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Light microscopic analysis of diatom frustules is widely used both in basic and applied research, notably taxonomy, morphometrics, water quality monitoring and paleo-environmental studies. In these application...
Whole-genome bisulfite sequencing currently provides the highest-precision view of the epigenome, with quantitative information about populations of cells down to single nucleotide resolution. Several studies ...
The life-science community faces a major challenge in handling “big data”, highlighting the need for high quality infrastructures capable of sharing and publishing research data. Data preservation, analysis, a...
Identification of protein-protein interactions (PPIs) is essential for a better understanding of biological processes, pathways and functions. However, experimental identification of the complete set of PPIs i...
Chickpea (Cicer arietinum) is a widely grown legume crop in tropical, sub-tropical and temperate regions. Molecular breeding approaches seem to be essential for enhancing crop productivity in chickpea. Until rece...
The recent introduction of the Pacific Biosciences RS single molecule sequencing technology has opened new doors to scaffolding genome assemblies in a cost-effective manner. The long read sequence information ...
Despite increased investment in pharmaceutical research and development, fewer and fewer new drugs are entering the marketplace. This has prompted studies in repurposing existing drugs for use against diseases...
Differential gene expression patterns in cells of the mammalian brain result in the morphological, connectional, and functional diversity of cells. A wide variety of studies have shown that certain genes are e...
Mass spectrometry-based metabolomic analysis depends upon the identification of spectral peaks by their mass and retention time. Statistical analysis that follows the identification currently relies on one mai...
In quantitative proteomics, peptide mapping is a valuable approach to combine positional quantitative information with topographical and domain information of proteins. Quantitative proteomic analysis of cell ...
Parsimony and maximum likelihood methods of phylogenetic tree estimation and parsimony methods for genome rearrangements are central to the study of genome evolution yet to date they have largely been pursued ...
In many applications, a family of nucleotide or protein sequences classified into several subfamilies has to be modeled. Profile Hidden Markov Models (pHMMs) are widely used for this task, modeling each subfam...
Developing suitable methods for the identification of protein complexes remains an active research area. It is important since it allows better understanding of cellular functions as well as malfunctions and i...
Non-specific feature selection is a dimension reduction procedure performed prior to cluster analysis of high dimensional molecular data. Not all measured features are expected to show biological variation, so...
Detection of large genomic rearrangements, such as large indels, duplications or translocations is now commonly achieved by next generation sequencing (NGS) approaches. Recently, several tools have been develo...
The characterization of protein binding sites is a major challenge in computational biology. Proteins interact with a wide variety of molecules and understanding of such complex interactions is essential to ga...
Gut microbiome metagenomics has revealed many protein families and domains found largely or exclusively in that environment. Proteins containing the GxGYxYP domain are over-represented in the gut microbiota, a...
Genome-wide association studies have revealed that rare variants are responsible for a large portion of the heritability of some complex human diseases. This highlights the increasing importance of detecting a...
Schizophrenia is a severe brain disorder, and SNPs (Single nucleotide polymorphism) in schizophrenia-associated miRNAs are believed to be one of the important reasons for dysregulation which might contribute t...
DNA methylation (DNAm) has important regulatory roles in many biological processes and diseases. It is the only epigenetic mark with a clear mechanism of mitotic inheritance and the only one easily available o...
RNA interference (RNAi) is an effective and important tool used to study gene function. For large-scale screens, RNAi is used to systematically down-regulate genes of interest and analyze their roles in a biol...
Meganucleases are important tools for genome engineering, providing an efficient way to generate DNA double-strand breaks at specific loci of interest. Numerous experimental efforts, ranging from in vivo selectio...
Data on single-nucleotide polymorphisms (SNPs) have been found to be useful in predicting phenotypes ranging from an individual’s class membership to his/her risk of developing a disease. In multi-class classi...
Accurate computational identification of eukaryotic gene organization is a long-standing problem. Despite the fundamental importance of precise annotation of genes encoded in newly sequenced genomes, the accur...
Transcriptome sequencing is a powerful tool for measuring gene expression, but as well as some other technologies, various artifacts and biases affect the quantification. In order to correct some of them, seve...
