Phillip Compeau

Biological Modeling: A Short Tour offers readers a deep but concise exploration of topics in modeling biological systems at multiple scales. Each chapter poses a single biological question, from why zebras have stripes, to how bacteria explore their world intelligently, to why the SARS-CoV-2 spike protein was so effective at binding to human cells. The book then introduces the modeling concepts needed to answer this question. The book website (http://biologicalmodeling.org) provides a free… Show more

Biological Modeling: A Short Tour offers readers a deep but concise exploration of topics in modeling biological systems at multiple scales. Each chapter poses a single biological question, from why zebras have stripes, to how bacteria explore their world intelligently, to why the SARS-CoV-2 spike protein was so effective at binding to human cells. The book then introduces the modeling concepts needed to answer this question. The book website (http://biologicalmodeling.org) provides a free online course containing dozens of interactive tutorials allowing readers to build and explore the models introduced in this book. The course was produced with the help of talented students at Carnegie Mellon University who appear in the book as chapter co-authors. Show less

The double-cut-and-join operation (DCJ) is a fundamental graph operation that is used to model a variety of genome rearrangements. However, DCJs are only useful when comparing genomes with equal (or nearly equal) gene content. One obvious extension of the DCJ framework supplements DCJs with insertions and deletions of chromosomes and chromosomal intervals, which implies a model in which DCJs receive unit cost, whereas insertions and deletions receive a nonnegative cost of ω. This paper proposes… Show more

The double-cut-and-join operation (DCJ) is a fundamental graph operation that is used to model a variety of genome rearrangements. However, DCJs are only useful when comparing genomes with equal (or nearly equal) gene content. One obvious extension of the DCJ framework supplements DCJs with insertions and deletions of chromosomes and chromosomal intervals, which implies a model in which DCJs receive unit cost, whereas insertions and deletions receive a nonnegative cost of ω. This paper proposes a unified model finding a minimum-cost transformation of one genome (with circular chromosomes) into another genome for any value of ω. In the process, it resolves the open case ω > 1. Show less

Bioinformatics Algorithms: an Active Learning Approach is one of the first textbooks to emerge from the recent Massive Open Online Course (MOOC) revolution. A light-hearted and analogy-filled companion to the authors’ acclaimed Bioinformatics Specialization on Coursera (http://coursera.org/specializations/bioinformatics), this book presents students with a dynamic approach to learning bioinformatics. It strikes a unique balance between practical challenges in modern biology and fundamental… Show more

Bioinformatics Algorithms: an Active Learning Approach is one of the first textbooks to emerge from the recent Massive Open Online Course (MOOC) revolution. A light-hearted and analogy-filled companion to the authors’ acclaimed Bioinformatics Specialization on Coursera (http://coursera.org/specializations/bioinformatics), this book presents students with a dynamic approach to learning bioinformatics. It strikes a unique balance between practical challenges in modern biology and fundamental algorithmic ideas, thus capturing the interest of students of both biology and computer science.

Each chapter begins with a central biological question, such as “Are There Fragile Regions in the Human Genome?” or “Which DNA Patterns Play the Role of Molecular Clocks?” and then steadily develops the algorithmic sophistication required to answer this question. Hundreds of exercises are incorporated directly into the text as soon as they are needed; readers can test their knowledge through automated coding challenges on the Rosalind Bioinformatics Textbook Track (http://rosalind.info/problems/list-view/?location=bioinformatics-textbook-track). Show less

The introduction of the double cut and join operation (DCJ) caused a flurry of research into the study of multichromosomal rearrangements. However, little of this work has incorporated indels (i.e., insertions and deletions of chromosomes and chromosomal intervals) into the calculation of genomic distance functions, with the exception of Braga et al., who provided a linear time algorithm for the problem of DCJ-indel sorting. Although their algorithm only takes linear time, its derivation is… Show more

The introduction of the double cut and join operation (DCJ) caused a flurry of research into the study of multichromosomal rearrangements. However, little of this work has incorporated indels (i.e., insertions and deletions of chromosomes and chromosomal intervals) into the calculation of genomic distance functions, with the exception of Braga et al., who provided a linear time algorithm for the problem of DCJ-indel sorting. Although their algorithm only takes linear time, its derivation is lengthy and depends on a large number of possible cases. Show less

A mathematical concept known as a de Bruijn graph turns the formidable challenge of assembling a contiguous genome from billions of short sequencing reads into a tractable computational problem.

While we can read a book one letter at a time, biologists still lack the ability to read a DNA sequence one nucleotide at a time. Instead, they can identify short fragments (approximately 100 nucleotides long) called reads; however, they do not know where these reads are located within the genome. Thus, assembling a genome from reads is like putting together a giant puzzle with a billion pieces, a formidable mathematical problem. We introduce some of the fascinating history underlying both… Show more

While we can read a book one letter at a time, biologists still lack the ability to read a DNA sequence one nucleotide at a time. Instead, they can identify short fragments (approximately 100 nucleotides long) called reads; however, they do not know where these reads are located within the genome. Thus, assembling a genome from reads is like putting together a giant puzzle with a billion pieces, a formidable mathematical problem. We introduce some of the fascinating history underlying both the mathematical and the biological sides of DNA sequencing. Show less

We consider four families of pancake graphs, which are Cayley graphs, whose vertex sets are either the symmetric group on n objects or the hyperoctahedral group on n objects and whose generating sets are either all reversals or all reversals inverting the first k elements (called prefix reversals). We find that the girth of each family of pancake graphs remains constant after some small threshold value of n.

A paper appearing in an undergraduate math journal describing how E. coli bacteria could be programmed to solve an instance of a computational problem called the "burnt pancake problem", which asks for the fewest number of reversals required to sort a signed permutation.