Research Output 1941 2018

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2018

Bacterial genome editing with CRISPR-Cas9: Taking clostridium beijerinckii as an example

Zhang, Z. T., Jiménez-Bonilla, P., Seo, S. O., Lu, T., Jin, Y. S., Blaschek, H. P. & Wang, Y. Jan 1 2018 Methods in Molecular Biology. Humana Press Inc., p. 297-325 29 p. (Methods in Molecular Biology; vol. 1772)

Research output: Chapter in Book/Report/Conference proceedingChapter

Clostridium beijerinckii
Clustered Regularly Interspaced Short Palindromic Repeats
Bacterial Genomes
Guide RNA
Streptococcus pyogenes

Bioinformatics for prohormone and neuropeptide discovery

Southey, B. R., Romanova, E. V., Rodriguez-Zas, S. L. & Sweedler, J. V. Jan 1 2018 Methods in Molecular Biology. Humana Press Inc., p. 71-96 26 p. (Methods in Molecular Biology; vol. 1719)

Research output: Chapter in Book/Report/Conference proceedingChapter

Computational Biology
Neuropeptides
Peptide Hormones
Post Translational Protein Processing
Proteomics

Coupling fluxes, enzymes, and regulation in genome-scale metabolic models

Jensen, P. A. Jan 1 2018 Methods in Molecular Biology. Humana Press Inc., p. 337-351 15 p. (Methods in Molecular Biology; vol. 1716)

Research output: Chapter in Book/Report/Conference proceedingChapter

Genome
Enzymes
Practice Guidelines
Software

Engineering and evolution of saccharomyces cerevisiae to produce biofuels and chemicals

Turner, T. L., Kim, H., Kong, I. I., Liu, J. J., Zhang, G. C. & Jin, Y. S. Jan 1 2018 Advances in Biochemical Engineering/Biotechnology. Springer Science and Business Media Deutschland GmbH, p. 175-215 41 p. (Advances in Biochemical Engineering/Biotechnology; vol. 162)

Research output: Chapter in Book/Report/Conference proceedingChapter

Biofuels
Yeast
Saccharomyces cerevisiae
Fossil Fuels
Bioconversion

Network dynamics theory of human intelligence

Nikolaidis, A. & Barbey, A. K. Jan 1 2018 The Cambridge Handbook of the Neuroscience of Creativity. Cambridge University Press, p. 382-404 23 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Intelligence
Creativity
Aptitude
Brain
Neuroimaging

Non-targeted identification of d-amino acid-containing peptides through enzymatic screening, chiral amino acid analysis, and LC-MS

Tai, H. C., Checco, J. W. & Sweedler, J. V. Jan 1 2018 Methods in Molecular Biology. Humana Press Inc., p. 107-118 12 p. (Methods in Molecular Biology; vol. 1719)

Research output: Chapter in Book/Report/Conference proceedingChapter

Amino Acids
Peptides
Post Translational Protein Processing
Mass Spectrometry

Pathway design, engineering, and optimization

Garcia-Ruiz, E., HamediRad, M. & Zhao, H. Jan 1 2018 Advances in Biochemical Engineering/Biotechnology. Springer Science and Business Media Deutschland GmbH, (Advances in Biochemical Engineering/Biotechnology; vol. 162)

Research output: Chapter in Book/Report/Conference proceedingChapter

Biofuels
Microorganisms
Enzymes
Pharmaceutical Preparations

Targeted gene knock out using nuclease-assisted vector integration: Hemi- and Homozygous deletion of JAG1

Gapinske, M., Tague, N., Winter, J., Underhill, G. H. & Perez-Pinera, P. Jan 1 2018 Methods in Molecular Biology. Humana Press Inc., p. 233-248 16 p. (Methods in Molecular Biology; vol. 1772)

Research output: Chapter in Book/Report/Conference proceedingChapter

Gene Knockout Techniques
Genome
Technology
Biotechnology
DNA
2017

Chapter 7: Computational Characterization of Molecular Mechanisms of Membrane Transporter Function

Trebesch, N., Vermaas, J. V. & Tajkhorshid, E. Jan 1 2017 Computational Biophysics of Membrane Proteins. 10 ed. Royal Society of Chemistry, p. 197-236 40 p. (RSC Theoretical and Computational Chemistry Series; vol. 2017-January, no. 10)

