2011

Adomako-Ankomah A†, Ettensohn CA*. P58-A and P58-B: novel proteins that mediate skeletogenesis in the sea urchin embryo. Dev Biol. 353(1):81-93, 2011 May 1. Epub 2011 Feb 26.

Ahrens ET*, Young WB, Xu H, Pusateri LK. Rapid quantification of inflammation in tissue samples using perfluorocarbon emulsion and fluorine-19 nuclear magnetic resonance. Biotechniques. 50(4):229-34, 2011 Apr.

Argimon S, Fanning S§ , Blankenship JR§, Mitchell AP*. Interaction between the Candida albicans High-Osmolarity Glycerol (HOG) Pathway and the Response to Human {beta}-defensins 2 and 3. Eukaryot Cell. 10(2):272-5, 2011 Feb. Epub 2010 Dec 3.

Bartoli KM, Jakovljevic J, Woolford JL Jr*, Saunders WS. Kinesin Molecular Motor Eg5 Functions during Polypeptide Synthesis. Mol Biol Cell. 2011 Jul 27. [Epub ahead of print]

Baudin-Creuza V, Ho C*, Marden MC. Hb Octamers by Introduction of Surface Cysteines, in Chemistry and Biochemistry of Oxygen Therapeutics:  From Transfusion to Artificial Blood  edited by Stefano Bettati and Andrea Mozzarelli, First Edition, John Wiley & Sons, Ltd., pp. 371-380, 2011.

Blankenship JR§, Mitchell AP*. Candida albicans Adds More Weight to Iron Regulation. Cell Host Microbe. 2011 Aug 18;10(2):93-4.

Bonetto F, Srinivas M, Heerschap A, Mailliard R, Ahrens ET*, Figdor CG, de Vries IJ. A novel (19)F agent for detection and quantification of human dendritic cells using magnetic resonance imaging. Int J Cancer. 2011 Jul 15;129(2):365-73. doi: 10.1002/ijc.25672. Epub 2010 Nov 3.

Brillet T, Baudin-Creuza V, Kettering R, Yeh JI, Shen, TJ, Ho NT,  Vasseur C, Domingues E, Ho C*, Marden MC. Interaction of Haptoglobin with Hemoglobin Octamers Based on the Mutation αAsn78Cys or βGly83Cys. American Journal of Molecular Biology, in press (2011).

Bruchez MP*. Quantum Dots Find Their Stride in Single Molecule Tracking. Current Opinion in Chemical Biology 2011. In press.

Cao W, Coman MM, Ding S, Henn A, Middleton ER, Bradley MJ, Rhoades E, Hackney DD*, Pyle AM, De La Cruz EM. Mechanism of Mss116 ATPase Reveals Functional Diversity of DEAD-Box Proteins. J. Mol. Biol. 409, 399-414, 2011.

Chen C-L, Zhang H, Ye Q, Hsieh W-Y, Hitchens TK, Shen H-H, Liu L, Wu Y-J, Foley LM, Wang S-J, Ho C*. A New Nano-Sized Iron Oxide Particle with High Sensitivity for Cellular Magnetic Resonance Imaging. Molecular Imaging & Biology 2011; 13, 825-839.

Cho HY, Srinivasan A, Hong J, Hsu E, Liu S, Shrivats A, Kwak D, Bohaty AK, Paik HJ, Hollinger JO*, Matyjaszewski K. Synthesis of Biocompatible PEG-Based Star Polymers with Cationic and Degradable Core for siRNA Delivery. Biomacromolecules. 2011 Oct 10;12(10):3478-86. Epub 2011 Sep 6.

Dagley MJ, Gentle IE, Beilharz TH, Pettolino FA, Djordjevic JT, Lo TL, Uwamahoro N, Rupasinghe T, Tull DL, McConville M, Beaurepaire C, Nantel A, Lithgow T, Mitchell AP, Traven A. Cell wall integrity is linked to mitochondria and phospholipid homeostasis in Candida albicans through the activity of the post-transcriptional regulator Ccr4-Pop2. Mol Microbiol. 79(4):968-989, 2011 Feb. Epub 2010 Dec 30.

