62 downloads
29 views

The “reproducibility crisis” has been a highly visible source of scientific controversy and dispute. Here, I propose and review several avenues for identifying and prioritizing research studies for the purpose of targeted validation. Of the various proposals discussed,...

["Bioinformatics","Evidence Based Medicine","Health Policy","Translational Medicine","Science Policy"]
doi:10.7287/peerj.preprints.2830v1
20 downloads
119 views

MerCat (“ Mer - Cat enate”) is a parallel, highly scalable and modular property software package for robust analysis of features in next-generation sequencing data. Using assembled contigs and raw sequence reads from any platform as input, MerCat performs k-mer...

["Bioinformatics","Computational Biology","Data Science","Scientific Computing and Simulation","Software Engineering"]
doi:10.7287/peerj.preprints.2825v1
1 download
31 views

Introduction Computational reproducibility refers to the possibility of reconstructing all the steps of a workflow that connects raw data, processed data and results: it is a fundamental issue in the omic studies because of the complex and high-dimensional nature...

["Bioinformatics","Computational Biology","Data Science"]
doi:10.7287/peerj.preprints.2823v1
43 downloads
298 views

Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations....

["Bioinformatics","Evolutionary Studies","Plant Science"]
doi:10.7287/peerj.preprints.2763v2
5 downloads
76 views

The importance of histidine tautomerism for an accurate drug/protein structure determination and their relevance for the interaction between biological systems is recognized. Consequently, here we used a recently introduced method to determine the pKa values of...

["Bioinformatics","Biophysics","Computational Biology","Molecular Biology"]
doi:10.7287/peerj.preprints.2816v1
13 downloads
91 views

Culture collections (CCs) manage fundamental data about preserved microorganisms. To enable the exploitation of these resources requires standardized, and simplified, access to the associated information. To this end, a European Microbial Resource Research Infrastructure,...

["Biodiversity","Bioinformatics","Microbiology","Mycology","Taxonomy"]
doi:10.7287/peerj.preprints.2815v1
12 downloads
78 views

Hydrolysis of ATP by Na+/K+-ATPase, a P-Type ATPase, catalyzing active Na+ and K+ transport through cellular membranes leads transiently to a phosphorylation of its catalytical α-subunit. Surprisingly, 3-dimensional molecular structure analysis of P-type ATPases...

["Biochemistry","Bioinformatics","Biophysics","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.2812v1
94 downloads
70 views

Prebiotics are selectively fermentable dietary compounds that result in changes in the composition and/or activity of the intestinal microbiota, thus conferring benefits upon host health. In veterinary medicine, commercially available products containing prebiotics...

["Bioinformatics","Microbiology","Veterinary Medicine","Gastroenterology and Hepatology","Nutrition"]
doi:10.7287/peerj.preprints.2814v1
127 downloads
656 views

Background De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is...

["Bioinformatics","Computational Biology","Genomics","Computational Science"]
doi:10.7717/peerj.2988
57 downloads
566 views

Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments and clinical diagnostics, and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics","Microbiology"]
doi:10.7717/peerj.2997
54 downloads
412 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
45 downloads
277 views

Type B trichothecenes, which pose a serious hazard to consumer health, occur worldwide in grains. These mycotoxins are produced mainly by three different trichothecene genotypes/chemotypes: 3ADON (3-acetyldeoxynivalenol), 15ADON (15-acetyldeoxynivalenol) and NIV...

["Bioinformatics","Mycology"]
doi:10.7717/peerj.2992
62 downloads
501 views

Metastatic cutaneous melanoma is an aggressive skin cancer with some progression-slowing treatments but no known cure. The omics data explosion has created many possible drug candidates; however, filtering criteria remain challenging, and systems biology approaches...

["Bioinformatics","Computational Biology","Data Science","World Wide Web and Web Science"]
doi:10.7717/peerj-cs.106
32 downloads
58 views

CodonGenie, freely available from http://codon.synbiochem.co.uk, is a simple web application for designing ambiguous codons to support protein mutagenesis applications. Ambiguous codons are derived from specific heterogeneous nucleotide mixtures, which create sequence...

["Bioengineering","Bioinformatics","Biotechnology","Computational Biology","Synthetic Biology"]
doi:10.7287/peerj.preprints.2797v1
35 downloads
108 views

Reproducibility has become one of biology’s most pressing issues. This impasse has been fuelled by the combined reliance on increasingly complex data analysis methods and the exponential growth of biological datasets. Nextflow is a pipeline orchestration tool that...

["Bioinformatics"]
doi:10.7287/peerj.preprints.2796v1

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