Research output: Chapter in Book/Report/Conference proceedingChapter

Membrane Transport Proteins
Membranes
Computational methods
Free energy
Adenosinetriphosphate

Electrokinetic Transport and Fluidic Manipulation in Three Dimensional Integrated Nanofluidic Networks

King, T. L., Jin, X., Nandigana, V. R., Aluru, N. & Bohn, P. W. Jan 1 2017 Nanofluidics, 2nd Edition. 41 ed. Royal Society of Chemistry, p. 37-75 39 p. (RSC Nanoscience and Nanotechnology; vol. 2017-January, no. 41)

Research output: Chapter in Book/Report/Conference proceedingChapter

Nanofluidics
fluidics
electrokinetics
Fluidics
manipulators

Enhanced Learning through Multimodal Training: Evidence from a Comprehensive Cognitive, Physical Fitness, and Neuroscience Intervention

Ward, N., Paul, E., Watson, P., Cooke, G. E., Hillman, C. H., Cohen, N. J., Kramer, A. F. & Barbey, A. K. Dec 1 2017 Scientific Reports. Nature Publishing Group, (Scientific Reports; vol. 7)

Research output: Chapter in Book/Report/Conference proceedingChapter

Physical Fitness
Neurosciences
Learning
Exercise
Cognition

Hydrothermal liquefaction (HTL): A promising pathway for biorefinery of algae

Tian, C., Liu, Z. & Zhang, Y. Jan 1 2017 Algal Biofuels: Recent Advances and Future Prospects. Springer International Publishing, p. 361-392 32 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Liquefaction
Algae
liquefaction
alga

Optical microscopy and spectroscopy for epigenetic modifications in single living cells

Cui, Y. & Irudayaraj, J. Jan 1 2017 Methods in Pharmacology and Toxicology. Humana Press Inc., p. 135-154 20 p. (Methods in Pharmacology and Toxicology)

Research output: Chapter in Book/Report/Conference proceedingChapter

Epigenomics
Microscopy
Spectrum Analysis
Optical Imaging
Physiological Phenomena

Qflow cytometry-based receptoromic screening: A high-throughput quantification approach informing biomarker selection and nanosensor development

Chen, S., Weddell, J., Gupta, P., Conard, G., Parkin, J. & Imoukhuede, P. I. Jan 1 2017 Methods in Molecular Biology. Humana Press Inc., p. 117-138 22 p. (Methods in Molecular Biology; vol. 1570)

Research output: Chapter in Book/Report/Conference proceedingChapter

Biomarkers
Immunohistochemistry
Calibration
Vascular Endothelial Growth Factor Receptor
Antibody Specificity

Strain development by whole-cell directed evolution

Si, T., Lian, J. & Zhao, H. Jan 1 2017 Directed Enzyme Evolution: Advances and Applications. Springer International Publishing, p. 173-200 28 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Phenotype
Workflow
Screening
Mutation

Surface treatment of metallic biomaterials in contact with blood to enhance hemocompatibility

Allain, J. P. & Echeverry-Rendón, M. Oct 31 2017 Hemocompatibility of Biomaterials for Clinical Applications: Blood-Biomaterials Interactions. Elsevier Inc., p. 279-326 48 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Ceramics
Biocompatible Materials
Polymers
Metals
Equipment and Supplies

“Dipstick” colorimetric detection of metal ions based on immobilization of DNAzyme and gold nanoparticles onto a lateral flow device

Mazumdar, D., Lan, T. & Lu, Y. Jan 1 2017 Methods in Molecular Biology. Humana Press Inc., p. 389-406 18 p. (Methods in Molecular Biology; vol. 1571)

Research output: Chapter in Book/Report/Conference proceedingChapter

Catalytic DNA
Immobilization
Gold
Nanoparticles
Metals
2016

Biocatalysis for Drug Discovery and Development

Liang, Y., Zhang, M. M., Ang, E. L. & Zhao, H. May 13 2016 Green Biocatalysis. wiley, p. 421-455 35 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Drug products
Enzymes
Pharmaceutical Preparations
Biocatalysts
Chemical reactions

