Preprints (not yet peer-reviewed)

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

It is now becoming feasible to determine the composition of an individual gut microbiota (gut microflora), as well as the individual genome. In addition, whole genome scale metabolic models (GEMs) exist for a range of bacteria, and also for human. In principle...

["Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.3267v1
4 downloads
58 views

The leading cause of permanent disability in developed countries is due to neurological injuries, such as stroke. While physical rehabilitation therapy is indispensable for treating neurological disabilities, repetitive and high intensity therapies place high physical...

["Human-Computer Interaction","Computational Science"]
doi:10.7287/peerj.preprints.3255v2
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
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
26 downloads
107 views

Standard procedures for NGS data analysis involve a pre-processing step of reads quality assessment, followed by the alignment of the filtered reads to a reference genome. Typically the amount of reads that correctly maps to the specific reference genome ranges...

["Bioinformatics","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.3230v1
212 downloads
592 views

RNA sequencing (RNA-Seq) is a powerful technique for thegene-expression profiling of organisms that uses the capabilities of next-generation sequencing technologies.Developing gene-expression-based classification algorithms is an emerging powerful method for diagnosis,...

["Bioinformatics","Genomics","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.2761v2
550 downloads
3,294 views

Traditionally, statistical training has focused primarily on mathematical derivations and proofs of statistical tests. The process of developing the technical artifact—that is, the paper, dashboard, or other deliverable—is much less frequently taught, presumably...

["Statistics","Human-Computer Interaction","Computational Science","Data Science"]
doi:10.7287/peerj.preprints.3210v1
795 downloads
2,416 views

Over the last three decades data has become ubiquitous and cheap. This transition has accelerated over the last five years and training in statistics, machine learning, and data analysis have struggled to keep up. In April 2014 we launched a program of nine courses,...

["Science and Medical Education","Statistics","Human-Computer Interaction","Computational Science"]
doi:10.7287/peerj.preprints.3195v1
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
224 downloads
1,437 views

Clustered regularly interspaced short palindromic repeat (CRISPR) systems are the adaptive immune systems of bacteria and archaea against viral infection. While CRISPRs have been exploited as a tool for genetic engineering, their spacer sequences can also provide...

["Bioinformatics","Genomics","Microbiology","Computational Science"]
doi:10.7287/peerj.preprints.2278v4
3,378 downloads
22,210 views

The website Sci-Hub provides access to scholarly literature via full text PDF downloads. The site enables users to access articles that would otherwise be paywalled. Since its creation in 2011, Sci-Hub has grown rapidly in popularity. However, until now, the extent...

["Bioinformatics","Legal Issues","Science and Medical Education","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.3100v1
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