Dahlen JE, Jimenez DA, Gerkin RC, Urban NN. Morphological analysis of activity-reduced adult-born neurons in the mouse olfactory bulb. Front Neurosci. 5:66, 2011. Epub 2011 May 9.

Dwivedi P, Thompson A, Xie Z, Kashleva H, Ganguly S†, Mitchell AP*, Dongari-Bagtzoglou A. Role of bcr1-activated genes hwp1 and hyr1 in Candida albicans oral mucosal biofilms and neutrophil evasion. PLoS One 6, e16218, 2011.

Ettensohn CA. Linking developmental gene regulatory networks to morphogenesis. Genesis, 2011, in press.

Finkel JS, Mitchell AP. Genetic control of Candida albicans biofilm development. Nat Rev Microbiol. 9(2):109-18, 2011 Feb. Epub 2010 Dec 29.

Finkel JS§, Yudanin N‡, Nett JE, Andes DR, Mitchell AP*. Application of the systematic "DAmP" approach to create a partially defective C. albicans mutant. Fungal Genet Biol. 48, 1056-1061, 2011 Jul 27.

Flynn CJ†, Sharma T†, Ruffins SW, Guerra SL‡, Crowley JC*, Ettensohn CA*. High-resolution, three-dimensional mapping of gene expression using GeneExpressMap (GEM). Dev Biol 357, 532-540. 2011 Jun 29. [Epub ahead of print].

Ganguly S†, Bishop AC, Xu W, Ghosh S, Nickerson KW, Lanni F*, Patton-Vogt J, Mitchell AP*. Zap1 control of cell-cell signaling in Candida albicans biofilms. Eukaryot Cell. 2011 Sep 2.

Ganguly S, Mitchell AP. Mucosal biofilms of Candida albicans. Curr Opin Microbiol, 14, 380-385. 2011 Jul 7.

Giridhar S, Doiron B, Urban NN*. Timescale-dependent shaping of correlation by olfactory bulb lateral inhibition. Proc Natl Acad Sci USA.;108(14):5843-8, 2011 Apr 5. Epub 2011 Mar 21.

Hitchens TK, Ye Q, Eytan DF, Janjic JM, Ahrens ET, Ho C. (19) F MRI detection of acute allograft rejection with in vivo perfluorocarbon labeling of immune cells. Magn Reson Med. 2011 Feb 8, 65, 11-45-1154.

Iordanova B§, Ahrens ET*. In vivo magnetic resonance imaging of ferritin-based reporter visualizes native neuroblast migration. Neuroimage. 2011 Sep 13.

Jackson C, Glory E, Murphy RF*, Kovacevic J. Model building and intelligent acquisition with application to protein subcellular location classification. Bioinformatics 27:1854-1859, 2011.

Kaan HY, Hackney DD*, Kozielski F. The structure of the kinesin-1 motor-tail complex reveals the mechanism of autoinhibition. Science. 333(6044):883-5, 2011 Aug 12.

Kadri S, Hinman V*, Benos PV. RNA Deep sequencing reveals differential microRNA expression during development of the sea urchin and sea star. PLOS ONE, in press.

Kang J, Steward R, Schwartz R*, Leduc PR*, Puskar K. Controlled response of actin filament networks under cyclic stress through a coarse grained Monte Carlo model. Journal of Theoretical Biology, 274:109-119, 2011.

Ker ED, Chu B, Phillippi JA, Gharaibeh B, Huard J, Weiss LE, Campbell PG. Engineering spatial control of multiple differentiation fates within a stem cell population. Biomaterials. 32(13):3413-22, 2011 May. Epub 2011 Feb 12.

Ker ED†, Nain AS, Weiss LE, Wang J, Suhan J, Amon CH, Campbell PG*. Bioprinting of growth factors onto aligned sub-micron fibrous scaffolds for simultaneous control of cell differentiation and alignment. Biomaterials. 2011 Aug 4.