Combined and iterative use of computational design and directed evolution for protein-ligand binding design

Wang, M. & Zhao, H. May 1 2016 Methods in Molecular Biology. Humana Press Inc., Vol. 1414, p. 139-153 15 p. (Methods in Molecular Biology; vol. 1414)

Research output: Chapter in Book/Report/Conference proceedingChapter

Protein Binding
Switch Genes
Ligands
Two-Hybrid System Techniques
Mutagenesis

Design of Heteronuclear Metalloenzymes

Bhagi-Damodaran, A., Hosseinzadeh, P., Mirts, E., Reed, J., Petrik, I. D. & Lu, Y. Jan 1 2016 Methods in Enzymology. Academic Press Inc., p. 501-537 37 p. (Methods in Enzymology; vol. 580)

Research output: Chapter in Book/Report/Conference proceedingChapter

Scaffolds
Metals
Proteins
Metal ions
Cytochrome-c Peroxidase

Engineered minicellulosomes for consolidated bioprocessing

Liang, Y., Ang, E. L. & Zhao, H. Jul 11 2016 Handbook of Carbohydrate-Modifying Biocatalysts. Pan Stanford Publishing Pte. Ltd., Vol. 2, p. 965-992 28 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Free D-aspartate in nonmammalian animals: Detection, localization, metabolism, and function

Patel, A. V., Kawai, T., Rubakhin, S. S. & Sweedler, J. V. Jan 1 2016 D-Amino Acids: Physiology, Metabolism, and Application. Springer Japan, p. 173-197 25 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

D-Aspartic Acid
Metabolism
Animals
Amino Acids
Neurotransmitter Agents

High-Efficiency Genome Editing of Streptomyces Species by an Engineered CRISPR/Cas System

Wang, Y., Cobb, R. E. & Zhao, H. Jan 1 2016 Methods in Enzymology. Academic Press Inc., p. 271-284 14 p. (Methods in Enzymology; vol. 575)

Research output: Chapter in Book/Report/Conference proceedingChapter

CRISPR-Cas Systems
Clustered Regularly Interspaced Short Palindromic Repeats
Streptomyces
Genes
Microbial Genome

Highly efficient SiRNA delivery mediated by cationic helical polypeptides and polypeptide-based nanosystems

Yin, L., Zheng, N. & Cheng, J. Jan 1 2016 Methods in Molecular Biology. Humana Press Inc., Vol. 1364, 1 p. (Methods in Molecular Biology; vol. 1364)

Research output: Chapter in Book/Report/Conference proceedingChapter

Small Interfering RNA
Peptides
RNA Interference
Oral Administration
Gene Expression

High-throughput screening or selection methods for evolutionary enzyme engineering

Shi, S., Zhang, H., Ang, E. L. & Zhao, H. May 17 2016 Understanding Enzymes: Function, Design, Engineering and Analysis. Pan Stanford Publishing Pte. Ltd., p. 707-744 38 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

High-throughput Screening
Enzymes
Engineering
Cracks

Microfluidic methods in single cell biology

Mukherjee, A. & Schroeder, C. M. Jan 1 2016 Microfluidic Methods for Molecular Biology. Springer International Publishing, p. 19-54 36 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Cytology
Microfluidics
Cell Biology
Cells
Molecular imaging

Microfluidics for Studying Pharmacodynamics of Antibiotics

Mohan, R., Desai, A. V., Sanpitakseree, C. & Kenis, P. J. A. Apr 29 2016 Micro- and Nanosystems for Biotechnology. Wiley, p. 177-202 26 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Microfluidics
Anti-Bacterial Agents
Microbial Sensitivity Tests
Prescriptions
Pharmacokinetics

Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation

Vermaas, J. V., Trebesch, N., Mayne, C. G., Thangapandian, S., Shekhar, M., Mahinthichaichan, P., Baylon, J. L., Jiang, T., Wang, Y., Muller, M. P., Shinn, E., Zhao, Z., Wen, P. C. & Tajkhorshid, E. Jan 1 2016 Computational Approaches for Studying Enzyme Mechanism Part B. Academic Press Inc., p. 373-428 56 p. (Methods in Enzymology; vol. 578)