The significant growth in the volume of electronic biomedical data in recent decades has pointed to the need for approximate string matching algorithms that can expedite tasks such as named entity recognition,...
Identification of protein complexes can help us get a better understanding of cellular mechanism. With the increasing availability of large-scale protein-protein interaction (PPI) data, numerous computational ...
Erroneous patient birthdates are common in health databases. Detection of these errors usually involves manual verification, which can be resource intensive and impractical. By identifying a frequent manifesta...
The high demanding computational requirements necessary to carry out protein motion simulations make it difficult to obtain information related to protein motion. On the one hand, molecular dynamics simulation...
Supertrees combine disparate, partially overlapping trees to generate a synthesis that provides a high level perspective that cannot be attained from the inspection of individual phylogenies. Supertrees can be...
Adapter trimming is a prerequisite step for analyzing next-generation sequencing (NGS) data when the reads are longer than the target DNA/RNA fragments. Although typically used in small RNA sequencing, adapter...
Various computer-based methods exist for the detection and quantification of protein spots in two dimensional gel electrophoresis images. Area-based methods are commonly used for spot quantification: an area i...
As resequencing projects become more prevalent across a larger number of species, accurate variant identification will further elucidate the nature of genetic diversity and become increasingly relevant in geno...
Understanding the molecular mechanisms involved in disease is critical for the development of more effective and individualized strategies for prevention and treatment. The amount of disease-related literature...
The ability of science to produce experimental data has outpaced the ability to effectively visualize and integrate the data into a conceptual framework that can further higher order understanding. Multidimens...
Networks of interacting genes and gene products mediate most cellular and developmental processes. High throughput screening methods combined with literature curation are identifying many of the protein-protei...
Ongoing advancements in cloud computing provide novel opportunities in scientific computing, especially for distributed workflows. Modern web browsers can now be used as high-performance workstations for query...
Social behavior has long been known to influence patterns of genetic diversity, but the effect of social processes on population genetics remains poorly quantified – partly due to limited community-level genet...
Gene expression in vertebrate cells may be controlled post-transcriptionally through regulatory elements in mRNAs. These are usually located in the untranslated regions (UTRs) of mRNA sequences, particularly t...
Human disease often arises as a consequence of alterations in a set of associated genes rather than alterations to a set of unassociated individual genes. Most previous microarray-based meta-analyses identifie...
Identification of recombination events and which chromosomal segments contributed to an individual is useful for a number of applications in genomic analyses including haplotyping, imputation, signatures of se...
Since proteins function by interacting with other molecules, analysis of protein-protein interactions is essential for comprehending biological processes. Whereas understanding of atomic interactions within a ...
The reproducibility of transcriptomic biomarkers across datasets remains poor, limiting clinical application. We and others have suggested that this is in-part caused by differential error-structure between da...
Retinal ganglion cell (RGC) loss is one of the earliest and most important cellular changes in glaucoma. The DARC (Detection of Apoptosing Retinal Cells) technology enables in vivo real-time non-invasive imaging ...
In vitro generated dose-response curves of human cancer cell lines are widely used to develop new therapeutics. The curves are summarised by simplified statistics that ignore the conventionally used dose-response...
High-throughput Next-Generation Sequencing (NGS) techniques are advancing genomics and molecular biology research. This technology generates substantially large data which puts up a major challenge to the scie...
Protein sequence similarities to any types of non-globular segments (coiled coils, low complexity regions, transmembrane regions, long loops, etc. where either positional sequence conservation is the result of...
HMMER is a commonly used bioinformatics tool based on Hidden Markov Models (HMMs) to analyze and process biological sequences. One of its main homology engines is based on the Viterbi decoding algorithm, which...
The haplotype phasing problem tries to screen for phenotype associated genomic variations from millions of candidate data. Most of the current computer programs handle this problem with high requirements of co...
Coronaviruses are the diverse group of RNA virus. From 1960, six strains of human coronaviruses have emerged that includes SARS-CoV and the recent infection by deadly MERS-CoV which is now going to cause anoth...
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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
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