Preprints (not yet peer-reviewed)

6 downloads
56 views

Protein sites present different amino acids during their evolution, whose number reflects the selective constraints operating on them. This evolutionary variability is strongly influenced by the structural properties of the site in the native structure, and it...

["Bioinformatics","Biophysics","Computational Biology","Evolutionary Studies"]
doi:10.7287/peerj.preprints.26868v1
52 downloads
150 views

Single-cell RNA-seq is revolutionizing our understanding of cell type heterogeneity in many fields of biology, ranging from neuroscience to cancer to immunology. In Immunology, one of the main promises of this approach is the ability to define cell types as clusters...

["Bioinformatics","Computational Biology","Evolutionary Studies","Immunology"]
doi:10.7287/peerj.preprints.26858v1
117 downloads
327 views

Many data include time or have longitudinal dimensionalilty. When these data include an index of time, i.e. measures at regular or periodically successive intervals, statistics that use time sequencing in some capacity are appropriate. Consequently, investing time...

["Bioinformatics","Computational Biology","Data Science"]
doi:10.7287/peerj.preprints.26842v1
223 downloads
562 views

Many pressing medical challenges -- such as diagnosing disease, enhancing directed stem cell differentiation, and classifying cancers -- have long been hindered by limitations in our ability to quantify proteins in single cells. Mass-spectrometry (MS) is poised...

["Bioengineering","Biotechnology","Cell Biology","Computational Biology","Genomics"]
doi:10.7287/peerj.preprints.26821v1
123 downloads
260 views

High-throughput sequencing of environmental DNA (eDNA) offers a simple and cost-effective solution for marine biodiversity assessments. Yet several analytical challenges remain, including the incorporation of statistical inference in the assignment of taxonomic...

["Biodiversity","Bioinformatics","Computational Biology","Marine Biology","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.26812v1
227 downloads
479 views

Potential Natural Vegetation (PNV) is the vegetation cover in equilibrium with climate, that would exist at a given location non-impacted by human activities. PNV is useful for raising public awareness about land degradation and for estimating land potential. This...

["Biogeography","Computational Biology","Plant Science","Data Mining and Machine Learning","Spatial and Geographic Information Science"]
doi:10.7287/peerj.preprints.26811v1
214 downloads
662 views

The development of methods to estimate rates of speciation and extinction from time- calibrated phylogenies has revolutionized evolutionary biology by allowing researchers to correlate diversification rate shifts with causal ecological factors. A growing number...

["Bioinformatics","Computational Biology","Evolutionary Studies"]
doi:10.7287/peerj.preprints.3206v2
1,640 downloads
3,823 views

Computers are a central tool in the research process, enabling complex and large scale data analysis. As computer-based research has increased in complexity, so have the challenges of ensuring that this research is reproducible. To address this challenge, we review...

["Anthropology","Computational Biology","Science and Medical Education","Computational Science","Data Science"]
doi:10.7287/peerj.preprints.3192v2
52 downloads
200 views

The ability of vertebrates to generate rhythm within their spinal neural networks is essential for walking, running, and other rhythmic behaviors. The central pattern generator (CPG) network responsible for these behaviors is well-characterized with experimental...

["Animal Behavior","Bioinformatics","Computational Biology","Neuroscience","Computational Science"]
doi:10.7287/peerj.preprints.26734v1
51 downloads
77 views

The classification of fresh fruits according to their ripeness is typically a subjective and tedious task; consequently, there is growing interest in the use of non-contact techniques such as those based on computer vision and machine learning. In this paper, we...

["Agricultural Science","Computational Biology","Food Science and Technology","Computational Science","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.26691v1
50 downloads
125 views

Analysing the relationships between biomolecules and the genetic diseases is a highly active area of research, where the aim is to identify the genes and their products that cause a particular disease due to functional changes originated from mutations. Biological...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.26663v1
57 downloads
191 views

The analysis of microbiome dynamics would allow us to elucidate patterns within microbial community evolution; however, microbiome state-transition dynamics have been scarcely studied. This is in part because a necessary first-step in such analyses has not been...

["Bioinformatics","Computational Biology","Microbiology","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.26657v1
85 downloads
159 views

R has many capabilities most of which are not known by many users, yet waiting to be discovered. For this reason we provide more tips on how to write really efficient code without having to program in C++, programming advice, and tips to avoid errors and numerical...

["Bioinformatics","Computational Biology","Computational Linguistics","Data Mining and Machine Learning","Data Science"]
doi:10.7287/peerj.preprints.26605v1
64 downloads
130 views

After transitioning to a new environment, species often exhibit rapid phenotypic innovation. One of the fastest mechanisms for this is duplication followed by specialization of existing genes, which leaves a phylogenetic signature of lineage-specific expansions...

["Bioinformatics","Computational Biology","Evolutionary Studies"]
doi:10.7287/peerj.preprints.26593v1
54 downloads
136 views

There are two basic forms of animal development: mosaic (as found in roundworms and sea squirts) and regulative (as found in amphibians and mammals). How might one distinguish between each type of development? Using a four-dimensional spatial representation (x,y,z,t),...

["Bioinformatics","Computational Biology","Developmental Biology"]
doi:10.7287/peerj.preprints.26587v1
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