Preprints (not yet peer-reviewed)

Fine-scale evolutionary dynamics can be challenging to tease out when focused on broad brush strokes of whole populations over long time spans. We propose a suite of diagnostic metrics that operate on lineages and phylogenies in digital evolution experiments with...

["Computational Biology","Adaptive and Self-Organizing Systems","Scientific Computing and Simulation"]
doi:10.7287/peerj.preprints.26883v1
10 downloads
81 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
66 downloads
181 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
126 downloads
351 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
228 downloads
585 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
125 downloads
272 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
231 downloads
493 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
220 downloads
682 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
1,660 downloads
3,851 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
210 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
86 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
134 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
203 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
164 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
66 downloads
145 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
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