Biochemistry & Molecular Biology

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Research Output 1961 2020

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2020

Oligonucleotide Enrichment of HSV-1 Genomic DNA from Clinical Specimens for Use in High-Throughput Sequencing

Shipley, M. M., Rathbun, M. M. & Szpara, M. L., Jan 1 2020, Methods in Molecular Biology. Humana Press Inc., p. 199-217 19 p. (Methods in Molecular Biology; vol. 2060).

Research output: Chapter in Book/Report/Conference proceedingChapter

Viral DNA
Human Herpesvirus 1
Oligonucleotides
High-Throughput Nucleotide Sequencing
Human Herpesvirus 2
2019
1 Citation (Scopus)

Bimolecular Fluorescence Complementation (BiFC) in Tissue Culture and in Developing Tissues of Drosophila to Study Protein-Protein Interactions

Matsui, Y. & Lai, Z., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 75-85 11 p. (Methods in Molecular Biology; vol. 1893).

Research output: Chapter in Book/Report/Conference proceedingChapter

Drosophila
Fluorescence
Proteins
Artifacts
1 Citation (Scopus)

Biosynthesis of chlorophylls and bacteriochlorophylls in green bacteria

Thweatt, J. L., Canniffe, D. P. & Bryant, D. A., Jan 1 2019, Advances in Botanical Research. Grimm, B. (ed.). Academic Press Inc., p. 35-89 55 p. (Advances in Botanical Research; vol. 90).

Research output: Chapter in Book/Report/Conference proceedingChapter

biosynthesis
chlorophyll
bacteria
Acidobacteria
chlorins

CryoEM reconstruction approaches to resolve asymmetric features

Goetschius, D. J., Lee, H. & Hafenstein, S., 2019, Advances in Virus Research. Rey, F. A. (ed.). Academic Press Inc., p. 73-91 19 p. (Advances in Virus Research; vol. 105).

Research output: Chapter in Book/Report/Conference proceedingChapter

Viruses
Capsid
Life Cycle Stages
Genome
Proteins

Information-Theoretic Inference of an Optimal Dictionary of Protein Supersecondary Structures

Konagurthu, A. S., Subramanian, R., Allison, L., Abramson, D., de la Banda, M. G., Stuckey, P. J. & Lesk, A., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 123-131 9 p. (Methods in Molecular Biology; vol. 1958).

Research output: Chapter in Book/Report/Conference proceedingChapter

Amino Acid Motifs
Data Compression
Protein Folding
Patient Selection

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
2018
13 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

Predicting Off-Target Effects of Therapeutic Antiviral Ribonucleosides: Inhibition of Mitochondrial RNA Transcription

Arnold, J. J. & Cameron, C. E., Feb 21 2018, Mitochondrial Dysfunction Caused by Drugs and Environmental Toxicants. wiley, Vol. 1-2. p. 407-417 11 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Ribonucleosides
Therapeutic Uses
Transcription
Antiviral Agents
Viruses
2 Citations (Scopus)

The biochemistry and physiology of respiratory-driven reversed methanogenesis

Nazem-Bokaee, H., Yan, Z., Maranas, C. D. & Ferry, J. G., Jun 20 2018, Methane Biocatalysis: Paving the Way to Sustainability. Springer International Publishing, p. 183-197 15 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Respiratory Physiological Phenomena
Biochemistry
Physiology

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

Anaerobic metabolism of aromatic compounds

Haddock, J. D. & Ferry, J. G., Jan 1 2017, Bioprocessing and Biotreatment of Coal. CRC Press, p. 393-416 24 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

metabolism
degradation
carbon
amino acid
microorganism
20 Citations (Scopus)

A panoply of phototrophs: An Overview of the thermophilic chlorophototrophs of the microbial mats of Alkaline siliceous hot springs in Yellowstone National Park, WY, USA

Tank, M., Thiel, V., Ward, D. M. & Bryant, D. A., Apr 18 2017, Modern Topics in the Phototrophic Prokaryotes: Environmental and Applied Aspects. Springer International Publishing, p. 87-137 51 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Hot Springs
hot springs
microbial mat
autotrophs
Chlorophyll

Biopiracy

Satheeshkumar, P. K. & Narayanan, A., May 10 2017, Status and Strategies for Exploration. Springer Singapore, Vol. 1. p. 185-204 20 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Intellectual Property
Internationality
Intellectual property
Inventors
Nimodipine

DNA analysis

Weedn, V. W., Lee, D. A., Roby, R. K. & Holland, M. M., Jan 1 2017, Handbook of Analytical Therapeutic Drug Monitoring and Toxicology. CRC Press, p. 35-49 15 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

DNA
Textbooks
4 Citations (Scopus)

Mechanism and Role of Globin-Coupled Sensor Signalling

Walker, J. A., Rivera, S. & Weinert, E., Jan 1 2017, Advances in Microbial Physiology. Academic Press, p. 133-169 37 p. (Advances in Microbial Physiology; vol. 71).

