Genetics

Semantic closure demonstrated by the evolution of a universal constructor architecture in an artificial chemistry.

We present a novel stringmol-based artificial chemistry system modelled on the universal constructor architecture (UCA) first explored by von Neumann. In a UCA, machines interact with an abstract description of themselves to replicate by copying the abstract description and constructing the machines that the abstract description encodes. DNA-based replication follows this architecture, with DNA be...

Feature selection using a one dimensional naïve Bayes' classifier increases the accuracy of support vector machine classification of CDR3 repertoires.

MOTIVATION: Somatic DNA recombination, the hallmark of vertebrate adaptive immunity, has the potential to generate a vast diversity of antigen receptor sequences. How this diversity captures antigen specificity remains incompletely understood. In this study we use high throughput sequencing to compare the global changes in T cell receptor β chain complementarity determining region 3 (CDR3β) sequen...

FARNA: knowledgebase of inferred functions of non-coding RNA transcripts.

Non-coding RNA (ncRNA) genes play a major role in control of heterogeneous cellular behavior. Yet, their functions are largely uncharacterized. Curren...

RBPPred: predicting RNA-binding proteins from sequence using SVM.

MOTIVATION: Detection of RNA-binding proteins (RBPs) is essential since the RNA-binding proteins play critical roles in post-transcriptional regulatio...

Application of supervised machine learning algorithms for the classification of regulatory RNA riboswitches.

Riboswitches, the small structured RNA elements, were discovered about a decade ago. It has been the subject of intense interest to identify riboswitc...

Gene essentiality prediction based on fractal features and machine learning.

Essential genes are required for the viability of an organism. Accurate and rapid identification of new essential genes is of substantial theoretical ...

Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning.

MOTIVATION: Many peak detection algorithms have been proposed for ChIP-seq data analysis, but it is not obvious which algorithm and what parameters ar...

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer.

CIViC is an expert-crowdsourced knowledgebase for Clinical Interpretation of Variants in Cancer describing the therapeutic, prognostic, diagnostic and...

A Sparse Learning Framework for Joint Effect Analysis of Copy Number Variants.

Copy number variants (CNVs), including large deletions and duplications, represent an unbalanced change of DNA segments. Abundant in human genomes, CN...

Community-Wide Evaluation of Computational Function Prediction.

A biological experiment is the most reliable way of assigning function to a protein. However, in the era of high-throughput sequencing, scientists are...

Visualizing GO Annotations.

Contemporary techniques in biology produce readouts for large numbers of genes simultaneously, the typical example being differential gene expression ...

Annotation Extensions.

The specificity of knowledge that Gene Ontology (GO) annotations currently can represent is still restricted by the legacy format of the GO annotation...

A Gene Selection Method for Microarray Data Based on Binary PSO Encoding Gene-to-Class Sensitivity Information.

Traditional gene selection methods for microarray data mainly considered the features' relevance by evaluating their utility for achieving accurate pr...

Identifying Biomarkers of Hepatocellular Carcinoma Based on Gene Co-Expression Network from High-Throughput Data.

In this paper, we proposed an approach systematically based on the use of gene co-expression network analyses to identify potential biomarkers for Hep...

Active Surveillance Use Among a Low-risk Prostate Cancer Population in a Large US Payer System: 17-Gene Genomic Prostate Score Versus Other Risk Stratification Methods.

Many men with low-risk prostate cancer (PCa) receive definitive treatment despite recommendations that have been informed by two large, randomized tri...

A neural network prediction of environmental determinants of Anopheles sinensis knockdown resistance mutation to pyrethroids in China.

Selection pressure caused by long-term intensive use of insecticides is the key driving force in resistance development. Additional parameters such as...

The Effects of First-Line Anti-Tuberculosis Drugs on the Actions of Vitamin D in Human Macrophages.

Tuberculosis (TB) is a major global health problem. Patients with TB have a high rate of vitamin D deficiency, both at diagnosis and during the course...

Metformin Alleviates Lipopolysaccharide-induced Acute Lung Injury through Suppressing Toll-like Receptor 4 Signaling.

Signaling AMP-activated protein kinase (AMPK), an energy sensing enzyme, has been implicated in controlling inflammation. In this study we investigate...

The Effect of Artemisia fragrans Willd: Essential Oil on Inducible Nitric Oxide Synthase Gene Expression and Nitric Oxide Production in Lipopolysaccharide-stimulated Murine Macrophage Cell Line.

The genus Artemisia is estimated to comprise over 800 species with anti-cancer, anti-fungal, anti-oxidant and anti-inflammatory properties. Artemisia ...

Cell Free DNA and Procalcitonin as Early Markers of Complications in ICU Patients with Multiple Trauma and Major Surgery.

BACKGROUND: Cell free DNA (cfDNA) was recently suggested as a new marker of sepsis and poor outcome in ICU patients. Procalcitonin has also been the f...