Biochemistry & Molecular Biology

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Research Output 1961 2020

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Review article
3 Citations (Scopus)

3D clustering of co-regulated genes and its effect on gene expression

Du, M. & Bai, L., Dec 1 2017, In : Current Genetics. 63, 6, p. 1017-1021 5 p.

Research output: Contribution to journalReview article

Cluster Analysis
Gene Expression
Genome
Genes
Saccharomycetales
46 Citations (Scopus)

A brilliant disguise for self RNA: 5′-End and internal modifications of primary transcripts suppress elements of innate immunity

Nallagatla, S. R., Toroney, R. & Bevilacqua, P. C., Jan 1 2008, In : RNA Biology. 5, 3

Research output: Contribution to journalReview article

Innate Immunity
RNA
Nucleosides
eIF-2 Kinase
Interferons
14 Citations (Scopus)

Acetate metabolism in anaerobes from the domain Archaea

Ferry, J. G., Jun 9 2015, In : Life. 5, 2, p. 1454-1471 18 p.

Research output: Contribution to journalReview article

anaerobes
Archaea
metabolism
Hydrothermal Vents
Metabolism
31 Citations (Scopus)

A common neuronal response to alphaherpesvirus infection

Szpara, M. L., Kobiler, O. & Enquist, L. W., Sep 1 2010, In : Journal of Neuroimmune Pharmacology. 5, 3, p. 418-427 10 p.

Research output: Contribution to journalReview article

Infection
Herpesviridae
Genes
Suid Herpesvirus 1
Neurons
54 Citations (Scopus)
Flavodoxin
Photosystem I Protein Complex
Ferredoxins
ferredoxins
photosystem I
272 Citations (Scopus)

Active repression mechanisms of eukaryotic transcription repressors

Hanna-Rose, W. & Hansen, U., Jun 1996, In : Trends in Genetics. 12, 6, p. 229-234 6 p.

Research output: Contribution to journalReview article

Biological Phenomena
RNA Polymerase II
DNA-Binding Proteins
Growth
54 Citations (Scopus)

Adaptive and acclimative responses of cyanobacteria to far-red light

Gan, F. & Bryant, D. A., Oct 1 2015, In : Environmental microbiology. 17, 10, p. 3450-3465 16 p.

Research output: Contribution to journalReview article

far-red light
Cyanobacteria
cyanobacterium
Light
chlorophyll
31 Citations (Scopus)

A genetic model for neurodevelopmental disease

Coe, B. P., Girirajan, S. & Eichler, E. E., Oct 1 2012, In : Current Opinion in Neurobiology. 22, 5, p. 829-836 8 p.

Research output: Contribution to journalReview article

Genetic Models
Genes
Technology
6 Citations (Scopus)

A model for the origin of protein synthesis as coreplicational scanning of nascent RNA

Yakhnin, A. V., Dec 1 2007, In : Origins of Life and Evolution of Biospheres. 37, 6, p. 523-536 14 p.

Research output: Contribution to journalReview article

ribonucleic acids
protein synthesis
translation (genetics)
peptides
RNA
89 Citations (Scopus)

Anaerobic functionalization of unactivated C-H bonds

Booker, S. J., Feb 1 2009, In : Current Opinion in Chemical Biology. 13, 1, p. 58-73 16 p.

Research output: Contribution to journalReview article

Enzymes
Alkanes
Methylation
Oxygen
Surveying
160 Citations (Scopus)

An atlas of serpin conformations

Whisstock, J., Skinner, R. & Lesk, A., Jan 1 1998, In : Trends in Biochemical Sciences. 23, 2, p. 63-67 5 p.

Research output: Contribution to journalReview article

Serpins
Atlases
Conformations
Chymotrypsin
Serine Proteases
27 Citations (Scopus)

An evolutionary approach reveals a high protein-coding capacity of the human genome

Nekrutenko, A., Chung, W. Y. & Li, W. H., Jun 1 2003, In : Trends in Genetics. 19, 6, p. 306-310 5 p.

Research output: Contribution to journalReview article

Human Genome
Exons
Proteins
Genes
64 Citations (Scopus)

An Intestinal Microbiota–Farnesoid X Receptor Axis Modulates Metabolic Disease

Gonzalez, F. J., Jiang, C. & Patterson, A. D., Nov 1 2016, In : Gastroenterology. 151, 5, p. 845-859 15 p.