Research output: Chapter in Book/Report/Conference proceedingChapter

Globins
Oxygen
Proteins
Heme
Protein Kinases
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
6 Citations (Scopus)

Molecular biology of lignin peroxidases from Phanerochaete chrysosporium

Holzbaur, E. L. F., Andrawis, A. & Tien, M., Jan 1 2017, Molecular Industrial Mycology: Systems and Applications for Filamentous Fungi. CRC Press, p. 197-223 27 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

lignin peroxidase
Phanerochaete
Phanerochaete chrysosporium
Lignin
biodegradation

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
3 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

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., Jan 1 2016, Methods in Molecular Biology. Humana Press Inc., 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
1 Citation (Scopus)

Induction and purification of c. Difficile phage tail-like particles

Hegarty, J. P., Sangster, W., Ashley, R. E., Myers, R., Hafenstein, S. & Stewart, D. B., Jan 1 2016, Methods in Molecular Biology. Humana Press Inc., p. 167-175 9 p. (Methods in Molecular Biology; vol. 1476).

Research output: Chapter in Book/Report/Conference proceedingChapter

Bacteriophages
Bacteriocins
Viral Genome
Capsid
Infection

Microbial cellulose synthesis

Nagachar, N. & McManus, J., Jan 1 2016, Microbial Factories: Biofuels, Waste treatment: Volume 1. Springer India, p. 203-216 14 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Cellulose
cellulose
synthesis
feedstocks
Carbon
2 Citations (Scopus)

Polymerase mechanism-based method of viral attenuation

Lee, C. A., August, A., Arnold, J. J. & Cameron, C. E., Jan 1 2016, Methods in Molecular Biology. Humana Press Inc., p. 83-104 22 p. (Methods in Molecular Biology; vol. 1349).

Research output: Chapter in Book/Report/Conference proceedingChapter

Vaccines
Viruses
Lysine
RNA Viruses
Mutation
3 Citations (Scopus)

Preparation, Crystallization, and Structure Determination of Chromatin Enzyme/Nucleosome Complexes

McGinty, R. K., Makde, R. D. & Tan, S., Jan 1 2016, Methods in Enzymology. Academic Press Inc., p. 43-65 23 p. (Methods in Enzymology; vol. 573).

Research output: Chapter in Book/Report/Conference proceedingChapter

Nucleosomes
Crystallization
Chromatin
Enzymes
Cryoelectron Microscopy
2015
1 Citation (Scopus)

Carbonic Anhydrases of Environmentally and Medically Relevant Anaerobic Prokaryotes

Ferry, J. G., Jan 8 2015, Carbonic Anhydrases as Biocatalysts: From Theory to Medical and Industrial Applications. Elsevier Inc., p. 325-336 12 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Carbonic anhydrase
Carbonic Anhydrases
Carbon Dioxide
Carbon dioxide
Mammals
31 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

Reconstitution of factor-dependent, promoter proximal pausing in Drosophila nuclear extracts

Li, J. & Gilmour, D. S., Feb 9 2015, Bacterial Transcriptional Control: Methods and Protocols. Springer New York, p. 133-152 20 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Drosophila
RNA
RNA Polymerase II
Transcription
Oligonucleotides
1 Citation (Scopus)

Re-routing redox chains for directed photocatalysis

Lubner, C. E., Applegate, A. M. & Golbeck, J. H., Jan 1 2015, Biohydrogen. Walter de Gruyter GmbH, p. 239-264 26 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Photocatalysis
Oxidation-Reduction

Selenium and Cancer Metastasis

Chen, Y. C. & Mastro, A. M., 2015, Betaine: Chemistry, Analysis, Function and Effects. 9 ed. Royal Society of Chemistry, Vol. 2015-January. p. 408-427 20 p. (Food and Nutritional Components in Focus; vol. 2015-January, no. 9).

Research output: Chapter in Book/Report/Conference proceedingChapter

Selenium
metastasis
selenium
Neoplasm Metastasis
neoplasms

Techniques Analyzing Chromatin Modifications at Specific Single Loci

Chen, X. A., Sun, J. & Wang, Y., Jun 17 2015, Epigenetic Technological Applications. Elsevier Inc., p. 79-100 22 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Histone Code
Chromatin
Histones
DNA
Lysine
2014
1 Citation (Scopus)

Applying UV crosslinking to study RNA-protein interactions in multicomponent ribonucleoprotein complexes

Krasilnikov, A. S., Jan 1 2014, RNA Folding: Methods and Protocols. Humana Press Inc., p. 193-207 15 p. (Methods in Molecular Biology; vol. 1086).

