AIMC Topic: Computational Biology

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Shape-to-graph mapping method for efficient characterization and classification of complex geometries in biological images.

PLoS computational biology
With the ever-increasing quality and quantity of imaging data in biomedical research comes the demand for computational methodologies that enable efficient and reliable automated extraction of the quantitative information contained within these image...

Discovery of Novel Type II Bacteriocins Using a New High-Dimensional Bioinformatic Algorithm.

Frontiers in immunology
Antimicrobial compounds first arose in prokaryotes by necessity for competitive self-defense. In this light, prokaryotes invented the first host defense peptides. Among the most well-characterized of these peptides are class II bacteriocins, ribosoma...

Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns.

Open biology
Biological processes are accomplished by the coordinated action of gene products. Gene products often participate in multiple processes, and can therefore be annotated to multiple Gene Ontology (GO) terms. Nevertheless, processes that are functionall...

Cone-beam computed tomography-based radiomics in prostate cancer: a mono-institutional study.

Strahlentherapie und Onkologie : Organ der Deutschen Rontgengesellschaft ... [et al]
PURPOSE: The purpose of the reported study was to investigate the value of cone-beam computed tomography (CBCT)-based radiomics for risk stratification and prediction of biochemical relapse in prostate cancer.

Impact of rescanning and normalization on convolutional neural network performance in multi-center, whole-slide classification of prostate cancer.

Scientific reports
Algorithms can improve the objectivity and efficiency of histopathologic slide analysis. In this paper, we investigated the impact of scanning systems (scanners) and cycle-GAN-based normalization on algorithm performance, by comparing different deep ...

A novel fusion based on the evolutionary features for protein fold recognition using support vector machines.

Scientific reports
Protein fold recognition plays a crucial role in discovering three-dimensional structure of proteins and protein functions. Several approaches have been employed for the prediction of protein folds. Some of these approaches are based on extracting fe...

DeepVariant-on-Spark: Small-Scale Genome Analysis Using a Cloud-Based Computing Framework.

Computational and mathematical methods in medicine
Although sequencing a human genome has become affordable, identifying genetic variants from whole-genome sequence data is still a hurdle for researchers without adequate computing equipment or bioinformatics support. GATK is a gold standard method fo...

Machine learning based refined differential gene expression analysis of pediatric sepsis.

BMC medical genomics
BACKGROUND: Differential expression (DE) analysis of transcriptomic data enables genome-wide analysis of gene expression changes associated with biological conditions of interest. Such analysis often provides a wide list of genes that are differentia...

Instance Transfer Subject-Dependent Strategy for Motor Imagery Signal Classification Using Deep Convolutional Neural Networks.

Computational and mathematical methods in medicine
In the process of brain-computer interface (BCI), variations across sessions/subjects result in differences in the properties of potential of the brain. This issue may lead to variations in feature distribution of electroencephalogram (EEG) across su...

A recurrent circuit implements normalization, simulating the dynamics of V1 activity.

Proceedings of the National Academy of Sciences of the United States of America
The normalization model has been applied to explain neural activity in diverse neural systems including primary visual cortex (V1). The model's defining characteristic is that the response of each neuron is divided by a factor that includes a weighte...