Research output: Contribution to journalReview article

choloylglycine hydrolase
Metabolic Diseases
Ceramides
High Fat Diet
Microbiota
3 Citations (Scopus)

An Introduction to the Structure and Function of the Catalytic Core Enzyme of Escherichia coli RNA Polymerase

Sutherland, C. & Murakami, K. S., Aug 1 2018, In : EcoSal Plus. 8, 1

Research output: Contribution to journalReview article

DNA-Directed RNA Polymerases
Catalytic Domain
Escherichia coli
Enzymes
Research Personnel
3 Citations (Scopus)

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
3 Citations (Scopus)

Another round of “clue” to uncover the mystery of complex traits

Verma, S. S. & Ritchie, M. D., Feb 2018, In : Genes. 9, 2, 61.

Research output: Contribution to journalReview article

Genome-Wide Association Study
Genetic Loci
Population

A Novel Biosynthetic Pathway Providing Precursors for Fatty Acid Biosynthesis and Secondary Metabolite Formation in Myxobacteria

Weinert, E. E. & Jarvis, B. B., Oct 1 2003, In : Chemtracts. 16, 11, p. 680-683 4 p.

Research output: Contribution to journalReview article

Biosynthesis
Metabolites
Fatty Acids
Biosynthetic Pathways
26 Citations (Scopus)

A physiological perspective on the origin and evolution of photosynthesis

Martin, W. F., Bryant, D. A. & Beatty, J. T., Jan 1 2018, In : FEMS Microbiology Reviews. 42, 2, p. 205-231 27 p.

Research output: Contribution to journalReview article

Photosynthesis
Chlorophyll
Ferredoxins
Phototrophic Processes
Hydrothermal Vents
32 Citations (Scopus)

Application of forensic DNA testing in the legal system

Primorac, D., Schanfield, M. S. & Primorac, D., Mar 1 2000, In : Croatian Medical Journal. 41, 1, p. 32-46 15 p.

Research output: Contribution to journalReview article

DNA
Forensic Sciences
Technology
Miniaturization
Forensic Medicine
28 Citations (Scopus)

Archaeal RNA polymerase

Hirata, A. & Murakami, K. S., Dec 1 2009, In : Current Opinion in Structural Biology. 19, 6, p. 724-731 8 p.

Research output: Contribution to journalReview article

Archaeal RNA
DNA-Directed RNA Polymerases
Eukaryota
General Transcription Factors
Archaea
1 Citation (Scopus)

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
25 Citations (Scopus)

A review of the determination of persistent organic pollutants for environmental forensics investigations

Megson, D., Reiner, E. J., Jobst, K. J., Dorman, F. L., Robson, M. & Focant, J. F., Oct 19 2016, In : Analytica Chimica Acta. 941, p. 10-25 16 p.

Research output: Contribution to journalReview article

Environmental Pollutants
Organic pollutants
Flame Retardants
Dioxins
Poisons
7 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
271 Citations (Scopus)

Aryl hydrocarbon receptor ligands in cancer: Friend and foe

Murray, I. A., Patterson, A. D. & Perdew, G. H., Nov 24 2014, In : Nature Reviews Cancer. 14, 12, p. 801-814 14 p.

Research output: Contribution to journalReview article

Aryl Hydrocarbon Receptors
Ligands
Neoplasms
Carcinogenesis
Dioxins
155 Citations (Scopus)

A structural and functional perspective of alphavirus replication and assembly

Jose, J., Snyder, J. E. & Kuhn, R., Sep 23 2009, In : Future microbiology. 4, 7, p. 837-856 20 p.

Research output: Contribution to journalReview article

Alphavirus
Arthropods
Viruses
Alphavirus Infections
Ross River virus

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
59 Citations (Scopus)

A three-dimensional osteogenic tissue model for the study of metastatic tumor cell interactions with bone

Mastro, A. M. & Vogler, E. A., May 15 2009, In : Cancer Research. 69, 10, p. 4097-4100 4 p.

