Lectures

Chapter 1 of ZB Book

A Biology Primer for Computer Scientists (Franco P. Preparata)

Scitable definition of DNA Transcription

What is a Gene? Colinearity and Transcription Units

Translation: DNA to mRNA to Protein

Tandem Repeats and Morphological Variation

RNA Splicing: Introns, Exons and Spliceosome

DNA Sequencing Fact Sheet

Coming of age: ten years of next-generation sequencing technologies (Goodwin et al. 2016, Nature Reviews Genetics)

DNA sequencing at 40: past, present and future (Shendure et al. 2017 Nature)

Must Watch Video (How DNA is copied)

Must Watch Video (Sequencing by Synthesis)

Alignment of Next-Generation Sequencing Reads (Reinert et al. 2015, Annual Review of Genomics and Human Genetics)

k-mer wiki

Concept of Hashing

Scribe Note

8.1, 9.1 and 9.2 of Genome-Scale Algorithm Design Book

Chapter 9 of Bioinformatics algorithms: an active learning approach book

FM-index for dummies (Grabowski et al. 2015)

FM-Index

A tutorial on Burrows-Wheeler indexing methods part 1

A tutorial on Burrows-Wheeler indexing methods part 2

A tutorial on Burrows-Wheeler indexing methods part 3

Suffix Array Code

FM Index Code

Scribe Notes 6.1 & 6.2

Short Read Mapping: An Algorithmic Tour (Canzar and Salzberg 2015)

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome (Langmead et al. 2009, Genome Biology)

Fast gapped-read alignment with Bowtie 2 (Langmead and Salzberg 2012, Nature Methods)

Fast and accurate short read alignment with Burrows–Wheeler transform (Li and Durbin 2009, Bioinformatics)

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs (Zerbino & Birney 2008 Genome Research)

Overlap graphs and de Bruijn graphs: data structures for de novo genome assembly in the big data era (Rizzi et al. 2019)

Chapter 3 of Bioinformatics: Active learning book

Why are de Bruijn graphs useful for genome assembly? (Compeau et al. 2011)

RNA sequencing data: hitchhiker's guide to expression analysis (Van Den Berge, Koen, et al. 2019)

RNA-Seq gene expression estimation with read mapping uncertainty (Li et al. 2010, Bioinformatics)

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome (Li & Dewey 2011, BMC Bioinformatics)

Near-optimal probabilistic RNA-seq quantification (Bray et al. 2016, Nature Biotech)

salmon provides fast and bias-aware quantification of transcript expression (Patro et al. 2017, Nature Methods)

A scaling normalization method for differential expression analysis of rna-seq data (Robinson & Oshlack 2010, Genome Biology)