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The competing endogenous RNA (ceRNA) regulation is a newly discovered post-transcriptional regulation mechanism and plays significant roles in physiological and pathological progress. CeRNA networks provide gl...
Citation: BMC Bioinformatics 2021 22:75
One component of precision medicine is to construct prediction models with their predicitve ability as high as possible, e.g. to enable individual risk prediction. In genetic epidemiology, complex diseases lik...
Citation: BMC Bioinformatics 2021 22:74
Oocyte quality decreases with aging, thereby increasing errors in fertilization, chromosome segregation, and embryonic cleavage. Oocyte appearance also changes with aging, suggesting a functional relationship ...
Citation: BMC Bioinformatics 2021 22:73
Bioimaging techniques offer a robust tool for studying molecular pathways and morphological phenotypes of cell populations subjected to various conditions. As modern high-resolution 3D microscopy provides acce...
Citation: BMC Bioinformatics 2021 22:72
Specialized data structures are required for online algorithms to efficiently handle large sequencing datasets. The counting quotient filter (CQF), a compact hashtable, can efficiently store k-mers with a skew...
Citation: BMC Bioinformatics 2021 22:71
The quantity of genomic data is expanding at an increasing rate. Tools for phylogenetic analysis which scale to the quantity of available data are required. To address this need, we present cognac, a user-frie...
Citation: BMC Bioinformatics 2021 22:70
Chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq), initially introduced more than a decade ago, is widely used by the scientific community to detect protein/DNA binding and histon...
Citation: BMC Bioinformatics 2021 22:69
The clustering of data produced by liquid chromatography coupled to mass spectrometry analyses (LC-MS data) has recently gained interest to extract meaningful chemical or biological patterns. However, recent i...
Citation: BMC Bioinformatics 2021 22:68
The search for statistically significant relationships between molecular markers and outcomes is challenging when dealing with high-dimensional, noisy and collinear multivariate omics data, such as metabolomic...
Citation: BMC Bioinformatics 2021 22:67
Conformational transitions are implicated in the biological function of many proteins. Structural changes in proteins can be described approximately as the relative movement of rigid domains against each other...
Citation: BMC Bioinformatics 2021 22:66
The advancement of SMRT technology has unfolded new opportunities of genome analysis with its longer read length and low GC bias. Alignment of the reads to their appropriate positions in the respective referen...
Citation: BMC Bioinformatics 2021 22:64
Human dicer is an enzyme that cleaves pre-miRNAs into miRNAs. Several models have been developed to predict human dicer cleavage sites, including PHDCleav and LBSizeCleav. Given an input sequence, these models...
Citation: BMC Bioinformatics 2021 22:63
Recent cancer genomic studies have generated detailed molecular data on a large number of cancer patients. A key remaining problem in cancer genomics is the identification of driver genes.
Citation: BMC Bioinformatics 2021 22:62
We present here a computational shortcut to improve a powerful wavelet-based method by Shim and Stephens (Ann Appl Stat 9(2):665–686, 2015.
Citation: BMC Bioinformatics 2021 22:61
Current high-throughput technologies—i.e. whole genome sequencing, RNA-Seq, ChIP-Seq, etc.—generate huge amounts of data and their usage gets more widespread with each passing year. Complex analysis pipelines ...
Citation: BMC Bioinformatics 2021 22:60
Long noncoding RNAs represent a large class of transcripts with two common features: they exceed an arbitrary length threshold of 200 nt and are assumed to not encode proteins. Although a growing body of evide...
Citation: BMC Bioinformatics 2021 22:59
Hub transcription factors, regulating many target genes in gene regulatory networks (GRNs), play important roles as disease regulators and potential drug targets. However, while numerous methods have been deve...
Citation: BMC Bioinformatics 2021 22:58
Mass spectrometry imaging (MSI) is a family of acquisition techniques producing images of the distribution of molecules in a sample, without any prior tagging of the molecules. This makes it a very interesting...
Citation: BMC Bioinformatics 2021 22:56
Identification and selection of protein particles in cryo-electron micrographs is an important step in single particle analysis. In this study, we developed a deep learning-based particle picking network to a...
Citation: BMC Bioinformatics 2021 22:55
The high variability in envelope regions of some viruses such as HIV allow the virus to establish infection and to escape subsequent immune surveillance. This variability, as well as increasing incorporation o...
Citation: BMC Bioinformatics 2021 22:54
Biological phenomena usually evolves over time and recent advances in high-throughput microscopy have made possible to collect multiple 3D images over time, generating
...
Citation: BMC Bioinformatics 2021 22:53
Drug repositioning refers to the identification of new indications for existing drugs. Drug-based inference methods for drug repositioning apply some unique features of drugs for new indication prediction. Com...
Citation: BMC Bioinformatics 2021 22:52
An inverted repeat is a DNA sequence followed downstream by its reverse complement, potentially with a gap in the centre. Inverted repeats are found in both prokaryotic and eukaryotic genomes and they have bee...
Citation: BMC Bioinformatics 2021 22:51
In the last decade, Genome-wide Association studies (GWASs) have contributed to decoding the human genome by uncovering many genetic variations associated with various diseases. Many follow-up investigations i...
Citation: BMC Bioinformatics 2021 22:50
Microbiomes consist of bacteria, viruses, and other microorganisms, and are responsible for many different functions in both organisms and the environment. Past analyses of microbiomes focused on using correla...
Citation: BMC Bioinformatics 2021 22:49
Various databases on genetically modified organisms (GMOs) exist, all with their specific focus to facilitate access to information needed for, e. g., the assistance in risk assessment, the development of dete...