Ker DF, Weiss LE, Junkers SN, Chen M, Yin Z, Sandbothe MF, Huh SI, Eom S, Bise R, Osuna-Highley E, Kanade T, Campbell PG. An engineered approach to stem cell culture: automating the decision process for real-time adaptive subculture of stem cells. PLoS One. 2011;6(11):e27672. Epub 2011 Nov 16.

Kim J, Magno MH, Alvarez P, Darr A, Kohn J, Hollinger JO*. Osteogenic differentiation of pre-osteoblasts on biomimetic tyrosine-derived polycarbonate scaffolds .Biomacromolecules. 2011 Oct 10;12(10):3520-7. Epub 2011 Sep 12.

Kim J, Sharma A, Runge B, Waters H, Doll B, McBride S, Alvarez P, Dadsetan M, Yaszemski MJ, Hollinger JO*. Osteoblast growth and bone-healing response to three-dimensional poly(ε-caprolactone fumarate) scaffolds. J Tissue Eng Regen Med. 2011 Jul 11.

Kumar A, Oswald AM, Urban N*, Doiron B.  Balanced synaptic input shapes the correlation between neural spike trains. PloS Computational Biology, In Press. 

Lanni F*, Keller HE. Microscope principles and optical systems. In: Imaging, A Laboratory Manual. RM Yuste Ed., Cold Spring Harbor Laboratory Press. Chapter 1, pp1-55, 2011.

Lanni F*.  Fluorescence grating imager systems for optical-sectioning microscopy.  In: Imaging, A Laboratory Manual.  RM Yuste Ed., Cold Spring Harbor Laboratory Press. Chapter 47, pp735-744, 2011.

Lee B§, LeDuc PR*, Schwartz R*. Unified regression model of binding equilibria in crowded environments. Scientific Reports, 1:97, 2011.

Lim JK, Lanni C, Evarts ER, Lanni F*, Tilton RD, Majetich SA.  Magnetophoresis of nanoparticles. ACS Nano 5: 217-226, 2011.

Lin T, Bar-Joseph Z*, Murphy RF*. Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs. Journal of Computational Biology, 2011, in press.

Lin TH, Murphy RF, Bar-Joseph Z. Discriminative motif finding for predicting protein subcellular localization. IEEE/ACM Trans Comput Biol Bioinform. 8(2):441-51, 2011 Mar-Apr.

Luo F, Dittrich M, Stiles JR*, Meriney SD. Luo F, Dittrich M, Stiles JR, Meriney SD. Single-pixel optical fluctuation analysis of calcium channel function in active zones of motor nerve terminals. J Neurosci. 31(31):11268-81, 2001 Aug 3.

Makowski L, Bardhan J, Gore D, Lal J, Mandava S, Park S, Rodi DJ, Ho NT, Ho C*, Fischetti RF.  WAXS Studies of the Structural Diversity of Hemoglobin in Solution. Journal of Molecular Biology 2011; 408, 909-921. 

May GE, Olson S, McManus CJ*, Graveley BR. Competing RNA secondary structures are required for mutually exclusive splicing of the Dscam exon 6 cluster. RNA 17(2):222-229,2011.

McManus CJ*, Graveley BR. RNA Structure and the mechanisms of alternative splicing. Curr Opin Genet Dev 21(4):373-9, 2011.

Micheva KD, Bruchez MP*. The gain in brain: novel imaging techniques and multiplexed proteomic imaging of brain tissue ultrastructure. Current Opinion in Neurobiology, 2011. 

Miller GL, Peng R, Schwartz R*, Tsourakakis C. Approximate dynamic programming using halfspace queries and multiscale Monge decomposition. ACM Symposium on Discrete Algorithms (SODA2011), 1675-1682, 2011.

Mills PH, Hitchens TK, Foley LM, Link T, Ye Q, Weiss CR, Thompson JD, Gilson WD, Arepally A, Melick JA, Kochanek PM, Ho C, Bulte JW, Ahrens ET. Automated detection and characterization of SPIO-labeled cells and capsules using magnetic field perturbations. Magn Reson Med. 2011 Jun 7.

