Peer-reviewed Articles - Biology

15 downloads
103 views

Background High myopia is a common ocular disease worldwide. To expand our current understanding of the genetic basis of high myopia, we carried out a whole exome sequencing (WES) study to identify potential causal gene mutations. Methods A total of 20 individuals...

["Bioinformatics","Computational Biology","Genetics","Genomics","Translational Medicine"]
doi:10.7717/peerj.5552
38 downloads
259 views

In single-cell RNA-sequencing, it is important to know the frequency at which the sequenced transcriptomes actually derive from multiple cells. A common method to estimate this multiplet frequency is to mix two different types of cells (e.g., human and mouse),...

["Bioinformatics","Computational Biology","Genomics","Mathematical Biology"]
doi:10.7717/peerj.5578
71 downloads
328 views

Background Optimization of transgene expression can be achieved by designing coding sequences with the synonymous codon usage of genes which are highly expressed in the host organism. The identification of the so-called “favoured codons” generally requires the...

["Bioinformatics","Biotechnology","Computational Biology","Genomics"]
doi:10.7717/peerj.5099
1 citation
150 downloads
594 views

Background Using DNA microarrays, we previously identified 451 genes expressed in 19 different human tissues. Although ubiquitously expressed, the variable expression patterns of these “housekeeping genes” (HKGs) could separate one normal human tissue type from...

["Bioinformatics","Computational Biology","Genomics","Oncology","Medical Genetics"]
doi:10.7717/peerj.4719
215 downloads
871 views

During the past decade, with the significant progress of computational power as well as ever-rising data availability, deep learning techniques became increasingly popular due to their excellent performance on computer vision problems. The size of the Protein Data...

["Bioinformatics","Computational Biology","Genomics","Computational Science"]
doi:10.7717/peerj.4750
182 downloads
1,599 views

RNA editing modifies transcripts and may alter their regulation or function. In humans, the most common modification is adenosine to inosine (A-to-I). We examined the global characteristics of RNA editing in 4,301 human tissue samples. More than 1.6 million A-to-I...

["Computational Biology","Genetics","Genomics","Cardiology","Computational Science"]
doi:10.7717/peerj.4466
159 downloads
934 views

C9orf72 is associated with frontotemporal dementia (FTD) and Amyotrophic Lateral Sclerosis (ALS), both of which are devastating neurodegenerative diseases. Findings suggest that an expanded hexanucleotide repeat in the non-coding region of the C9orf72 gene is the...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7717/peerj.4391
4 citations
120 downloads
1,004 views

We introduce LEISR (Likehood Estimation of Individual Site Rates, pronounced “laser”), a tool to infer relative evolutionary rates from protein and nucleotide data, implemented in HyPhy. LEISR is based on the popular Rate4Site (Pupko et al., 2002) approach for...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics"]
doi:10.7717/peerj.4339
4 citations
335 downloads
1,320 views

The ubiquitous daily rhythms in mammalian physiology are guided by progression of the circadian clock. In mice, systemic disruption of the clock can promote tumor growth. In vitro, multiple oncogenes can disrupt the clock. However, due to the difficulties of studying...

["Bioinformatics","Computational Biology","Genomics","Oncology"]
doi:10.7717/peerj.4327
192 downloads
1,093 views

Plasma lipid levels are risk factors for cardiovascular disease, a leading cause of death worldwide. While many studies have been conducted on lipid genetics, they mainly focus on Europeans and thus their transferability to diverse populations is unclear. We performed...

["Computational Biology","Genetics","Genomics"]
doi:10.7717/peerj.4314
420 downloads
1,296 views

Genomic signal processing (GSP) methods which convert DNA data to numerical values have recently been proposed, which would offer the opportunity of employing existing digital signal processing methods for genomic data. One of the most used methods for exploring...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7717/peerj.4264
218 downloads
987 views

The etiology of cancer includes aberrant cellular homeostasis where a compromised RNA regulatory network is a prominent contributing factor. In particular, noncoding RNAs including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) were recently shown to play...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7717/peerj.4254
238 downloads
1,386 views

The amino acid content of the proteins encoded by a genome may predict the coding potential of that genome and may reflect lifestyle restrictions of the organism. Here, we calculated the Kullback–Leibler divergence from the mean amino acid content as a metric to...

["Bioinformatics","Computational Biology","Genomics","Microbiology","Statistics"]
doi:10.7717/peerj.4026
195 downloads
905 views

Recently, Docker technology has received increasing attention throughout the bioinformatics community. However, its implementation has not yet been mastered by most biologists; accordingly, its application in biological research has been limited. In order to popularize...

["Bioinformatics","Computational Biology","Genomics","Microbiology"]
doi:10.7717/peerj.3948
1 citation
527 downloads
1,923 views

Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers. ATAC-seq surmounted a major technical barrier and enabled epigenome profiling of clinical...

["Bioinformatics","Computational Biology","Genomics","Human-Computer Interaction","Computational Science"]
doi:10.7717/peerj.4040

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