Peer-reviewed Articles - Biology

29 downloads
228 views

Transcription factors (TFs) and microRNAs (miRNAs) are well-characterized trans-acting essential players in gene expression regulation. Growing evidence indicates that TFs and miRNAs can work cooperatively, and their dysregulation has been associated with many...

["Bioinformatics","Computational Biology","Genomics","Computational Science"]
doi:10.7717/peerj.5951
29 downloads
181 views

We present PromoterPredict, a dynamic multiple regression approach to predict the strength of Escherichia coli promoters binding the σ70 factor of RNA polymerase. σ70 promoters are ubiquitously used in recombinant DNA technology, but characterizing their strength...

["Bioinformatics","Computational Biology","Genomics","Synthetic Biology","Data Mining and Machine Learning"]
doi:10.7717/peerj.5862
38 downloads
238 views

Background The need for read-based phasing arises with advances in sequencing technologies. The minimum error correction (MEC) approach is the primary trend to resolve haplotypes by reducing conflicts in a single nucleotide polymorphism-fragment matrix. However,...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7717/peerj.5852
65 downloads
306 views

Background Osteoclast differentiation in the inflamed synovium of rheumatoid arthritis (RA) affected joints leads to the formation of bone lesions. Reconstruction and analysis of protein interaction networks underlying specific disease phenotypes are essential...

["Bioinformatics","Computational Biology","Genomics","Immunology","Rheumatology"]
doi:10.7717/peerj.5743
58 downloads
198 views

Xeno-miRNAs are microRNAs originating from exogenous species detected in host biofluids. A growing number of studies have suggested that many of these xeno-miRNAs may be involved in cross-species interactions and manipulations. To date, hundreds of xeno-miRNAs...

["Bioinformatics","Computational Biology","Genetics","Genomics","Parasitology"]
doi:10.7717/peerj.5650
142 downloads
573 views

Background Dengue fever has rapidly manifested into a serious global health concern. The emergence of various viral serotypes has prompted the urgent need for innovative drug design techniques. Of the viral non-structural enzymes, the NS5 RNA-dependent RNA polymerase...

["Bioinformatics","Computational Biology","Genomics","Infectious Diseases"]
doi:10.7717/peerj.5068
77 downloads
351 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
70 downloads
351 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
89 downloads
378 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
2 citations
177 downloads
697 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
1 citation
287 downloads
1,008 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
206 downloads
1,759 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
180 downloads
1,022 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
135 downloads
1,092 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
5 citations
361 downloads
1,503 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

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