Research output: Contribution to journalReview article

Osteoblasts
Cell Communication
Bone and Bones
Bioreactors
Osteocytes
39 Citations (Scopus)

Auxiliary iron-sulfur cofactors in radical SAM enzymes

Lanz, N. D. & Booker, S. J., Jun 1 2015, In : Biochimica et Biophysica Acta - Molecular Cell Research. 1853, 6, p. 1316-1334 19 p.

Research output: Contribution to journalReview article

Sulfur
Methionine
Iron
Enzymes
Protein S
2 Citations (Scopus)

Back into the fold. Modernizing Croatian science and education

Primorac, D., Jul 1 2008, In : EMBO Reports. 9, 7, p. 596-599 4 p.

Research output: Contribution to journalReview article

International Cooperation
Croatia
Internet
Teaching
Education
345 Citations (Scopus)

Bacterial RNA polymerases: The wholo story

Murakami, K. S. & Darst, S. A., Feb 1 2003, In : Current Opinion in Structural Biology. 13, 1, p. 31-39 9 p.

Research output: Contribution to journalReview article

Bacterial RNA
DNA-Directed RNA Polymerases
Holoenzymes
47 Citations (Scopus)

Basal transcription factors

Reese, J. C., Jan 1 2003, In : Current Opinion in Genetics and Development. 13, 2, p. 114-118 5 p.

Research output: Contribution to journalReview article

RNA Polymerase II
Transcription Factors
1 Citation (Scopus)

Basic statistics.

Moore, J. H., Thornton, T. A. & Ritchie, M. D., Jan 1 2003, In : Current protocols in human genetics / editorial board, Jonathan L. Haines ... [et al.]. Appendix 3

Research output: Contribution to journalReview article

Software Design
Software
Datasets
3 Citations (Scopus)

Battle for the bulge: Directing small molecules to DNA and RNA defects

Bevilacqua, P. C., Jan 1 2002, In : Chemistry and Biology. 9, 8, p. 854-855 2 p.

Research output: Contribution to journalReview article

RNA
Defects
Molecules
DNA
Nucleotides
2 Citations (Scopus)

Between form and function: The complexity of genome folding

Oudelaar, A. M., Hanssen, L. L. P., Hardison, R. C., Kassouf, M. T., Hughes, J. R. & Higgs, D. R., Oct 1 2017, In : Human Molecular Genetics. 26, R2, p. R208-R215

Research output: Contribution to journalReview article

Chromatin
Genome
Globins
Multigene Family
DNA
62 Citations (Scopus)

Beyond ribosome rescue: tmRNA and co-translational processes

Hayes, C. S. & Keiler, K. C., Jan 21 2010, In : FEBS Letters. 584, 2, p. 413-419 7 p.

Research output: Contribution to journalReview article

Ribosomes
Protein folding
Peptides
Protein Folding
Transfer RNA
118 Citations (Scopus)

Beyond the Hofmeister Series: Ion-Specific Effects on Proteins and Their Biological Functions

Okur, H. I., Hladílková, J., Rembert, K. B., Cho, Y., Heyda, J., Dzubiella, J., Cremer, P. S. & Jungwirth, P., Mar 9 2017, In : Journal of Physical Chemistry B. 121, 9, p. 1997-2014 18 p.

Research output: Contribution to journalReview article

Ions
proteins
Proteins
ions
Salts
15 Citations (Scopus)

Bifunctional transfer-messenger RNA

Keiler, K. C. & Ramadoss, N. S., Nov 1 2011, In : Biochimie. 93, 11, p. 1993-1997 5 p.

Research output: Contribution to journalReview article

Transfer RNA
Messenger RNA
Bacteria
RNA
Gene Expression Regulation
77 Citations (Scopus)

Biochemical models for S-RNase-based self-incompatibility

Hua, Z. H., Fields, A. & Kao, T. H., Jul 2008, In : Molecular plant. 1, 4, p. 575-585 11 p.

Research output: Contribution to journalReview article

Pollen Tube
pollen tubes
Petunia integrifolia
Petunia
Solanaceae
10 Citations (Scopus)

Biochemistry of the oxidation of lignin by Phangerochate chrysosporium

Kirk, T. K., Tien, M. & Faison, B. D., 1984, In : Biotechnology Advances. 2, 2, p. 183-199 17 p.

Research output: Contribution to journalReview article

Chrysosporium
Biochemistry
Lignin
Oxidation
Oxygen
16 Citations (Scopus)

Bioinformatics approaches for detecting gene-gene and gene-environment interactions in studies of human disease.

