Research Output 1949 2019

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2019

Chapter 11: Collective Behaviour of Artificial Microswimmers in Response to Environmental Conditions

Altemose, A. & Sen, A., Jan 1 2019, Self-organized Motion: Physicochemical Design based on Nonlinear Dynamics. Lagzi, I., Pimienta, V., Suematsu, N. J., Nakata, S. & Kitahata, H. (eds.). 14 ed. Royal Society of Chemistry, p. 250-283 34 p. (RSC Theoretical and Computational Chemistry Series; vol. 2019-January, no. 14).

Research output: Chapter in Book/Report/Conference proceedingChapter

Biological systems
Fish

In Vivo Genome-Wide RNA Structure Probing with Structure-seq

Ritchey, L. E., Su, Z., Assmann, S. M. & Bevilacqua, P. C., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 305-341 37 p. (Methods in Molecular Biology; vol. 1933).

Research output: Chapter in Book/Report/Conference proceedingChapter

Genome
RNA
Glyoxal
Transcriptome
Bacteria

Metabolon formation by chemotaxis

Zhao, X. & Sen, A., Jan 1 2019, Methods in Enzymology. Academic Press Inc., p. 45-62 18 p. (Methods in Enzymology; vol. 617).

Research output: Chapter in Book/Report/Conference proceedingChapter

Chemotaxis
Enzymes
Substrates
Glucose-6-Phosphate Isomerase
Phosphofructokinases

Monitoring proteome stress in live cells using halotag-based fluorogenic sensor

Liu, Y., Fares, M. & Zhang, X., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 171-182 12 p. (Methods in Molecular Biology; vol. 1873).

Research output: Chapter in Book/Report/Conference proceedingChapter

Proteome
Fluorescence
Hot Temperature
Pharmaceutical Preparations

The Alstoscholarisine Alkaloids: Isolation, Structure Determination, Biogenesis, Biological Evaluation, and Synthesis

Mason, J. D. & Weinreb, S. M., Jan 1 2019, Alkaloids: Chemistry and Biology. Knölker, H-J. (ed.). Academic Press Inc., p. 115-150 36 p. (Alkaloids: Chemistry and Biology; vol. 81).

Research output: Chapter in Book/Report/Conference proceedingChapter

Alkaloids
Alstonia
Secologanin Tryptamine Alkaloids
Biosynthesis
Metabolites
2018
5 Citations (Scopus)

Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a “Plug and Play” Domain

Holliday, G. L., Akiva, E., Meng, E. C., Brown, S. D., Calhoun, S., Pieper, U., Sali, A., Booker, S. J. & Babbitt, P. C., Jan 1 2018, Methods in Enzymology. Bandarian, V. (ed.). Academic Press Inc., p. 1-71 71 p. (Methods in Enzymology; vol. 606).

Research output: Chapter in Book/Report/Conference proceedingChapter

Atlases
Nucleic Acids
Databases
Enzymes
Metabolism
1 Citation (Scopus)

Biochemical Approaches for Understanding Iron–Sulfur Cluster Regeneration in Escherichia coli Lipoyl Synthase During Catalysis

McCarthy, E. L. & Booker, S. J., Jan 1 2018, Methods in Enzymology. Bandarian, V. (ed.). Academic Press Inc., p. 217-239 23 p. (Methods in Enzymology; vol. 606).

Research output: Chapter in Book/Report/Conference proceedingChapter

Catalysis
Escherichia coli
Regeneration
S-Adenosylmethionine
Sulfur

Chemical Tools for Studying the Impact of cis/trans Prolyl Isomerization on Signaling: A Case Study on RNA Polymerase II Phosphatase Activity and Specificity

Burkholder, N. T., Medellin, B., Irani, S., Matthews, W., Showalter, S. A. & Zhang, Y. J., Jan 1 2018, Methods in Enzymology. Allen, K. N. (ed.). Academic Press Inc., p. 269-297 29 p. (Methods in Enzymology; vol. 607).

Research output: Chapter in Book/Report/Conference proceedingChapter

RNA Polymerase II
Isomerization
Phosphoric Monoester Hydrolases
Proline
Conformations

Detecting purinosome metabolon formation with fluorescence microscopy

Pedley, A. M. & Benkovic, S., Jan 1 2018, Methods in Molecular Biology. Humana Press Inc., p. 279-289 11 p. (Methods in Molecular Biology; vol. 1764).

