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Boosting the extraction of elementary flux modes in genome-scale metabolic networks using the linear programming approach

AbstractMotivationElementary flux modes (EFMs) are a key tool for analyzing genome-scale metabolic networks, and several methods have been proposed to compute them. Among them, those based on solving linear programming (LP) problems are known to be very efficient if the main interest lies in computing large enough sets of EFMs.ResultsHere, we propose...

SpaCell: integrating tissue morphology and spatial gene expression to predict disease cells

AbstractMotivationSpatial transcriptomics (ST) technology is increasingly being applied because it enables the measurement of spatial gene expression in an intact tissue along with imaging morphology of the same tissue. However, current analysis methods for ST data do not use image pixel information, thus missing the quantitative links between gene...

EPIP: a novel approach for condition-specific enhancer–promoter interaction prediction

AbstractMotivationThe identification of enhancer–promoter interactions (EPIs), especially condition-specific ones, is important for the study of gene transcriptional regulation. Existing experimental approaches for EPI identification are still expensive, and available computational methods either do not consider or have low performance in predicting...

Sub-dominant principal components inform new vaccine targets for HIV Gag

AbstractMotivationPatterns of mutational correlations, learnt from patient-derived sequences of human immunodeficiency virus (HIV) proteins, are informative of biochemically linked networks of interacting sites that may enable viral escape from the host immune system. Accurate identification of these networks is important for rationally designing vaccines...

relax: the analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data

Bioinformatics, (2014) doi: 10.1093/bioinformatics/btu166

Corrigendum to: A new cis-acting regulatory element driving gene expression in the zebrafish pineal gland

Bioinformatics (2009) doi:10.1093/bioinformatics/btp031

Modelling G×E with historical weather information improves genomic prediction in new environments

AbstractMotivationInteraction between the genotype and the environment (G×E) has a strong impact on the yield of major crop plants. Although influential, taking G×E explicitly into account in plant breeding has remained difficult. Recently G×E has been predicted from environmental and genomic covariates, but existing works have not shown that generalization...

Protein multiple alignments: sequence-based versus structure-based programs

AbstractMotivationMultiple sequence alignment programs have proved to be very useful and have already been evaluated in the literature yet not alignment programs based on structure or both sequence and structure. In the present article we wish to evaluate the added value provided through considering structures.ResultsWe compared the multiple alignments...

Discovery of tandem and interspersed segmental duplications using high-throughput sequencing

AbstractMotivationSeveral algorithms have been developed that use high-throughput sequencing technology to characterize structural variations (SVs). Most of the existing approaches focus on detecting relatively simple types of SVs such as insertions, deletions and short inversions. In fact, complex SVs are of crucial importance and several have been...

Developing structural profile matrices for protein secondary structure and solvent accessibility prediction

AbstractMotivationPredicting secondary structure and solvent accessibility of proteins are among the essential steps that preclude more elaborate 3D structure prediction tasks. Incorporating class label information contained in templates with known structures has the potential to improve the accuracy of prediction methods. Building a structural profile...

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