Biochemistry & Molecular Biology

  • United States

Research Output 1961 2019

2019

Adaptive Shape Ripening and Interparticle Bridging of L-Arginine-Stabilized Silica Nanoparticles during Evaporative Colloidal Crystal Assembly

Russell, J. L., Tran, N. L. L. & Mallouk, T. E., Jan 30 2019, In : ACS Applied Materials and Interfaces. 11, 4, p. 4568-4577 10 p.

Research output: Contribution to journalArticle

Arginine
Silicon Dioxide
Colloids
Silica
Nanoparticles

A machine-learning approach for accurate detection of copy number variants from exome sequencing

Pounraja, V. K., Jayakar, G., Jensen, M., Kelkar, N. & Girirajan, S., Jan 1 2019, In : Genome research. 29, 7, p. 1134-1143 10 p.

Research output: Contribution to journalArticle

Open Access
Exome
Inborn Genetic Diseases
Base Composition
Machine Learning

Analysis of RNA Methylation by Phylogenetically Diverse Cfr Radical S-Adenosylmethionine Enzymes Reveals an Iron-Binding Accessory Domain in a Clostridial Enzyme

Gumkowski, J. D., Martinie, R. J., Corrigan, P. S., Pan, J., Bauerle, M. R., Almarei, M., Booker, S. J., Silakov, A., Krebs, C. & Boal, A. K., Jun 27 2019, In : Biochemistry. 58, 29, p. 3169-3184 16 p.

Research output: Contribution to journalArticle

tRNA Methyltransferases
S-Adenosylmethionine
Methylation
Accessories
Rubredoxins

Analysis of RNAPII complexes

Reese, J. C., Apr 15 2019, In : Methods. 159-160, p. 1-3 3 p.

Research output: Contribution to journalEditorial

1 Citation (Scopus)

A New Microbial Pathway for Organophosphonate Degradation Catalyzed by Two Previously Misannotated Non-Heme-Iron Oxygenases

Rajakovich, L. J., Pandelia, M. E., Mitchell, A. J., Chang, W. C., Zhang, B., Boal, A. K., Krebs, C. & Bollinger, Jr., J. M., Mar 26 2019, In : Biochemistry. 58, 12, p. 1627-1647 21 p.

Research output: Contribution to journalArticle

Organophosphonates
Oxygenases
Iron
Degradation
gamma-Butyrobetaine Dioxygenase
1 Citation (Scopus)

An interaction-based model for neuropsychiatric features of copy-number variants

Jensen, M. & Girirajan, S., Jan 1 2019, In : PLoS genetics. 15, 1, e1007879.

Research output: Contribution to journalArticle

phenotype
Phenotype
gene
Genes
genes
5 Citations (Scopus)

An N-nitrosating metalloenzyme constructs the pharmacophore of streptozotocin

Ng, T. L., Rohac, R., Mitchell, A. J., Boal, A. K. & Balskus, E. P., Feb 7 2019, In : Nature. 566, 7742, p. 94-99 6 p.

Research output: Contribution to journalLetter

Streptozocin
Iron
Synthetic Chemistry Techniques
Guanidine
Enzymes

An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes

Bevilacqua, P. C., Harris, M. E., Piccirilli, J. A., Gaines, C., Ganguly, A., Kostenbader, K., Ekesan, Ş. & York, D. M., Jun 21 2019, In : ACS chemical biology. 14, 6, p. 1068-1076 9 p.

Research output: Contribution to journalReview article

RNA Cleavage
Catalytic RNA
Ontology
RNA
Enzymes

An optimal O(nm) algorithm for enumerating all walks common to all closed edge-covering walks of a graph

Cairo, M., Medvedev, P., Acosta, N. O., Rizzi, R. & Tomescu, A. I., Jul 1 2019, In : ACM Transactions on Algorithms. 15, 4, 48.