Research output: Chapter in Book/Report/Conference proceedingChapter

Fluorescence Microscopy
Enzymes
Multienzyme Complexes
Purines
Biosynthetic Pathways

Polyphosphazenes as an example of the element-blocks approach to new materials

Allcock, H. R., Jan 1 2018, New Polymeric Materials Based on Element-Blocks. Springer Singapore, p. 167-188 22 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Polymers
Organometallics
Phosphorus
Substitution reactions
Thermoplastic elastomers

The Use of 13C Direct-Detect NMR to Characterize Flexible and Disordered Proteins

Cook, E. C., Usher, G. A. & Showalter, S. A., Jan 1 2018, Methods in Enzymology. Rhoades, E. (ed.). Academic Press Inc., p. 81-100 20 p. (Methods in Enzymology; vol. 611).

Research output: Chapter in Book/Report/Conference proceedingChapter

Intrinsically Disordered Proteins
Nuclear magnetic resonance
Nuclear magnetic resonance spectroscopy
Magnetic Resonance Spectroscopy
Proteins
2 Citations (Scopus)

Using Peptide Mimics to Study the Biosynthesis of the Side-Ring System of Nosiheptide

Wang, B., LaMattina, J. W., Badding, E. D., Gadsby, L. K., Grove, T. L. & Booker, S. J., Jan 1 2018, Methods in Enzymology. Bandarian, V. (ed.). Academic Press Inc., p. 241-268 28 p. (Methods in Enzymology; vol. 606).

Research output: Chapter in Book/Report/Conference proceedingChapter

Biosynthesis
S-Adenosylmethionine
Peptides
Pharmacokinetics
Antimalarials
2017

Chapter 3: Structural Diversity in Fluorinated Polyphosphazenes: Exploring the Change from Crystalline Thermoplastics to High-performance Elastomers and Other New Materials

Allcock, H. R., Jan 1 2017, Fluorinated Polymers, Volume 1: Synthesis, Properties, Processing and Simulation. Ameduri, B., Sawada, H. & Tang, B. Z. (eds.). 24 ed. Royal Society of Chemistry, p. 54-79 26 p. (RSC Polymer Chemistry Series; vol. 2017-January, no. 24).

Research output: Chapter in Book/Report/Conference proceedingChapter

Elastomers
Thermoplastics
Polymers
Crystalline materials
Block copolymers
1 Citation (Scopus)

Mechanism-Based Strategies for Structural Characterization of Radical SAM Reaction Intermediates

Davis, K. M. & Boal, A. K., Jan 1 2017, Methods in Enzymology. Academic Press Inc., p. 331-359 29 p. (Methods in Enzymology; vol. 595).

Research output: Chapter in Book/Report/Conference proceedingChapter

S-Adenosylmethionine
Reaction intermediates
Enzymes
Substrate Specificity
Crystal structure

The role of iron-sulfur clusters in the biosynthesis of the lipoyl cofactor

Lanz, N. D. & Booker, S. J., Aug 21 2017, Characterization, Properties and Applications. Walter de Gruyter GmbH, Vol. 1. p. 327-358 32 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Biosynthesis
Sulfur
Iron
7 Citations (Scopus)

TsrM as a Model for Purifying and Characterizing Cobalamin-Dependent Radical S-Adenosylmethionine Methylases

Blaszczyk, A. J., Wang, R. X. & Booker, S. J., Jan 1 2017, Methods in Enzymology. Academic Press Inc., p. 303-329 27 p. (Methods in Enzymology; vol. 595).

Research output: Chapter in Book/Report/Conference proceedingChapter

S-Adenosylmethionine
Vitamin B 12
Enzymes
Proteins
Biosynthesis
2016
2 Citations (Scopus)

A High-Throughput Biological Calorimetry Core: Steps to Startup, Run, and Maintain a Multiuser Facility

Yennawar, N., Fecko, J. A., Showalter, S. A. & Bevilacqua, P. C., Jan 1 2016, Methods in Enzymology. Academic Press Inc., p. 435-460 26 p. (Methods in Enzymology; vol. 567).

Research output: Chapter in Book/Report/Conference proceedingChapter

Calorimetry
Throughput
Chemical Engineering
Ligands
Bioengineering
2 Citations (Scopus)

Assessing Coupled Protein Folding and Binding Through Temperature-Dependent Isothermal Titration Calorimetry

Sahu, D., Bastidas, M., Lawrence, C. W., Noid, W. G. & Showalter, S. A., Jan 1 2016, Methods in Enzymology. Academic Press Inc., p. 23-45 23 p. (Methods in Enzymology; vol. 567).

