Peer-reviewed Articles - Computer sci

14 downloads
96 views

The AP2/ERF superfamily of transcription factors is one of the largest transcription factor families in plants and plays an important role in plant development processes and stress responses. In this study, BjABR1, an AP2/ERF superfamily gene, from tuber mustard...

["Bioinformatics","Molecular Biology","Plant Science"]
doi:10.7717/peerj.6071
72 downloads
675 views

Modern scientific studies from many diverse areas of research abound with multiple hypothesis testing concerns. The false discovery rate (FDR) is one of the most commonly used approaches for measuring and controlling error rates when performing multiple tests....

["Bioinformatics","Statistics","Data Science"]
doi:10.7717/peerj.6035
31 downloads
121 views

Next-Generation Sequencing (NGS) technologies provide unique possibilities for the comprehensive assessment of the environmental diversity of bacteriophages. Several Bacillus bacteriophages have been isolated, but very few Bacillus megaterium bacteriophages have...

["Agricultural Science","Bioinformatics","Genomics","Virology"]
doi:10.7717/peerj.5687
26 downloads
110 views

Background Understanding hub genes involved in gastric cancer (GC) metastasis could lead to effective approaches to diagnose and treat cancer. In this study, we aim to identify the hub genes and investigate the underlying molecular mechanisms of GC. Methods To...

["Bioinformatics","Gastroenterology and Hepatology"]
doi:10.7717/peerj.6092
81 downloads
136 views

Protein structure is not static; residues undergo conformational rearrangements and, in doing so, create, stabilize or break non-covalent interactions. Molecular dynamics (MD) is a technique used to simulate these movements with atomic resolution. However, given...

["Bioinformatics","Biophysics","Computational Biology"]
doi:10.7717/peerj.5998
17 downloads
131 views

Background Colorectal cancer remains a serious public health problem due to the poor prognosis. In the present study, we attempted to develop and validate a prognostic signature to predict the individual mortality risk in colorectal cancer patients. Materials and...

["Bioinformatics","Molecular Biology","Gastroenterology and Hepatology","Oncology"]
doi:10.7717/peerj.6061
27 downloads
245 views

Reverse engineering metabolome data to infer metabolic interactions is a challenging research topic. Here we introduce JacLy, a Jacobian-based method to infer metabolic interactions of small networks (<20 metabolites) from the covariance of steady-state metabolome...

["Bioengineering","Bioinformatics","Biotechnology","Computational Biology","Computational Science"]
doi:10.7717/peerj.6034
66 downloads
179 views

Use of environmental DNA (eDNA) to assess distributions of aquatic and semi-aquatic macroorganisms is promising, but sampling schemes may need to be tailored to specific objectives. Given the potentially high variance in aquatic eDNA among replicate grab samples,...

["Aquaculture, Fisheries and Fish Science","Bioinformatics","Ecosystem Science","Freshwater Biology"]
doi:10.7717/peerj.5871
50 downloads
459 views

The family Miridae is the most diverse and one of the most economically important groups in Heteroptera. However, identification of mirid species on the basis of morphology is difficult and time-consuming. In the present study, we evaluated the effectiveness of...

["Agricultural Science","Bioinformatics","Entomology","Molecular Biology","Taxonomy"]
doi:10.7717/peerj.6070
57 downloads
255 views

Background Bladder cancer is a malignant tumor in the urinary system with high mortality and recurrence rates. However, the causes and recurrence mechanism of bladder cancer are not fully understood. In this study, we used integrated bioinformatics to screen for...

["Bioinformatics","Oncology","Data Mining and Machine Learning"]
doi:10.7717/peerj.6036
39 downloads
269 views

Motivation The identification of functional sequence variations in regulatory DNA regions is one of the major challenges of modern genetics. Here, we report results of a combined multifactor analysis of properties characterizing functional sequence variants located...

["Bioinformatics","Genomics","Data Mining and Machine Learning"]
doi:10.7717/peerj.5742
74 downloads
546 views

Background and Objective Docker is a light containerization program that shows almost the same performance as a local environment. Recently, many bioinformatics tools have been distributed as Docker images that include complex settings such as libraries, configurations,...

["Bioinformatics","Genomics"]
doi:10.7717/peerj.5954
107 downloads
602 views

We have sequenced a partial transcriptome of the Northern Wheatear (Oenanthe oenanthe), a species with one of the longest migrations on Earth. The transcriptome was constructed de novo using RNA-Seq sequence data from the pooled mRNA of six different tissues: brain,...

["Animal Behavior","Bioinformatics","Conservation Biology","Genetics","Genomics"]
doi:10.7717/peerj.5860
297 downloads
1,342 views

Scorpions have evolved a variety of toxins with a plethora of biological targets, but characterizing their evolution has been limited by the lack of a comprehensive phylogenetic hypothesis of scorpion relationships grounded in modern, genome-scale datasets. Disagreements...

["Bioinformatics","Evolutionary Studies","Genomics"]
doi:10.7717/peerj.5902
50 downloads
336 views

Background In our previous study, Melaleuca alternifolia essential oil (EO) was considered to have an insecticidal effect by acting on the mitochondrial respiratory chain in insects. However, the mode of action is not fully understood. Methods In this study, we...

["Bioinformatics","Entomology","Toxicology"]
doi:10.7717/peerj.5693

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