Research output: Contribution to journalArticle

Open Access
Walk
Covering
Closed
Graph in graph theory
Dihydroxyacetone Phosphate
Quinolinic Acid
X ray crystallography
X Ray Crystallography
Phosphates

A review of analytical platforms for accurate bile acid measurement

Dutta, M., Cai, J., Gui, W. & Patterson, A. D., Jul 19 2019, In : Analytical and Bioanalytical Chemistry. 411, 19, p. 4541-4549 9 p.

Research output: Contribution to journalReview article

Bile Acids and Salts
Clinical laboratories
Intestinal Diseases
Molecules
Liquid chromatography
2 Citations (Scopus)

Arf GTPases and their GEFs and GAPS: Concepts and challenges

Sztul, E., Chen, P. W., Casanova, J. E., Cherfils, J., Dacks, J. B., Lambright, D. G., Lee, F. J. S., Randazzo, P. A., Santy, L. C., Schürmann, A., Wilhelmi, I., Yohe, M. E. & Kahn, R. A., Jan 1 2019, In : Molecular biology of the cell. 30, 11, p. 1249-1271 23 p.

Research output: Contribution to journalReview article

Open Access
GTP Phosphohydrolases
Proteins
GTPase-Activating Proteins
Guanine Nucleotide Exchange Factors
Pliability

A small-molecule inhibitor of trans-translation synergistically interacts with cathelicidin antimicrobial peptides to impair survival of staphylococcus aureus

Huang, Y., Alumasa, J., Callaghan, L. T., Samuel Baugh, R., Rae, C. D., Keiler, K. C. & McGillivray, S. M., Apr 1 2019, In : Antimicrobial agents and chemotherapy. e02362-18.

Research output: Contribution to journalArticle

Staphylococcus aureus
Survival
Daptomycin
Anti-Bacterial Agents
Methicillin

A stepwise mechanism for aqueous two-phase system formation in concentrated antibody solutions

Rogers, B. A., Rembert, K. B., Poyton, M. F., Okur, H. I., Kale, A. R., Yang, T., Zhang, J. & Cremer, P. S., Aug 6 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 32, p. 15784-15791 8 p.

Research output: Contribution to journalArticle

Open Access
Temperature
Antibodies
Gels
Suspensions
Proteins

Asymmetry in icosahedral viruses

Goetschius, D. J., Parrish, C. R. & Hafenstein, S., Jun 1 2019, In : Current Opinion in Virology. 36, p. 67-73 7 p.

Research output: Contribution to journalReview article

Leviviridae
Genome
Viruses
Picornaviridae
Capsid Proteins

A traction force threshold signifies metastatic phenotypic change in multicellular epithelia

Zhang, Y., Shi, X., Zhao, T., Huang, C., Wei, Q., Tang, X., Santy, L. C., Saif, M. T. A. & Zhang, S., Jan 1 2019, In : Soft Matter. 15, 36, p. 7203-7210 8 p.

Research output: Contribution to journalArticle

epithelium
traction
Stiffness
Phase diagrams
thresholds
4 Citations (Scopus)

Berberine directly affects the gut microbiota to promote intestinal farnesoid X receptor activation

Tian, Y., Cai, J., Gui, W., Nichols, R. G., Koo, I., Zhang, J., Anitha, M. & Patterson, A. D., Feb 1 2019, In : Drug Metabolism and Disposition. 47, 2, p. 86-93 8 p.

Research output: Contribution to journalArticle

Berberine
Bacteria
choloylglycine hydrolase
Metabolomics
Bile Acids and Salts
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)

Biochemical and Structural Characterization of XoxG and XoxJ and Their Roles in Lanthanide-Dependent Methanol Dehydrogenase Activity

Featherston, E. R., Rose, H. R., McBride, M. J., Taylor, E. M., Boal, A. K. & Cotruvo, Jr., J. A., Jan 1 2019, (Accepted/In press) In : ChemBioChem.