Research output: Chapter in Book/Report/Conference proceedingChapter

Protein folding
Calorimetry
Protein Folding
Titration
Protein Binding
1 Citation (Scopus)

Protein conformational motions: Enzyme catalysis

Huang, X., Tony Liu, C. & Benkovic, S., May 17 2016, Understanding Enzymes: Function, Design, Engineering and Analysis. Pan Stanford Publishing Pte. Ltd., p. 21-46 26 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Catalysis
Enzymes
Protein
Motion
Proteins
2015
29 Citations (Scopus)

Mechanisms of 2-oxoglutarate-dependent oxygenases: The hydroxylation paradigm and beyond

Bollinger, Jr., J. M., Chang, W. C., Matthews, M. L., Martinie, R. J., Boal, A. K. & Krebs, C., Jan 1 2015, 2-Oxoglutarate-Dependent Oxygenases. Hausinger, R. P. & Schofield, C. J. (eds.). 3 ed. Royal Society of Chemistry, p. 95-122 28 p. (RSC Metallobiology; vol. 2015-January, no. 3).

Research output: Chapter in Book/Report/Conference proceedingChapter

Oxygenases
Hydroxylation
Dehydrogenation
Halogenation
Alkenes

Quantitative point-of-care (POC) assays using measurements of time as the readout: A new type of readout for mHealth

Lewis, G. G. & Phillips, S. T., Jan 27 2015, Mobile Health Technologies: Methods and Protocols. Springer New York, p. 213-229 17 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Point-of-Care Systems
Telemedicine
Assays
Equipment and Supplies
Capillary Action
1 Citation (Scopus)

Supramolecular Polymers

Elacqua, E., Ten Brummelhuis, N. & Weck, M., Jan 1 2015, Volume 3: Polymer Synthesis. wiley, Vol. 3-3. p. 71-92 22 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Polymers
Self assembly
Rotaxanes
Ring opening polymerization
Alkenes
2014

Cluster secondary ion mass spectrometrys

Kozole, J. & Winograd, N., Jan 1 2014, Surface Analysis and Techniques in Biology. Springer International Publishing, p. 71-98 28 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Secondary Ion Mass Spectrometry
Projectiles
Secondary ion mass spectrometry
Ions
Imaging techniques
20 Citations (Scopus)

Experimental approaches for measuring pKa's in RNA and DNA

Thaplyal, P. & Bevilacqua, P. C., Jan 1 2014, Methods in Enzymology. C ed. Academic Press Inc., p. 189-219 31 p. (Methods in Enzymology; vol. 549, no. C).

Research output: Chapter in Book/Report/Conference proceedingChapter

RNA
DNA
Nucleic Acids
Hydroxides
RNA Folding

Fluorinated Polyphosphazenes

Allcock, H. R., May 27 2014, Handbook of Fluoropolymer Science and Technology. Wiley-Blackwell, p. 1-20 20 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Polymers
Fluorine
Organic polymers
Block copolymers
Tuning
21 Citations (Scopus)

Phase separation as a possible means of nuclear compartmentalization

Aumiller, W. M., Davis, B. W. & Keating, C. D., Jan 1 2014, International Review of Cell and Molecular Biology. Elsevier Inc., p. 109-149 41 p. (International Review of Cell and Molecular Biology; vol. 307).

Research output: Chapter in Book/Report/Conference proceedingChapter

Phase separation
Eukaryotic Cells
Organelles
Polymers
Polymer solutions
5 Citations (Scopus)

The role of iron-sulfur clusters in the biosynthesis of the lipoyl cofactor

Lanz, N. D. & Booker, S. J., Jan 1 2014, Iron-Sulfur Clusters in Chemistry and Biology. Walter de Gruyter GmbH, p. 211-238 28 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Sulfur
Iron
2013
12 Citations (Scopus)

An integrated picture of HDV ribozyme catalysis

Golden, B. L., Hammes-Schiffer, S., Carey, P. R. & Bevilacqua, P. C., Jan 1 2013, Biophysics of RNA Folding. Springer New York, p. 135-167 33 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Hepatitis Delta Virus
Catalytic RNA
Catalysis
Viruses
Crystallography
11 Citations (Scopus)

Cluster TOF-SIMS Imaging and the Characterization of Biological Materials

Vickerman, J. & Winograd, N., Apr 15 2013, Cluster Secondary Ion Mass Spectrometry: Principles and Applications. John Wiley and Sons, p. 269-312 44 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Secondary ion mass spectrometry
Biological materials
Imaging techniques
Mass spectrometers
Ions

DNA Replication Fork, Bacterial

Spiering, M. M. & Benkovic, S., Feb 15 2013, Encyclopedia of Biological Chemistry: Second Edition. Elsevier Inc., p. 114-117 4 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

DNA Replication
DNA
Escherichia coli
Base Pairing
Clamping devices
3 Citations (Scopus)

Enzyme-gold nanoparticle bioconjugates: Quantification of particle stoichiometry and enzyme specific activity

Keighron, J. D. & Keating, C. D., Sep 3 2013, NanoBiotechnology Protocols. p. 163-174 12 p. (Methods in Molecular Biology; vol. 1026).

