Biochemistry and Molecular Biology

Publications 1975 2018

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2018

Automated inference of chemical discriminants of biological activity

Raschka, S., Scott, A. M., Huertas, M., Li, W. & Kuhn, L. A. Jan 1 2018 Methods in Molecular Biology. Humana Press Inc., p. 307-338 32 p. (Methods in Molecular Biology; vol. 1762)

Research output: Chapter in Book/Report/Conference proceedingChapter

Synthetic Chemistry Techniques
Decision Trees
Quantitative Structure-Activity Relationship
Biological Assay
Vertebrates

XEN and the Art of Stem Cell Maintenance: Molecular Mechanisms Maintaining Cell Fate and Self-Renewal in Extraembryonic Endoderm Stem (XEN) Cell Lines

Ralston, A. Jan 1 2018 Advances in Anatomy Embryology and Cell Biology. Springer Verlag, Vol. 229, p. 69-78 10 p. (Advances in Anatomy Embryology and Cell Biology; vol. 229)

Research output: Chapter in Book/Report/Conference proceedingChapter

Endoderm
Art
Stem Cells
Maintenance
Cell Line
2017

Lactate Racemase and Its Niacin-Derived, Covalently-Tethered, Nickel Cofactor

Desguin, B., Soumillion, P., Hols, P., Hu, J. & Hausinger, R. P. 2017 Molybdenum and Tungsten Enzymes: Biochemistry. 10 ed. Royal Society of Chemistry, Vol. 2017-January, p. 220-236 17 p. (RSC Metallobiology; vol. 2017-January, no. 10)

Research output: Chapter in Book/Report/Conference proceedingChapter

lactate racemase
Niacin
Nickel
Accessories
Lactic Acid
1 Citations

Pluripotency-What Does Cell Polarity Have to Do With It?

Frum, T. & Ralston, A. Nov 2 2017 Cell Polarity in Development and Disease. Elsevier Inc., p. 31-60 30 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Cell Polarity
Polarization
Stem cells
Embryonic Structures
Pluripotent Stem Cells
2016
2 Citations

Biolayer interferometry: A novel method to Elucidate Protein-Protein and Protein-DNA interactions in the Mitochondrial DNA Replisome

Ciesielski, G. L., Hytönen, V. P. & Kaguni, L. S. 2016 Methods in Molecular Biology. Humana Press Inc., Vol. 1351, p. 223-231 9 p. (Methods in Molecular Biology; vol. 1351)

Research output: Chapter in Book/Report/Conference proceedingChapter

Interferometry
Mitochondrial Diseases
Mitochondrial DNA
Holoenzymes
DNA

Differential geometry-based solvation and electrolyte transport models for biomolecular modeling: A review

Wei, G. W. & Baker, N. A. Mar 14 2016 Many-Body Effects and Electrostatics in Biomolecules. Pan Stanford Publishing Pte. Ltd., p. 417-461 45 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

differential geometry
solvation
electrolytes

Expression and purification of mitochondrial RNA polymerase and transcription factor a from drosophila melanogaster

Gajewski, J. P., Arnold, J. J., Salminen, T. S., Kaguni, L. S. & Cameron, C. E. 2016 Methods in Molecular Biology. Humana Press Inc., Vol. 1351, p. 199-210 12 p. (Methods in Molecular Biology; vol. 1351)

Research output: Chapter in Book/Report/Conference proceedingChapter

DNA-Directed RNA Polymerases
Drosophila melanogaster
Transcription Factors
Mitochondrial Genes
Small Ubiquitin-Related Modifier Proteins

Nickel Toxicity, Regulation, and Resistance in Bacteria

Macomber, L. & Hausinger, R. P. Aug 12 2016 Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria. Wiley Blackwell, Vol. 2, p. 1131-1144 14 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Nickel
Bacteria
Poisons
Metals
Metalloproteins
1 Citations

Purification and Comparative assay of Human Mitochondrial single-stranded DNA-binding protein

Ciesielski, G. L., Rosado-Ruiz, F. A. & Kaguni, L. S. 2016 Methods in Molecular Biology. Humana Press Inc., Vol. 1351, p. 211-222 12 p. (Methods in Molecular Biology; vol. 1351)

