Research Output 1960 2018

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Review article
2017

27-Hydroxycholesterol, an endogenous selective estrogen receptor modulator

He, S. & Nelson, E. R. Oct 1 2017 In : Maturitas. 104, p. 29-35 7 p.

Research output: Research - peer-reviewReview article

Selective Estrogen Receptor Modulators
Estrogen Receptors
Cholesterol
27-hydroxycholesterol
Pharmacology

A New Era of Genome Integration - Simply Cut and Paste!

Liu, Z., Liang, Y., Ang, E. L. & Zhao, H. Apr 21 2017 In : ACS Synthetic Biology. 6, 4, p. 601-609 9 p.

Research output: Research - peer-reviewReview article

Ointments
Genome
Genes
Homologous Recombination
Synthetic Biology

Bacteriophage removal efficiency as a validation and operational monitoring tool for virus reduction in wastewater reclamation: Review

Amarasiri, M., Kitajima, M., Nguyen, T. H., Okabe, S. & Sano, D. 2017 In : Water Research. 121, p. 258-269 12 p.

Research output: Research - peer-reviewReview article

bacteriophage
virus
wastewater
monitoring
removal

Bio-nano interface: The impact of biological environment on nanomaterials and their delivery properties

Cai, K., Wang, A. Z., Yin, L. & Cheng, J. Oct 10 2017 In : Journal of Controlled Release. 263, p. 211-222 12 p.

Research output: Research - peer-reviewReview article

Nanomedicine
Nanostructures
Medicine

Biosynthetic approach to modeling and understanding metalloproteins using unnatural amino acids

Yu, Y., Cui, C., Wang, J. & Lu, Y. Feb 1 2017 In : Science China Chemistry. 60, 2, p. 188-200 13 p.

Research output: Research - peer-reviewReview article

Metalloproteins
Amino Acids
Azurin
Ribonucleotide Reductases
Catalysts

Breaking the silence: new strategies for discovering novel natural products

Ren, H., Wang, B. & Zhao, H. Dec 1 2017 In : Current Opinion in Biotechnology. 48, p. 21-27 7 p.

Research output: Research - peer-reviewReview article

Biological Products
Genes
Multigene Family
Throughput
Pharmaceutical Preparations

Categorizing Cells on the Basis of their Chemical Profiles: Progress in Single-Cell Mass Spectrometry

Comi, T. J., Do, T. D., Rubakhin, S. S. & Sweedler, J. V. Mar 22 2017 In : Journal of the American Chemical Society. 139, 11, p. 3920-3929 10 p.

Research output: Research - peer-reviewReview article

amplification
metabolite
mass spectrometry
chemical
Metabolites

Computational optical coherence tomography [invited]

Liu, Y. Z., South, F. A., Xu, Y., Scott Carney, P. & Boppart, S. A. Mar 1 2017 In : Biomedical Optics Express. 8, 3, p. 1549-1574 26 p.

Research output: Research - peer-reviewReview article

imaging techniques
tomography
Optical Coherence Tomography
aberration
high speed

Developmental Origins of Hypothalamic Cells Controlling Reproduction

Biehl, M. J. & Raetzman, L. T. Mar 1 2017 In : Seminars in Reproductive Medicine. 35, 2, p. 121-129 9 p.

Research output: Research - peer-reviewReview article

Hypothalamus
Reproduction
Kisspeptins
Gonadal Hormones
Anterior Hypothalamus

Dietary fiber and prebiotics and the gastrointestinal microbiota

Holscher, H. D. Mar 4 2017 In : Gut Microbes. 8, 2, p. 172-184 13 p.

Research output: Research - peer-reviewReview article

Prebiotics
Dietary Fiber
Gastrointestinal Microbiome
Microbiota
Polysaccharides

DNAzyme sensors for detection of metal ions in the environment and imaging them in living cells

McGhee, C. E., Loh, K. Y. & Lu, Y. Jun 1 2017 In : Current Opinion in Biotechnology. 45, p. 191-201 11 p.

Research output: Research - peer-reviewReview article

Metal ions
Cells
Imaging techniques
Sensors
Catalytic DNA

Dynamic Thermal management for aerospace technology: Review and outlook

Doty, J., Yerkes, K., Byrd, L., Murthy, J., Alleyne, A., Wolff, M., Heister, S. & Fisher, T. S. 2017 In : Journal of Thermophysics and Heat Transfer. 31, 1, p. 86-98 13 p.

Research output: Research - peer-reviewReview article

energy
electric power
aerospace vehicles
chemical energy
propulsion

Engineering biological systems using automated biofoundries

Chao, R., Mishra, S., Si, T. & Zhao, H. Jul 1 2017 In : Metabolic Engineering. 42, p. 98-108 11 p.

