[PhD] Bioinformatics 101
Want to get started with bioinformatics, but don't know how? Start here!
Ever felt overwhelmed with wanting to get into bioinformatics and not knowing where to start? I wrote the Bioinformatics Fundamentals 101 so you don’t have to be!
I enjoy creating guides for things that took me a long time to figure out so that others have to struggle less. This notion page provides a summary of courses, textbooks, and concrete skills you can learn, should you want to get started in bioinformatics.
Bioinformatics
Definition: Interdisciplinary field combining biology, computer science, and statistics to analyze biological data.
Techniques:
Sequence Alignment: Arranging sequences to identify similarities (e.g., BLAST). It helps in comparing DNA, RNA, or protein sequences to find evolutionary or functional relationships.
Protein Structure Prediction: Predicting the 3D structure of proteins from their amino acid sequences (e.g., AlphaFold). This is crucial for understanding protein function and interaction.
Gene Expression Analysis: Examining the levels of gene activity (e.g., RNA-seq). This technique measures the quantity and sequences of RNA to understand gene function and regulation.
Single-cell RNA-seq: Analyzing gene expression in individual cells. This provides insights into cellular diversity and functions within tissues.
Machine Learning: Using algorithms to analyze biological data. Machine learning helps in pattern recognition, predictions, and uncovering complex relationships within the data.
Analysis:
Annotation: Identifying and attaching biological information to genome elements, such as genes, proteins, and regulatory elements.
Statistical Analysis: Applying statistical methods and models to interpret complex biological data, enhancing the understanding of genetic and genomic phenomena.
Genomics
Definition: Study of genomes, the complete DNA set of an organism.
Techniques:
Whole-genome Sequencing: Determining the order of nucleotides in an entire genome. This provides comprehensive information about the genetic blueprint of an organism.
Comparative Genomics: Comparing genomes of different species to identify similarities and differences. This technique is used to understand evolutionary relationships and functional genomics.
Genome-wide Association Studies (GWAS): Identifying genetic variants associated with traits by scanning the genomes from many individuals. This is used to find genetic contributions to diseases and traits.
Phylogenetics: Study of evolutionary relationships using tools like LCA trees (Least Common Ancestor trees). Phylogenetics helps in understanding the evolutionary history and relationships among species.
Analysis:
Phylogenetic Tree Construction: Building evolutionary trees to illustrate relationships among various biological species or entities.
Identifying genetic variants: Detecting differences in DNA sequences among individuals that may contribute to different traits or diseases.
Mapping genes to traits: Linking specific genes to particular traits or diseases to understand genetic underpinnings.
Studying genome evolution: Analyzing changes in genomes over time to understand the mechanisms of evolution and adaptation.
Tools and Methods
Unix Shell: A command-line interface for interacting with the operating system, essential for running bioinformatics scripts and pipelines efficiently.
R Programming: A language and environment for statistical computing and graphics, widely used for analyzing and visualizing biological data.
Specialized Fields
Metagenomics: Study of genetic material recovered directly from environmental samples, providing insights into the microbial communities without the need for culturing.
Transcriptomics: Study of the complete set of RNA transcripts produced by the genome, providing insights into gene expression patterns and regulatory mechanisms.
Proteomics: Large-scale study of proteins, including their structures, functions, and interactions, essential for understanding cellular processes and disease mechanisms.
Do you have any questions? Did I miss a technique or get a definition wrong? Please let me know and I will update the post.