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This paper presents a novel approach for Generative Anatomy Modeling Language (GAML). This approach automatically detects the geometric partitions in 3D anatomy that in turn speeds up integrated non-linear opt...
Several methods to handle data generated from bottom-up proteomics via liquid chromatography-mass spectrometry, particularly for peptide-centric quantification dealing with post-translational modification (PTM...
Reference genome selection is a prerequisite for successful analysis of next generation sequencing (NGS) data. Current practice employs one of the two most recent human reference genome versions: HG19 or HG38....
Gene families are sets of structurally and evolutionarily related genes – in one or multiple species – that typically share a conserved biological function. As such, the identification and subsequent analyses ...
The number of publicly available metagenomic experiments in various environments has been rapidly growing, empowering the potential to identify similar shifts in species abundance between different experiments...
Genetic structural variation underpins a multitude of phenotypes, with significant implications for a range of biological outcomes. Despite their crucial role, structural variants (SVs) are often neglected and...
A revolutionary diversion from classical vaccinology to reverse vaccinology approach has been observed in the last decade. The ever-increasing genomic and proteomic data has greatly facilitated the vaccine des...
Balancer chromosomes are tools used by fruit fly geneticists to prevent meiotic recombination. Recently, CRISPR/Cas9 genome editing has been shown capable of generating inversions similar to the chromosomal re...
Next-generation sequencing (NGS) technologies have produced large volumes of genomic data. One common operation on heterogeneous genomic data is genomic interval intersection. Most of the existing tools impose...
In bacterial genomes, there are two mechanisms to terminate the DNA transcription: the “intrinsic” or Rho-independent termination and the Rho-dependent termination. Intrinsic terminators are characterized by a...
Principal component analysis (PCA) is a standard method to correct for population stratification in ancestry-specific genome-wide association studies (GWASs) and is used to cluster individuals by ancestry. Usi...
RNA-seq, wherein RNA transcripts expressed in a sample are sequenced and quantified, has become a widely used technique to study disease and development. With RNA-seq, transcription abundance can be measured, ...
The standard genetic code is a recipe for assigning unambiguously 21 labels, i.e. amino acids and stop translation signal, to 64 codons. However, at early stages of the translational machinery development, the...
High-throughput sequencing often provides a foundation for experimental analyses in the life sciences. For many such methods, an intermediate layer of bioinformatics data analysis is the genomic signal track c...
As an important type of post-translational modification (PTM), protein glycosylation plays a crucial role in protein stability and protein function. The abundance and ubiquity of protein glycosylation across t...
Cell direct reprogramming technology has been rapidly developed with its low risk of tumor risk and avoidance of ethical issues caused by stem cells, but it is still limited to specific cell types. Direct repr...
Existing tools for the aggregation and visualization of differential expression data have discrete functionality and require that end-users rely on multiple software packages with complex dependencies or manua...
Blood pressure diseases have increasingly been identified as among the main factors threatening human health. How to accurately and conveniently measure blood pressure is the key to the implementation of effec...
The accurate determination of parent-progeny relationships within both in situ natural populations and ex situ genetic resource collections can greatly enhance plant breeding/domestication efforts and support ...
Recent comparative studies have brought to our attention how somatic mutation detection from next-generation sequencing data is still an open issue in bioinformatics, because different pipelines result in a lo...
A large fraction of human and mouse autosomal genes are subject to random monoallelic expression (MAE), an epigenetic mechanism characterized by allele-specific gene expression that varies between clonal cell ...
Group structures among genes encoded in functional relationships or biological pathways are valuable and unique features in large-scale molecular data for survival analysis. However, most of previous approache...
Ligand-binding proteins play key roles in many biological processes. Identification of protein-ligand binding residues is important in understanding the biological functions of proteins. Existing computational...
Accurate identification of perturbed signaling pathways based on differentially expressed genes between sample groups is one of the key factors in the understanding of diseases and druggable targets. Most path...
Next-Generation Sequencing (NGS) is now widely used in biomedical research for various applications. Processing of NGS data requires multiple programs and customization of the processing pipelines according to...
The investigation of intracellular metabolism is the mainstay in the biotechnology and physiology settings. Intracellular metabolic rates are commonly evaluated using labeling pattern of the identified metabol...
