Preprints (not yet peer-reviewed)

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
24 downloads
60 views

During software maintenance, developers usually deal with a significant number of software change requests. As a part of this, they often formulate an initial query from the request texts, and then attempt to map the concepts discussed in the request to relevant...

["Software Engineering"]
doi:10.7287/peerj.preprints.3186v2
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
1 download
4 views

Melanoma is a highly immunogenic tumor. Therefore, in recent years physicians have incorporated drugs that alter the immune system into their therapeutic arsenal against this disease, revolutionizing in the treatment of patients in an advanced stage of the disease....

["Bioinformatics","Algorithms and Analysis of Algorithms","Databases","Visual Analytics"]
doi:10.7287/peerj.preprints.3260v1
3 downloads
9 views

Irreducible Polynomials (IPs) have been of utmost importance in generation of substitution boxes in modern cryptographic ciphers. In this paper an algorithm entitled Composite Algorithm using both multiplication and division over Galois fields have been demonstrated...

["Cryptography","Scientific Computing and Simulation","Security and Privacy"]
doi:10.7287/peerj.preprints.3259v1
3 downloads
8 views

Searching for Monic Irreducible Polynomials (IPs) over extended Galois Field GF(p^q) for large value of prime moduli p and extension to Galois Field q is a well needed solution in the field of Cryptography. In this paper a new algorithm to obtain Monic IPs over...

["Cryptography","Security and Privacy"]
doi:10.7287/peerj.preprints.3258v1
6 downloads
31 views

The growth function is the generating function for sizes of spheres around the identity in Cayley graphs of groups. We present a novel method to calculate growth functions for automatic groups with normal form recognizing automata that recognize a single normal...

["Theory and Formal Methods"]
doi:10.7287/peerj.preprints.3256v1
4 downloads
11 views

4-bit Linear Relations play an important role in Cryptanalysis of 4-bit Bijective S-Boxes. Count of existence of all 4-bit Linear Relations, for all of 16 input and output 4-bit bit patterns of 4-bit Bijective S-Boxes said as S-Boxes has been reported in Linear...

["Cryptography"]
doi:10.7287/peerj.preprints.3249v1
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
138 downloads
545 views

Despite most Spatial Data Infrastructures are offering service-based visualization of geospatial data, requirements are often at a very basic level leading to poor quality of maps. This is a general observation for any geospatial architecture as soon as open standards...

["Spatial and Geographic Information Systems","World Wide Web and Web Science"]
doi:10.7287/peerj.preprints.2415v4
80 downloads
770 views

We describe best practices for providing convenient, high-speed, secure access to large data via research data portals. We capture these best practices in a new design pattern, the Modern Research Data Portal, that disaggregates the traditional monolithic web-based...

["Computer Networks and Communications","Data Science","Distributed and Parallel Computing","Security and Privacy","World Wide Web and Web Science"]
doi:10.7287/peerj.preprints.3194v2
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
11 downloads
32 views

The increasing amount of -omics data leads to development of models to interpret and analyse them. A common approach consists in representing data as PPI Networks. These models can be very complex and informatics tools are needed to analyse them. In this abstract,...

["Bioinformatics"]
doi:10.7287/peerj.preprints.3229v1
52 downloads
477 views

The geology and mineralogy of the Apollo 12 landing site has been the subject of recent studies that this research attempts to complement from a remote sensing point of view using the Moon Mineralogy Mapper (M3) sensor data, onboard the Chandrayaan-1 lunar orbiter....

["Algorithms and Analysis of Algorithms","Data Science","Scientific Computing and Simulation","Spatial and Geographic Information Systems"]
doi:10.7287/peerj.preprints.2124v2
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
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