Preprints (not yet peer-reviewed)

172 downloads
596 views

Evolutionary biology has entered an era of unprecedented amounts of DNA sequence data, as new sequencing platforms such as Massive Parallel Sequencing (MPS) can generate billions of nucleotides within less than a day. The current bottleneck is how to efficiently...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genetics"]
doi:10.7287/peerj.preprints.26477v3
29 downloads
113 views

Background: Zika virus (ZIKV) is an arbovirus that belongs to family Flaviviridae. The virus has emerged as a global threat and no FDA approved vaccine is available, so an efficient vaccine needs to be designed in order to prevent the infection. Computationally...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.26499v1
114 downloads
452 views

Exogenous sequence contamination presents a challenge in first-draft genomes because it can lead to non-contiguous, chimeric assembled sequences. This can mislead downstream analyses reliant on synteny, such as linkage-based analyses. Recently, the Mojave Desert...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.3266v4
643 downloads
1,742 views

Building the Tree of Life (ToL) is a major challenge of modern biology, requiring major advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging...

["Biodiversity","Computational Biology","Evolutionary Studies","Genomics"]
doi:10.7287/peerj.preprints.26449v3
23 downloads
75 views

A significant approach for the discovery of biological regulatory rules of genes, protein and their inheritance relationships is the extraction of meaningful patterns from biological sequence data.The existing algorithms of sequence pattern discovery, like MSPM...

["Computational Biology","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.26471v1
36 downloads
117 views

High-throughput phenotype assays are a cornerstone of systems biology as they allow direct measurements of mutations, genes, strains, or even different genera. High-throughput methods also require data analytic methods that reduce complex time-series data to a...

["Computational Biology","Microbiology"]
doi:10.7287/peerj.preprints.26469v1
14 downloads
76 views

Background. Hepatitis C Virus (HCV) is a major causative agent of liver infection leading to critical liver damage. In response to HCV, the improper regulation of host immune system leads to chronic infection. The host immune system employs multiple cell types,...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.26456v1
41 downloads
100 views

The general purpose of this paper is to build up on our understanding of the basic mathematical principles that underlie the emergence of biological rhythms, in particular, the circadian clock. To do so, we study the role that the coupling strength and noise play...

["Computational Biology","Mathematical Biology"]
doi:10.7287/peerj.preprints.26447v1
113 downloads
569 views

Background. The phytohormone jasmonates (JAs) regulate fundamental plant processes; such as the anthocyanin accumulation during ripening of strawberry, a non-climacteric fruit model. Jasmonoyl-isoleucine (JA-Ile), one of the bioactive JA molecules, mediates binding...

["Biochemistry","Bioinformatics","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.2772v2
54 downloads
148 views

Microbes are identified based on their distinguishing characteristics such as gene sequence or metabolic profile. Nucleic acid approaches such as 16S rRNA gene sequencing provide the gold standard method for microbial identification in the contemporary era. However,...

["Biochemistry","Bioinformatics","Biotechnology","Computational Biology","Microbiology"]
doi:10.7287/peerj.preprints.3524v1
114 downloads
541 views

The 2nd Argentine Symposium of Young Bioinformatics Researchers (2SAJIB, according to its acronym in Spanish) took place on November 2017 in Buenos Aires, Argentina. SAJIB is the main annual student-based activity in the field of Bioinformatics and Computational...

["Bioinformatics","Computational Biology","Science and Medical Education"]
doi:10.7287/peerj.preprints.3504v2
379 downloads
510 views

Generating heatmaps of genetic datasets is a 2D graphical visualization of data where the individual expression values contained in a matrix are represented as colors. Herein, we describe AFCMHeatMap a shiny web App that integrates quantitative interaction of genomics...

["Bioinformatics","Computational Biology","Genetics","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.2961v2
52 downloads
101 views

The reconstruction of genomes using mapping based approaches with short reads experiences difficulties when resolving repetitive regions. These repetitive regions in genomes result in low mapping qualities of the respective reads, which in turn lead to many unresolved...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.3480v1
67 downloads
122 views

Background. Real-time quantitative PCR (qPCR) is a broadly used technique in the biomedical research. Currently, few different analysis models are used to determine the quality of data and to quantify the mRNA level across the experimental conditions. Methods....

["Bioinformatics","Cell Biology","Computational Biology","Molecular Biology"]
doi:10.7287/peerj.preprints.3477v1
68 downloads
152 views

The increasing move towards open access full-text scientific literature enhances our ability to utilize advanced text-mining methods to construct information-rich networks that no human will be able to grasp simply from 'reading the literature'. The utility of...

["Computational Biology","Microbiology","Plant Science"]
doi:10.7287/peerj.preprints.3472v1
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