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Clustering of protein sequences is of key importance in predicting the structure and function of newly sequenced proteins and is also of use for their annotation. With the advent of multiple high-throughput se...
The nearest neighbor model and associated dynamic programming algorithms allow for the efficient estimation of the RNA secondary structure Boltzmann ensemble. However because a given RNA secondary structure on...
Integration of transcriptomic and metabolomic data improves functional interpretation of disease-related metabolomic phenotypes, and facilitates discovery of putative metabolite biomarkers and gene targets. Fo...
When many (up to millions) of statistical tests are conducted in discovery set analyses such as genome-wide association studies (GWAS), approaches controlling family-wise error rate (FWER) or false discovery r...
Automated bioinformatics workflows are more robust, easier to maintain, and results more reproducible when built with command-line utilities than with custom-coded scripts. Command-line utilities further benef...
The application of high-throughput sequencing in a broad range of quantitative genomic assays (e.g., DNA-seq, ChIP-seq) has created a high demand for the analysis of large-scale read-count data. Typically, the...
In the field of biomarker validation with mass spectrometry, controlling the technical variability is a critical issue. In selected reaction monitoring (SRM) measurements, this issue provides the opportunity o...
Quantitative trait locus (QTL) mapping in genetic data often involves analysis of correlated observations, which need to be accounted for to avoid false association signals. This is commonly performed by model...
The exponential accumulation of new sequences in public databases is expected to improve the performance of all the approaches for predicting protein structural and functional features. Nevertheless, this was ...
Fungi have diverse biotechnological applications in, among others, agriculture, bioenergy generation, or remediation of polluted soil and water. In this context, culture media based on color change in response...
Crm1-dependent Nuclear Export Signals (NESs) are clusters of alternating hydrophobic and non-hydrophobic amino acid residues between 10 to 15 amino acids in length. NESs were largely thought to follow simple c...
Pathological angiogenesis has been identified in many malignancies as a potential prognostic factor and target for therapy. In most cases, angiogenic analysis is based on the measurement of microvessel density...
Protein crystal structures are potentially over-interpreted since they are routinely refined without any restraint on the upper limit of atomic B-factors. Consequently, some of their atoms, undetected in the e...
Prioritization of sequence variants for diagnosis and discovery of Mendelian diseases is challenging, especially in large collections of whole genome sequences (WGS). Fast, scalable solutions are needed for di...
The analysis of modular gene co-expression networks is a well-established method commonly used for discovering the systems-level functionality of genes. In addition, these studies provide a basis for the disco...
The haplotype assembly problem for diploid is to find a pair of haplotypes from a given set of aligned Single Nucleotide Polymorphism (SNP) fragments (reads). It has many applications in association studies, d...
The read length of single-molecule DNA sequencers is reaching 1 Mb. Popular alignment software tools widely used for analyzing such long reads often take advantage of single-instruction multiple-data (SIMD) op...
DNA damage causes aging, cancer, and other serious diseases. The comet assay can detect multiple types of DNA lesions with high sensitivity, and it has been widely applied. Although comet assay platforms have ...
While next-generation sequencing (NGS) costs have fallen in recent years, the cost and complexity of computation remain substantial obstacles to the use of NGS in bio-medical care and genomic research. The rap...
Bioinformatics research for finding biological mechanisms can be done by analysis of transcriptome data with pathway based interpretation. Therefore, researchers have tried to develop tools to analyze transcri...
LncRNAs are long regulatory non-coding RNAs, some of which are arguably predicted to have coding potential. Despite coding potential classifiers that utilize ribosome profiling data successfully detected activ...
Aberrant mutations in KRAS play a critical role in tumor initiation and progression, and are a negative prognosis factor in lung adenocarcinoma (LUAD).
Since many proteins become functional only after they interact with their partner proteins and form protein complexes, it is essential to identify the sets of proteins that form complexes. Therefore, several c...
It is known that functional RNAs often switch their functions by forming different secondary structures. Popular tools for RNA secondary structures prediction, however, predict the single ‘best’ structures, an...