Research output: Research - peer-reviewReview article

Foundries
Biological systems
Biotechnology
Industrial plants
Networks (circuits)

Escapement mechanisms and the conversion of disequilibria; the engines of creation

Branscomb, E., Biancalani, T., Goldenfeld, N. & Russell, M. Mar 17 2017 In : Physics Reports. 677, p. 1-60 60 p.

Research output: Research - peer-reviewReview article

engines
energy
cascades
free energy
causes

Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function

Thor, S., Peterson, J. R. & Luthey-Schulten, Z. 2017 In : Archaea. 2017, 9763848

Research output: Research - peer-reviewReview article

Archaea
Metabolic Networks and Pathways
Genome
genome
modeling

Glucocorticoids and gut bacteria: “The GALF Hypothesis” in the metagenomic era

Morris, D. J. & Ridlon, J. M. Sep 1 2017 In : Steroids. 125, p. 1-13 13 p.

Research output: Research - peer-reviewReview article

11-beta-Hydroxysteroid Dehydrogenases
Metagenomics
Glucocorticoids
Bacteria
Acids

Go it alone: four-electron oxidations by mononuclear non-heme iron enzymes

Peck, S. C. & van der Donk, W. A. Apr 1 2017 In : Journal of Biological Inorganic Chemistry. 22, 2-3, p. 381-394 14 p.

Research output: Research - peer-reviewReview article

Iron
Oxidation
Electrons
Enzymes
Substrates

Human milk oligosaccharides influence neonatal mucosal and systemic immunity

Donovan, S. M. & Comstock, S. S. Jan 1 2017 In : Annals of Nutrition and Metabolism. 69, 2, p. 42-51 10 p.

Research output: Research - peer-reviewReview article

Mucosal Immunity
Human Milk
Oligosaccharides
Infant Formula
Milk

Innovative techniques for evaluating behavioral nutrition interventions

Scherr, R. E., Laugero, K. D., Graham, D. J., Cunningham, B. T., Jahns, L., Lora, K. R., Reicks, M. & Mobley, A. R. 2017 In : Advances in Nutrition. 8, 1, p. 113-125 13 p.

Research output: Research - peer-reviewReview article

nutritional intervention
methodology
Biosensing Techniques
Carotenoids
Research Personnel

Intersections of post-transcriptional gene regulatory mechanisms with intermediary metabolism

Arif, W., Datar, G. & Kalsotra, A. Mar 1 2017 In : Biochimica et Biophysica Acta - Gene Regulatory Mechanisms. 1860, 3, p. 349-362 14 p.

Research output: Research - peer-reviewReview article

Regulator Genes
Enzymes
Metabolism
Genes
Allosteric Regulation

Lamina-Associated Domains: Links with Chromosome Architecture, Heterochromatin, and Gene Repression

van Steensel, B. & Belmont, A. S. May 18 2017 In : Cell. 169, 5, p. 780-791 12 p.

Research output: Research - peer-reviewReview article

Nuclear Lamina
Heterochromatin
Chromosomes
Genes
Gene expression

Limb development: A paradigm of gene regulation

Petit, F., Sears, K. E. & Ahituv, N. Apr 1 2017 In : Nature Reviews Genetics. 18, 4, p. 245-258 14 p.

Research output: Research - peer-reviewReview article

Extremities
Genes
Developmental Biology
Systems Biology
Forelimb

Long-term evolution of viruses: A Janus-faced balance

Nasir, A., Kim, K. M. & Caetano-Anollés, G. Aug 1 2017 In : BioEssays. 39, 8, 1700026

Research output: Research - peer-reviewReview article

Viruses
Long Term Evolution (LTE)
Virus Latency
Symbiosis
Metagenomics

Mechanisms of gene flow in archaea

Wagner, A., Whitaker, R. J., Krause, D. J., Heilers, J. H., Van Wolferen, M., Van Der Does, C. & Albers, S. V. Aug 1 2017 In : Nature Reviews Microbiology. 15, 8, p. 492-501 10 p.

Research output: Research - peer-reviewReview article

Gene Flow
Archaea
Genes
Archaeal DNA
Horizontal Gene Transfer

Mechanisms of Salmonella pathogenesis in animal models

Palmer, A. D. & Slauch, J. M. Nov 17 2017 In : Human and Ecological Risk Assessment. 23, 8, p. 1877-1892 16 p.

Research output: Research - peer-reviewReview article

Salmonella
Animal Models
animal
salmonella
Animals

Mimivirus: Leading the way in the discovery of giant viruses of amoebae

Colson, P., La Scola, B., Levasseur, A., Caetano-Anollés, G. & Raoult, D. Mar 13 2017 In : Nature Reviews Microbiology. 15, 4, p. 243-254 12 p.

