Journal of Computational Biology

Lysine glycation is one of the most significant protein post-translational modifications, which changes the properties of the proteins and causes them to be dysfunctional. Accurately identifying glycation sites helps to understand the biological function and potential mechanism of glycation in disease treatments. Nonetheless, the experimental methods are ordinarily inefficient and costly, so effective computational methods need to be developed. In this study, we proposed the new model called iGly-IDN based on the improved densely connected convolutional networks (DenseNet)...

Due to uncertainty in tumor phylogeny inference from sequencing data, many methods infer multiple, equally plausible phylogenies for the same cancer. To summarize the solution space <mml:math xmlns:mml="https://www.w3.org/1998/Math/MathML"><mml:mstyle/><mml:mi>T</mml:mi></mml:math> of tumor phylogenies, consensus tree methods seek a single best representative tree S under a specified pairwise tree distance function. One such distance function is the ancestor-descendant (AD) distance [Formula: see text] , which equals the size of the symmetric difference of the transitive closures of the edge sets [Formula: see text] and [Formula: see text] ...

Intratumoral heterogeneity and the presence of cancer stem cells are challenging issues in cancer therapy. An appropriate quantification of the stemness of individual cells for assessing the potential for self-renewal and differentiation from the cell of origin can define a measurement for quantifying different cell states, which is important in understanding the dynamics of cancer evolution, and might further provide possible targeted therapies aimed at tumor stem cells. Nevertheless, it is usually difficult to quantify the stemness of a cell based on molecular information associated with the cell...

The analysis of gene expression data has made significant contributions to understanding disease mechanisms and developing new drugs and therapies. In such analysis, gene selection is often required for identifying informative and relevant genes and removing redundant and irrelevant ones. However, this is not an easy task as gene expression data have inherent challenges such as ultra-high dimensionality, biological noise, and measurement errors. This study focuses on the measurement errors in gene selection problems...

Interleukins (ILs) are a group of multifunctional cytokines, which play important roles in immune regulations and inflammatory responses. Recently, IL-6 has been found to affect the development of COVID-19, and significantly elevated levels of IL-6 cytokines have been reported in patients with severe COVID-19. IL-10 and IL-17 are anti-inflammatory and proinflammatory cytokines, respectively, which play multiple protective roles in host defense against pathogens. At present, a number of machine learning methods have been proposed to predict ILs inducing peptides, but their predictive performance needs to be further improved, and the inducing peptides of different ILs are predicted separately, rather than using a general approach...

Genetic component assembly is key in the simulation and implementation of genetic circuits. Automating this process, thus accelerating prototyping, is a necessity. We present pyBrick-DNA, a software written in Python, that assembles components for the construction of genetic circuits. pyBrick-DNA (colab.pyBrick.com) is a user-friendly environment where scientists can select genetic sequences or input custom sequences to build genetic assemblies. All components are modularly fused to generate a ready-to-go single DNA fragment...

Minimizers and syncmers are sketching methods that sample representative k -mer seeds from a long string. The minimizer scheme guarantees a well-spread k -mer sketch (high coverage) while seeking to minimize the sketch size (low density). The syncmer scheme yields sketches that are more robust to base substitutions (high conservation) on random sequences, but do not have the coverage guarantee of minimizers. These sketching metrics are generally adversarial to one another, especially in the context of sketch optimization for a specific sequence, and thus are difficult to be simultaneously achieved...

The itca Python package offers an information-theoretic criterion to assist practitioners in combining ambiguous outcome labels by balancing the tradeoff between prediction accuracy and classification resolution. This article provides instructions for installing the itca Python package, demonstrates how to evaluate the criterion, and showcases its application in real-world scenarios for guiding the combination of ambiguous outcome labels.

No abstract text is available yet for this article.

Statistical models that accurately predict the binding affinity of an input ligand-protein pair can greatly accelerate drug discovery. Such models are trained on available ligand-protein interaction data sets, which may contain biases that lead the predictor models to learn data set-specific, spurious patterns instead of generalizable relationships. This leads the prediction performances of these models to drop dramatically for previously unseen biomolecules. Various approaches that aim to improve model generalizability either have limited applicability or introduce the risk of degrading overall prediction performance...

Robust generalization of drug-target affinity (DTA) prediction models is a notoriously difficult problem in computational drug discovery. In this article, we present pydebiaseddta: a computational software for improving the generalizability of DTA prediction models to novel ligands and/or proteins. pydebiaseddta serves as the practical implementation of the DebiasedDTA training framework, which advocates modifying the training distribution to mitigate the effect of spurious correlations in the training data set that leads to substantially degraded performance for novel ligands and proteins...

