Category: 2015 WS Online Lectures

Introduction to RNA-seq – Paul Gardner

In this talk I will introduce the relatively new method for identifying and quantifying RNA, called RNA-seq. I will discuss different RNA-seq approaches, some exciting questions that are being tested with RNA-seq methods and some limitations of the method and … Read more


K-mers in metagenomics – Donovan Parks

K-mers play a critical role in the exploration of metagenomic data. They have been widely used to assign taxonomic attributions to the short genomic fragments characteristic of shotgun (metagenomic) sequencing. These approaches provide an assembly-free method for profiling microbial communities, … Read more


K-mers in genome assembly – Benjamin Woodcroft

K-mers are central to eukaryotic, microbial and metagenome assembly, with their use enabling genome assembly to be feasible. Given the central importance of k-mers there have been several recent advances. This talk will outline some of these advances, including the … Read more


Blue: correcting sequencing errors using k-mers – Paul Greenfield

Blue is an error-correction algorithm based on the concepts of k-mer consensus and context. Blue can correct substitution, deletion and insertion errors, as well as uncalled bases. It accepts both FASTQ and FASTA formats, and corrects quality scores for corrected … Read more


The distribution of the D2 statistic and its close relatives: A review – Conrad Burden

The D2 statistic is defined as the number of k-mer matches for some pre-specified length k between two sequences of letters. It is potentially a useful statistic for measuring similarity of DNA or protein sequences in cases where long alignments … Read more


Analysing correlated time-course data – Katya (Kathy) Ruggiero

Time-course experiments involve the collection of data through time and are used to study dynamic changes in a biological system or process, e.g. the molecular changes that occur during the progression of an acute disease such as sepsis. Temporal measurements … Read more


Statistical experiment design – basic principles for biological studies – Alexander (Alec) Zwart

“To consult the statistician after an experiment is finished is often merely to ask them to conduct a post mortem examination. They can perhaps say what the experiment died of.” ‐ Sir Ronald Aylmer Fisher, the “father of modern statistics”. … Read more


A web-based personal assistant for designing statistically sound experiments – Katya (Kathy) Ruggiero

“Right question. Wrong data!” Being advised that the data you have collected cannot answer the questions for which they were intended can be disastrous! These disasters can be avoided by carefully planning how an experiment will be conducted, placing particular … Read more


Big data in health care and biomedical research – John Quackenbush

Every major scientific and technological revolution in history has been driven by one thing: access to data. Today, the availability of Big Data from a wide variety of sources is transforming health and biomedical research into an information science, where … Read more


Using whole-genome sequencing to map mutations from mutagenic screens in zebrafish – Gregory Baillie

TThe zebrafish (Danio rerio) is a popular model for vertebrate development and genetics, due to its ease of maintenance, the ability to observe developmental aberrations in the early embryo, and the simplicity of mutagenesis techniques. The Hogan and Smith labs … Read more