Research output: Chapter in Book/Report/Conference proceedingChapter

Mitochondrial DNA
DNA-Binding Proteins
DNA Helicases
Single-Stranded DNA
Electrophoretic Mobility Shift Assay

Purification and comparative assay of the human mitochondrial replicative DNA helicase

Rosado-Ruiz, F. A., So, M. & Kaguni, L. S. 2016 Methods in Molecular Biology. Humana Press Inc., Vol. 1351, p. 185-198 14 p. (Methods in Molecular Biology; vol. 1351)

Research output: Chapter in Book/Report/Conference proceedingChapter

DNA Helicases
Mitochondrial DNA
Enzyme Stability
Mitochondrial Genome
DNA-Binding Proteins
2015
2 Citations

AlkB and its homologues - DNA repair and beyond

Müller, T. A. & Hausinger, R. P. 2015 2-Oxoglutarate-Dependent Oxygenases. 3 ed. Royal Society of Chemistry, Vol. 2015-January, p. 246-262 17 p. (RSC Metallobiology; vol. 2015-January, no. 3)

Research output: Chapter in Book/Report/Conference proceedingChapter

Plant Viruses
Dioxygenases
Lyases
Alkylating Agents
Archaea
2 Citations

Axonal Regeneration and Myelination: Applicabilityof the Layer-by-Layer Technology

Liu, C., Pyne, R., Baek, S., Sakamoto, J., Tuszynski, M. H. & Chan, C. Jan 30 2015 Layer-by-Layer Films for Biomedical Applications. wiley, p. 525-546 22 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Scaffolds
Repair
Cell adhesion
Tissue engineering
Pharmaceutical Preparations
11 Citations

Biochemical diversity of 2-oxoglutarate-dependent oxygenases

Hausinger, R. P. 2015 2-Oxoglutarate-Dependent Oxygenases. 3 ed. Royal Society of Chemistry, Vol. 2015-January, p. 1-58 58 p. (RSC Metallobiology; vol. 2015-January, no. 3)

Research output: Chapter in Book/Report/Conference proceedingChapter

Oxygenases
Enzymes
Biosynthesis
Phytanic Acid
5-Methylcytosine
3 Citations

Production of Bacterial Cellulose with Controlled Deuterium-Hydrogen Substitution for Neutron Scattering Studies

O'Neill, H., Shah, R., Evans, B. R., He, J., Pingali, S. V., Chundawat, S. P. S., Jones, A. D., Langan, P., Davison, B. H. & Urban, V. 2015 Methods in Enzymology. Academic Press Inc., Vol. 565, p. 123-146 24 p. (Methods in Enzymology; vol. 565)

Research output: Chapter in Book/Report/Conference proceedingChapter

Deuterium
Neutrons
Neutron scattering
Cellulose
Hydrogen
2013

Biomedical and clinical networks of cancer

Dalkic, E. & Chan, C. 2013 Network Topologies: Types, Performance Impact and Advantages/Disadvantages. Nova Science Publishers, Inc., p. 131-140 10 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Systems science
Chemotherapy
Radiotherapy
Electric network analysis
Surgery

DNA Replication: Initiation in Bacteria

Kaguni, J. M. Feb 15 2013 Encyclopedia of Biological Chemistry: Second Edition. Elsevier Inc., p. 121-125 5 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Replication Origin
DNA Replication
Escherichia coli
Bacteria
Cell Cycle
13 Citations

Elicitation of jasmonate-mediated defense responses by mechanical wounding and insect herbivory

Herde, M., Koo, A. J. K. & Howe, G. A. 2013 Methods in Molecular Biology. Humana Press Inc., Vol. 1011, p. 51-61 11 p. (Methods in Molecular Biology; vol. 1011)

Research output: Chapter in Book/Report/Conference proceedingChapter

Herbivory
Insects
Plant Immunity
Mastication
Growth and Development
12 Citations

Measuring transmembrane helix interaction strengths in lipid bilayers using steric trapping

Hong, H., Chang, Y. C. & Bowie, J. U. 2013 Methods in Molecular Biology. Vol. 1063, p. 37-56 20 p. (Methods in Molecular Biology; vol. 1063)

