Preprints (not yet peer-reviewed)

83 downloads
215 views

Bioinformatics algorithms are now crucial for processing high throughput “-omics” data and deriving meaningful interpretations in most biomedical and life science research domains. Bioinformatics-related training and research mostly take place in nations with higher...

["Bioinformatics","Computational Biology","Genomics","Science and Medical Education"]
doi:10.7287/peerj.preprints.27415v1
110 downloads
223 views

Increasingly, big data, coding, and quantitative methods contribute to contemporary ecological and evolutionary endeavours. This is not in opposition to effective ideation nor does it play to the false dichotomy of theory versus data. Computational expeditions...

["Computational Biology","Computer Education","Data Science"]
doi:10.7287/peerj.preprints.27408v1
17 downloads
67 views

Clinical bioinformatics, translational bioinformatics and personalised medicine are connected by the common task of analysing and integrating clinical data and results, in order to find important biomarkers related to pathologies and facilitate their prediction,...

["Bioinformatics","Computational Biology","Pathology","Statistics","Data Science"]
doi:10.7287/peerj.preprints.27398v1
3,409 downloads
5,397 views

Gene expression is the fundamental level at which the result of various genetic and regulatory programs are observable. The measurement of transcriptome-wide gene expression has convincingly switched from microarrays to sequencing in a matter of years. RNA sequencing...

["Bioinformatics","Computational Biology","Genomics","Data Science"]
doi:10.7287/peerj.preprints.27283v2
229 downloads
359 views

The rapid decrease in DNA sequencing cost is revolutionizing medicine and science. In medicine, genome sequencing has revealed millions of missense variants that change protein sequences, yet we only understand the molecular and phenotypic consequences of a small...

["Bioinformatics","Biophysics","Computational Biology","Genomics","Medical Genetics"]
doi:10.7287/peerj.preprints.27379v1
1,494 downloads
3,486 views

This article proposes quantitative answers to meta-scientific questions including "how much knowledge is attained by a research field?","how rapidly is a field making progress?", "what is the expected reproducibility of a result?", "how much knowledge is lost from...

["Computational Biology","Ethical Issues","Science Policy","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.1968v5
52 downloads
106 views

Crowding research has become a hotbed of vision research and some fundamentals are now widely agreed upon. It is highly likely that you would agree with the following statements. 1) Bouma’s Law can be sensibly stated as saying that ‘critical distance for crowding...

["Computational Biology","Neuroscience","Anatomy and Physiology","Ophthalmology","Psychiatry and Psychology"]
doi:10.7287/peerj.preprints.27353v1
29 downloads
58 views

Next-generation sequencing (NGS) technologies are greatly facilitating the sequencing of whole genomes leading to the production of different gene annotations, released often from both reference resources (such as NCBI or Ensembl) and specific consortia. All these...

["Computational Biology","Data Science","Databases"]
doi:10.7287/peerj.preprints.27347v1
27 downloads
77 views

Explaining the variability in drug sensitivity across a panel of cell lines using genomic information is a key aspect of cancer drug discovery. The results of such analyses may ultimately determine which patients are likely to benefit from a new treatment. There...

["Bioinformatics","Computational Biology","Genomics","Drugs and Devices","Oncology"]
doi:10.7287/peerj.preprints.27345v1
28 downloads
98 views

To compare multiple genome sequences, we transform each primary genome sequence into corresponding k-mer-based vectors. According to the principle of independent component analysis (ICA), the operation can be regarded as mixing multiple source genomic signals via...

["Bioinformatics","Computational Biology","Genomics","Mathematical Biology","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.27333v1
29 downloads
109 views

Several programs have been developed that are able to replace a residue with another one in a protein structure, but usually they are not able to simulate the short- and long-range effects of a real single point mutation. We tested if the approach of re-modelling...

["Biochemistry","Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.27326v1
39 downloads
72 views

One of the most challenging fields in Life Science research is to deeply understand how complex cellular functions arise from the interactions of molecules in living cells. Mathematical and computational methods in Systems Biology are fundamental to study the complex...

["Computational Biology"]
doi:10.7287/peerj.preprints.27327v1
34 downloads
99 views

Neurological diseases (NDs) are progressive disorder often advances with age and comorbidities of Type 2 diabetes (T2D). Epidemiological, clinical and neuropathological evidence advocate that patients with T2D are at an increased risk of getting NDs. However, it...

["Bioinformatics","Computational Biology","Genetics","Genomics","Diabetes and Endocrinology"]
doi:10.7287/peerj.preprints.27323v1
40 downloads
124 views

We propose a biologically-inspired research agenda with parallel tracks aimed at AI and AI safety. The bottom-up component consists of building a sequence of biophysically realistic simulations of simple organisms such as the nematode Caenorhabditis elegans, the...

["Animal Behavior","Computational Biology","Entomology","Neuroscience","Zoology"]
doi:10.7287/peerj.preprints.27321v1
71 downloads
102 views

There are many methods available for each phase of the RNA-Seq analysis and each of them uses different algorithms. It is therefore useful to identify a pipeline that combines the best tools in terms of time and results. For this purpose, we compared five different...

["Bioinformatics","Computational Biology","Data Science"]
doi:10.7287/peerj.preprints.27317v2
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