High-throughput amplicon sequencing of environmental DNA (eDNA metabarcoding) has become a routine tool for biodiversity survey and ecological studies. By including sample-specific tags in the primers prior PC...
Long non-coding RNAs play an important role in human complex diseases. Identification of lncRNA-disease associations will gain insight into disease-related lncRNAs and benefit disease diagnoses and treatment. ...
Protein ubiquitination occurs when the ubiquitin protein binds to a target protein residue of lysine (K), and it is an important regulator of many cellular functions, such as signal transduction, cell division...
The identification of prognostic genes that can distinguish the prognostic risks of cancer patients remains a significant challenge. Previous works have proven that functional gene sets were more reliable for ...
Prioritisation of gene ontology terms from differential gene expression analyses in a two-dimensional format remains a challenge with exponentially growing data volumes. Typically, gene ontology terms are repr...
Drug combinations have the potential to improve efficacy while limiting toxicity. To robustly identify synergistic combinations, high-throughput screens using full dose-response surface are desirable but requi...
Dynamic modelling is a core element in the systems biology approach to understanding complex biosystems. Here, we consider the problem of parameter estimation in models of biological oscillators described by d...
Life science research is moving quickly towards large-scale experimental designs that are comprised of multiple tissues, time points, and samples. Omic time-series experiments offer answers to three big questi...
Cell counting from cell cultures is required in multiple biological and biomedical research applications. Especially, accurate brightfield-based cell counting methods are needed for cell growth analysis. With ...
Functional annotation of genes is an essential step in omics data analysis. Multiple databases and methods are currently available to summarize the functions of sets of genes into higher level representations,...
Functional characterization of single nucleotide variants (SNVs) involves two steps, the first step is to convert DNA to protein and the second step is to visualize protein sequences with their structures. As ...
Genetic sequence database retrieval benchmarks play an essential role in evaluating the performance of sequence searching tools. To date, all phylogenetically diverse benchmarks known to the authors include on...
The advance of next generation sequencing enables higher throughput with lower price, and as the basic of high-throughput sequencing data analysis, variant calling is widely used in disease research, clinical ...
With the availability of well-assembled genomes of a growing number of organisms, identifying the bioinformatic basis of whole genome duplication (WGD) is a growing field of genomics. The most extant software ...
Biomarker discovery studies have been moving the focus from a single target gene to a set of target genes. However, the number of target genes in a drug should be minimum to avoid drug side-effect or toxicity....
Reconstruction of protein-protein interaction networks (PPIN) has been riddled with controversy for decades. Particularly, false-negative and -positive interactions make this progress even more complicated. Al...
Given the importance of relation or event extraction from biomedical research publications to support knowledge capture and synthesis, and the strong dependency of approaches to this information extraction tas...
A large number of computational methods have been proposed for predicting protein functions. The underlying techniques adopted by most of these methods revolve around predicting the functions of an unannotated...
Understanding the genetic networks and their role in chronic diseases (e.g., cancer) is one of the important objectives of biological researchers. In this work, we present a text mining system that constructs ...
Determining which target to pursue is a challenging and error-prone first step in developing a therapeutic treatment for a disease, where missteps are potentially very costly given the long-time frames and hig...
It is possible to predict whether a tuberculosis (TB) patient will fail to respond to specific antibiotics by sequencing the genome of the infecting Mycobacterium tuberculosis (Mtb) and observing whether the path...
Non-coding RNAs (ncRNAs) are emerging as key regulators and play critical roles in a wide range of tumorigenesis. Recent studies have suggested that long non-coding RNAs (lncRNAs) could interact with microRNAs...
Harmonization techniques make different gene expression profiles and their sets compatible and ready for comparisons. Here we present a new bioinformatic tool termed Shambhala for harmonization of multiple hum...
We previously reported on CERENKOV, an approach for identifying regulatory single nucleotide polymorphisms (rSNPs) that is based on 246 annotation features. CERENKOV uses the xgboost classifier and is designed...
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Citation Impact 2023
Journal Impact Factor: 2.9
5-year Journal Impact Factor: 3.6
Source Normalized Impact per Paper (SNIP): 0.821
SCImago Journal Rank (SJR): 1.005
Speed 2023
Submission to first editorial decision (median days): 12
Submission to acceptance (median days): 146
Usage 2023
Downloads: 5,987,678
Altmetric mentions: 4,858