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Feature screening plays a critical role in handling ultrahigh dimensional data analyses when the number of features exponentially exceeds the number of observations. It is increasingly common in biomedical res...
As regulators of gene expression, microRNAs (miRNAs) are increasingly recognized as critical biomarkers of human diseases. Till now, a series of computational methods have been proposed to predict new miRNA-di...
Genome-wide studies of DNA methylation across the epigenetic landscape provide insights into the heterogeneity of pluripotent embryonic stem cells (ESCs). Differentiating into embryonic somatic and germ cells,...
Transcriptome analysis by next-generation sequencing has become a popular technique in recent years. This approach is quite suitable for non-model organism study, as de novo assembly is independent of prior ge...
In shotgun proteomics, database searching of tandem mass spectra results in a great number of peptide-spectrum matches (PSMs), many of which are false positives. Quality control of PSMs is a multiple hypothesi...
In the last decade, a large number of common variants underlying complex diseases have been identified through genome-wide association studies (GWASs). Summary data of the GWASs are freely and publicly availab...
High-throughput sequencing experiments followed by differential expression analysis is a widely used approach for detecting genomic biomarkers. A fundamental step in differential expression analysis is to mode...
Whenever suitable template structures are not available, usage of fragment-based protein structure prediction becomes the only practical alternative as pure ab initio techniques require massive computational r...
Analysing whole genome bisulfite sequencing datasets is a data-intensive task that requires comprehensive and reproducible workflows to generate valid results. While many algorithms have been developed for tas...
An amendment to this paper has been published and can be accessed via the original article.
An amendment to this paper has been published and can be accessed via the original article.
Motility in bacteria forms the basis for taxis and is in some pathogenic bacteria important for virulence. Video tracking of motile bacteria allows the monitoring of bacterial swimming behaviour and taxis on t...
Network motifs are connectivity structures that occur with significantly higher frequency than chance, and are thought to play important roles in complex biological networks, for example in gene regulation, in...
Circular RNAs (circRNAs) are a newly appreciated class of non-coding RNA molecules. Numerous tools have been developed for the detection of circRNAs, however computational tools to perform downstream functiona...
While clinical trials are considered the gold standard for detecting adverse events, often these trials are not sufficiently powered to detect difficult to observe adverse events. We developed a preliminary ap...
The reconstruction of metabolic networks and the three-dimensional coverage of protein structures have reached the genome-scale in the widely studied Escherichia coli K-12 MG1655 strain. The combination of the tw...
Technological developments in the emerging field of spatial transcriptomics have opened up an unexplored landscape where transcript information is put in a spatial context. Clustering commonly constitutes a ce...
Cytochrome P450 monooxygenases (termed CYPs or P450s) are hemoproteins ubiquitously found across all kingdoms, playing a central role in intracellular metabolism, especially in metabolism of drugs and xenobiot...
Genomic islands are associated with microbial adaptations, carrying genomic signatures different from the host. Some methods perform an overall test to identify genomic islands based on their local features. H...
With the rapid development of single-cell RNA sequencing technology, it is possible to dissect cell-type composition at high resolution. A number of methods have been developed with the purpose to identify rar...
Quality assessment of protein tertiary structure prediction models, in which structures of the best quality are selected from decoys, is a major challenge in protein structure prediction, and is crucial to det...
Binary classification rules based on a small-sample of high-dimensional data (for instance, gene expression data) are ubiquitous in modern bioinformatics. Constructing such classifiers is challenging due to (a...
Breast cancer is one of the common kinds of cancer among women, and it ranks second among all cancers in terms of incidence, after lung cancer. Therefore, it is of great necessity to study the detection method...
The Sackin indexS of a rooted phylogenetic tree, defined as the sum of its leaves’ depths, is one of the most popular balance indices in phylogenetics, and Sackin’s paper (Syst Zool 21:225–6, 1972) is usually cit...
Nanopore sequencing is a rapidly developing third-generation sequencing technology, which can generate long nucleotide reads of molecules within a portable device in real-time. Through detecting the change of ...