Research output: Research - peer-reviewReview article

Mimiviridae
Amoeba
Giant Viruses
Viruses
Virophages

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Bowers, R. M. , Kyrpides, N. C. , Stepanauskas, R. , Harmon-Smith, M. , Doud, D. , Reddy, T. B. K. , Schulz, F. , Jarett, J. , Rivers, A. R. , Eloe-Fadrosh, E. A. , Tringe, S. G. , Ivanova, N. N. , Copeland, A. , Clum, A. , Becraft, E. D. , Malmstrom, R. R. , Birren, B. , Podar, M. , Bork, P. , Weinstock, G. M. & 35 others Garrity, G. M., Dodsworth, J. A., Yooseph, S., Sutton, G., Glöckner, F. O., Gilbert, J. A., Nelson, W. C., Hallam, S. J., Jungbluth, S. P., Ettema, T. J. G., Tighe, S., Konstantinidis, K. T., Liu, W. T., Baker, B. J., Rattei, T., Eisen, J. A., Hedlund, B., McMahon, K. D., Fierer, N., Knight, R., Finn, R., Cochrane, G., Karsch-Mizrachi, I., Tyson, G. W., Rinke, C., Lapidus, A., Meyer, F., Yilmaz, P., Parks, D. H., Eren, A. M., Schriml, L., Banfield, J. F., Hugenholtz, P., Woyke, T. & The Genome Standards Consortium Aug 8 2017 In : Nature Biotechnology. 35, 8, p. 725-731 7 p.

Research output: Research - peer-reviewReview article

Metagenome
Archaea
Genome
Bacteria
Genes

Modification of the Genome of Domestic Animals

Lotti, S. N., Polkoff, K. M., Rubessa, M. & Wheeler, M. B. Jul 3 2017 In : Animal Biotechnology. 28, 3, p. 198-210 13 p.

Research output: Research - peer-reviewReview article

domestic animals
genome
methodology
Domestic Animals
Genome
Myotonic Dystrophy
Penetrance
Genetic Testing
Age of Onset
Phenotype

Nanodiscs in Membrane Biochemistry and Biophysics

Denisov, I. G. & Sligar, S. G. Mar 22 2017 In : Chemical Reviews. 117, 6, p. 4669-4713 45 p.

Research output: Research - peer-reviewReview article

Biochemistry
Membranes
Metabolism
Chemical analysis

Photonic crystals: Emerging biosensors and their promise for point-of-care applications

Inan, H., Poyraz, M., Inci, F., Lifson, M. A., Baday, M., Cunningham, B. T. & Demirci, U. Jan 21 2017 In : Chemical Society Reviews. 46, 2, p. 366-388 23 p.

Research output: Research - peer-reviewReview article

Photonic crystals
Biosensors
Telemedicine
Intelligent materials
Metamaterials

Potential impacts of changing supply-water quality on drinking water distribution: A review

Liu, G., Zhang, Y., Knibbe, W. J., Feng, C., Liu, W., Medema, G. & van der Meer, W. 2017 In : Water Research. 116, p. 135-148 14 p.

Research output: Research - peer-reviewReview article

drinking water
water quality
distribution
Potable water
Water

Potential of global croplands and bioenergy crops for climate change mitigation through deployment for enhanced weathering

Kantola, I. B., Masters, M. D., Beerling, D. J., Long, S. P. & DeLucia, E. H. Apr 1 2017 In : Biology Letters. 13, 4, 0714

Research output: Research - peer-reviewReview article

energy crops
weathering
climate change
cropland
Climate Change

Production of fuels and chemicals from xylose by engineered Saccharomyces cerevisiae: A review and perspective

Kwak, S. & Jin, Y. S. May 11 2017 In : Microbial Cell Factories. 16, 1, 82

Research output: Research - peer-reviewReview article

Xylose
Saccharomyces cerevisiae
Yeasts
Metabolism
Glucose

Recent advances in DNAzyme-based gene silencing

Fan, H., Zhang, X. & Lu, Y. May 1 2017 In : Science China Chemistry. 60, 5, p. 591-601 11 p.

Research output: Research - peer-reviewReview article

Genes
RNA
DNA
Phosphorylation
Single-Stranded DNA

Review of cellular mechanotransduction

Wang, N. May 17 2017 In : Journal of Physics D: Applied Physics. 50, 23, 233002

Research output: Research - peer-reviewReview article

Gene expression
Cells
Tissue
gene expression
human body

Ribosomally synthesized and post-translationally modified peptide natural product discovery in the genomic era

Hetrick, K. J. & van der Donk, W. A. Jun 1 2017 In : Current Opinion in Chemical Biology. 38, p. 36-44 9 p.

