About State-of-the-Art Bioinformatics: From Sequencing Reads to Predicted Biology

Maximum-Likelihood Phylogenetic Inference AlphaFold2: Evolutionary Couplings, the Evoformer, and End-to-End Structure Local Pairwise Sequence Alignment: The Smith-Waterman Algorithm Profile Hidden Markov Models for Protein Family Search Substitution Matrices: Scoring Amino Acid Change with PAM and BLOSUM AlphaFold3: Diffusion-Based Prediction of Biomolecular Complexes Variant Calling: From Bayesian Genotypers to DeepVariant Long-Read Sequencing and Haplotype-Resolved Assembly Short-Read Mapping with the Burrows-Wheeler Transform and FM-Index De Novo Genome Assembly with de Bruijn Graphs Pangenome Graphs: Beyond a Single Linear Reference Protein Language Models: ESM and Learned Sequence Representations BLAST Algorithm Sequencing Reads and the FASTQ Format RNA-seq Quantification and Differential Expression Single-Cell Foundation Models: scGPT and Geneformer Multiple Sequence Alignment Single-Cell RNA-seq: From Count Matrix to Cell Types BLAST Sequence Search Reproducible Bioinformatics Workflows with Nextflow and Containers Global Pairwise Sequence Alignment: The Needleman-Wunsch Algorithm in EMBL-EBI Variant Effect Prediction with Genomic Foundation Models Genomic Foundation Models: DNABERT, Nucleotide Transformer, and Evo Spatial Transcriptomics: Expression With Coordinates Attached