Indirect Estimation of its Parameters from Fluorescence Microscopy Images. Cytometry 77A:457-466, 2010.

Sharma T, Ettensohn CA*. Activation of the skeletogenic gene regulatory network in the early sea urchin embryo. Development 137, 1149-1157, 2010.

Srinivas M, Heerschap A, Ahrens ET*, Figdor CG, de Vries IJ. 19)F MRI for quantitative in vivo cell tracking. Trends Biotechnol. 28(7):363-70, 2010 Jul. Epub 2010 Apr 26.

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.

Szent-Gyorgyi C, Schmidt BF, Fitzpatrick JAJ, Bruchez MP*. Fluorogenic Dyedrons with Multiple Donor Chromophores as Bright Genetically Targeted and Activated Probes. Journal of the American Chemical Society, 2010.

Talkowski ME, McCann KL, Chen, M Y-M, McClain L, Bamne M, Wood J, Chowdari KV, Kirov G, Georgieva L, Toncheva D, Mansour H, Lewis DA, Owen M, O’Donovan M, Papasaikas P, Sullivan P, Sklar P, Ruderfer D and ISC consortium, Yao JK, Leonard S, Thomas P, Miyajima F, Quinn J, Lopez AJ*, Nimgaonkar VL. Fine mapping reveals novel alternative splicing of the dopamine transporter. Am J Med Genet B Neuropsychiatr Genet. 153B(8):1434-1447, 2010.

Tolliver D, Tsourakakis C, Subramanian A, Shackney S, Schwartz R*. Robust unmixing of tumor states in array comparative genomic hybridization data. Bioinformatics (Proceedings Issue for Intelligent Systems for Molecular Biology (ISMB 2010)), 26(12):i106-i114, 2010.

Tristram-Nagle S, Chan R, Kooijman E, Uppamoochikkal P, Qiang W, Weliky DP, Nagle JF*. HIV fusion peptide penetrates, disorders, and softens T-cell membrane mimics. J Mol Biol. 402(1):139-53, 2010 Sep 10. Epub 2010 Jul 22.

Tristram-Nagle S, Kim DJ, Akhunzada N, Kucerka N, Mathai JC, Katsaras J, Zeidel M, Nagle JF*. Structure and water permeability of fully hydrated diphytanoylPC. Chem. Phys. Lipids 163, 630-637, 2010.

Uppamoochikkal P, Tristram-Nagle S, Nagle JF*. Orientation of tie-lines in the phase diagram of DOPC/DPPC/cholesterol model biomembranes. Langmuir. 26(22):17363-8, 2010 Nov 16. Epub 2010 Oct 22.

Urban NN*, Castro JB. Functional polarity in neurons: what can we learn from studying an exception? Curr Opin Neurobiol. 20(5):538-42, 2010 Oct. Epub 2010 Aug 17.

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.

Yassin L, Benedetti BL, Jouhanneau JS, Wen JA, Poulet JF, Barth AL*. An embedded subnetwork of highly active neurons in the neocortex. Neuron. 68(6):1043-50, 2010 Dec 22.

Yuan Y, Simplaceanu V, Ho NT, Ho C*. An Investigation of the Distal Histidyl H-bonds in Oxyhemoglobin: Effects of Temperature, pH, and Organic Phosphate. Biochemistry 49, 10606-10615, 2010. Selected by the Library of Faculty of 1000

Zanotti KJ, Silva GL, Creeger Y, Robertson KL, Waggoner AS*, Berget PB*, Armitage BA*. Blue fluorescent dye-protein complexes based on fluorogenic cyanine dyes and single chain antibody fragments. Org Biomol Chem. 9(4):1012-20, 2011. Epub 2010 Dec 22.

Zhang X, Badea CT, Hood G, Wetzel AW, Stiles JR*, Johnson GA. Free-space fluorescence tomography with adaptive sampling based on anatomical information from microCT. Proc Soc Photo Opt Instrum Eng. 7757(775706), 2010. pii: 755706 (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 340:54-66, 2010.