Peer-reviewed Articles

141 downloads
671 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
60 downloads
577 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
56 downloads
436 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
47 downloads
282 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
63 downloads
503 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
68 downloads
333 views

A metabolomic study has been performed to identify sensitive and robust biomarkers of malnutrition in farmed fish, using gilthead sea bream (Sparus aurata) as a model. The metabolomic fingerprinting of serum from fasted fish was assessed by means of ultra-high...

["Aquaculture, Fisheries and Fish Science","Biochemistry","Bioinformatics","Nutrition","Metabolic Sciences"]
doi:10.7717/peerj.2920
57 downloads
305 views

Background Transposable element (TE) polymorphisms are important components of population genetic variation. The functional impacts of TEs in gene regulation and generating genetic diversity have been observed in multiple species, but the frequency and magnitude...

["Bioinformatics","Genomics","Plant Science"]
doi:10.7717/peerj.2942
70 downloads
459 views

Bioinformaticians have implemented different strategies to distinguish cancer driver genes from passenger genes. One of the more recent advances uses a pathway-oriented approach. Methods that employ this strategy are highly dependent on the quality and size of...

["Bioinformatics","Computational Biology","Statistics","Computational Science"]
doi:10.7717/peerj.2568
46 downloads
228 views

Snakebite envenomings represent a neglected public health issue in many parts of the rural tropical world. Animal-derived antivenoms have existed for more than a hundred years and are effective in neutralizing snake venom toxins when timely administered. However,...

["Bioinformatics","Biotechnology","Toxicology","Immunology","Synthetic Biology"]
doi:10.7717/peerj.2924
193 downloads
694 views

Single-cell RNA-Sequencing (scRNA-Seq) is a fast-evolving technology that enables the understanding of biological processes at an unprecedentedly high resolution. However, well-suited bioinformatics tools to analyze the data generated from this new technology are...

["Bioinformatics","Genomics"]
doi:10.7717/peerj.2888
95 downloads
672 views

Autophagy serves as a turnover mechanism for the recycling of redundant and/or damaged macromolecules present in eukaryotic cells to re-use them under starvation conditions via a double-membrane structure known as autophagosome. A set of eukaryotic genes called...

["Bioinformatics","Cell Biology","Computational Biology"]
doi:10.7717/peerj.2878
452 downloads
1,028 views

Recently, there has been a move encouraged by many stakeholders towards generating big, open data in many areas of research. One area where big, open data is particularly valuable is in research relating to complex heterogeneous disorders such as Autism Spectrum...

["Bioinformatics","Neuroscience","Psychiatry and Psychology"]
doi:10.7717/peerj.2880
266 downloads
990 views

The importance of 16S rRNA gene amplicon profiles for understanding the influence of microbes in a variety of environments coupled with the steep reduction in sequencing costs led to a surge of microbial sequencing projects. The expanding crowd of scientists and...

["Bioinformatics","Ecology","Microbiology"]
doi:10.7717/peerj.2836
93 downloads
392 views

Biomaterial scaffolds have the potential to enhance neuronal development and regeneration. Understanding the genetic responses of astrocytes and neurons to biomaterials could facilitate the development of synthetic environments that enable the specification of...

["Bioengineering","Bioinformatics","Cell Biology","Genomics","Neuroscience"]
doi:10.7717/peerj.2829
65 downloads
648 views

Solar salterns are excellent model ecosystems for studying virus-microbial interactions because of their low microbial diversity, environmental stability, and high viral density. By using the power of CRISPR spacers to link viruses to their prokaryotic hosts, we...

["Bioinformatics","Computational Biology","Ecology","Genomics","Microbiology"]
doi:10.7717/peerj.2844

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