Research output: Chapter in Book/Report/Conference proceedingChapter

Lipid Bilayers
Streptavidin
Competitive Binding
Biotin
Membrane Proteins
1 Citations

Relevance of Network Hierarchy in Cancer Drug-Target Selection

Nath, A. & Chan, C. Aug 1 2013 Systems Biology in Cancer Research and Drug Discovery. Springer Netherlands, p. 339-362 24 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Pharmaceutical Preparations
Neoplasms
Neoplasm Genes
Prostatic Neoplasms
Therapeutics
3 Citations

SiRNA therapeutic design: Tools and challenges

Malefyt, A. P., Angart, P. A., Chan, C. & Walton, S. P. Aug 1 2013 Regulatory RNAs: Basics, Methods and Applications. Springer-Verlag Berlin Heidelberg, p. 475-503 29 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

RNA Interference
RNA
Small Interfering RNA
Therapeutics
Clinical Trials
2012
29 Citations

Genomic approaches for interrogating the biochemistry of medicinal plant species

Góngora-Castillo, E., Fedewa, G., Yeo, Y., Chappell, J., Dellapenna, D. & Buell, C. R. 2012 Methods in Enzymology. Vol. 517, p. 139-159 21 p. (Methods in Enzymology; vol. 517)

Research output: Chapter in Book/Report/Conference proceedingChapter

Biochemistry
Medicinal Plants
Transcriptome
Genes
Computational methods

Network-Based Information Synergy Analysis for Alzheimer Disease

Wang, X., Geekiyanage, H. & Chan, C. Jun 21 2012 Statistical and Machine Learning Approaches for Network Analysis. John Wiley and Sons, p. 245-259 15 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Alzheimer's Disease
Synergy
6 Citations

Rapid LC-MS/MS profiling of protein amino acids and metabolically related compounds for large-scale assessment of metabolic phenotypes

Gu, L., Jones, A. D. & Last, R. L. 2012 Methods in Molecular Biology. Vol. 828, p. 1-11 11 p. (Methods in Molecular Biology; vol. 828)

Research output: Chapter in Book/Report/Conference proceedingChapter

Homoserine
Phenotype
Amino Acids
Isoleucine
Threonine
2011

Biochemical and molecular techniques for the study of photosynthetic processes

Parry, M. A. J., Andralojc, P. J., Foyer, C. H., Galmés, J. & Sharkey, T. D. Jan 1 2011 Terrestrial Photosynthesis in a Changing Environment a Molecular, Physiological and Ecological Approach. Cambridge University Press, p. 186-205 20 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Cues
Biochemical Phenomena
metabolites
Plant Physiological Phenomena
Genes

Biochemistry and photochemistry of terrestrial photosynthesis: A synopsis

Sharkey, T. D., Ducruet, J. M. & Parry, M. Jan 1 2011 Terrestrial Photosynthesis in a Changing Environment a Molecular, Physiological and Ecological Approach. Cambridge University Press, p. 9-19 11 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Photochemistry
photochemistry
Photosynthesis
Carbon Monoxide
Biochemistry
8 Citations

Chloroplast phenomics: Systematic phenotypic screening of chloroplast protein mutants in Arabidopsis

Lu, Y., Savage, L. J. & Last, R. L. 2011 Methods in Molecular Biology. Vol. 775, p. 161-185 25 p. (Methods in Molecular Biology; vol. 775)

Research output: Chapter in Book/Report/Conference proceedingChapter

Chloroplast Proteins
Chloroplasts
Arabidopsis
Seed Storage Proteins
Controlled Vocabulary
4 Citations

Conformational sampling in structure prediction and refinement with atomistic and coarse-grained models

Feig, M., Gopal, S. M., Vadivel, K. & Stumpff-Kane, A. 2011 Multiscale Approaches to Protein Modeling: Structure Prediction, Dynamics, Thermodynamics and Macromolecular Assemblies. Springer New York, p. 85-109 25 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Sampling
Proteins
Atoms
Conformations
2 Citations