Research output: Chapter in Book/Report/Conference proceedingChapter

Biological Transport
Molecular Docking Simulation
Protein Conformation
Membrane Transport Proteins
Active Biological Transport

Molecular imaging with spectral CT nanoprobes

Pan, D., Schmieder, A. H., SenPan, A., Yang, X., Wickline, S. A., Roessl, E., Proksa, R., Schirra, C. O. & Lanza, G. M. Jan 1 2016 Design and Applications of Nanoparticles in Biomedical Imaging. Springer International Publishing, p. 385-402 18 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Nanoprobes
Molecular imaging
Molecular Imaging
Tomography
Contrast Media

Noninvasive optical imaging of stem cell differentiation in biomaterials using photonic crystal surfaces

Choi, J. S., Zhuo, Y., Cunningham, B. T. & Harley, B. A. C. Nov 14 2016 Monitoring and Evaluation of Biomaterials and their Performance In Vivo. Elsevier Inc., p. 195-207 13 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Optics and Photonics
Optical Imaging
Biocompatible Materials
Cell Differentiation
Stem Cells
2015

Biomaterial Scaffolds for Tendon Tissue Engineering

Hortensius, R., Mozdzen, L. & Harley, B. Jan 1 2015 Tendon Regeneration: Understanding Tissue Physiology and Development to Engineer Functional Substitutes. Elsevier Inc., p. 349-380 32 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Biocompatible Materials
Tissue Engineering
Tendons
Cicatrix
Extracellular Matrix

Biophotonics for assessing breast cancer

Erickson-Bhatt, S. J. & Boppart, S. A. Jun 25 2015 Biophotonics for Medical Applications. Elsevier Inc., p. 175-214 40 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Imaging techniques
Optical tomography
Tumors
Infrared radiation
Mammography

Data analysis and signal postprocessing for optical coherence tomography

Ralston, T. S., Marks, D. L., Ahmad, A. & Boppart, S. A. Jan 1 2015 Optical Coherence Tomography: Technology and Applications, Second Edition. Springer International Publishing, p. 407-436 30 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Optical tomography
Optical Coherence Tomography
tomography
signal processing
Signal processing

Design and quality control for translating 3D-printed scaffolds

Hollister, S. J., Flanagan, C. L., Zopf, D. A., Morrison, R. J., Nasser, H., Wheeler, M. B. & Green, G. E. Aug 7 2015 Essentials of 3D Biofabrication and Translation. Elsevier Inc., p. 43-59 17 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Splints
Scaffolds
Quality Control
Quality control
Lasers

Detection of protein biomarker using a blood glucose meter

Lan, T., Xiang, Y. & Lu, Y. Jan 27 2015 Mobile Health Technologies: Methods and Protocols. Springer New York, p. 99-109 11 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Biomarkers
Blood Glucose
Assays
beta-Fructofuranosidase
Monitoring

Development of microfluidic devices for the manipulation of neuronal synapses

Jain, A. & Gillette, M. U. Mar 10 2015 Microfluidic and Compartmentalized Platforms for Neurobiological Research. Springer New York, p. 127-137 11 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Lab-On-A-Chip Devices
synapse
Synapses
Microfluidics
Cues

Development of polyester-drug nanoconjugates for cancer targeting and treatment

Yin, Q., Tong, R., Wang, H. & Cheng, J. Jan 1 2015 Biodegradable Polymers. Volume 1: Advancement in Biodegradation Study and Applications. Nova Science Publishers, Inc., p. 239-261 23 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Nanoconjugates
Polyesters
Nanoparticles
Pharmaceutical Preparations
Medical nanotechnology

DSP technology and methods for OCT

Ali, M., Ahmad, A. & Boppart, S. A. Jan 1 2015 Optical Coherence Tomography: Technology and Applications, Second Edition. Springer International Publishing, p. 437-458 22 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Optical tomography
Optical Coherence Tomography
Digital signal processors
central processing units
Semiconductors

Image Reconstruction in MRI

Ying, L. & Liang, Z. P. Feb 14 2015 Acquisition Methods, Methods and Modeling. Elsevier Inc., Vol. 1, p. 223-229 7 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Computer-Assisted Image Processing

