Archives

Haplotype-based prediction of gene alleles using pedigrees and SNP genotypes, Yuri Pirola, ACM-BCB 2013 (slides). Computational methods for gene allele prediction have been proposed to substitute dedicated and expensive assays with cheaper in-silico analyses that operate on routinely collected data, such as SNP genotypes. Most of these methods are tailored to the needs and characteristics […]

A fast and practical approach to genotype phasing and imputation on a pedigree with erroneous and incomplete information, Yuri Pirola, ICCABS 2012. This work proposes the Min-Recombinant Haplotype Configuration with Bounded Errors problem (MRHCE), which extends the original Min-Recombinant Haplotype Configuration formulation by incorporating two common characteristics of real data: errors and missing genotypes (including […]

PIntron: a fast method for gene structure prediction via maximal pairings of a pattern and a text, Yuri Pirola, ICCABS 2011 (slides). In this work, we propose a novel pipeline for computational gene-structure prediction based on spliced alignment of expressed sequences (ESTs and mRNAs). This pipeline, called PIntron, is composed by four steps: Firstly, alternative […]

Haplotype Inference on Pedigrees with Recombinations and Mutations, Yuri Pirola, WABI 2010 (slides). The work proposes a new combinatorial formulation for haplotype inference on general pedigrees that generalizes the existing combinatorial ones to a more realistic settings. We prove an approximation-preserving reduction from this problem, called Minimum Change Haplotype Configuration (MCHC), to a well-known coding […]

Pure Parsimony Xor Haplotyping, Yuri Pirola, ISBRA 2009 (slides). In this work we addressed the problem of haplotype inference from xor genotypes under the pure parsimony assumption. Exact algorithms for restricted instances, a fixed parameter algorithm, an approximation algorithm, and an effective heuristic have been proposed. A prototypical implementation of the heuristic is freely available […]

Minimum Factorization Agreement of Spliced ESTs, Yuri Pirola, WABI 2009 (slides). The work presents a new parsimony-based formulation for the problem of choosing the best alignment of an expressed sequence against a genomic sequence exploiting the redundancy of current expressed sequence databases. A preliminary experimental evaluation of the formulation and the related algorithm shows their […]