Models of photosynthesis

Diaz-Espejo, A., Bernacchi, C. J., Collatz, G. J. & Sharkey, T. D. Jan 1 2011 Terrestrial Photosynthesis in a Changing Environment a Molecular, Physiological and Ecological Approach. Cambridge University Press, p. 98-112 15 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Photosynthesis
photosynthesis
canopy
Chemical Phenomena
Physical Phenomena
1 Citations

Optical methods for investigation of leaf photosynthesis

Ducruet, J. M., Baron, M., Delucia, E. H., Morales, F. & Sharkey, T. D. Jan 1 2011 Terrestrial Photosynthesis in a Changing Environment a Molecular, Physiological and Ecological Approach. Cambridge University Press, p. 131-151 21 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Photosynthesis
photosynthesis
Light
Fluorescence
Energy Metabolism
2 Citations

Photosynthetic responses to high temperature

Sharkey, T. D. & Bernacchi, C. J. Jan 1 2011 Terrestrial Photosynthesis in a Changing Environment a Molecular, Physiological and Ecological Approach. Cambridge University Press, p. 290-298 9 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Temperature
Photosynthesis
temperature
photosynthesis
Droughts

Photosynthetic responses to increased co2 and air pollutants

Calfapietra, C., Bernacchi, C. J., Centritto, M. & Sharkey, T. D. Jan 1 2011 Terrestrial Photosynthesis in a Changing Environment a Molecular, Physiological and Ecological Approach. Cambridge University Press, p. 257-271 15 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Air Pollutants
pollutants
climate change
air
Carbon Monoxide
4 Citations

Regulation during adaptation of cyanobacteria to changes in iron availability: A case study of responses to iron limitation in Fremyella diplosiphon

Montgomery, B. L. & Pattanaik, B. Jan 2011 Biometals: Molecular Structures, Binding Properties and Applications. Nova Science Publishers, Inc., p. 215-226 12 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

availability
iron
physiological effects
homeostasis
scavenging
13 Citations

SELEX (systematic evolution of ligands by exponential enrichment), as a powerful tool for deciphering the protein-DNA interaction space

Chai, C., Xie, Z. & Grotewold, E. Jul 29 2011 Plant Transcription Factors: Methods and Protocols. p. 249-258 10 p. (Methods in Molecular Biology; vol. 754)

Research output: Chapter in Book/Report/Conference proceedingChapter

SELEX Aptamer Technique
DNA
Transcription Factors
Nucleotide Aptamers
Biological Phenomena
10 Citations

Spatially Resolved Plant Metabolomics

Sumner, L. W., Yang, D. S., Bench, B. J., Watson, B. S., Li, C. & Daniel Jones, A. Mar 17 2011 Annual Plant Reviews Volume 43: Biology of Plant Metabolomics. wiley, Vol. 43, p. 343-366 24 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Metabolomics
Metabolites
Tissue
Secondary Metabolism
Systems Biology
7 Citations

Studying arabidopsis envelope protein localization and topology using thermolysin and trypsin proteases

Froehlich, J. 2011 Methods in Molecular Biology. Vol. 774, p. 351-367 17 p. (Methods in Molecular Biology; vol. 774)

Research output: Chapter in Book/Report/Conference proceedingChapter

Arabidopsis Proteins
Thermolysin
Trypsin
Peptide Hydrolases
Membranes

Sulfur Metabolism

Takahashi, H. Mar 28 2011 Plant Metabolism and Biotechnology. John Wiley and Sons, p. 103-133 31 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Inversion layers
Sulfur
O-acetylhomoserine (thiol)-lyase
2010
1 Citations

Biomolecular Solvation in Theory and Experiment

Feig, M. Jan 27 2010 Modeling Solvent Environments: Applications to Simulations of Biomolecules. Wiley-VCH, p. 1-29 29 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Protein folding
Crystallography
Solvation
Neutron scattering
Glycerol
9 Citations

Glycosyltransferases of the GT34 and GT37 Families

Keegstra, K. & Cavalier, D. Nov 23 2010 Annual Plant Reviews. Wiley-Blackwell, Vol. 41, p. 235-249 15 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Glycosyltransferases
glycosyltransferases
Genes
Fucosyltransferases
genes
6 Citations

