History and Scope of Bioinformatics

This set of vocabulary flashcards covers the historical milestones, key pioneers, essential algorithms, and modern applications of bioinformatics as detailed in the lecture.

Bioinformatics

A multidimensional and interdisciplinary tool that extracts information from biological data using concepts of mathematics, physics, and chemistry for analysis with computational assistance.

Nuclein

A phosphorus-rich substance extracted from the nuclei of white blood cells by Friedrich Miescher in $1869$, which was later renamed nucleic acid.

Nucleotides

Identified by Phoebus Levene as the core building blocks of nucleic acids, consisting of a sugar, a phosphate group, and four nitrogenous bases.

Chargaff's Rules

The principle discovered by Erwin Chargaff that base ratios are conserved, with adenine pairing with thymine and guanine pairing with cytosine.

Margaret Dayhoff

Considered the founder of bioinformatics; she published the first collection of protein sequences in $1965$ and created the one-letter amino acid code and PAM scoring matrices.

Needleman-Wunsch Algorithm

A dynamic programming algorithm for global sequence alignment published by Saul Needleman and Christian Wunsch in $1970$.

Bioinformatic (Term)

A term coined in $1970$ by Ben Hesper and Pauline Hogeweg to describe the study of informatic processes in biotic systems.

Sanger Sequencing

The chain-termination method for sequencing DNA developed by Frederick Sanger in $1977$, frequently called the gold standard due to its $99.9\%$ accuracy.

Smith-Waterman Algorithm

A modification of the Needleman-Wunsch algorithm introduced in $1981$ by Temple Smith and Michael Waterman to allow for local sequence alignment.

GenBank

A public repository for DNA sequences established by the National Institutes of Health (NIH) in $1982$.

FASTA

An algorithm and format introduced by David Lipman and William Pearson in $1984$ that drastically sped up database searches.

NCBI

The National Center for Biotechnology Information, established in the US in $1988$ to oversee GenBank and develop molecular biology information systems.

BLAST

The Basic Local Alignment Search Tool, published in $1990$, used for rapid sequence database searching to identify regions of local similarity.

DNA Microarrays

A technology developed in $1994$ that allows for the simultaneous measurement of expression levels for thousands of genes, forming the field of transcriptomics.

Next-Generation Sequencing (NGS)

Massive parallel sequencing technologies, such as $454$ and Illumina, that entered the market in $2005$ and significantly reduced the cost of sequencing.

AlphaFold2

A breakthrough by DeepMind that solved the $50$-year-old protein folding problem in $2020$ by predicting $3D$ protein structures from amino acid sequences.

Multi-Omics

The integration of various data types including genomics, proteomics, metabolomics, and spatial transcriptomics for biological discovery.

De Bruijn Graphs

A genome assembly algorithm that breaks sequencing reads into smaller sequences known as k-mers.

Burrows-Wheeler Transform (BWT)

A string-matching algorithm that compresses data and enables fast mapping of short sequencing reads to a reference genome.

Hidden Markov Models (HMM)

Probabilistic models used in machine learning to model probability distributions over sequences of observed events.

UPGMA

Unweighted Pair Group Method with Arithmetic Mean; a simple hierarchical clustering method used to construct phylogenetic trees based on genetic distance.

Neighbor-Joining

A distance-based method for creating phylogenetic trees that corrects for varying rates of evolution across different lineages.

Drug Repurposing

The strategy of finding new therapeutic targets or indications for existing drugs, such as using Thalidomide for multiple myeloma.

MAKER

An automated genome annotation pipeline that integrates sequence alignment tools to annotate protein-coding genes and non-coding RNAs.

Gene Ontology (GO)

A standardized framework for gene product attributes, encompassing molecular functions, biological processes, and cellular components.

PLINK

A computational toolset designed for the analysis of large-scale genotype-phenotype data and association studies.

MEGA

Molecular Evolutionary Genetics Analysis; a software suite for sequence alignment, phylogenetic tree construction, and evolutionary hypothesis testing.