Genetics

Changing techniques in crop plant classification: molecularization at the National Institute of Agricultural Botany during the 1980s.

Modern methods of analysing biological materials, including protein and DNA sequencing, are increasingly the objects of historical study. Yet twentieth-century taxonomic techniques have been overlooked in one of their most important contexts: agricultural botany. This paper addresses this omission by harnessing unexamined archival material from the National Institute of Agricultural Botany (NIAB),...

Bayesian Machine Learning Techniques for revealing complex interactions among genetic and clinical factors in association with extra-intestinal Manifestations in IBD patients.

The objective of the study is to assess the predictive performance of three different techniques as classifiers for extra-intestinal manifestations in 152 patients with Crohn's disease. Naïve Bayes, Bayesian Additive Regression Trees and Bayesian Networks implemented using a Greedy Thick Thinning algorithm for learning dependencies among variables and EM algorithm for learning conditional probabil...

Who's Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy.

The potential for genetic discovery in human DNA sequencing studies is greatly diminished if DNA samples from a cohort are mislabeled, swapped, or con...

Multi-Instance Metric Transfer Learning for Genome-Wide Protein Function Prediction.

Multi-Instance (MI) learning has been proven to be effective for the genome-wide protein function prediction problems where each training example is a...

A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma.

BACKGROUND: We have identified molecules that exhibit synthetic lethality in cells with loss of the neurofibromin 1 (NF1) tumor suppressor gene. Howev...

Recognition of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks.

Accurate computational identification of promoters remains a challenge as these key DNA regulatory regions have variable structures composed of functi...

Gene selection for microarray cancer classification using a new evolutionary method employing artificial intelligence concepts.

Gene selection is a demanding task for microarray data analysis. The diverse complexity of different cancers makes this issue still challenging. In th...

Continuous Adaptive Population Reduction (CAPR) for Differential Evolution Optimization.

Differential evolution (DE) has been applied extensively in drug combination optimization studies in the past decade. It allows for identification of ...

Bosco: Boosting Corrections for Genome-Wide Association Studies With Imbalanced Samples.

In genome-wide association studies (GWAS), the acquired sequential data may exhibit imbalance structure: abundant control vs. limited case samples. Su...

Sequence-specific bias correction for RNA-seq data using recurrent neural networks.

BACKGROUND: The recent success of deep learning techniques in machine learning and artificial intelligence has stimulated a great deal of interest amo...

Simultaneous Identification of Multiple Causal Mutations in Rice.

Next-generation sequencing technologies (NGST) are being used to discover causal mutations in ethyl methanesulfonate (EMS)-mutagenized plant populatio...

Detecting N-methyladenosine sites from RNA transcriptomes using ensemble Support Vector Machines.

As one of the most abundant RNA post-transcriptional modifications, N-methyladenosine (mA) involves in a broad spectrum of biological and physiologica...

Novel Mutation Sites in the Development of Vancomycin- Intermediate Resistance in .

Increased use of vancomycin has led to the emergence of vancomycin-intermediate (VISA). To investigate the mechanism of VISA development, 39 methicil...

Neural-Network-Biased Genetic Algorithms for Materials Design: Evolutionary Algorithms That Learn.

Machine learning has the potential to dramatically accelerate high-throughput approaches to materials design, as demonstrated by successes in biomolec...

Enumerateblood - an R package to estimate the cellular composition of whole blood from Affymetrix Gene ST gene expression profiles.

BACKGROUND: Measuring genome-wide changes in transcript abundance in circulating peripheral whole blood is a useful way to study disease pathobiology ...

Retinoic Acid Excess Impairs Amelogenesis Inducing Enamel Defects.

Abnormalities of enamel matrix proteins deposition, mineralization, or degradation during tooth development are responsible for a spectrum of either g...

PaPrBaG: A machine learning approach for the detection of novel pathogens from NGS data.

The reliable detection of novel bacterial pathogens from next-generation sequencing data is a key challenge for microbial diagnostics. Current computa...

Antibacterial Activity and Mechanism of Action of Black Pepper Essential Oil on Meat-Borne .

The aim of this study was to investigate the antibacterial activity of black pepper essential oil (BPEO) on , further evaluate the potential mechanism...

Natural language processing to ascertain two key variables from operative reports in ophthalmology.

PURPOSE: Antibiotic prophylaxis is critical to ophthalmology and other surgical specialties. We performed natural language processing (NLP) of 743 838...

Diaryltriazenes as antibacterial agents against methicillin resistant Staphylococcus aureus (MRSA) and Mycobacterium smegmatis.

Diaryltriazene derivatives were synthesized and evaluated for their antimicrobial properties. Initial experiments showed some of these compounds to ha...