Minden JS*. DIGE: past and future. In Difference Gel Electrophoresis (DIGE): Methods and Protocols, Cramer and Westermeier (Eds), Humnan Press. NY, 2011.

Minden JS*. Two-dimensional difference gel electrophoresis. in Protein Electrophoresis: Methods and Protocols, Kurien and Scofield (Eds), Humnan Press. NY, 2011.

Misra N, Blelloch G, Ravi R, Schwartz R*. An optimization-based sampling scheme for phylogenetic trees. Journal of Computational Biology, in press, 2011. (extended version of RECOMB 2011 conference paper)

Misra N, Blelloch G, Ravi R, Schwartz R. Generalized buneman pruning for inferring the most parsimonious multi-state phylogeny. J Comput Biol. 18(3):445-57, 2011 Mar.

Mittal R, Bruchez MP*. Biotin-4-Fluorescein Based Fluorescence Quenching Assay for Determination of Biotin Binding Capacity of Streptavidin Conjugated Quantum Dots. Bioconjugate Chemistry 2011.

Morel PA, Srinivas M, Turner MS, Fuschiotti P, Munshi R, Bahar I, Feili-Hariri M, Ahrens ET*. Gene expression analysis of dendritic cells that prevent diabetes in NOD mice: analysis of chemokines and costimulatory molecules. J Leukoc Biol. 2011 Sep;90(3):539-50. Epub 2011 May 31.

Morin-Leisk J†, Saini SG, Meng X, Makhov AM, Zhang P, Lee TH*. An intramolecular salt bridge drives the soluble domain of GTP-bound atlastin into the postfusion conformation. The Journal of Cell Biology, 195(4): 605-615, 2011.

Mukhopadhyay S, Linstedt AD. Identification of a gain-of-function mutation in a Golgi P-type ATPase that enhances Mn2+ efflux and protects against toxicity. Proc Natl Acad Sci U S A. 2011 Jan 11;108(2):858-63. Epub 2010 Dec 27.

Murphy RF*. An active role for machine learning in drug development. Nat Chem Biol. 7(6):327-30, 2011 Jun.

Murphy RF* CellOrganizer: Image-derived Models of Subcellular Organization and Protein Distribution. Methods in Cell Biology, 2011, in press.

Nimgaonkar VL, Chowdari KV, Prasad KM, Watson A, Mansour H, Wood JA, Lopez AJ*. What can be learned from nominally significant/discrepant associations? An illustration using dopamine gene variants and schizophrenia. in “Schizophrenia: The Final Frontier”. Edited by A.S. David, S. Kapur and P. McGuffin. Taylor and Francis Ltd., 2011. ISBN-13: 978-1848720770.

Peng T, Murphy RF*. Image-derived, Three-dimensional Generative Models of Cellular Organization. Cytometry Part A 79A:383-391, 2011.

Rafiq K†, Cheers M, Ettensohn CA*. The genomic regulatory control of skeletal morphogenesis in the sea urchin. Development, 2011, in press.

Rao A and Murphy RF*. Determination of Protein Location Diversity Via Analysis of Immunohistochemical Images from the Human Protein Atlas. Proceedings of the 2011 IEEE International Symposium on Biomedical Imaging  (ISBI 2011), 1727-1729, 2011.

Sahasranaman A, Dembowski J, Strahler J, Andrews P, Maddock J, Woolford JL Jr*. Assembly of Saccharomyces cerevisiae 60S ribosomal subunits: role of factors required for 27S pre-rRNA processing. EMBO J. 2011 Sep 16.

Sengupta D, Linstedt AD. Control of Organelle Size: The Golgi Complex. Annu Rev Cell Dev Biol. 2011 May 31.

Shariff A, Murphy RF*, Rohde GK. Automated Estimation of Microtubule Model Parameters from 3-D Live Cell Microscopy Images. Proc IEEE Int Symp Biomed Imaging. 2011 Jun 9;2011(March 30 2011-April 2 2011):1330-1333.

Sharma T, Ettensohn CA. Regulative deployment of the skeletogenic gene regulatory network during sea urchin development. Development. 138(12):2581-90, 2011 Jun.

