IEEE/ACM Transactions on Computational Biology and Bioinformatics

Ranked gene trees, which consider both the gene tree topology and the sequence in which gene lineages separate, can potentially provide a new source of information for use in modeling genealogies and performing inference of species trees. Recently, we ...

Controlling regions in cortical networks, which serve as key nodes to control the dynamics of networks to a desired state, can be detected by minimizing the eigenratio R and the maximum imaginary part \sigma of an extended connection matrix. Until now, ...

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 that have improved ...

Bioreductive drugs are a class of hypoxia selective drugs that are designed to eradicate the hypoxic fraction of solid tumors. Their activity depends upon a number of biological and pharmacological factors and we used a mathematical modeling approach to ...

Epithelia are sheets of connected cells that are essential across the animal kingdom. Experimental observations suggest that the dynamical behavior of many single-layered epithelial tissues has strong analogies with that of specific mechanical systems, ...

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Structural alignment has been shown to be an effective computational method to identify structural noncoding RNA (ncRNA) candidates as ncRNAs are known to be conserved in secondary structures. However, the complexity of the structural alignment ...

The accelerating increase in the biomedical literature makes keeping up with recent advances challenging for researchers thus making automatic extraction and discovery of knowledge from this vast literature a necessity. Building such systems requires ...

Biomarker identification and cancer classification are two closely related problems. In gene expression data sets, the correlation between genes can be high when they share the same biological pathway. Moreover, the gene expression data sets may contain ...

In many bioinformatics applications, it is important to assess and compare the performances of algorithms trained from data, to be able to draw conclusions unaffected by chance and are therefore significant. Both the design of such experiments and the ...

Side effect machines produce features for classifiers that distinguish different types of DNA sequences. They have the, as yet unexploited, potential to give insight into biological features of the sequences. We introduce several innovations to the ...

Protein-protein interaction (PPI) database curation requires text-mining systems that can recognize and normalize interactor genes and return a ranked list of PPI pairs for each article. The order of PPI pairs in this list is essential for ease of ...

Reconstructing the topology of a signaling network by means of RNA interference (RNAi) technology is an underdetermined problem especially when a single gene in the network is knocked down or observed. In addition, the exponential search space limits ...

In this work, the problem of representing a stochastic forward model output with respect to a large number of input parameters is considered. The methodology is applied to a stochastic reaction network of competence dynamics in Bacillus subtilis ...

A central biological process in all living organisms is gene translation. Developing a deeper understanding of this complex process may have ramifications to almost every biomedical discipline. Reuveni et al. recently proposed a new computational model ...

We present a comprehensive review on probabilistic arithmetic automata (PAAs), a general model to describe chains of operations whose operands depend on chance, along with two algorithms to numerically compute the distribution of the results of such ...

In order to perform successful diagnosis and treatment of cancer, discovering, and classifying cancer types correctly is essential. One of the challenging properties of class discovery from cancer data sets is that cancer gene expression profiles not ...

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Discovering network motifs could provide a significant insight into systems biology. Interestingly, many biological networks have been found to have a high degree of symmetry (automorphism), which is inherent in biological network topologies. The ...

Many emerging database applications entail sophisticated graph-based query manipulation, predominantly evident in large-scale scientific applications. To access the information embedded in graphs, efficient graph matching tools and algorithms have ...

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Ranking genes in functional networks according to a specific biological function is a challenging task raising relevant performance and computational complexity problems. To cope with both these problems we developed a transductive gene ranking method ...

An important objective of modeling biological phenomena is to develop therapeutic intervention strategies to move an undesirable state of a diseased network toward a more desirable one. Such transitions can be achieved by the use of drugs to act on some ...

Triplex forming oligonucleotides (TFOs) represent a class of drug candidates for antigene therapy. Based on strict criteria, we investigated the potential of 25 known oncogenes to be regulated by TFOs in the mRNA synthesis level and we report specific ...

In recent years a particular class of probabilistic graphical models—called topic models—has proven to represent an useful and interpretable tool for understanding and mining microarray data. In this context, such models have been almost only applied in ...

Nowadays storing data derived from deep sequencing experiments has become pivotal and standard compression algorithms do not exploit in a satisfying manner their structure. A number of reference-based compression algorithms have been developed but they ...

Given a set S of n strings, each of length \ell , and a nonnegative value d , we define a center string as a string of length \ell that has Hamming distance at most d from each string in S . The \#{\rm CLOSEST STRING} problem aims to determine the ...

"Pull moves” is a popular move set for lattice polymer model simulations. We show that the proof given for its reversibility earlier is flawed, and some moves are irreversible, which leads to biases in the parameters estimated from the simulations. We ...

In [CHECK END OF SENTENCE], the authors proposed a framework for automated clustering and visualization of biological data sets named AUTO-HDS. This letter is intended to complement that framework by showing that it is possible to get rid of a user-...