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Systems Biology and Bioinformatics

Computational approaches to analyzing biological systems

P
pipeline_bio 22 terms Jan 28, 2026
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Terms 22

1
Systems Biology
Integrative study of complex biological systems using mathematical modeling and data analysis
2
Genome
Complete genetic information of an organism; ~3 billion bp in humans; 20,000-25,000 genes
3
Transcriptome
Complete set of RNA transcripts; quantified by RNA-seq; reveals gene expression patterns
4
Proteome
Complete set of proteins; studied by mass spectrometry; more complex than genome due to modifications
5
Metabolome
Complete set of small-molecule metabolites; profiled by NMR or mass spec; functional readout of cell state
6
BLAST
Basic Local Alignment Search Tool; finds similar sequences in databases; E-value measures significance
7
Multiple Sequence Alignment
Aligns 3+ sequences simultaneously; MUSCLE, MAFFT; reveals conserved regions and phylogenetic signal
8
Phylogenetic Tree Construction
Maximum likelihood, Bayesian, neighbor-joining; infers evolutionary relationships from sequence data
9
RNA-seq
High-throughput sequencing of RNA; quantifies transcript abundance; requires normalization (RPKM, TPM)
10
Differential Expression Analysis
Identifies genes with significantly different expression between conditions; DESeq2, edgeR; FDR correction
11
Gene Ontology (GO)
Hierarchical controlled vocabulary for gene function; biological process, molecular function, cellular component
12
Pathway Analysis
Tests if genes cluster in known pathways; KEGG, Reactome; over-representation analysis
13
Protein Structure Prediction
AlphaFold2 (DeepMind) predicts 3D structure from sequence; near-experimental accuracy; revolutionized biology
14
ChIP-seq
Chromatin immunoprecipitation + sequencing; identifies protein-DNA binding sites across genome
15
ATAC-seq
Maps open chromatin (accessible DNA); identifies regulatory regions; used for single-cell epigenomics
16
Single-Cell RNA-seq (scRNA-seq)
Transcriptomics at single-cell resolution; reveals cell type heterogeneity; Seurat, Scanpy
17
UMAP/t-SNE
Dimensionality reduction for single-cell data; visualizes high-dimensional expression in 2D
18
Gene Regulatory Network
Map of transcription factor-target gene relationships; inferred from expression data and binding data
19
Protein-Protein Interaction Network
Graph of protein interactions; STRING, BioGRID; hub proteins often essential
20
Network Centrality
Betweenness, degree, eigenvector centrality; identifies important nodes in biological networks
21
Machine Learning in Bioinformatics
Random forests, neural networks for gene expression classification, variant effect prediction
22
SNP (Single Nucleotide Polymorphism)
Single base-pair variant; millions in human genome; used in GWAS, pharmacogenomics