Table 3.
Summary of biology and genetics concepts and methods
| Reference | Concepts | Method |
| Beck et al., 2007 | Global gene expression and shoot apical meristem | |
| Butler et al., 2008 | Microscopy | |
| Cattley and Arthur, 2007 | Multiple sequence alignment, PCR primer design, restriction mapping, evolution, phylogeny, gene detection, microarray analysis, protein structure and function prediction, proteomics, protein identification and characterization, motif searching, and sequence assembly | |
| Craddock et al., 2007 | Obtain pathogen information from Patho-Systems Resource Integration Center and Center for Pathogen Information | |
| Doom et al., 2003 | Chemistry, biochemistry, molecular biology, genetics, DNA sequencing, gene expression, X-ray crystallography, protein structure and function, gene structure and density, introns and exons, transposition and repetitive elements, introduction to gene microarrays, and proteomics | Comparative model of protein structure, DNA isolation, gel electrophoresis, molecular visualization, structural modeling, ligand screening, inhibition, and drug design |
| Feig and Jabri, 2002 | Exploring concepts of information content of different biopolymers, the relationship between primary sequence and tertiary structure, and how sequence conservation can be used to find an enzyme active site | |
| Fetrow and John, 2006 | Pairwise sequence alignment, protein secondary structure prediction, gene expression, gene prediction, and gene sequencing | |
| Fuselier et al., 2011 | Sequencing and PCR | NCBI and BLASTN |
| Goode and Trajkovski, 2007 | Organic chemistry | |
| Harmon et al., 2002 | Genomics and proteomics | DNA research and sequencing |
| Honts, 2003 | Phylogenetic trees, molecular biology, cellular biology, DNA sequence, protein structure and function, gene structure and expression, and genome | |
| Howard et al., 2007 | Biochemistry, genetics, cell biology, molecular biology, bacterial diversity, microbial genetics, microbiology, genes, protein sequence, protein structure, nucleotide sequence, amino acid sequence, DNA sequence, genetic mutation, and proteomics | |
| Hughey and Karplus, 2003 | Molecular biology, chemistry, biochemistry, organic chemistry, cell biology, basics of DNA, RNA, protein sequence and structure, enzymes, regulation, metabolism, amino acids, genomics, phylogeny, and proteomics | Biochemistry laboratory, protein structure prediction, mRNA expression analysis, gene finding, RNA prediction and alignment, X-ray crystallography, and NMR spectroscopy |
| Kane and Brewer, 2007 | Amino acids, nucleotides, genes, proteins, and single-nucleotide polymorphisms | Pairwise sequence alignments, multiple sequence alignments, and DNA microarray |
| Kane et al., 2006 | Single nucleotide polymorphisms, protein sequence and function, genomics, DNA microarrays, proteomics, and atomic force | Mass spectrometry and cellular imaging |
| Kerfeld and Scott, 2011 | Evolution and biological principles | BLAST |
| Khuri, 2008 | Genetics, molecular biology, biochemistry, genomics, and proteomics | Macromolecular structures and machines and DNA microarray technology |
| Koch and Fuellen, 2008 | Sequence/structure analysis, microarray data, and phylogenetic tree inference | |
| Krilowicz et al., 2007 | Molecular biology, biochemistry, genetics, microarrays, molecular life science, and bioethics | |
| Luo, 2013 | Data mining, DNA and protein sequence analysis, motif identification, gene structure prediction, tree construction, and protein structure visualization and analysis | PubMed searches, UniProt database queries, sequence alignments, dot plots, BLAST, WebLab, Jemboss, MEGA, and SPDBV |
| Medin and Nolin, 2011 | Primers and data mining | Blast, GenBank, Protein Data Bank, Science Direct, PubMed |
| Miskowski et al., 2007 | Biology, transcription, translation, mutations, microbiology, genetics, evolutionary conservation, biochemistry, protein structure and function, enzyme kinetics, cell biology, phylogeny, protein sequence alignments, conserved protein domains, molecular biology, genomics, developmental biology, model organisms/comparative genomics, bacterial diversity, diversity of morphologies, physiologies and ecological niches throughout the microbial phylogenetic tree, DNA replication, structural RNA, and proteomics | Gene expression |
| MacMullen and Denn, 2005 | Microarray gene expression, gene function, and molecular biology | |
| Nehm and Budd, 2006 | Evolution, geochemistry, molecular biology, paleobiology, and genetics | |
| Nichols et al., 2003 | Illustrate the different percentage of guanine-cytosine content present in the same gene across various organisms; variations in codon usage for each amino acid among organisms; relationships between nucleotide frequency, codon usage, and melting temperatures; and building phylogenetic trees based on a single gene from different organisms | |
| Obom and Cummings, 2009 | Molecular biology, cell biology, human genetics, immunology, stem cell biology, proteomics, microbial genomics, molecular structure, and systems biology | Gene organization and expression, genome analysis, microarrays and analysis, and simulation of biological complex systems |
| Perez-Iratxeta et al., 2007 | Genomics and protein sequences | DNA microarray data |
| Rao et al., 2008 | Genomics | DNA microarray technology and gene-specific measurements and detections |
| Robertson and Phillips, 2008 | PCR | |
| Sahinidis et al., 2005 | Proteomics, metabolic networks, biochemistry, molecular biology, cell biology, organic chemistry, and genomics | DNA microarray data, complex feedback and control mechanisms |
| Saier, 2003 | Bioinformatic and biosystematic approaches to address fundamental questions about transmembrane transport systems and to develop probable answers based on systematic phylogenetic analyses | Bioinformatic tools applied to macromolecular evolution |
| Tolvanen and Vihinen, 2004 | Biochemistry, molecular biology, proteins, and DNA | |
| Toth and Connelly, 2006 | Molecular biology | |
| Wefer and Sheppard, 2008 | Evolution, nucleotide sequences, amino acid sequences, DNA sequences, and mutations and variations | Evolutionary models |
| Wightman and Hark, 2012 | Data mining and sequences | PubMed, NCBI, OMIM, and Blast |
| Yang et al., 2008 | Transmembrane proteins, amino acid, amino acid pair composition, RNA, and RNase digestion | Microarray data analysis, Bayesian biclustering model, Gibbs sampling procedure, protein structure prediction and classification, and protein disorder predictor |
| Yang and Zhang, 2008 | Protein structure and function and genomes | Sequence analysis, pairwise sequence alignment, multiple sequence alignment, protein structure comparison and classification, protein structure prediction, and gene expression |
| Zhang et al., 2007 | PCR, DNA, theory of molecular evolution, comparative genomics, phylogenetic trees, sequence alignment, biochemistry, and biology | Isolation of cell DNA and preparation of PCRs |