Research output: Research - peer-reviewReview article

Biological Products
Genome
Peptides
Genes
Bacterial Genomes

RNA modifications and structures cooperate to guide RNA-protein interactions

Lewis, C. J. T., Pan, T. & Kalsotra, A. Mar 1 2017 In : Nature Reviews Molecular Cell Biology. 18, 3, p. 202-210 9 p.

Research output: Research - peer-reviewReview article

Guide RNA
RNA
Proteins
Transcriptome
Gene Expression

Rooting for cassava: insights into photosynthesis and associated physiology as a route to improve yield potential

De Souza, A. P., Massenburg, L. N., Jaiswal, D., Cheng, S., Shekar, R. & Long, S. P. Jan 1 2017 In : New Phytologist. 213, 1, p. 50-65 16 p.

Research output: Research - peer-reviewReview article

cassava
rooting
physiology
photosynthesis
Manihot

Serration and noise behaviors in materials

Zhang, Y., Liu, J. P., Chen, S. Y., Xie, X., Liaw, P. K., Dahmen, K. A., Qiao, J. W. & Wang, Y. L. Oct 1 2017 In : Progress in Materials Science. 90, p. 358-460 103 p.

Research output: Research - peer-reviewReview article

Functional materials
Steel
Metallic glass
Stress-strain curves
Plasticity

Targeting Specificity of the CRISPR/Cas9 System

Tasan, I. & Zhao, H. Sep 15 2017 In : ACS Synthetic Biology. 6, 9, p. 1609-1613 5 p.

Research output: Research - peer-reviewReview article

Clustered Regularly Interspaced Short Palindromic Repeats
Therapeutics
Genes
Insertional Mutagenesis
Research Personnel

The 4D nucleome project

Dekker, J., Belmont, A. S., Guttman, M., Leshyk, V. O., Lis, J. T., Lomvardas, S., Mirny, L. A., O'Shea, C. C., Park, P. J., Ren, B., Ritland Politz, J. C., Shendure, J., Zhong, S. & 4D Nucleome Network Sep 13 2017 In : Nature. 549, 7671, p. 219-226 8 p.

Research output: Research - peer-reviewReview article

Genome
Benchmarking
Human Genome
Technology
Population

The "ok, molly" chemistry

Lu, Y. 2017 In : Accounts of Chemical Research. 50, 3, p. 647-651 5 p.

Research output: Research - peer-reviewReview article

The role of early life nutrition in the establishment of gastrointestinal microbial composition and function

Davis, E. C., Wang, M. & Donovan, S. M. Mar 4 2017 In : Gut Microbes. 8, 2, p. 143-171 29 p.

Research output: Research - peer-reviewReview article

Gastrointestinal Microbiome
Dysbiosis
Prebiotics
Infant Formula
Microbiota

The ultrastructure of bone and its relevance to mechanical properties

Schwarcz, H. P., Abueidda, D. & Jasiuk, I. Sep 5 2017 In : Frontiers in Physics. 5, SEP, 39

Research output: Research - peer-reviewReview article

Ultrastructure
Bone
Mechanical Properties
Relevance
bones

Using natural products for drug discovery: the impact of the genomics era

Zhang, M. M., Qiao, Y., Ang, E. L. & Zhao, H. May 4 2017 In : Expert Opinion on Drug Discovery. 12, 5, p. 475-487 13 p.

Research output: Research - peer-reviewReview article

Drug Discovery
Genomics
Biological Products
Synthetic Biology
Metagenomics

YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function

Burkhart, B. J., Schwalen, C. J., Mann, G., Naismith, J. H. & Mitchell, D. A. Apr 26 2017 In : Chemical Reviews. 117, 8, p. 5389-5456 68 p.

Research output: Research - peer-reviewReview article

Biosynthesis
Amides
Chemical activation
Proteins
Nucleophiles
2016

Accelerated genome engineering through multiplexing

Bao, Z., Cobb, R. E. & Zhao, H. Jan 1 2016 In : Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 8, 1, p. 5-21 17 p.

Research output: Research - peer-reviewReview article

Genome
Multiplexing
Genes
Bioengineering
Biological Science Disciplines

A comprehensive empirical study of data privacy, trust, and consumer autonomy

Kesan, J. P., Hayes, C. M. & Bashir, M. N. 2016 In : Indiana Law Journal. 91, 2, p. 267-352 86 p.

Research output: Research - peer-reviewReview article

ACS Catalysis and the Scope of Papers Sought in Three Catalysis Subdisciplines: Biocatalysis and Enzymology, Molecular Catalysis for Organic Synthesis, and Heterogeneous Photocatalysis

Chang, S., Fornasiero, P., Gunnoe, T. B., Jones, C. W., Linic, S., Ooi, T., Williams, R. M. & Zhao, H. Jul 1 2016 In : ACS Catalysis. 6, 7, p. 4782-4785 4 p.

Research output: Research - peer-reviewReview article