Peer-reviewed Articles - Biology

63 downloads
279 views

Protein backbones occupy diverse conformations, but compact metrics to describe such conformations and transitions between them have been missing. This report re-introduces the Ramachandran number (ℛ) as a residue-level structural metric that could simply the life...

["Bioinformatics","Computational Biology","Mathematical Biology"]
doi:10.7717/peerj.5745
80 downloads
393 views

In single-cell RNA-sequencing, it is important to know the frequency at which the sequenced transcriptomes actually derive from multiple cells. A common method to estimate this multiplet frequency is to mix two different types of cells (e.g., human and mouse),...

["Bioinformatics","Computational Biology","Genomics","Mathematical Biology"]
doi:10.7717/peerj.5578
1 citation
240 downloads
976 views

Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports...

["Bioinformatics","Genomics","Mathematical Biology"]
doi:10.7717/peerj.4545
792 downloads
1,463 views

Sigmoidal and double-sigmoidal dynamics are commonly observed in many areas of biology. Here we present sicegar, an R package for the automated fitting and classification of sigmoidal and double-sigmoidal data. The package categorizes data into one of three categories,...

["Bioinformatics","Computational Biology","Mathematical Biology","Statistics","Data Science"]
doi:10.7717/peerj.4251
4 citations
507 downloads
1,980 views

Background Colorectal cancer (CRC) is one of the leading cancers worldwide. Several studies have performed microarray data analyses for cancer classification and prognostic analyses. Microarray assays also enable the identification of gene signatures for molecular...

["Bioinformatics","Mathematical Biology","Molecular Biology","Oncology","Statistics"]
doi:10.7717/peerj.3003
11 citations
744 downloads
3,471 views

In biological mass spectrometry, crude instrumental data need to be converted into meaningful theoretical models. Several data processing and data evaluation steps are required to come to the final results. These operations are often difficult to reproduce, because...

["Bioinformatics","Biophysics","Computational Biology","Mathematical Biology","Statistics"]
doi:10.7717/peerj.1401
619 downloads
1,814 views

Two Component Systems and Phosphorelays (TCS/PR) are environmental signal transduction cascades in prokaryotes and, less frequently, in eukaryotes. The internal domain organization of proteins and the topology of TCS/PR cascades play an important role in shaping...

["Bioinformatics","Computational Biology","Mathematical Biology","Synthetic Biology"]
doi:10.7717/peerj.1183
6 citations
847 downloads
3,278 views

Background. Establishing health-related causal relationships is a central pursuit in biomedical research. Yet, the interdependent non-linearity of biological systems renders causal dynamics laborious and at times impractical to disentangle. This pursuit is further...

["Bioinformatics","Mathematical Biology","Computational Science","Coupled Natural and Human Systems"]
doi:10.7717/peerj.824
1 citation
456 downloads
1,817 views

The impetus for this work was the need to analyse nucleotide diversity in a viral mix taken from honeybees. The paper has two findings. First, a method for correction of next generation sequencing error in the distribution of nucleotides at a site is developed....

["Biodiversity","Bioinformatics","Computational Biology","Genetics","Mathematical Biology"]
doi:10.7717/peerj.645
9 citations
627 downloads
2,548 views

Multi-parameter models in systems biology are typically ‘sloppy’: some parameters or combinations of parameters may be hard to estimate from data, whereas others are not. One might expect that parameter uncertainty automatically leads to uncertain predictions,...

["Bioinformatics","Computational Biology","Mathematical Biology","Statistics"]
doi:10.7717/peerj.433
1 citation
406 downloads
2,029 views

The arrangement of nucleotides within a bacterial chromosome is influenced by numerous factors. The degeneracy of the third codon within each reading frame allows some flexibility of nucleotide selection; however, the third nucleotide in the triplet of each codon...

["Bioinformatics","Computational Biology","Genomics","Mathematical Biology","Molecular Biology"]
doi:10.7717/peerj.127
4 citations
518 downloads
2,237 views

The inference of gene regulatory networks gained within recent years a considerable interest in the biology and biomedical community. The purpose of this paper is to investigate the influence that environmental conditions can exhibit on the inference performance...

["Bioinformatics","Computational Biology","Mathematical Biology","Statistics"]
doi:10.7717/peerj.10

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