Sinha K, Jen-Jacobson L, Rule G*. Site-Specific Labeling of Threonine Methyl Groups for NMR Studies of Protein-Nucleic Acid Complexes. Biochemistry, 2011, in press.

Stadler AL, Delos Santos JO, Stensrud ES§, Dembska A, Silva GL, Liu S, Shank NI, Kunttas-Tatli E†, Sobers CJ, Gramlich PM, Carell T, Peteanu LA, McCartney BM*, Armitage BA*. Fluorescent DNA Nanotags Featuring Covalently Attached Intercalating Dyes: Synthesis, Antibody Conjugation and Intracellular Imaging. Bioconjugate Chemistry 22(8):1491-1502, 2011 Aug 17.

Subramanian A†, Shackney S, Schwartz R*. Inference of tumor phylogenies from genomic assays on heterogeneous samples. Proceedings of the ACM Conference on Bioinformatics and Computational Biology, 2011.

Tiso M, Tejero J, Basu S, Azarov I, Wang X, Simplaceanu V, Frizzell S, Jayaraman T, Geary L, Shapiro C, Ho C*, Shiva S, Kim-Shapiro DB, Gladwin MT. Human Neuroglobin Functions as a Redox-regulated Nitrite Reductase. Journal of Biological Chemistry 2011; 286, 18277-18289. 

Truschel ST§, Sengupta D, Foote A‡, Heroux A, Macbeth M*, Linstedt AD*. Structure of the membrane-tethering GRASP domain reveals a unique PDZ ligand interaction that mediates Golgi biogenesis. J Biol Chem. 2011 Jun 10;286(23):20125-9. Epub 2011 Apr 22.

Tsai MC, Blelloch G, Ravi R, Schwartz R*. A consensus tree approach for reconstructing human evolutionary history and detecting population substructure. IEEE/ACM Trans Comput Biol Bioinform. 8(4):918-28, 2011 Jul-Aug.

Tsourakakis CE, Peng R, Tsiarli MA, Miller GL, Schwartz R*. Approximation algorithms for speeding up dynamic programming and denoising aCGH data. Journal of Experimental Algorithmics, accepted for publication, 2011.

Wen JA and Barth AL. Input-Specific Critical Periods for Experience-Dependent Plasticity in Layer 2/3 Pyramidal Neurons. J Neurosci. 31(12):4456-65, 2011 March 23.

Wren NS, Schwartz R*, Dahl KN*. Modeling nuclear blebs in a nucleoskeleton of independent filament networks. Cellular and Molecular Bioengineering, accepted for publication, 2011.

Wu YJL, Ye Q, Zhang H, Hitchens TK, Ho C*. Other Non-Stem Cell Therapies for Cellular Tracking – Inflammatory Cell Tracking in Stem Cell Labeling for Delivery and Tracking Using Non-Invasive Imaging, edited by Dara L. Kraitchman and Joseph C. Wu, Taylor & Francis Group, in press, 2011.

Wu YL, Ye Q, Ho C. Cellular and Functional Imaging of Cardiac Transplant Rejection. Curr Cardiovasc Imaging Rep. 4(1):50-62, 2011 Feb 1.

Yadav S and Linstedt AD. Golgi Positioning. Cold Spring Harb Perspect Biol. pii: cshperspect.a005322v1, 2011 Apr 6.

Yuan Y, Shen T-J, Gupta P‡, Ho NT, Simplaceanu V, Tam TCS, Hofreiter M, Cooper A, Campbell KL, Ho C*. A Biochemical-Biophysical Study of Hemoglobins from Woolly Mammoth, Asian Elephant, and Humans. Biochemistry. 2011 Aug 2.

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. 2011 Feb 21;9(4):1012-20. Epub 2010 Dec 22.

Zhou M-N, Kunttas-Tatli E, Zimmerman S, Zhouzheng F, McCartney BM. Cortical localization of APC2 plays a role in actin organization but not in Wnt signaling in Drosophila. Journal of Cell Science, 124(Pt 9):1589-600, 2011 May 1.