Preprints (not yet peer-reviewed)

1 download
4 views

Background. Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease primarily affecting upper and lower motor neurons in the brain and spinal cord. The heterogeneity in the course of ALS clinical progression and ultimately survival, coupled...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning","Scientific Computing and Simulation"]
doi:10.7287/peerj.preprints.3262v1
4 downloads
39 views

The mutational processes responsible for the somatic mutations observed in tumor samples can significantly vary not only between tumor types but also among the individual cancers within a tumor class. Mutational processes can be represented by so called “mutational...

["Bioinformatics","Computational Biology","Genomics","Oncology"]
doi:10.7287/peerj.preprints.3257v1
4 downloads
70 views

Horizontal gene transfer (HGT) is a powerful mechanism that allows bacteria to directly transfer long stretches of genomic sequence from one individual to another. The transfer of antimicrobial resistance genes is a prominent example of HGT events in the context...

["Bioinformatics","Computational Biology","Public Health","Computational Science"]
doi:10.7287/peerj.preprints.3248v1
4 downloads
28 views

The process of inferring a full haplotype of a cell is known as haplotyping, which consists in assigning all heterozygous Single Nucleotide Polymorphisms (SNPs) to exactly one of the two chromosomes. In this work, we propose a novel computational method for haplotype...

["Bioinformatics","Computational Biology","Artificial Intelligence","Distributed and Parallel Computing","Optimization Theory and Computation"]
doi:10.7287/peerj.preprints.3246v1
12 downloads
42 views

In complex phenotypes (e.g., psychiatric diseases) single locus tests, commonly performed with Genome-Wide Association Studies, have proven to be limited in discovering strong gene associations. A growing body of evidence suggests that epistatic non-linear effects...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.3242v1
9 downloads
96 views

Computational biology is rapidly advancing thanks to the many new tools developed and published each month. A systematic benchmarking practice would help biomedical researchers leverage this technological expansion to optimize their projects. Several aspects of...

["Computational Biology","Genetics","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.3236v1
107 downloads
344 views

Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed...

["Agricultural Science","Bioinformatics","Computational Biology","Plant Science","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.3225v1
13 downloads
190 views

Epigenetic research focuses on understanding non-inheritable factors influencing gene regulation and covers various cellular mechanisms such as DNA methylation, histone modification, miRNA function and transcription factor binding sites. Recent advances in high-throughput...

["Bioinformatics","Computational Biology","Genetics","Molecular Biology","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.3224v1
8 downloads
48 views

The immune system protects a host from foreign pathogens. In rare cases, the immune system can attack the cells of the host organism causing autoimmune diseases. We outline a computational framework that combines bioinformatics and network analysis with an emerging...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.3217v2
11 downloads
72 views

Algal blooms have been the subject of considerable research as they occur over various spatial and temporal scales and can produce toxins that disrupt their ecosystem. Algal blooms are often governed by nutrient availability however other limitations exist. Algae...

["Biodiversity","Computational Biology","Ecology","Marine Biology","Mathematical Biology"]
doi:10.7287/peerj.preprints.3218v1
55 downloads
277 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. We use rigorous simulations...

["Bioinformatics","Computational Biology","Evolutionary Studies"]
doi:10.7287/peerj.preprints.3206v1
4 downloads
46 views

We propose a series of ODE systems to model the various dynamics of human-Borg interaction during a Borg invasion. These models, progressively developed one after the other, could provide humanity and other peace-loving intergalactic species the necessary mathematical...

["Computational Biology","Adaptive and Self-Organizing Systems","Scientific Computing and Simulation"]
doi:10.7287/peerj.preprints.3198v1
356 downloads
1,597 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.3192v1
28 downloads
135 views

The regulatory code that determines whether and how a given genetic variant affects the function of a regulatory element remains poorly understood for most classes of regulatory variation. Indeed the large majority of bioinformatics tools have been developed to...

["Bioinformatics","Computational Biology","Computational Science","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.3185v1
589 downloads
2,427 views

Spreadsheets are widely used software tools for data entry, storage, analysis, and visualization. Focusing on the data entry and storage aspects, this paper offers practical recommendations for organizing spreadsheet data to reduce errors and ease later analyses....

["Computational Biology","Science and Medical Education","Statistics","Computational Science","Data Science"]
doi:10.7287/peerj.preprints.3183v1
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