Research output: Contribution to journalArticle

Lanthanoid Series Elements
Assays
Methylobacterium extorquens
Crystal structure
Periplasmic Binding Proteins
2 Citations (Scopus)

Biochemical methods to characterize RNA polymerase II elongation complexes

Brooks Crickard, J. & Reese, J. C., Apr 15 2019, In : Methods. 159-160, p. 70-81 12 p.

Research output: Contribution to journalArticle

RNA Polymerase II
Elongation
Transcription
Peptide Elongation Factors
DNA

Bioresponsive peptide-polysaccharide nanogels — A versatile delivery system to augment the utility of bioactive cargo

Simonson, A. W., Lawanprasert, A., Goralski, T. D. P., Keiler, K. C. & Medina, S. H., Apr 1 2019, In : Nanomedicine: Nanotechnology, Biology, and Medicine. 17, p. 391-400 10 p.

Research output: Contribution to journalArticle

Hyaluronic acid
Polysaccharides
Peptides
Cells
Proteins
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

Bipartite graphs of small readability

Chikhi, R., Jovičić, V., Kratsch, S., Medvedev, P., Milanič, M., Raskhodnikova, S. & Varma, N., Jan 1 2019, In : Theoretical Computer Science.

Research output: Contribution to journalArticle

Bioinformatics
Bipartite Graph
Chain Graph
Graph in graph theory
Polynomials
1 Citation (Scopus)

"Candidates thermonerobacter thiotrophicus," a non-phototrophic member of the Bacteroidetes/Chlorobi with dissimilatory sulfur metabolism in hot spring mat communities

Thiel, V., Costas, A. M. G., Fortney, N. W., Martinez, J. N., Tank, M., Roden, E. E., Boyd, E. S., Ward, D. M., Hanada, S. & Bryant, D. A., Jan 1 2019, In : Frontiers in Microbiology. 10, JAN, 3159.

Research output: Contribution to journalArticle

Open Access
Chlorobi
Hot Springs
Bacteroidetes
Sulfur
Sulfates
1 Citation (Scopus)
S-Adenosylmethionine
Biosynthesis
Peptides
C1 peptide
Acids
1 Citation (Scopus)

Ccr4–not maintains genomic integrity by controlling the ubiquitylation and degradation of arrested RNAPII

Jiang, H., Wolgast, M., Beebe, L. M. & Reese, J. C., Jun 1 2019, In : Genes and Development. 33, 11-12, p. 705-717 13 p.

Research output: Contribution to journalArticle

Open Access
RNA Polymerase II
Ubiquitination
DNA Damage
Ligases
Ubiquitin
6 Citations (Scopus)

Characterization of chlorophyll f synthase heterologously produced in Synechococcus sp. PCC 7002

Shen, G., Canniffe, D. P., Ho, M. Y., Kurashov, V., van der Est, A., Golbeck, J. H. & Bryant, D. A., Apr 1 2019, In : Photosynthesis research. 140, 1, p. 77-92 16 p.

Research output: Contribution to journalArticle

Synechococcus sp. PCC 7002
Synechococcus
chlorophyll
Genes
Light

Characterizing protein-DNA binding event subtypes in ChIP-exo data

Yamada, N., Lai, W., Farrell, N., Pugh, B. F. & Mahony, S. A., Mar 15 2019, In : Bioinformatics. 35, 6, p. 903-913 11 p.

Research output: Contribution to journalArticle

DNA-binding Protein
Chromatin Immunoprecipitation
Chromatin
DNA-Binding Proteins
DNA
1 Citation (Scopus)

Charge Transfer Dynamics in Aqueous Dye-Sensitized Photoelectrochemical Cells: Implications for Water Splitting Efficiency

Xu, P. & Mallouk, T. E., Oct 1 2019, In : Journal of Physical Chemistry C. 123, 1, p. 299-305 7 p.

