Swiftly Computing Center Strings

Background  

The center string (or closest string) problem is a classic computer science problem with important applications in computational biology. Given k input strings and a distance threshold d, we search for a string within Hamming distance at most d to each input string. This problem is NP complete.     

Gene finding in novel genomes

Background  

Computational gene prediction continues to be an important problem, especially for genomes with little experimental data.     

On the persistence of supplementary resources in biomedical publications

Background  

Providing for long-term and consistent public access to scientific data is a growing concern in biomedical research. One aspect of this problem can be demonstrated by evaluating the persistence of supplementary data associated with published biomedical papers.     

Categorizing and comparing psychophysical detection strategies based on biomechanical responses to short postural perturbations

Background  

A fundamental unsolved problem in psychophysical detection experiments is in discriminating guesses from the correct responses. This paper proposes a coherent solution to this problem by presenting a novel classification method that compares biomechanical and psychological responses.     

Theoretical analysis of the mechanisms of a gender differentiation in the propensity for orthostatic intolerance after spaceflight

Background  

A tendency to develop reentry orthostasis after a prolonged exposure to microgravity is a common problem among astronauts. The problem is 5 times more prevalent in female astronauts as compared to their male counterparts. The mechanisms responsible for this gender differentiation are poorly understood despite many detailed and complex investigations directed toward an analysis of the physiologic control systems involved.     

Constraint Logic Programming approach to protein structure prediction

Background  

The protein structure prediction problem is one of the most challenging problems in biological sciences. Many approaches have been proposed using database information and/or simplified protein models. The protein structure prediction problem can be cast in the form of an optimization problem. Notwithstanding its importance, the problem has very seldom been tackled by Constraint Logic Programming, a declarative programming paradigm suitable for solving combinatorial optimization problems.     

Effective ambiguity checking in biosequence analysis

Background  

Ambiguity is a problem in biosequence analysis that arises in various analysis tasks solved via dynamic programming, and in particular, in the modeling of families of RNA secondary structures with stochastic context free grammars. Several types of analysis are invalidated by the presence of ambiguity. As this problem inherits undecidability (as we show here) from the namely problem for context free languages, there is no complete algorithmic solution to the problem of ambiguity checking.     

Identification of biomarkers from mass spectrometry data using a "common" peak approach

Background  

Proteomic data obtained from mass spectrometry have attracted great interest for the detection of early-stage cancer. However, as mass spectrometry data are high-dimensional, identification of biomarkers is a key problem.     

Clustering gene expression data with a penalized graph-based metric

Background  

The search for cluster structure in microarray datasets is a base problem for the so-called "-omic sciences". A difficult problem in clustering is how to handle data with a manifold structure, i.e. data that is not shaped in the form of compact clouds of points, forming arbitrary shapes or paths embedded in a high-dimensional space, as could be the case of some gene expression datasets.     

ANMM4CBR: a case-based reasoning method for gene expression data classification

Background  

Accurate classification of microarray data is critical for successful clinical diagnosis and treatment. The "curse of dimensionality" problem and noise in the data, however, undermines the performance of many algorithms.     

HaploRec: efficient and accurate large-scale reconstruction of haplotypes

Background  

Haplotypes extracted from human DNA can be used for gene mapping and other analysis of genetic patterns within and across populations. A fundamental problem is, however, that current practical laboratory methods do not give haplotype information. Estimation of phased haplotypes of unrelated individuals given their unphased genotypes is known as the haplotype reconstruction or phasing problem.     

Identification of metabolic system parameters using global optimization methods

Background  

The problem of estimating the parameters of dynamic models of complex biological systems from time series data is becoming increasingly important.     

BioWarehouse: a bioinformatics database warehouse toolkit

Background  

This article addresses the problem of interoperation of heterogeneous bioinformatics databases.     

Tableau-based protein substructure search using quadratic programming

Background  

Searching for proteins that contain similar substructures is an important task in structural biology. The exact solution of most formulations of this problem, including a recently published method based on tableaux, is too slow for practical use in scanning a large database.     

IDSS: deformation invariant signatures for molecular shape comparison

Background  

The conventional superposition methods use an ordinary least squares (LS) fit for structural comparison of two different conformations of the same protein. The main problem of the LS fit that it is sensitive to outliers, i.e. large displacements of the original structures superimposed.     

Real time electrocardiogram QRS detection using combined adaptive threshold

Background  

QRS and ventricular beat detection is a basic procedure for electrocardiogram (ECG) processing and analysis. Large variety of methods have been proposed and used, featuring high percentages of correct detection. Nevertheless, the problem remains open especially with respect to higher detection accuracy in noisy ECGs     

An Entropy-based gene selection method for cancer classification using microarray data

Background  

Accurate diagnosis of cancer subtypes remains a challenging problem. Building classifiers based on gene expression data is a promising approach; yet the selection of non-redundant but relevant genes is difficult.     

Machine learning methods for metabolic pathway prediction

Background  

A key challenge in systems biology is the reconstruction of an organism's metabolic network from its genome sequence. One strategy for addressing this problem is to predict which metabolic pathways, from a reference database of known pathways, are present in the organism, based on the annotated genome of the organism.     

<Emphasis Type="Italic">M. tuberculosis</Emphasis> genotypic diversity and drug susceptibility pattern in HIV- infected and non-HIV-infected patients in northern Tanzania

Background  

Tuberculosis (TB) is a major health problem and HIV is the major cause of the increase in TB. Sub-Saharan Africa is endemic for both TB and HIV infection. Determination of the prevalence of M. tuberculosis strains and their drug susceptibility is important for TB control.     

A novel scoring function for discriminating hyperthermophilic and mesophilic proteins with application to predicting relative thermostability of protein mutants

Background  

The ability to design thermostable proteins is theoretically important and practically useful. Robust and accurate algorithms, however, remain elusive. One critical problem is the lack of reliable methods to estimate the relative thermostability of possible mutants.