Research Output 1969 2020

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Review article

‘Democratized’ genomic enzymology web tools for functional assignment

Zallot, R., Oberg, N. O. & Gerlt, J. A., Dec 2018, In : Current Opinion in Chemical Biology. 47, p. 77-85 9 p.

Research output: Contribution to journalReview article

Protein Databases
Genome
Genes
Proteins
Costs and Cost Analysis

β-sheet folding mechanisms from perturbation energetics

Deechongkit, S., Nguyen, H., Jager, M., Powers, E. T., Gruebele, M. & Kelly, J. W., Feb 1 2006, In : Current Opinion in Structural Biology. 16, 1, p. 94-101 8 p.

Research output: Contribution to journalReview article

Thermodynamics
Data Mining
Hydrogen Bonding
Hydrophobic and Hydrophilic Interactions
Amides

Zooming in on biological processes with fluorescence nanoscopy

Agrawal, U., Reilly, D. T. & Schroeder, C. M., Aug 1 2013, In : Current Opinion in Biotechnology. 24, 4, p. 646-653 8 p.

Research output: Contribution to journalReview article

Biological Phenomena
Fluorescent Dyes
Fluorescence
Proteins
Imaging techniques

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: Contribution to journalReview article

Biosynthesis
Amides
Chemical activation
Nucleophiles
Proteins

Xylan degradation, a metabolic property shared by rumen and human colonic Bacteroidetes

Dodd, D., Mackie, R. I. & Cann, I., Jan 1 2011, In : Molecular Microbiology. 79, 2, p. 292-304 13 p.

Research output: Contribution to journalReview article

Bacteroidetes
Xylans
Rumen
Polysaccharides
Physiological Phenomena

Xenobiotic detoxification pathways in honey bees

Berenbaum, M. R. & Johnson, R. M., May 16 2015, In : Current Opinion in Insect Science. 10, p. 51-58 8 p.

Research output: Contribution to journalReview article

honey
xenobiotics
detoxification
bee
honey bees
Ribulose-Bisphosphate Carboxylase
C3 plants
Photosynthesis
ribulose-bisphosphate carboxylase
photosynthesis

Wing shape and size of the western corn rootworm (Coleoptera: Chrysomelidae) is related to sex and resistance to soybean-maize crop rotation

Mikac, K. M., Douglas, J. & Spencer, J. L., Aug 1 2013, In : Journal of economic entomology. 106, 4, p. 1517-1524 8 p.

Research output: Contribution to journalReview article

Diabrotica virgifera virgifera
crop rotation
Chrysomelidae
soybean
maize

Why experiment with success? Opportunities and risks in applying assessment and adaptive management to the Emiquon floodplain restoration project

Sparks, R. E., Douglas Blodgett, K., Casper, A. F., Hagy, H., Lemke, M. J., Velho, L. F. M. & Rodrigues, L. C., Dec 1 2017, In : Hydrobiologia. 804, 1, p. 177-200 24 p.

Research output: Contribution to journalReview article

adaptive management
floodplains
risk assessment
floodplain
planning process

Why does the magnitude of genotype-by-environment interaction vary?

Saltz, J. B., Bell, A. M., Flint, J., Gomulkiewicz, R., Hughes, K. A. & Keagy, J., Jun 2018, In : Ecology and Evolution. 8, 12, p. 6342-6353 12 p.

Research output: Contribution to journalReview article

genotype
evolutionary biology
phenotypic plasticity
genetic variation
environmental change

When Osama became Saddam: Origins and consequences of the change in America's public enemy #1

Althaus, S. & Largio, D. M., Oct 2004, In : PS - Political Science and Politics. 37, 4, p. 795-799 5 p.

Research output: Contribution to journalReview article

What's bugging brood parasites?

Clayton, D. H. & Johnson, K. P., Jan 1 2001, In : Trends in Ecology and Evolution. 16, 1, p. 9-10 2 p.

Research output: Contribution to journalReview article

foster care
Molothrus ater
parasite
parasites
louse

What is the maximum efficiency with which photosynthesis can convert solar energy into biomass?

Zhu, X. G., Long, S. P. & Ort, D. R., Apr 1 2008, In : Current Opinion in Biotechnology. 19, 2, p. 153-159 7 p.