Research output: Contribution to journalArticle

Photoelectrochemical cells
water splitting
Charge transfer
Coloring Agents
Dyes

Commitment Isn't for Everyone

Josling, G. A. & Llinas, M., Jun 1 2019, In : Trends in Parasitology. 35, 6, p. 381-383 3 p.

Research output: Contribution to journalShort survey

Parasites
Culicidae
Malaria
Infection

Comparative genomics of the genus Methanohalophilus, including a newly isolated strain from Kebrit deep in the Red Sea

Guan, Y., Ngugi, D. K., Vinu, M., Blom, J., Alam, I., Guillot, S., Ferry, J. G. & Stingl, U., Jan 1 2019, In : Frontiers in Microbiology. 10, APR, 839.

Research output: Contribution to journalArticle

Open Access
Indian Ocean
Genomics
Genome
Carbon Cycle
Archaea
1 Citation (Scopus)

Comparison of herpes simplex virus 1 strains circulating in Finland demonstrates the uncoupling of whole-genome relatedness and phenotypic outcomes of viral infection

Bowen, C. D., Paavilainen, H., Renner, D. W., Palomäki, J., Lehtinen, J., Vuorinen, T., Norberg, P., Hukkanen, V. & Szpara, M. L., Jan 1 2019, In : Journal of virology. 93, 8, Y.

Research output: Contribution to journalArticle

Open Access
Human herpesvirus 1
Human Herpesvirus 1
Virus Diseases
Finland
Genome
1 Citation (Scopus)

Competing Polar and Antipolar Structures in the Ruddlesden-Popper Layered Perovskite Li2SrNb2O7

Uppuluri, R., Akamatsu, H., Sen Gupta, A., Wang, H., Brown, C. M., Agueda Lopez, K. E., Alem, N., Gopalan, V. & Mallouk, T. E., Jun 25 2019, In : Chemistry of Materials. 31, 12, p. 4418-4425 8 p.

Research output: Contribution to journalArticle

Perovskite
Antiferroelectric materials
Ferroelectricity
Neutron diffraction
Synchrotrons

Convergent evolution of hetero-oligomeric cellulose synthesis complexes in mosses and seed plants

Li, X., Speicher, T. L., Dees, D. C. T., Mansoori, N., McManus, J. B., Tien, M., Trindade, L. M., Wallace, I. S. & Roberts, A. W., Jan 1 2019, In : Plant Journal. 99, 5, p. 862-876 15 p.

Research output: Contribution to journalArticle

Bryophyta
convergent evolution
Spermatophytina
Cellulose
mosses and liverworts
Toll-Like Receptor 2
Acylation
Listeria monocytogenes
Lipoproteins
Copper
Catalytic RNA
Nucleotides
Catalysis
Molecules
Open Access
Microbiology
Light
corrigendum

Corrigendum to: ProtaBank: A repository for protein design and engineering data (Protein Science, (2018), 27, 6, (1113-1124), 10.1002/pro.3406)

Wang, C. Y., Chang, P. M., Ary, M. L., Allen, B. D., Chica, R. A., Mayo, S. L. & Olafson, B. D., Mar 1 2019, In : Protein Science. 28, 3, 1 p.

Research output: Contribution to journalComment/debate

Protein Engineering
Databases
Technology
Proteins
Ownership
3 Citations (Scopus)

Counter Cations Affect Transport in Aqueous Hydroxide Solutions with Ion Specificity

Drexler, C. I., Miller, T. C., Rogers, B. A., Li, Y. C., Daly, C. A., Yang, T., Corcelli, S. A. & Cremer, P. S., May 1 2019, In : Journal of the American Chemical Society. 141, 17, p. 6930-6936 7 p.

Research output: Contribution to journalArticle

Cations
Protons
Lithium
Positive ions
Sodium

Crossing the Thauer limit: Rewiring cyanobacterial metabolism to maximize fermentative H2 production

Kumaraswamy, K. G., Krishnan, A., Ananyev, G., Zhang, S., Bryant, D. A. & Dismukes, G. C., Mar 1 2019, In : Energy and Environmental Science. 12, 3, p. 1035-1045 11 p.

