Preprints (not yet peer-reviewed)

DNA metabarcoding provides species composition data for entire communities, yet information on intraspecific diversity is usually lost during data analysis. The capacity to infer intraspecific genetic diversity within whole communities would, however, represent...

["Biogeography","Bioinformatics","Molecular Biology","Freshwater Biology"]
doi:10.7287/peerj.preprints.3269v1

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

The annual German Conference on Bioinformatics (GCB) has brought together renowned international scientists in bioinformatics, computational biology, biostatistics, biology and medicine since 1993. The 25th GCB was held in Tübingen from 18th to 21st of September...

["Bioinformatics"]
doi:10.7287/peerj.preprints.3268v1
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
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
16 downloads
159 views

Bacterial surfaces are complex, built of from membranes, peptide-glycans and, importantly, proteins. The proteins play crucial roles as the key regulator of how the bacterium interacts with its environment. A full catalog of the motifs in coiled-coil proteins and...

["Bioinformatics","Infectious Diseases","Data Science"]
doi:10.7287/peerj.preprints.3118v2
4 downloads
68 views

Finding and enumerating common molecular substructures is an important task in cheminformatics, where small molecules are often modeled as molecular graphs. We introduce the problem of enumerating all maximal k-common molecular fragments of a pair of molecular...

["Bioinformatics","Computational Science"]
doi:10.7287/peerj.preprints.3250v1
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
3 downloads
46 views

Background. Actinobacillus pleuropneumonia is a gram-negative bacterium that serves as the major etiological agent for porcine pleuropneumonia, one of critical diseases causing substantial socio-economic losses in swine rearing industry world-wide. Apx exotoxins...

["Bioinformatics","Veterinary Medicine"]
doi:10.7287/peerj.preprints.3244v1
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
104 views

Background: Due to the interplay between many factors, systems medicine of complex diseases is most often centered either on individual genes, or on statistical associations. Complex network analysis could potentially explain systems-wide differences between patients...

["Bioinformatics"]
doi:10.7287/peerj.preprints.3241v1
7 downloads
126 views

Contemporary proteins can be traced back to a basic set of a few thousand domain prototypes. The origin of these domain prototypes, however, remains poorly understood. We have proposed that they arose from an ancestral set of peptides, which acted as cofactors...

["Biochemistry","Bioinformatics","Evolutionary Studies"]
doi:10.7287/peerj.preprints.3234v1
23 downloads
123 views

The gastro-intestinal (GI) microbiota of abalone contains a highly complex bacterial assemblage playing an essential role in the overall health of these gastropods. The gut bacterial communities characterized so far reveal considerable interspecific variability,...

["Bioinformatics","Microbiology","Molecular Biology"]
doi:10.7287/peerj.preprints.3233v1
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