Ritchie, M. D., Jan 1 2005, In : Neurosurgical Focus. 19, 4

Research output: Contribution to journalReview article

Gene-Environment Interaction
Nervous System Diseases
Computational Biology
Multifactor Dimensionality Reduction
Mental Disorders
96 Citations (Scopus)

Biological contexts for DNA charge transport chemistry

Merino, E. J., Boal, A. K. & Barton, J. K., Apr 1 2008, In : Current Opinion in Chemical Biology. 12, 2, p. 229-237 9 p.

Research output: Contribution to journalReview article

Charge transfer
DNA
DNA Repair
Mitochondria
Genome
153 Citations (Scopus)

Biology of trans-translation

Keiler, K. C., Oct 20 2008, In : Annual Review of Microbiology. 62, p. 133-151 19 p.

Research output: Contribution to journalReview article

Quality Control
Messenger RNA
Ribosomal Frameshifting
Bacteria
Ribonucleoproteins
13 Citations (Scopus)
Photosystem I Protein Complex
Membrane Proteins
Thermodynamics
Sulfur
Iron
51 Citations (Scopus)

Breast cancer cells induce osteoblast apoptosis: A possible contributor to bone degradation

Mastro, A. M., Gay, C. V., Welch, D. R., Donahue, H. J., Jewell, J., Mercer, R., DiGirolamo, D., Chislock, E. M. & Guttridge, K., Dec 1 2004, In : Journal of cellular biochemistry. 91, 2, p. 265-276 12 p.

Research output: Contribution to journalReview article

Osteoblasts
Bone
Cells
Apoptosis
Breast Neoplasms
14 Citations (Scopus)

Breast cancer metastasis to bone: Evolving models and research challenges

Welch, D. R., Harms, J. F., Mastro, A. M., Gay, C. V. & Donahue, H. J., Mar 1 2003, In : Journal of Musculoskeletal Neuronal Interactions. 3, 1, p. 30-38 9 p.

Research output: Contribution to journalReview article

Osteonectin
Parathyroid Hormone-Related Protein
Osteolysis
Osteopontin
Osteoclasts
128 Citations (Scopus)

Breast cancer metastasis to the bone: Mechanisms of bone loss

Chen, Y. C., Sosnoski, D. M. & Mastro, A. M., Dec 16 2010, In : Breast Cancer Research. 12, 6, 215.

Research output: Contribution to journalReview article

Osteoclasts
Osteoblasts
Breast Neoplasms
Neoplasm Metastasis
Bone and Bones
217 Citations (Scopus)

Catabolite activator protein: DNA binding and transcription activation

Lawson, C. L., Swigon, D., Murakami, K. S., Darst, S. A., Berman, H. M. & Ebright, R. H., Feb 2004, In : Current Opinion in Structural Biology. 14, 1, p. 10-20 11 p.

Research output: Contribution to journalReview article

Cyclic AMP Receptor Protein
Protein Binding
Transcriptional Activation
DNA
Protein C
120 Citations (Scopus)

Catalytic Roles for Proton Transfer and Protonation in Ribozymes

Bevilacqua, P. C., Brown, T. S., Nakano, S. I. & Yajima, R., Jan 1 2004, In : Biopolymers. 73, 1, p. 90-109 20 p.

Research output: Contribution to journalReview article

Catalytic RNA
Proton transfer
Protonation
Catalysis
Protons
29 Citations (Scopus)

Causes and consequences of nuclear envelope alterations in tumour progression

Bell, E. S. & Lammerding, J., Nov 1 2016, In : European journal of cell biology. 95, 11, p. 449-464 16 p.

Research output: Contribution to journalReview article

Nuclear Envelope
Lamin Type A
Neoplasms
Nuclear Proteins
Lamins
83 Citations (Scopus)

Ccr4-Not complex: The control freak of eukaryotic cells

Miller, J. E. & Reese, J. C., Jul 1 2012, In : Critical Reviews in Biochemistry and Molecular Biology. 47, 4, p. 315-333 19 p.

Research output: Contribution to journalReview article

Catabolite Repression
Eukaryotic Cells
Carbon
Gene expression
Messenger RNA