Research output: Chapter in Book/Report/Conference proceedingChapter

Gold
Nanoparticles
Enzymes
Research Personnel

Polyphosphazenes as biomaterials

Deng, M., Laurencin, C. T., Allcock, H. R. & Kumbar, S. G., Jan 1 2013, Polymeric Biomaterials: Structure and Function. CRC Press, Vol. 1. p. 84-126 43 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Biocompatible Materials
Biomaterials
Tissue
Tissue engineering
Controlled drug delivery
33 Citations (Scopus)

Systematic methods for structurally consistent coarse-grained models

Noid, W. G., Jan 1 2013, Biomolecular Simulations: Biomolecular Simulations. Humana Press Inc., p. 487-531 45 p. (Methods in Molecular Biology; vol. 924).

Research output: Chapter in Book/Report/Conference proceedingChapter

Entropy
Mechanics
3 Citations (Scopus)

Three-dimensional, paper-based micro fluidic devices containing internal timers for running time-based diagnostic assays

Phillips, S. T. & Thom, N. K., Jan 1 2013, Microfluidic Diagnostics: Methods and Protocols. Humana Press Inc., p. 185-196 12 p. (Methods in Molecular Biology; vol. 949).

Research output: Chapter in Book/Report/Conference proceedingChapter

Equipment and Supplies
Waxes
Adhesives
Food
3 Citations (Scopus)

Ultrafast infrared probes of electronic processes in materials

Asbury, J. B., Jan 1 2013, Ultrafast Infrared Vibrational Spectroscopy. CRC Press, p. 239-267 29 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Infrared radiation
probes
electronics
emerging
Flexible electronics
2012
7 Citations (Scopus)

Analysis of rna folding and ligand binding by conventional and high-throughput calorimetry

Sokoloski, J. E. & Bevilacqua, P. C., Jul 27 2012, Bacterial Regulatory RNA: Methods and Protocols. Keiler, K. C. (ed.). p. 145-174 30 p. (Methods in Molecular Biology; vol. 905).

Research output: Chapter in Book/Report/Conference proceedingChapter

RNA Folding
Calorimetry
Ligands
Differential Scanning Calorimetry
RNA
3 Citations (Scopus)

Mechanistic analysis of the Hepatitis Delta Virus (HDV) ribozyme: Methods for RNA preparation, structure mapping, solvent isotope effects, and co-transcriptional cleavage

Chadalavada, D. M., Cerrone-Szakal, A. L., Wilcox, J. L., Siegfried, N. A. & Bevilacqua, P. C., Mar 19 2012, Ribozymes: Methods and Protocols. Hartig, J. (ed.). p. 21-40 20 p. (Methods in Molecular Biology; vol. 848).

Research output: Chapter in Book/Report/Conference proceedingChapter

Hepatitis Delta Virus
Catalytic RNA
Isotopes
RNA
Reverse Transcription
1 Citation (Scopus)

Molecular self-assemblies in co-crystals: Engineering chemical reactivity and organic semiconductors

Friščić, T., Varshney, D. B., Elacqua, E., Sumrak, J. C., Sokolov, A. N. & MacGillivray, L. R., Oct 31 2012, Molecular Self-Assembly: Advances and Applications. Pan Stanford Publishing Pte. Ltd., p. 223-238 16 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Crystal engineering
chemical engineering
Chemical reactivity
Semiconducting organic compounds
organic semiconductors
59 Citations (Scopus)

RlmN and AtsB as models for the overproduction and characterization of radical SAM proteins

Lanz, N. D., Grove, T. L., Gogonea, C. B., Lee, K. H., Krebs, C. & Booker, S. J., Jan 1 2012, Methods in Enzymology. Academic Press Inc., p. 125-152 28 p. (Methods in Enzymology; vol. 516).

