Preprints (not yet peer-reviewed)

4 downloads
29 views

Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on the comparison of single DNA sequences, or a concatenation of a number of these. However, with the advent of next-generation DNA sequencing technologies, the...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.3271v1
19 downloads
164 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.3266v3
3 downloads
29 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
11 downloads
66 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
46 downloads
99 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
13 downloads
39 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
15 downloads
46 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
135 downloads
400 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
16 downloads
205 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
11 downloads
50 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
59 downloads
292 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
28 downloads
139 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
24 downloads
200 views

Analysis of DNA microarray data has been very useful for experimental molecular biology, as it provides unprecedented opportunities to study a wide variety of biological processes. As a part of this analysis, biclustering has been consolidated as one of the first...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.3110v2
49 downloads
198 views

Sigmoidal and double-sigmoidal dynamics are commonly observed in many areas of biology. Here we present sicegar, an R package for the automated fitting and classification of sigmoidal and double-sigmodial data. The package categorizes data into one of three categories,...

["Bioinformatics","Computational Biology","Mathematical Biology","Statistics","Data Science"]
doi:10.7287/peerj.preprints.3116v1
41 downloads
237 views

We have developed a machine learning approach to predict context specific enhancer-promoter interactions using evidence from changes in genomic protein occupancy over time. The occupancy of estrogen receptor alpha (ERα), RNA polymerase (Pol II) and histone marks...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7287/peerj.preprints.3093v1
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