Research output: Contribution to journalReview article

Solar Energy
Photosynthesis
Biomass
Solar energy
Economic Development
Photosynthesis
carbon dioxide
Air
photosynthesis
canopy

What counts as the evidence for three-dimensional and four-dimensional spatial representations?

Wang, R. F. & Street, W. N., Oct 1 2013, In : Behavioral and Brain Sciences. 36, 5, p. 567-568 2 p.

Research output: Contribution to journalReview article

evidence
coding
animal
trend
performance

What can whole genome expression data tell us about the ecology and evolution of personality?

Bell, A. M. & Aubin-Horth, N., Dec 27 2010, In : Philosophical Transactions of the Royal Society B: Biological Sciences. 365, 1560, p. 4001-4012 12 p.

Research output: Contribution to journalReview article

Ecology
Personality
Genes
Genome
ecology
Cognition
Research
Geese
Theory of Mind
Pain

What can machine learning do for antimicrobial peptides, and what can antimicrobial peptides do for machine learning?

Lee, E. Y., Lee, M. W., Fulan, B. M., Ferguson, A. & Wong, G. C. L., Dec 6 2017, In : Interface Focus. 7, 6, 20160153.

Research output: Contribution to journalReview article

Peptides
Learning systems
Membranes
Machine Learning
Taxonomies

Weak-lensing mass calibration of the Atacama Cosmology Telescope equatorial Sunyaev-Zeldovich cluster sample with the Canada-France-Hawaii telescope stripe 82 survey

Battaglia, Leauthaud, A., Miyatake, H., Hasselfield, M., Gralla, M. B., Allison, R., Bond, J. R., Calabrese, E., Crichton, D., Devlin, M. J., Dunkley, J., Dünner, R., Erben, T., Ferrara, S., Halpern, M., Hilton, M., Hill, J. C., Hincks, A. D., Hložek, R., Huffenberger, K. M. & 22 others, Hughes, J. P., Kneib, J. P., Kosowsky, A., Makler, M., Marriage, T. A., Menanteau, F., Miller, L., Moodley, K., Moraes, B., Niemack, M. D., Page, L., Shan, H., Sehgal, N., Sherwin, B. D., Sievers, J. L., Sifón, C., Spergel, D. N., Staggs, S. T., Taylor, J. E., Thornton, R., Waerbeke, L. V. & Wollack, E. J., Aug 8 2016, In : Journal of Cosmology and Astroparticle Physics. 2016, 8, 013.

Research output: Contribution to journalReview article

France
Canada
cosmology
telescopes
galaxies
Proteins
Biomolecules
Biological systems
Nucleic Acids
Free energy

Water Use Efficiency as a Constraint and Target for Improving the Resilience and Productivity of C 3 and C 4 Crops

Leakey, A., Ferguson, J. N., Pignon, C. P., Wu, A., Jin, Z., Hammer, G. L. & Lobell, D. B., Apr 2019, In : Annual Review of Plant Biology. 70, p. 781-808 28 p.

Research output: Contribution to journalReview article

water use efficiency
Water
crops
Photosynthesis
photosynthesis

Waterborne Viruses: A Barrier to Safe Drinking Water

Gall, A. M., Mariñas, B. J., Lu, Y. & Shisler, J. L., Jun 1 2015, In : PLoS pathogens. 11, 6, e1004867.

Research output: Contribution to journalReview article

Drinking Water
Disease Outbreaks
Viruses

Visual sensing is seeing: Why "mindsight," in hindsight, is blind

Simons, D. J., Nevarez, G. & Boot, W. R., Jul 1 2005, In : Psychological Science. 16, 7, p. 520-524 5 p.

Research output: Contribution to journalReview article

Blindness
Research Personnel
Psychology

Visualizing the proteome: Mapping protein changes in disease states with mass spectrometry imaging

Lanni, E. J., Rubakhin, S. & Sweedler, J. V., Mar 1 2013, In : Journal of Neurochemistry. 124, 5, p. 581-583 3 p.

Research output: Contribution to journalReview article

Matrix-Assisted Laser Desorption-Ionization Mass Spectrometry
Amyotrophic Lateral Sclerosis
Proteome
Neuroimaging
Mass Spectrometry

Visualizing chromosome dynamics with GFP

Belmont, A. S., Jun 2001, In : Trends in Cell Biology. 11, 6, p. 250-257 8 p.