The function of many noncoding RNAs (ncRNAs) depend upon their secondary structures. Over the last decades, several methodologies have been developed to predict such structures or to use them to functionally a...
Small RNA molecules play important roles in many biological processes and their dysregulation or dysfunction can cause disease. The current method of choice for genome-wide sRNA expression profiling is deep se...
Completion of genome-scale flux-balance models using computational reaction gap-filling is a widely used approach, but its accuracy is not well known.
The ease at which influenza virus sequence data can be used to estimate antigenic relationships between strains and the existence of databases containing sequence data for hundreds of thousands influenza strai...
Long read sequencing is changing the landscape of genomic research, especially de novo assembly. Despite the high error rate inherent to long read technologies, increased read lengths dramatically improve the con...
Prioritizing disease genes is trying to identify potential disease causing genes for a given phenotype, which can be applied to reveal the inherited basis of human diseases and facilitate drug development. Our...
The advent of modern high-throughput genetics continually broadens the gap between the rising volume of sequencing data, and the tools required to process them. The need to pinpoint a small subset of functiona...
The associations between genes and diseases are of critical significance in aspects of prevention, diagnosis and treatment. Although gene-disease relationships have been investigated extensively, much of the u...
Over the last few decades, computational genomics has tremendously contributed to decipher biology from genome sequences and related data. Considerable effort has been devoted to the prediction of transcriptio...
The correct determination of protein–protein interaction interfaces is important for understanding disease mechanisms and for rational drug design. To date, several computational methods for the prediction of ...
Consumers increasingly use online resources for their health information needs. While current search engines can address these needs to some extent, they generally do not take into account that most health inf...
Word representations support a variety of Natural Language Processing (NLP) tasks. The quality of these representations is typically assessed by comparing the distances in the induced vector spaces against hum...
Genomic islands play an important role in microbial genome evolution, providing a mechanism for strains to adapt to new ecological conditions. A variety of computational methods, both genome-composition based ...
Identification of differentially methylated regions (DMRs) is the initial step towards the study of DNA methylation-mediated gene regulation. Previous approaches to call DMRs suffer from false prediction, use ...
Application Programming Interfaces (APIs) are now widely used to distribute biological data. And many popular biological APIs developed by many different research teams have adopted Javascript Object Notation ...
Protein structure can be described by backbone torsion angles: rotational angles about the N-Cα bond (φ) and the Cα-C bond (ψ) or the angle between Cαi-1-Cαi-Cαi + 1 (θ) and the rotational angle about the Cαi-Cαi...
The clinical sequencing of cancer genomes to personalize therapy is becoming routine across the world. However, concerns over patient re-identification from these data lead to questions about how tightly acces...
Biocatalysis in organic solvents is nowadays a common practice with a large potential in Biotechnology. Several studies report that proteins which are co-crystallized or soaked in organic solvents preserve the...
Genome assemblies across all domains of life are being produced routinely. Initial analysis of a new genome usually includes annotation and comparative genomics. Synteny provides a framework in which conservat...
GenIO is a novel web-server, designed to assist clinical genomics researchers and medical doctors in the diagnostic process of rare genetic diseases. The tool identifies the most probable variants causing a ra...
Protein or nucleic acid sequences contain a multitude of associated annotations representing continuous sequence elements (CSEs). Comparing these CSEs is needed, whenever we want to match identical annotations...
The uncovering of genes linked to human diseases is a pressing challenge in molecular biology and precision medicine. This task is often hindered by the large number of candidate genes and by the heterogeneity...
Contact-guided protein structure prediction methods are becoming more and more successful because of the latest advances in residue-residue contact prediction. To support contact-driven structure prediction, e...
Molecular biomarkers that can predict drug efficacy in cancer patients are crucial components for the advancement of precision medicine. However, identifying these molecular biomarkers remains a laborious and ...
The consensus emerging from the study of microbiomes is that they are far more complex than previously thought, requiring better assemblies and increasingly deeper sequencing. However, current metagenomic asse...
Feature selection is commonly employed for identifying collectively-predictive biomarkers and biosignatures; it facilitates the construction of small statistical models that are easier to verify, visualize, an...
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Citation Impact 2023
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