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bioinformatics
48 downloads
118 views

Whole genome bisulfite sequencing (WGBS) is the current method of choice to obtain the methylation status of each single CpG dinucleotide in a genome. The typical analysis asks for regions that are differentially methylated (DMRs) between samples of two classes,...

["Bioinformatics","Computational Biology","Optimization Theory and Computation"]
doi:10.7287/peerj.preprints.1287v3
3 views

Perilipins are lipid droplet surface proteins that contribute to fat metabolism by controlling the access of lipids to lipolytic enzymes. Perilipins have been identified in organisms as diverse as metazoa, fungi, and amoebas but strikingly not in nematodes. Here...

["Bioinformatics","Cell Biology","Genomics"]
doi:10.7717/peerj.1213
16 downloads
64 views

In this study, we sequenced the genome of Pandoraea pnomenusa RB38 using Pacific Biosciences RSII (PacBio) Single Molecule Real Time (SMRT) sequencing technology. A pair of cognate luxI/R homologs was identified where the luxI homolog, ppnI, was found adjacent...

["Bioinformatics","Genomics","Microbiology","Molecular Biology"]
doi:10.7717/peerj.1225
39 downloads
541 views

Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. Because of the complex nature of these communities,...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7717/peerj.1165
11 downloads
58 views

The analysis of next-generation sequence (NGS) data is often a fragmented step-wise process. For example, multiple pieces of software are typically needed to map NGS reads, extract variant sites, and construct a DNA sequence matrix containing only single nucleotide...

["Bioinformatics"]
doi:10.7717/peerj-cs.20
23 downloads
59 views

Plants are a hyperdiverse clade that plays a key role in maintaining ecological and evolutionary processes as well as human livelihoods. Glaring biases, gaps, and uncertainties in plant occurrence information remain a central problem in ecology and conservation,...

["Biogeography","Bioinformatics","Conservation Biology","Ecology","Plant Science"]
doi:10.7287/peerj.preprints.1326v2
19 downloads
160 views

The inconvenience operation of EEG P300 or functional magnetic resonance imaging (FMRI) will be overcome, when the deceptive information can be effectively detected from speech signal analysis. In this paper, the fractional Mel cepstral coefficient (FrCC) is proposed...

["Bioinformatics","Computational Biology","Psychiatry and Psychology","Computational Science"]
doi:10.7717/peerj.1194
21 downloads
49 views

Enterobacter cancerogenus strain M004 genome size is 5.67 Mb. Here, its luxI homologue, designated as ecnI which is ecnI gene (633 bp) was cloned and overexpressed. Its AHL synthesis activity was verified using the high-resolution liquid chromatography-mass spectrometry...

["Bioinformatics","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.1310v1
76 downloads
120 views

For producing ATP, tumor cells rely on glycolysis leading to lactate to about the same extent as on respiration. Thus, they use a higher fraction of glycolysis than the corresponding healthy cells. This is known as the Warburg effect (named after German biochemist...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.1309v1
5 downloads
49 views

In personalized medicine, one major goal is the identification of yet unknown patient subgroups with specific gene or protein expression. Different subgroups can indicate different molecular subtypes of a disease. These subtypes might correlate with disease progression,...

["Bioinformatics","Computational Biology","Molecular Biology","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.1305v1
26 downloads
66 views

Treatment with broadly neutralizing antibodies (bNAbs) has recently proven effective against HIV-1 infections in humanized mice, non-human primates, and humans. For optimal treatment, susceptibility of the patient's viral strains to a particular bNAb has to be...

["Bioinformatics","Computational Biology","Virology","HIV","Statistics"]
doi:10.7287/peerj.preprints.1304v1
26 downloads
91 views

Dysfunctional protein complexes are often associated with diseases. To develop effective treatments it is essential to understand the composition, formation and functionality of protein complexes. Novel techniques like complexome profiling give an overview of possible...

["Bioinformatics","Computational Biology","Visual Analytics"]
doi:10.7287/peerj.preprints.1303v1
26 downloads
95 views

High-throughput data, for instance ChIP-seq data, measure binding of transcription factors (TFs) or other proteins to DNA and have become a widespread data source for de-novo motif discovery. Often, several ChIP-seq data sets study the same TF under different conditions...

["Bioinformatics","Computational Biology","Molecular Biology","Computational Science"]
doi:10.7287/peerj.preprints.1302v1
17 downloads
79 views

Genomic structural variations play key roles in genetic diversity and disease. Despite recent advances in structural variation discovery, many variants are yet to be discovered. Midsize insertions and deletions pose particularly involved algorithmic challenges....

["Bioinformatics","Computational Biology","Algorithms and Analysis of Algorithms","Data Science"]
doi:10.7287/peerj.preprints.1301v1
17 downloads
177 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

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