Research output: Contribution to journalReview article

Bacterial Chromosomes
Chromosome Segregation
Centromere
Interphase
Nuclear Proteins

Visual hallucinations, thalamocortical physiology and Lewy body disease: A review

Esmaeeli, S., Murphy, K., Swords, G. M., Ibrahim, B. A., Brown, J. W. & Llano, D. A., Aug 2019, In : Neuroscience and Biobehavioral Reviews. 103, p. 337-351 15 p.

Research output: Contribution to journalReview article

Lewy Body Disease
Hallucinations
Thalamic Nuclei
Thalamus
Arousal

Visible and invisible bodies: The architectural patronage of Shajar al-Durr

Ruggles, D. F., Jan 1 2015, In : Muqarnas. 32, 1, p. 63-78 16 p.

Research output: Contribution to journalReview article

clientelism
Patronage
Invisible
Visible

Visibility-based pursuit-evasion in an unknown planar environment

Sachs, S., Lavalle, S. M. & Rajko, S., Dec 1 2004, In : International Journal of Robotics Research. 23, 1, p. 3-26 24 p.

Research output: Contribution to journalReview article

Pursuit-evasion
Visibility
Unknown
Robot
Perfect Map

Virtual Issue on Metal-Halide Perovskite Nanocrystals - A Bright Future for Optoelectronics

Buriak, J. M., Kamat, P. V., Schanze, K. S., Alivisatos, A. P., Murphy, C. J., Schatz, G. C., Scholes, G. D., Stang, P. J. & Weiss, P. S., Nov 14 2017, In : Chemistry of Materials. 29, 21, p. 8915-8917 3 p.

Research output: Contribution to journalReview article

Metal halides
Optoelectronic devices
Nanocrystals
perovskite

Viewpoint from computational thinking to computational action

Tissenbaum, M. B., Sheldon, J. & Abelson, H., Mar 2019, In : Communications of the ACM. 62, 3, p. 34-36 3 p.

Research output: Contribution to journalReview article

Education computing

Utilization and control of bioactuators across multiple length scales

Chan, V., Asada, H. H. & Bashir, R., Feb 21 2014, In : Lab on a chip. 14, 4, p. 653-670 18 p.

Research output: Contribution to journalReview article

Tissue
Muscle
Cells
Protozoa
Kinesin

Using the phase-field crystal method in the multi-scale modeling of microstructure evolution

Provatas, N., Dantzig, J. A., Athreya, B., Chan, P., Stefanovic, P., Goldenfeld, N. & Elder, K. R., Jul 1 2007, In : JOM. 59, 7, p. 83-90 8 p.

Research output: Contribution to journalReview article

Crystals
Microstructure
Binary alloys
Elastic deformation
Grain growth

Using resting state functional connectivity to unravel networks of tinnitus

Husain, F. T. & Schmidt, S. A., Jan 1 2014, In : Hearing Research. 307, p. 153-162 10 p.

Research output: Contribution to journalReview article

Tinnitus
Brain
Nervous System Diseases
Hearing Loss
Neuroimaging

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: Contribution to journalReview article

Drug Discovery
Genomics
Biological Products
Synthetic Biology
Metagenomics

Using genomics for natural product structure elucidation

Tietz, J. I. & Mitchell, D. A., Jun 1 2016, In : Current Topics in Medicinal Chemistry. 16, 15, p. 1645-1694 50 p.

Research output: Contribution to journalReview article

Genomics
Biological Products
Crystallography
Multigene Family
Computational Biology

Using Biosynthetic Models of Heme-Copper Oxidase and Nitric Oxide Reductase in Myoglobin to Elucidate Structural Features Responsible for Enzymatic Activities

Bhagi-Damodaran, A., Petrik, I. & Lu, Y., Oct 1 2016, In : Israel Journal of Chemistry. 56, 9-10, p. 773-790 18 p.

Research output: Contribution to journalReview article

Myoglobin
Heme
Electrons
Nitrous Oxide
copper oxidase

Use of the progesterone receptor antagonist RU 486 to identify novel progesterone receptor-regulated pathways in implantation

Bagchi, I. C., Li, Q., Cheon, Y. P., Mantena, S. R., Kannan, A. & Bagchi, M. K., Feb 1 2005, In : Seminars in Reproductive Medicine. 23, 1, p. 38-45 8 p.

