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YHap: a population model for probabilistic assignment of Y haplogroups from re-sequencing data.
We developed a new algorithm, YHap, which uses an imputation framework to jointly predict Y chromosome genotypes and assign Y haplogroups using low coverage population sequence data. We use data from the 1000 genomes project to demonstrate that YHap provides accurate Y haplogroup assignment with les...
Evaluating a linear k-mer model for protein-DNA interactions using high-throughput SELEX data.
We implemented the standard cross-validation scheme to reduce the number of k-mers in the model and observed that the number of k-mers can often be reduced significantly without a great negative effect on prediction accuracy. We also found that the later SELEX enrichment cycles provide a much better...
Comparative studies of differential gene calling using RNA-Seq data.
We examined the performance of differential gene-calling methods using RNA-Seq data in practical situations. We focused on two representative methods: one parametric method, DESeq, and one nonparametric method, NOISeq. We examined their performance using both simulated and real datasets. Our simulat...
VarRanker: rapid prioritization of sequence variations associated with human disease.
We describe an algorithm and web-based application which take into account both the probability that a variant damages the function of a gene as well as the relevance of the gene to a given phenotype. Phenotypes are described by a list of scored terms supplied by the user. These terms are then used...
A study and benchmark of DNcon: a method for protein residue-residue contact prediction using deep networks.
We evaluated several sequence based residue-residue contact predictors that participated in the tenth Critical Assessment of protein Structure Prediction (CASP) experiment. The evaluation was performed using standard assessment techniques such as those used by the official CASP assessors as well as...
Argudas: lessons for argumentation in biology based on a gene expression use case
From the work described in this paper it is clear that for argumentation to be effective in the biological domain the argumentation community need to develop further the tools and resources they provide. Additionally, the biological community must tackle the incongruity between overlapping and adjac...
Correction: Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity.
PCI-SS: MISO dynamic nonlinear protein secondary structure prediction.
Using PSI-BLAST divergent evolutionary profiles as input data, dynamic nonlinear systems are built through a black-box approach to model the process of protein folding. Genetic algorithms (GAs) are applied in order to optimize the architectural parameters of the PCI models. The three-state predictio...
Comparison of sequence-dependent tiling array normalization approaches.
We compared three different sequence-dependent probe level normalization procedures to a naÃ¯ve sequence-independent normalization technique. In order to achieve maximal comparability, we used the normalized intensity values as input to a single peak detection algorithm. A so-called "spike-in" dat...
A novel R-package graphic user interface for the analysis of metabonomic profiles.
We made complex multivariate analysis user-friendly for both experienced and novice users, which could help to expand the use of NMR-based metabonomics....