Research output: Chapter in Book/Report/Conference proceedingChapter

Methionine
Enzymes
Proteins
Iron
Explosions
16 Citations (Scopus)

Silver nanoparticle antimicrobials and related materials

Zhang, H., Wu, M. & Sen, A., Apr 1 2012, Nano-Antimicrobials: Progress and Prospects. Springer-Verlag Berlin Heidelberg, Vol. 9783642244285. p. 3-45 43 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Silver
Nanoparticles
Antimicrobial agents
Biofouling
Coatings
2011

Calculating the Raman and HyperRaman Spectra of Large Molecules and Molecules Interacting with Nanoparticles

Valley, N., Jensen, L., Autschbach, J. & Schatz, G. C., Jul 5 2011, Computational Methods for Large Systems: Electronic Structure Approaches for Biotechnology and Nanotechnology. John Wiley and Sons, p. 493-514 22 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Density functional theory
Nanoparticles
Molecules
Uracil
Excited states
10 Citations (Scopus)

Towards a minimal cytoplasm

Keighron, J. D. & Keating, C. D., Dec 1 2011, The Minimal Cell: The Biophysics of Cell Compartment and the Origin of Cell Functionality. Springer Netherlands, p. 3-30 28 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Cytoplasm
Cells
2010
8 Citations (Scopus)

Computational Spectroscopy in Environmental Chemistry

Kubicki, J. D. & Mueller, K. T., Oct 11 2010, Computational Spectroscopy: Methods, Experiments and Applications. John Wiley and Sons, p. 323-351 29 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Spectroscopy

Design and assembly of high-aspect-ratio silica-encapsulated nanostructures for nanoelectronics applications

Kovtyukhova, N. I., Dec 1 2010, Nanomaterials and Supramolecular Structures: Physics, Chemistry, and Applications. Springer Netherlands, p. 329-345 17 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Nanoelectronics
Silicon Dioxide
Aspect ratio
Nanostructures
Silica
12 Citations (Scopus)

Lipid detection, identification, and imaging single cells with SIMS

Heien, M. L., Piehowski, P. D., Winograd, N. & Ewing, A. G., Dec 1 2010, Mass Spectrometry Imaging: Principles and Protocols. Rubakhin, S. & Sweedler, J. (eds.). p. 85-97 13 p. (Methods in Molecular Biology; vol. 656).

Research output: Chapter in Book/Report/Conference proceedingChapter

Lipids
Tetrahymena thermophila
Secondary Ion Mass Spectrometry
Oligodendroglia
Membrane Lipids
4 Citations (Scopus)

Lipoic acid biosynthesis and enzymology

Billgren, E. S., Cicchillo, R. M., Nesbitt, N. M. & Booker, S. J., Mar 1 2010, Comprehensive Natural Products II: Chemistry and Biology. Elsevier Ltd, Vol. 7. p. 181-212 32 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

enzymology
lipoic acid
Thioctic Acid
Biosynthesis
biosynthesis
25 Citations (Scopus)

Magnetic Tweezers for the Study of DNA Tracking Motors

Manosas, M., Meglio, A., Spiering, M. M., Ding, F., Benkovic, S., Barre, F. X., Saleh, O. A., Allemand, J. F., Bensimon, D. & Croquette, V., Jan 1 2010, Methods in Enzymology. C ed. Academic Press Inc., p. 297-320 24 p. (Methods in Enzymology; vol. 475, no. C).

Research output: Chapter in Book/Report/Conference proceedingChapter

DNA
Molecules
2009
3 Citations (Scopus)

1,2-Thiazines and their Benzo Derivatives

Garigipati, R. S. & Weinreb, S. M., Sep 1 2009, Six-membered Rings with Two or More Heteroatoms and Fused Carbocyclic Derivatives. Elsevier Ltd, Vol. 6. p. 349-382 34 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Thiazines
Derivatives
18 Citations (Scopus)

Chapter 13 Thinking Inside the Box. Designing, Implementing, and Interpreting Thermodynamic Cycles to Dissect Cooperativity in RNA and DNA Folding

Siegfried, N. A. & Bevilacqua, P. C., Mar 16 2009, Biothermodynamics, Part A. Johnson, M., Holt, J. & Ackers, G. (eds.). A ed. p. 365-393 29 p. (Methods in Enzymology; vol. 455, no. A).

Research output: Chapter in Book/Report/Conference proceedingChapter

RNA Folding
Thermodynamics
RNA
DNA
Freezing
1 Citation (Scopus)

Hydrophobic and superhydrophobic polyphosphazenes

Allcock, H. R., Steely, L., Singh, A. & Hindenlang, M., Jan 1 2009, Superhydrophobic Surfaces. CRC Press, p. 127-138 12 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Polymers
Siloxanes
Inorganic polymers
Organic polymers
Graft copolymers