Research output: Contribution to journalReview article

Mifepristone
Progesterone Receptors
Gene Regulatory Networks
Uterus
Pregnancy Maintenance

Use of Pig as a Model for Mesenchymal Stem Cell Therapies for Bone Regeneration

Rubessa, M., Polkoff, K., Bionaz, M., Monaco, E., Milner, D. J., Holllister, S. J., Goldwasser, M. S. & Wheeler, M. B., Oct 2 2017, In : Animal Biotechnology. 28, 4, p. 275-287 13 p.

Research output: Contribution to journalReview article

Bone Regeneration
Cell- and Tissue-Based Therapy
Stem cells
Mesenchymal Stromal Cells
stem cells

Use of genome-editing tools to treat sickle cell disease

Tasan, I., Jain, S. & Zhao, H., Sep 1 2016, In : Human Genetics. 135, 9, p. 1011-1028 18 p.

Research output: Contribution to journalReview article

Sickle Cell Anemia
Globins
CRISPR-Associated Proteins
Therapeutics
Clustered Regularly Interspaced Short Palindromic Repeats
Testing
Demonstrations

Urban Neighborhood and Residential Factors Associated with Breast Cancer in African American Women: a Systematic Review

Smith, B. P. & Madak-Erdogan, Z., Apr 1 2018, In : Hormones and Cancer. 9, 2, p. 71-81 11 p.

Research output: Contribution to journalReview article

African Americans
Breast Neoplasms
Delayed Diagnosis
Mammography
Social Class

Urban land-cover change detection through sub-pixel imperviousness mapping using remotely sensed data

Yang, L., Xian, G., Klaver, J. M. & Deal, B. M., Sep 1 2003, In : Photogrammetric Engineering and Remote Sensing. 69, 9, p. 1003-1010 8 p.

Research output: Contribution to journalReview article

Land use
pixel
land cover
Pixels
land use change

Updating a cautionary tale of masked priming: Reply to Klapp (2005)

Lleras, A. & Enns, J. T., Aug 1 2005, In : Journal of Experimental Psychology: General. 134, 3, p. 436-440 5 p.

Research output: Contribution to journalReview article

Unraveling the surface chemistry processes in lithiated and boronized plasma material interfaces under extreme conditions

Krstic, P. S., Allain, J. P., Dominguez-Gutierrez, F. J. & Bedoya, F., Jul 2018, In : Matter and Radiation at Extremes. 3, 4, p. 165-187 23 p.

Research output: Contribution to journalReview article

Surface chemistry
chemistry
Plasmas
Fusion reactions
fusion

Unraveling atomic-level self-organization at the plasma-material interface

Allain, J. P. & Shetty, A., Jun 28 2017, In : Journal of Physics D: Applied Physics. 50, 28, 283002.

Research output: Contribution to journalReview article

Plasmas
Irradiation
Beam plasma interactions
irradiation
Surface treatment

Understanding the relationship between brain gene expression and social behavior: Lessons from the honey bee

Zayed, A. & Robinson, G. E., Dec 3 2012, In : Annual Review of Genetics. 46, p. 591-615 25 p.

Research output: Contribution to journalReview article

Honey
Social Behavior
Bees
Gene Expression
Brain
Fluorescence microscopy
Fluorescence Microscopy
Epigenomics
Molecules
Gene expression

Understanding TERT promoter mutations: A common path to immortality

Bell, R. J. A., Rube, H. T., Xavier-Magalhães, A., Costa, B. M., Mancini, A., Song, J. S. & Costello, J. F., Apr 2016, In : Molecular Cancer Research. 14, 4, p. 315-323 9 p.

Research output: Contribution to journalReview article

Mutation
Telomerase
Neoplasms
Transcriptional Activation
Carcinogenesis

Understanding enzymic catalysis: The importance of short, strong hydrogen bonds

Gerlt, J. A., Kreevoy, M. M., Cleland, W. W. & Frey, P. A., Apr 1997, In : Chemistry and Biology. 4, 4, p. 259-267 9 p.

Research output: Contribution to journalReview article

Catalysis
Hydrogen
Hydrogen bonds
Catalytic Domain
Enzymes
Azurin
amino acids
Amino acids
Copper
electron transfer