Research output: Chapter in Book/Report/Conference proceedingChapter

Ribonucleoproteins
RNA
His-His-His-His-His-His
Ribonuclease P
Proteins
2 Citations (Scopus)

Bosnia and Herzegovina: Forensic Archaeology in Support of National and International Organisations Undertaking Criminal Investigations and Identifying the Missing from 1996 to 2013

Hanson, I., Rizviç, A. & Parsons, T. J., Jan 1 2014, Forensic Archaeology: A Global Perspective. Wiley-Blackwell, p. 19-31 13 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Bosnia and Herzegovina
archaeology
war crime
Yugoslavia
prosecution
23 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
3 Citations (Scopus)

Finding the epistasis needles in the genome-wide haystack

Ritchie, M. D., Nov 17 2014, Epistasis: Methods and Protocols. Springer New York, p. 19-33 15 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Genome-Wide Association Study
Needles
Genes
Genome
Single Nucleotide Polymorphism
3 Citations (Scopus)

Histone, nucleosome, and chromatin structure

McGinty, R. K. & Tan, S., May 1 2014, Fundamentals of Chromatin. Springer New York, p. 1-28 28 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Nucleosomes
Histones
Chromatin
DNA
Cell Nucleus

Metabolomics

Belton, B. R., Correll, J. B. & Patterson, A. D., Jan 1 2014, Applications of High-Resolution Mass Spectrometry in Drug Discovery and Development. Future Medicine Ltd., p. 106-118 13 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Tissue Extracts
Plasmas
Molecules
Metabolomics
10 Citations (Scopus)

Prioritized Sampling of Bone and Teeth for DNA Analysis in Commingled Cases

Hines, D. Z. C., Vennemeyer, M., Amory, S., Huel, R. L. M., Hanson, I., Katzmarzyk, C. & Parsons, T. J., Jun 17 2014, Commingled Human Remains: Methods in Recovery, Analysis, and Identification. Elsevier Inc., p. 275-305 31 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

genetic test
human being
Yugoslavia
experience
costs

Reducing Dimensionality in the Search for Gene-Gene Interactions

Ritchie, M. D., Jan 1 2014, Between the Lines of Genetic Code: Genetic Interactions in Understanding Disease and Complex Phenotypes. Elsevier Inc., p. 25-37 13 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Genes
Data Mining
Explosions
Sample Size
Data mining
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

Biosynthesis
Sulfur
Iron
1 Citation (Scopus)

Using the split-ubiquitin yeast two-hybrid system to test protein-protein interactions of transmembrane proteins

Bashline, L. & Gu, Y., Nov 18 2014, Plant Cell Expansion: Methods and Protocols. Springer New York, p. 143-158 16 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

two hybrid system techniques
Two-Hybrid System Techniques
transmembrane proteins
protein-protein interactions
ubiquitin
2013
6 Citations (Scopus)

Analytical Methodology of POPs

Reiner, E. J., Jobst, K. J., Megson, D., Dorman, F. L. & Focant, J. F., Dec 1 2013, Environmental Forensics for Persistent Organic Pollutants. Elsevier B.V., p. 59-139 81 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Organic pollutants
Flame Retardants
Environmental Pollutants
Poisons
Flame retardants
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

Biomonitoring for POPs

Patterson, D. G., Aylward, L. L., Covaci, A. & Franzblau, A., Dec 1 2013, Environmental Forensics for Persistent Organic Pollutants. Elsevier B.V., p. 163-197 35 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Beef
Metabolism
Dust
Clay
Contamination
1 Citation (Scopus)

Electron paramagnetic resonance spectroscopy

Golbeck, J. H. & van der Est, A., Jan 1 2013, Molecular Biophysics for the Life Sciences. Springer New York, p. 175-213 39 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

electron paramagnetic resonance spectroscopy
Electron Spin Resonance Spectroscopy
Paramagnetic resonance
Spectrum Analysis
Spectroscopy
6 Citations (Scopus)

Extraction of hydrophilic metabolites from plasmodium falciparum -infected erythrocytes for metabolomic analysis

Olszewski, K. L. & Llinas, M., Jan 1 2013, Malaria: Methods and Protocols. Humana Press Inc., p. 259-266 8 p. (Methods in Molecular Biology; vol. 923).

Research output: Chapter in Book/Report/Conference proceedingChapter

Metabolomics
Plasmodium falciparum
Parasites
Erythrocytes
Metabolic Networks and Pathways