Research output: Contribution to journalArticle

Metabolism
Glucose
glucose
Pentoses
metabolism

CryoEM reconstruction approaches to resolve asymmetric features

Goetschius, D. J., Lee, H. & Hafenstein, S., Jan 1 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
Open Access
adducts
Crystal structure
chlorides
Atoms
crystal structure

Crystal structures of two isomeric 2-aryl-3-phenyl-1,3-thiazepan-4-ones

Yennawar, H. P., Peterson, S. D. & Silverberg, L. J., Jan 1 2019, In : Acta Crystallographica Section E: Crystallographic Communications. 75, p. 1270-1276 7 p.

Research output: Contribution to journalArticle

Open Access
Crystal structure
crystal structure
Molecules
Conformations
rings

De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality-Value Based Algorithm

Sahlin, K. & Medvedev, P., Jan 1 2019, Research in Computational Molecular Biology - 23rd Annual International Conference, RECOMB 2019, Proceedings. Cowen, L. J. (ed.). Springer Verlag, p. 227-242 16 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11467 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Clustering
Nanopore
Nanopores
Breadth
Reconstruction Algorithm

Design of highly active double-pseudoknotted ribozymes: A combined computational and experimental study

Yamagami, R., Kayedkhordeh, M., Mathews, D. H. & Bevilacqua, P. C., Jan 10 2019, In : Nucleic acids research. 47, 1, p. 29-42 14 p.

Research output: Contribution to journalArticle

Catalytic RNA
RNA Folding
Riboswitch
RNA
Synthetic Biology
2 Citations (Scopus)

Dissociation rate compensation mechanism for budding yeast pioneer transcription factors

Donovan, B. T., Chen, H., Jipa, C., Bai, L. & Poirier, M. G., Mar 1 2019, In : eLife. 8, e43008.

Research output: Contribution to journalArticle

Open Access
Saccharomycetales
Nucleosomes
Yeast
Transcription Factors
Yeasts

Draft genome sequences of type VI secretion system-encoding vibrio fischeri strains FQ-A001 and ES401

Bultman, K. M., Cecere, A. G., Miyashiro, T. I., Septer, A. N. & Mandel, M. J., May 16 2019, In : Microbiology Resource Announcements. 8, 20, e00385-19.

Research output: Contribution to journalArticle

Open Access
Aliivibrio fischeri
Genome
Decapodiformes
Genomics
Bacteria

Dual role of a C-terminally truncated isoform of large tumor suppressor kinase 1 in the regulation of hippo signaling and tissue growth

Matsui, Y., Zhang, Y., Paulson, R. & Lai, Z., Jan 1 2019, In : DNA and Cell Biology. 38, 1, p. 91-106 16 p.

Research output: Contribution to journalArticle

Protein Isoforms
Phosphotransferases
Growth
Neoplasms
Drosophila
3 Citations (Scopus)
Photosystem I Protein Complex
far-red light
Energy Transfer
photosystem I
energy transfer
1 Citation (Scopus)

Engineering of B800 bacteriochlorophyll binding site specificity in the Rhodobacter sphaeroides LH2 antenna

Swainsbury, D. J. K., Faries, K. M., Niedzwiedzki, D. M., Martin, E. C., Flinders, A. J., Canniffe, D. P., Shen, G., Bryant, D. A., Kirmaier, C., Holten, D. & Hunter, C. N., Mar 1 2019, In : Biochimica et Biophysica Acta - Bioenergetics. 1860, 3, p. 209-223 15 p.

Research output: Contribution to journalArticle

Light-Harvesting Protein Complexes
Bacteriochlorophylls
Rhodobacter sphaeroides
Binding Sites
Antennas