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Laboratory Methods

 

Nanoparticles

Use of cell morphology as early bioindicator for viral infection. IET Nanobiotechnol. 2014 Mar;8(1):24-30 (Ding et al., 2014).

Quantification of biomass and cell motion in human pluripotent stem cell colonies. Biophys J. 2013 Aug 6;105(3):593-601 (Zangle et al.,2013).

Self-assembly of Phospholipid-PEG Coating on Nanoparticles through Dual Solvent Exchange. Nano Letters, 11: 3720-6. (Tong et al., 2011).

Bright and compact alloyed quantum dots with broadly tunable near-Infrared absorption and fluorescence spectra through mercury cation exchange. J. Am. Chem. Soc. 133:24-26. (Smith et al., 2011).

Quantum Dot-Fluorescent Protein FRET Probe for Monitoring Intracellular pH. ACS Nano, 6: 2917-24. (Dennis et al., 2012).

 

Bioengineering and Biophysics

Synthesis of nanostructured and biofunctionalized water-in-oil droplets as tools for homing T cells. J Am Chem Soc. 2013 Mar 6;135(9):3339-42 (Platzman et al., 2013).

Simplified prototyping of perfusable polystyrene microfluidics. Biomicrofluidics 8, 046501 (Tran et al., 2014).

Nanolithographic Control of the Spatial Organization of Cellular Adhesion Receptors at the Single-Molecule Level. Nano Lett. 11(3):1306-12. (Schvartzman et al., 2011).

Probing single biomolecules in solution using the Anti-Brownian ELectrokinetic (ABEL) trap. Acc Chem Res. 45:1955-1964. (Wang et al., 2012).

Forming giant vesicles with controlled membrane composition, asymmetry, and contents. Proc Nat Acad Sci. 108(23): 9431-6. (Richmond et al., 2011).

 

Gene Correction

Quantifying genome-editing outcomes at endogenous loci with SMRT sequencing. Cell Rep. 2014 Apr 10;7(1):293-305. (Hendel et al., 2014).

An unbiased method for detection of genome-wide off target effects in cell lines treated with zinc finger nucleases. Methods in Molecular Biology Genome Res. 22(3): 539–548. (Lindsay et al., 2013).

Use of a microscope stagemounted Nickel-63 microirradiator for real-time observation of the DNA double-strand break response. Nucleic Acids Res. 38:e144. (Cao et al., (2010).

“Intranuclear delivery of a novel antibody-derived radiosensitizer targeting the DNA-dependent protein kinase catalytic subunit.” Int. J, Radiat. Oncol. Biol. Phys. (Xiong et al., 2011).

 

Optical Control

A red-shifted, fast-relaxing azobenzene photoswitch for visible light control of an ionotropic glutamate receptor. J Am Chem Soc. 2013 Nov 27;135(47):17683-6. (Kienzler et al., 2013).

Photochromic potassium channel blockers: design and electrophysiological characterization. Methods Mol Biol. 995, 89-105 (Mourot et al., 2013).

A (1)H NMR assay for measuring the photostationary states of photoswitchable ligands. Methods Mol Biol. 995,107-20 (Banghart et al. 2013).

Optical control of endogenous proteins with a photoswitchable conditional subunit reveals a role for TREK1 channel in GABAB signaling. Neuron 74, 1005-14 (Sandoz et al. 2012).

 “Light-based feedback for controlling intracellular signaling dynamics”, Nat Methods. Sep 11; 8(10): 837-9 (Toettcher et al., 2011).

 

Electrophysiology/Imaging

Imaging light responses of retinal ganglion cells in the living mouse eye. J. Neurophysiol. 109:2415-21 (Yin et al. 2013).

Scanless two-photon excitation of channelrhodopsin-2. Nat Meth 7:848-854 (Papagiakoumou et al., 2010).

 

Structural Biology

A rotamer library to enable modeling and design of peptoid foldamers J Am Chem Soc. 2014 Jun 18;136(24):8772-82 (Renfrew et al., 2014).

Peptidomimetic design— Adding diverse noncanonical backbones to rosetta PLoS One. 2013 Jul 15;8(7):e67051 (Drew et al., 2013).

Cryo-EM model validation using independent map reconstructions. Protein Sci. 2013 Jun;22(6):865-8 (DiMaio et al., 2013).

Cryo-EM of macromolecular assemblies at near atomic resolution. Nature Protocols 5: 1697-1708 (Baker et al., 2010).

Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering and fitting of structures by alignment to regions. J Struct Biol 170(3):427-38 (Pintilie et al., 2010).

Cryo-EM model validation using independent map reconstructions. Protein Sci 22:865-868 (Dimaio et al., 2013).

Zernike phase contrast cryo-electron microscopy and tomography for structure determination at nanometer and subnanometer resolutions. Structure 18(8):903-912. (Murata et al. 2010).

 

Vectors

Biologically active homo-oligomers of human CCT4 and CCT5 chaperonin subunits expressed in Escherichia coli J Biol Chem. 2013 Jun 14;288(24):17734-44 (Sergeeva et al., 2013).

Purified Human TRiC complex Cell Stress Chaperones. 2013 Mar;18(2):137-44 (Knee et al., 2013).

In Vivo–Directed Evolution of a New Adeno-Associated Virus for Therapeutic Outer Retinal Gene Delivery from the Vitreous. Science Transl. Med. 5, 189ra76. (Dalkara et al., 2013).

Adeno-associated viral vectors for gene therapy of inherited retinal degenerations. Methods Mol Biol. 935, 351-69 (Flannery et al. 2013).

 

Computational

SCISSORS: A Linear-Algebraical Technique to Rapidly Approximate Chemical Similarities. JCIM. 28;50(6):1075-88. (Haque et al. 2010).

Parametric Bayesian priors and better choice of negative examples improve protein function prediction. Bioinformatics. May 1;29(9):1190-8 (Youngs et al. 2013).

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