Citation: BMC Bioinformatics 2021 22:48
Survival analysis is an important part of cancer studies. In addition to the existing Cox proportional hazards model, deep learning models have recently been proposed in survival prediction, which directly int...
Citation: BMC Bioinformatics 2021 22:47
The development of genetically modified crops (GM) includes the discovery of candidate genes through bioinformatics analysis using genomics data, gene expression, and others. Proteins of unknown function (PUFs...
Citation: BMC Bioinformatics 2021 22:46
Several bioinformatics pipelines have been developed to detect sequences from viruses that integrate into the human genome because of the health relevance of these integrations, such as in the persistence of v...
Citation: BMC Bioinformatics 2021 22:45
Differential expression and feature selection analyses are essential steps for the development of accurate diagnostic/prognostic classifiers of complicated human diseases using transcriptomics data. These step...
Citation: BMC Bioinformatics 2021 22:44
Transposable elements (TEs) constitute a significant part of eukaryotic genomes. Short interspersed nuclear elements (SINEs) are non-autonomous TEs, which are widely represented in mammalian genomes and also f...
Citation: BMC Bioinformatics 2021 22:42
The drive to understand how microbial communities interact with their environments has inspired innovations across many fields. The data generated from sequence-based analyses of microbial communities typicall...
Citation: BMC Bioinformatics 2021 22:41
Generating and analysing single-cell data has become a widespread approach to examine tissue heterogeneity, and numerous algorithms exist for clustering these datasets to identify putative cell types with shar...
Citation: BMC Bioinformatics 2021 22:39
Due to the complexity of the biological systems, the prediction of the potential DNA binding sites for transcription factors remains a difficult problem in computational biology. Genomic DNA sequences and expe...
Citation: BMC Bioinformatics 2021 22:38
IsomiRs are miRNA variants that vary in length and/or sequence when compared to their canonical forms. These variants display differences in length and/or sequence, including additions or deletions of one or m...
Citation: BMC Bioinformatics 2021 22:37
Phylogenetic analysis strongly depends on evolutionary models. Most evolutionary models for estimating genetic differences and phylogenetic relationships do not treat gap sites in the alignment of sequences. A...
Citation: BMC Bioinformatics 2021 22:36
Assigning chromatin states genome-wide (e.g. promoters, enhancers, etc.) is commonly performed to improve functional interpretation of these states. However, computational methods to assign chromatin state suf...
Citation: BMC Bioinformatics 2021 22:35
Network alignment (NA) can transfer functional knowledge between species’ conserved biological network regions. Traditional NA assumes that it is topological similarity (isomorphic-like matching) between netwo...
Citation: BMC Bioinformatics 2021 22:34
Predicting the response of cancer cell lines to specific drugs is an essential problem in personalized medicine. Since drug response is closely associated with genomic information in cancer cells, some large p...
Citation: BMC Bioinformatics 2021 22:33
Anatomical distance has been identified as a key factor in the organizational principles of the human brain. On the other hand, criticality was proposed to accommodate the multiscale properties of human brain ...
Citation: BMC Bioinformatics 2021 22:32
Driven by deep learning, inter-residue contact/distance prediction has been significantly improved and substantially enhanced ab initio protein structure prediction. Currently, most of the distance prediction ...
Citation: BMC Bioinformatics 2021 22:30
Due to continued advances in sequencing technology, the limitation in understanding biological systems through an “-omics” lens is no longer the generation of data, but the ability to analyze it. Importantly, ...
Citation: BMC Bioinformatics 2021 22:29
Drug repositioning is an emerging approach in pharmaceutical research for identifying novel therapeutic potentials for approved drugs and discover therapies for untreated diseases. Due to its time and cost eff...
Citation: BMC Bioinformatics 2021 22:28
Currently, large-scale gene expression profiling has been successfully applied to the discovery of functional connections among diseases, genetic perturbation, and drug action. To address the cost of an ever-e...
Citation: BMC Bioinformatics 2021 22:27
Brain Computer Interfaces (BCIs) translate the activity of the nervous system to a control signal which is interpretable for an external device. Using continuous motor BCIs, the user will be able to control a ...
Citation: BMC Bioinformatics 2021 22:26
Diverse microbiome communities drive biogeochemical processes and evolution of animals in their ecosystems. Many microbiome projects have demonstrated the power of using metagenomics to understand the structur...
Citation: BMC Bioinformatics 2021 22:25
Long non-coding RNAs (lncRNAs) regulate diverse biological processes via interactions with proteins. Since the experimental methods to identify these interactions are expensive and time-consuming, many computa...
Citation: BMC Bioinformatics 2021 22:24
Copy number alterations (CNAs), due to their large impact on the genome, have been an important contributing factor to oncogenesis and metastasis. Detecting genomic alterations from the shallow-sequencing data...
Citation: BMC Bioinformatics 2021 22:23
In this study, we demonstrate that our modified Gene Set Enrichment Analysis (GSEA) method, drug perturbation GSEA (dpGSEA), can detect phenotypically relevant drug targets through a unique transcriptomic enri...
Citation: BMC Bioinformatics 2021 22:22
Computational modelling of cell biological processes is a frequently used technique to analyse the underlying mechanisms and to generally understand the behaviour of these processes in the context of a pathway...
Citation: BMC Bioinformatics 2021 22:21
View featured videos from across the BMC-series journals
Speed
70 days to first decision for reviewed manuscripts only
44 days to first decision for all manuscripts
163 days from submission to acceptance
36 days from acceptance to publication
Citation Impact
3.242 - 2-year Impact Factor
3.213 - 5-year Impact Factor
1.156 - Source Normalized Impact per Paper (SNIP)
1.626 - SCImago Journal Rank (SJR)
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