Predicting of chemical compounds is one of the fundamental tasks in bioinformatics and chemoinformatics, because it contributes to various applications in metabolic engineering and drug discovery. The recent r...
Protein succinylation has recently emerged as an important and common post-translation modification (PTM) that occurs on lysine residues. Succinylation is notable both in its size (e.g., at 100 Da, it is one o...
Membrane transport proteins (transporters) play an essential role in every living cell by transporting hydrophilic molecules across the hydrophobic membranes. While the sequences of many membrane proteins are ...
Molecular characters have been added in integrative taxonomic approaches in recent years. Nevertheless, taxon diagnoses are still widely restricted to morphological characters. The inclusion of molecular chara...
G protein-coupled receptors (GPCRs) mediate a variety of important physiological functions, are closely related to many diseases, and constitute the most important target family of modern drugs. Therefore, the...
Typical experimental design advice for expression analyses using RNA-seq generally assumes that single-end reads provide robust gene-level expression estimates in a cost-effective manner, and that the addition...
After publication of this supplement article [1], it is requested the grant ID in the Funding section should be corrected from NSF grant IIS-7811367 to NSF grant IIS-1902617. Therefore, the correct ‘Funding’ s...
Detection of DNA copy number alterations (CNAs) is critical to understand genetic diversity, genome evolution and pathological conditions such as cancer. Cancer genomes are plagued with widespread multi-level ...
Recent years have witnessed an increasing interest in multi-omics data, because these data allow for better understanding complex diseases such as cancer on a molecular system level. In addition, multi-omics d...
The advent of mass cytometry has dramatically increased the parameter limit for immunological analysis. New approaches to analysing high parameter cytometry data have been developed to ease analysis of these c...
The study of cancer genomics continually matures as the number of patient samples sequenced increases. As more data is generated, oncogenic drivers for specific cancer types are discovered along with their ass...
Protein-protein interactions (PPIs) are fundamental in many biological processes and understanding these interactions is key for a myriad of applications including drug development, peptide design and identifi...
An important process for plant survival is the immune system. The induced systemic resistance (ISR) triggered by beneficial microbes is an important cost-effective defense mechanism by which plants are primed ...
Multiple co-inertia analysis (mCIA) is a multivariate analysis method that can assess relationships and trends in multiple datasets. Recently it has been used for integrative analysis of multiple high-dimensio...
High-throughput omics technologies have enabled the comprehensive reconstructions of genome-scale metabolic networks for many organisms. However, only a subset of reactions is active in each cell which differs...
Functional enrichment of genes and pathways based on Gene Ontology (GO) has been widely used to describe the results of various -omics analyses. GO terms statistically overrepresented within a set of a large n...
Epistasis is defined as the interaction between different genes when expressing a specific phenotype. The most common way to characterize an epistatic relationship is using a penetrance table, which contains t...
Hinge-bending movements in proteins comprising two or more domains form a large class of functional movements. Hinge-bending regions demarcate protein domains and collectively control the domain movement. Cons...
Microarray technology provides the expression level of many genes. Nowadays, an important issue is to select a small number of informative differentially expressed genes that provide biological knowledge and m...
Diseases like cancer will lead to changes in gene expression, and it is relevant to identify key regulatory genes that can be linked directly to these changes. This can be done by computing a Regulatory Impact...
Despite the great advance of protein structure prediction, accurate prediction of the structures of mainly β proteins is still highly challenging, but could be assisted by the knowledge of residue-residue pair...
Processing and analysis of DNA sequences obtained from next-generation sequencing (NGS) face some difficulties in terms of the correct prediction of DNA sequencing outcomes without the implementation of bioinf...
Admixed populations arise when two or more previously isolated populations interbreed. A powerful approach to addressing the genetic complexity in admixed populations is to infer ancestry. Ancestry inference i...
DNA damage accumulates over the course of cancer development. The often-substantial amount of somatic mutations in cancer poses a challenge to traditional methods to characterize tumors based on driver mutatio...
Hybrid capture-based next-generation sequencing of DNA has been widely applied in the detection of circulating tumor DNA (ctDNA). Various methods have been proposed for ctDNA detection, but low-allelic-fractio...
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Citation Impact 2023
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