Jasmonates

Howe, G. A. 2010 Plant Hormones: Biosynthesis, Signal Transduction, Action!. Springer Netherlands, p. 646-680 35 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

jasmonic acid
Physiological Phenomena
Biosynthetic Pathways
proteinase inhibitors
biochemical pathways
2009
23 Citations

Glycerolipid Biosynthesis

Riekhof, W. R. & Benning, C. 2009 The Chlamydomonas Sourcebook 3-Vol set. Elsevier Inc., Vol. 2, p. 41-68 28 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Chlamydomonas
biosynthesis
Phosphatidylcholines
Lipids
phosphatidylcholines

Synthesis of Chiral sec-Alcohols by Ketone Reduction

Pollard, D., Truppo, M., Moore, J., Kosjek, B., Tellers, D., Moore, J., Smonou, I., Kalaitzakis, D., Musa, M. M., Ziegelmann-Fjeld, K. I., Vieille, C., Zeikus, J. G., Phillipsa, R. S., Truppo, M., Morley, K., Devine, P., Ema, T., Okita, N., Ide, S. & Sakai, T. Dec 15 2009 Practical Methods for Biocatalysis and Biotransformations. John Wiley & Sons, Ltd, p. 273-275 3 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Ketones
Alcohols
2008
5 Citations

Action of plant defensive enzymes in the insect midgut

Chen, H., Gonzales-Vigil, E. & Howe, G. A. 2008 Induced Plant Resistance to Herbivory. Springer Netherlands, p. 271-284 14 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Plant Proteins
threonine
midgut
Insects
arginase
5 Citations

Bioinformatics: Databasing and gene annotation

Burgoon, L. D. & Zacharewski, T. R. 2008 Methods in Molecular Biology. Humana Press, Vol. 460, p. 145-157 13 p. (Methods in Molecular Biology; vol. 460)

Research output: Chapter in Book/Report/Conference proceedingChapter

Molecular Sequence Annotation
Computational Biology
Information Storage and Retrieval
Genes
Research Personnel
49 Citations

Direct defenses in plants and their induction by wounding and insect herbivores

Howe, G. A. & Schaller, A. 2008 Induced Plant Resistance to Herbivory. Springer Netherlands, p. 7-29 23 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Herbivory
Insects
herbivores
insects
jasmonic acid
18 Citations

Implicit membrane models for membrane protein simulation

Feig, M. 2008 Methods in Molecular Biology. Humana Press, Vol. 443, p. 181-196 16 p. (Methods in Molecular Biology; vol. 443)

Research output: Chapter in Book/Report/Conference proceedingChapter

Membrane Proteins
Membranes
Static Electricity
Lipids
Peptides

Nuclear and Cytoplasmic Localization of Galectin-1 and Galectin-3 and Their Roles in Pre-mRNA Splicing

Wang, J. L., Haudek, K. C., Voss, P. G. & Patterson, R. J. Jan 29 2008 Galectins. John Wiley & Sons, Inc., p. 87-95 9 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Galectin 1
Galectin 3
RNA Precursors
2007

An introduction to proteomics data analysis

Wilkerson, C. G. 2007 Plant Proteomics. Springer-Verlag Berlin Heidelberg, p. 29-40 12 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Proteomics
Software
Proteins
Research Personnel
Datasets
10 Citations

Cell Wall Structure, Biosynthesis and Assembly

Liepman, A. H., Cavalier, D. M., Lerouxel, O. & Keegstra, K. Nov 12 2007 Plant Cell Separation and Adhesion. Wiley Blackwell, Vol. 25, p. 8-39 32 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Cell Wall
Polysaccharides
polysaccharides
cell walls
biosynthesis
12 Citations

Chaperones of Nickel Metabolism

Quiroz, S., Kim, J. K., Mulrooney, S. B. & Hausinger, R. P. Mar 12 2007 Nickel and Its Surprising Impact in Nature. wiley, Vol. 2, p. 519-544 26 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Nickel
Metabolism
Apoproteins
Enzymes
Accessories

Strength in flexibility: Modeling side-chain conformational change in docking and screening

Kuhn, L. A. 2007 RSC Biomolecular Sciences. p. 181-191 11 p. (RSC Biomolecular Sciences)

Research output: Chapter in Book/Report/Conference proceedingChapter