Related papers: Optimal Haplotype Assembly from High-Throughput Ma…
Clinical adoption of human genome sequencing requires methods with known accuracy of genotype calls at millions or billions of positions across a genome. Previous work showing discordance amongst sequencing methods and algorithms has made…
The perennial problem of "how many clusters?" remains an issue of substantial interest in data mining and machine learning communities, and becomes particularly salient in large data sets such as populational genomic data where the number…
The usefulness of a `total-evidence' approach to human population genetics was assessed through a clustering analysis of combined genome-wide SNP datasets. The combination contained only 3146 SNPs. Detailed examination of the results…
Genome assembly is a prominent problem studied in bioinformatics, which computes the source string using a set of its overlapping substrings. Classically, genome assembly uses assembly graphs built using this set of substrings to compute…
In genetic studies, haplotype data provide more refined information than data about separate genetic markers. However, large-scale studies that genotype hundreds to thousands of individuals may only provide results of pooled data, where…
For a genomically unstable cancer, a single tumour biopsy will often contain a mixture of competing tumour clones. These tumour clones frequently differ with respect to their genomic content (copy number of each gene) and structure (order…
Correlation of gene histories in the human genome determines the patterns of genetic variation (haplotype structure) and is crucial to understanding genetic factors in common diseases. We derive closed analytical expressions for the…
We investigate the role of assortative mating in speciation using the sympatric model of Derrida and Higgs. The model explores the idea that genetic differences create incompatibilities between individuals, preventing mating if the number…
Inside a cell, heterotypic proteins assemble in inhomogeneous, crowded systems where the abundance of these proteins vary with cell types. While some protein complexes form putative structures that can be visualized with imaging, there are…
We study the genetic behaviour of a population formed by haploid individuals which reproduce asexually. The genetic information for each individual is stored along a bit-string (or chromosome) with L bits, where 0-bits represent the…
Structural variants compose the majority of human genetic variation, but are difficult to assess using current genomic sequencing technologies. Optical mapping technologies, which measure the size of chromosomal fragments between labeled…
The Minimum-Recombinant Haplotype Configuration problem (MRHC) has been highly successful in providing a sound combinatorial formulation for the important problem of genotype phasing on pedigrees. Despite several algorithmic advances and…
Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking…
Correspondence homomorphisms are both a generalization of standard homomorphisms and a generalization of correspondence colourings. For a fixed target graph $H$, the problem is to decide whether an input graph $G$, with each edge labeled by…
The Spliced Alignment Problem (SAP) that consists in finding an optimal semi-global alignment of a spliced RNA sequence on an unspliced genomic sequence has been largely considered for the prediction and the annotation of gene structures in…
The evolution of the full repertoire of proteins encoded in a given genome is mostly driven by gene duplications, deletions, and sequence modifications of existing proteins. Indirect information about relative rates and other intrinsic…
Whole-genome sequencing in an isolated population with few founders directly ascertains variants from the population bottleneck that may be rare elsewhere. In such populations, shared haplotypes allow imputation of variants in unsequenced…
About 2% of human genetic polymorphisms have been hypothesized to arise via multinucleotide mutations (MNMs), complex events that generate SNPs at multiple sites in a single generation. MNMs have the potential to accelerate the pace at…
We examine the distribution of heterozygous sites in nine European and nine Yoruban individuals whose genomic sequences were made publicly available by Complete Genomics. We show that it is possible to obtain detailed information about…
Polynomial systems occur in many areas of science and engineering. Unlike general nonlinear systems, the algebraic structure enables to compute all solutions of a polynomial system. We describe our massive parallel predictor-corrector…