Signaling and metabolic pathways, which consist of chains of reactions that produce target molecules from source compounds, are cornerstones of cellular biology. Properly modeling the reaction networks that represent such pathways requires directed hypergraphs , where each molecule or compound maps to a vertex, and each reaction maps to a hyperedge directed from its set of input reactants to its set of output products. Inferring the most likely series of reactions that produces a given set of targets from a given set of sources, where for each reaction its reactants are produced by prior reactions in the series, corresponds to finding a shortest hyperpath in a directed hypergraph, which is NP-complete...

We address the problem of rooting an unrooted species tree given a set of unrooted gene trees, under the assumption that gene trees evolve within the model species tree under the multispecies coalescent (MSC) model. Quintet Rooting (QR) is a polynomial time algorithm that was recently proposed for this problem, which is based on the theory developed by Allman, Degnan, and Rhodes that proves the identifiability of rooted 5-taxon trees from unrooted gene trees under the MSC. However, although QR had good accuracy in simulations, its statistical consistency was left as an open problem...

A pangenome graph can serve as a better reference for genomic studies because it allows a compact representation of multiple genomes within a species. Aligning sequences to a graph is critical for pangenome-based resequencing. The seed-chain-extend heuristic works by finding short exact matches between a sequence and a graph. In this heuristic, colinear chaining helps identify a good cluster of exact matches that can be combined to form an alignment. Colinear chaining algorithms have been extensively studied for aligning two sequences with various gap costs, including linear, concave, and convex cost functions...

Models of gene regulatory networks (GRNs) capture the dynamics of the regulatory processes that occur within the cell as a means to understanding the variability observed in gene expression between different conditions. Arguably the simplest mathematical construct used for modeling is the Boolean network, which dictates a set of logical rules for transition between states described as Boolean vectors. Due to the complexity of gene regulation and the limitations of experimental technologies, in most cases knowledge about regulatory interactions and Boolean states is partial...

The transposition distance problem is a classical problem in genome rearrangements, which seeks to determine the minimum number of transpositions needed to transform a linear chromosome into another represented by the permutations <mml:math xmlns:mml="https://www.w3.org/1998/Math/MathML"><mml:mi>π</mml:mi></mml:math> and <mml:math xmlns:mml="https://www.w3.org/1998/Math/MathML"><mml:mi>σ</mml:mi></mml:math>, respectively. This article focuses on the equivalent problem of sorting by transpositions (SBT), where <mml:math xmlns:mml="https://www...

In silico identification of long noncoding RNAs (lncRNAs) is a multistage process including filtering of transcripts according to their physical characteristics (e.g., length, exon-intron structure) and determination of the coding potential of the sequence. A common issue within this process is the choice of the most suitable method of coding potential analysis for the conducted research. Selection of tools on the sole basis of their single performance may not provide the most effective choice for a specific problem...

RNA secondary structures are essential abstractions for understanding spacial folding behaviors of those macromolecules. Many secondary structure algorithms involve a common dynamic programming setup to exploit the property that secondary structures can be decomposed into substructures. Dirks et al. noted that this setup cannot directly address an issue of distinguishability among secondary structures, which arises for classes of sequences that admit nontrivial symmetry. Circular sequences are among these. We examine the problem of counting distinguishable secondary structures...

This article deals with the numerical positivity, boundedness, convergence, and dynamical behaviors for stochastic susceptible-infected-susceptible (SIS) model. To guarantee the biological significance of the split-step backward Euler method applied to the stochastic SIS model, the numerical positivity and boundedness are investigated by the truncated Wiener process. Motivated by the almost sure boundedness of exact and numerical solutions, the convergence is discussed by the fundamental convergence theorem with a local Lipschitz condition...

In this article, we investigate the algebraic structure of double cyclic codes of length <mml:math xmlns:mml="https://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mo>(</mml:mo><mml:mrow><mml:mi>α</mml:mi><mml:mo>,</mml:mo><mml:mi>β</mml:mi></mml:mrow><mml:mo>)</mml:mo></mml:mrow></mml:math> over <mml:math xmlns:mml="https://www.w3.org/1998/Math/MathML"><mml:msub><mml:mrow><mml:mstyle><mml:mi>F</mml:mi></mml:mstyle></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub><mml:mo>+</mml:mo><mml:mi>u</mml:mi><mml:msub><mml:mrow><mml:mstyle><mml:mi>F</mml:mi></mml:mstyle></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:math> with <mml:math xmlns:mml="https://www...