Interferometric synthetic aperture microscopy (ISAM)

Adie, S. G., Shemonski, N. D., Ralston, T. S., Carney, P. S. & Boppart, S. A. Jan 1 2015 Optical Coherence Tomography: Technology and Applications, Second Edition. Springer International Publishing, p. 965-1004 40 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Synthetic apertures
synthetic apertures
Microscopy
Microscopic examination
aberration

Intraoperative OCT in surgical oncology

South, F. A., Marjanovic, M. & Boppart, S. A. Jan 1 2015 Optical Coherence Tomography: Technology and Applications, Second Edition. Springer International Publishing, p. 2393-2412 20 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Oncology
Tumors
tumors
cancer
Tissue

Molecular optical coherence tomography contrast enhancement and imaging

Oldenburg, A. L., Applegate, B. E., Tucker-Schwartz, J. M., Skala, M. C., Kim, J. & Boppart, S. A. Jan 1 2015 Optical Coherence Tomography: Technology and Applications, Second Edition. Springer International Publishing, p. 1429-1454 26 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Optical tomography
Optical Coherence Tomography
Molecular imaging
Microscopy
Microscopic examination

Nanomaterials for diagnostic imaging of the brain

Qin, E. & Kong, H. Jul 23 2015 Biomedical Engineering: Frontier Research and Converging Technologies. Springer International Publishing, Vol. 9, p. 77-89 13 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Nanostructures
Diagnostic Imaging
Nanostructured materials
Brain
Imaging techniques

Nonlinear interferometric vibrational imaging (NIVI) with novel optical sources

Boppart, S. A., King, M. D., Liu, Y., Tu, H. & Gruebele, M. Jan 1 2015 Optical Coherence Tomography: Technology and Applications, Second Edition. Springer International Publishing, p. 1237-1256 20 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Molecular Imaging
Raman Spectrum Analysis
Optical Imaging
imaging techniques
Nanoparticles

Optical coherence elastography

Kennedy, B. F., Kennedy, K. M., Oldenburg, A. L., Adie, S. G., Boppart, S. A. & Sampson, D. D. Jan 1 2015 Optical Coherence Tomography: Technology and Applications, Second Edition. Springer International Publishing, p. 1007-1054 48 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Elasticity Imaging Techniques
Tissue
Mechanical properties
Optical tomography
mechanical properties

Optical coherence tomography in tissue engineering

Zhao, Y., Yang, Y., Wang, R. K. & Boppart, S. A. Jan 1 2015 Optical Coherence Tomography: Technology and Applications, Second Edition. Springer International Publishing, p. 1965-2001 37 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

tissue engineering
Optical tomography
Optical Coherence Tomography
Tissue Engineering
Tissue engineering

Stereolithographic 3D bioprinting for biomedical applications

Raman, R. & Bashir, R. Aug 7 2015 Essentials of 3D Biofabrication and Translation. Elsevier Inc., p. 89-121 33 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Bioprinting
Technology
Stereolithography
Medical applications
Biomedical Technology
2014

Advances in Animal Biotechnology

Schook, L. B., Rund, L. A., Hu, W., Darfour-Oduro, K. A., Knapp, L. A., Rodrigues, F. M. & Schachtschneider, K. M. Jan 1 2014 Agriculture and Science. Elsevier, p. 1-16 16 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

disease resistance
biotechnology
animal
animal welfare
medicine

A two-plasmid bacterial selection system for characterization and engineering of homing endonucleases

Sun, N. & Zhao, H. 2014 Homing Endonucleases: Methods and Protocols. Humana Press Inc., Vol. 1123, p. 87-96 10 p. (Methods in Molecular Biology; vol. 1123)

Research output: Chapter in Book/Report/Conference proceedingChapter

Endonucleases
Plasmids
DNA Cleavage
Double-Stranded DNA Breaks
Cell Survival

Directed evolution of enzymes for industrial biocatalysis

Liang, Y., Ang, E. L. & Zhao, H. Jan 1 2014 Industrial Biocatalysis. Pan Stanford Publishing Pte. Ltd., p. 73-114 42 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Biocatalysis
Enzymes
Cracks