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Methodology Article
The development of single-cell RNA sequencing has enabled profound discoveries in biology, ranging from the dissection of the composition of complex tissues to the identification of novel cell types and dynami...
BMC Bioinformatics 2017 18:270
Published on: 23 May 2017
Software
The sequence logo has been widely used to represent DNA or RNA motifs for more than three decades. Despite its intelligibility and intuitiveness, the traditional sequence logo is unable to display the intra-mo...
BMC Bioinformatics 2017 18:269
Published on: 22 May 2017
Methodology article
The stress fibers are prominent organization of actin filaments that perform important functions in cellular processes such as migration, polarization, and traction force generation, and whose collective organ...
BMC Bioinformatics 2017 18:268
Published on: 22 May 2017
Research article
With the development of Next Generation Sequencing technologies, the number of predicted proteins from entire (meta-) genomes has risen exponentially. While for some of these sequences protein functions can be...
BMC Bioinformatics 2017 18:267
Published on: 22 May 2017
Software
Analysis of genome-wide association studies (GWAS) with “time to event” outcomes have become increasingly popular, predominantly in the context of pharmacogenetics, where the survival endpoint could be death, ...
BMC Bioinformatics 2017 18:265
Published on: 19 May 2017
Research Article
It has been proposed that future reference genomes should be graph structures in order to better represent the sequence diversity present in a species. However, there is currently no standard method to represe...
BMC Bioinformatics 2017 18:263
Published on: 18 May 2017
Software
Many biological pathways have been created to represent different types of knowledge, such as genetic interactions, metabolic reactions, and gene-regulating and physical-binding relationships. Biologists are u...
BMC Bioinformatics 2017 18:262
Published on: 18 May 2017
Research Article
A visualization referred to as rainfall plot has recently gained popularity in genome data analysis. The plot is mostly used for illustrating the distribution of somatic cancer mutations along a reference geno...
BMC Bioinformatics 2017 18:264
Published on: 18 May 2017
Methodology Article
Different phenomena like the spread of a disease, social interactions or the biological relation between genes can be thought of as dynamic networks. These can be represented as a sequence of static graphs (so...
BMC Bioinformatics 2017 18:261
Published on: 16 May 2017
Software
Spectral imaging with polarity-sensitive fluorescent probes enables the quantification of cell and model membrane physical properties, including local hydration, fluidity, and lateral lipid packing, usually ch...
BMC Bioinformatics 2017 18:254
Published on: 12 May 2017
Research Article
Deciphering complete networks of interactions between proteins is the key to comprehend cellular regulatory mechanisms. A significant effort has been devoted to expanding the coverage of the proteome-wide inte...
BMC Bioinformatics 2017 18:257
Published on: 12 May 2017
Methodology Article
Several recent studies showed that next-generation sequencing (NGS)-based human leukocyte antigen (HLA) typing is a feasible and promising technique for variant calling of highly polymorphic regions. To date, ...
BMC Bioinformatics 2017 18:258
Published on: 12 May 2017
Methodology Article
Exponentially increasing numbers of NGS-based epigenomic datasets in public repositories like GEO constitute an enormous source of information that is invaluable for integrative and comparative studies of gene...
BMC Bioinformatics 2017 18:259
Published on: 12 May 2017
Research Article
There exist many methods for describing the complex relation between changes of gene expression in molecular pathways or gene ontologies under different experimental conditions. Among them, Gene Set Enrichment...
BMC Bioinformatics 2017 18:256
Published on: 12 May 2017
Commentary
Despite the long-anticipated possibility of putting sequence alignment on the same footing as statistical phylogenetics, theorists have struggled to develop time-dependent evolutionary models for indels that a...
BMC Bioinformatics 2017 18:255
Published on: 12 May 2017
Software
Species-level classification for 16S rRNA gene sequences remains a serious challenge for microbiome researchers, because existing taxonomic classification tools for 16S rRNA gene sequences either do not provid...
BMC Bioinformatics 2017 18:247
Published on: 10 May 2017
Research Article
Mathematical modeling and in silico analysis are widely acknowledged as complementary tools to biological laboratory methods, to achieve a thorough understanding of emergent behaviors of cellular processes in ...
BMC Bioinformatics 2017 18:246
Published on: 10 May 2017
Software
Immunoinformatics has become a crucial part in biomedical research. Yet many immunoinformatics tools have command line interfaces only and can be difficult to install. Web-based immunoinformatics tools, on the...
BMC Bioinformatics 2017 18:242
Published on: 8 May 2017
Research Article
Reconstructing gene regulatory networks (GRNs) from expression data plays an important role in understanding the fundamental cellular processes and revealing the underlying relations among genes. Although many...
BMC Bioinformatics 2017 18:241
Published on: 8 May 2017
Research Article
Recent studies have shown that the crosstalk between microRNA (miRNA) sponges plays an important role in human cancers. However, the co-regulation roles of miRNA sponges in protein-protein interactions (PPIs) ...
BMC Bioinformatics 2017 18:243
Published on: 8 May 2017
Database
The Geminiviridae family encompasses a group of single-stranded DNA viruses with twinned and quasi-isometric virions, which infect a wide range of dicotyledonous and monocotyledonous plants and are responsible fo...
BMC Bioinformatics 2017 18:240
Published on: 5 May 2017
Software
A major challenge of high throughput transcriptome studies is presenting the data to researchers in an interpretable format. In many cases, the outputs of such studies are gene lists which are then examined fo...
BMC Bioinformatics 2017 18:237
Published on: 4 May 2017
Methodology Article
Sample size calculation and power estimation are essential components of experimental designs in biomedical research. It is very challenging to estimate power for RNA-Seq differential expression under complex ...
BMC Bioinformatics 2017 18:234
Published on: 3 May 2017
Software
A common challenge in bioinformatics is to identify short sub-sequences that are unique in a set of genomes or reference sequences, which can efficiently be achieved by k-mer (k consecutive nucleotides) counting....
BMC Bioinformatics 2017 18:228
Published on: 2 May 2017
Methodology Article
Reconstructing transcript models from RNA-sequencing (RNA-seq) data and establishing these as independent transcriptional units can be a challenging task. Current state-of-the-art tools for long non-coding RNA...
BMC Bioinformatics 2017 18:231
Published on: 2 May 2017
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