Preprints (not yet peer-reviewed)

19 downloads
83 views

The analysis of large numbers of sequences requires the reduction of ambiguities during the analytical work to ensure that the effort will focus only on confirmed sequences. Performing this work automatically may help to minimize potential errors associated with...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.3364v1
20 downloads
147 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.3217v3
21 downloads
138 views

Personalized medicine is in great part enabled by the progress in data acquisition technologies for modern biology, such as next-generation sequencing (NGS). Conventional NGS processing workflows are composed by independent tools implementing shared-memory parallelism...

["Bioinformatics","Computational Biology","Distributed and Parallel Computing"]
doi:10.7287/peerj.preprints.3338v1
18 downloads
131 views

MicroRNAs (miRNAs) are small non-coding RNA molecules mediating the translational repression and degradation of target mRNAs in the cell. Mature miRNAs are used as a template by the RNA-induced silencing complex (RISC) to recognize the complementary mRNAs to be...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7287/peerj.preprints.3337v1
187 downloads
541 views

Computational models in biology encode molecular and cell biological processes. These models often can be represented as biochemical reaction networks. Studying such networks, one is mostly interested in systems that share similar reactions and mechanisms. Typical...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning","Data Science"]
doi:10.7287/peerj.preprints.1479v3
32 downloads
193 views

As the costs of high-throughput measurement technologies continue to fall, experimental approaches in biomedicine are increasingly data intensive and the advent of big data is justifiably seen as holding the promise to transform medicine. However, as data volumes...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.3328v1
27 downloads
107 views

Celiac disease is a chronic condition, which can be described as inflammatory and autoimmune. The well-known treatment is a lifelong gluten-free diet, but it can be not totally effective for a high percentage of the patients. The aim of this work is to approach...

["Bioinformatics","Biotechnology","Computational Biology","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.3315v1
40 downloads
186 views

Network Diffusion has been proposed in several applications, thanks to its ability of amplifying biological signals and prioritizing genes that may be associated with a disease. Not surprising, the success of Network Diffusion on a “single layer” led to the first...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7287/peerj.preprints.3310v1
32 downloads
71 views

We present GenotypeAnalytics (GA), a RESTFul service that makes it possible to mine association rules from Single Nucleotide Polymorphism (SNP) datasets using standard web browsers. GA can speed up and simplify the analysis of this massive amount of data, highlighting...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning","Data Science","World Wide Web and Web Science"]
doi:10.7287/peerj.preprints.3299v1
35 downloads
78 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
53 downloads
240 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
34 downloads
102 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
58 downloads
126 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
69 downloads
181 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
25 downloads
74 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
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