Genetics

gammaBOriS: Identification and Taxonomic Classification of Origins of Replication in Gammaproteobacteria using Motif-based Machine Learning.

The biology of bacterial cells is, in general, based on information encoded on circular chromosomes. Regulation of chromosome replication is an essential process that mostly takes place at the origin of replication (oriC), a locus unique per chromosome. Identification of high numbers of oriC is a prerequisite for systematic studies that could lead to insights into oriC functioning as well as the i...

Combination Strategies for Immune-Checkpoint Blockade and Response Prediction by Artificial Intelligence.

The therapeutic concept of unleashing a pre-existing immune response against the tumor by the application of immune-checkpoint inhibitors (ICI) has resulted in long-term survival in advanced cancer patient subgroups. However, the majority of patients do not benefit from single-agent ICI and therefore new combination strategies are eagerly necessitated. In addition to conventional chemotherapy, kin...

Dendrite P systems.

It was recently found that dendrites are not just a passive channel. They can perform mixed computation of analog and digital signals, and therefore c...

Fold-Change-Specific Enrichment Analysis (FSEA): Quantification of Transcriptional Response Magnitude for Functional Gene Groups.

Gene expression profiling data contains more information than is routinely extracted with standard approaches. Here we present Fold-Change-Specific En...

PredDBP-Stack: Prediction of DNA-Binding Proteins from HMM Profiles using a Stacked Ensemble Method.

DNA-binding proteins (DBPs) play vital roles in all aspects of genetic activities. However, the identification of DBPs by using wet-lab experimental a...

A comparative study of machine learning and deep learning algorithms to classify cancer types based on microarray gene expression data.

Cancer classification is a topic of major interest in medicine since it allows accurate and efficient diagnosis and facilitates a successful outcome i...

Random forest machine learning algorithm predicts virologic outcomes among HIV infected adults in Lausanne, Switzerland using electronically monitored combined antiretroviral treatment adherence.

Machine Learning (ML) can improve the analysis of complex and interrelated factors that place adherent people at risk of viral rebound. Our aim was to...

Predicting the short-term success of human influenza virus variants with machine learning.

Seasonal influenza viruses are constantly changing and produce a different set of circulating strains each season. Small genetic changes can accumulat...

Biohorology and biomarkers of aging: Current state-of-the-art, challenges and opportunities.

The aging process results in multiple traceable footprints, which can be quantified and used to estimate an organism's age. Examples of such aging bio...

The International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019): computational methods and applications in medical genomics.

In this editorial, we briefly summarized the International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019) that was held on June 9-11...

Machine learning and clinical epigenetics: a review of challenges for diagnosis and classification.

BACKGROUND: Machine learning is a sub-field of artificial intelligence, which utilises large data sets to make predictions for future events. Although...

A fast conformal predictive system with regularized extreme learning machine.

A conformal predictive system(CPS) is based on the learning framework of conformal prediction, which outputs cumulative distribution functions(CDFs) f...

Meta-Analysis Based on Nonconvex Regularization.

The widespread applications of high-throughput sequencing technology have produced a large number of publicly available gene expression datasets. Howe...

Development of a Bioinformatics Framework for Identification and Validation of Genomic Biomarkers and Key Immunopathology Processes and Controllers in Infectious and Non-infectious Severe Inflammatory Response Syndrome.

Sepsis is defined as dysregulated host response caused by systemic infection, leading to organ failure. It is a life-threatening condition, often requ...

Where medical education meets artificial intelligence: 'Does technology care?'.

'COLD' TECHNOLOGIES AND 'WARM' HANDS-ON MEDICINE NEED TO WALK HAND-IN-HAND: Technologies, such as deep learning artificial intelligence (AI), promise ...

Estimating gene expression from DNA methylation and copy number variation: A deep learning regression model for multi-omics integration.

Gene expression analysis plays a significant role for providing molecular insights in cancer. Various genetic and epigenetic factors (being dealt unde...

Brain MRI analysis using a deep learning based evolutionary approach.

Convolutional neural network (CNN) models have recently demonstrated impressive performance in medical image analysis. However, there is no clear unde...

HMMPred: Accurate Prediction of DNA-Binding Proteins Based on HMM Profiles and XGBoost Feature Selection.

Prediction of DNA-binding proteins (DBPs) has become a popular research topic in protein science due to its crucial role in all aspects of biological ...

DDBJ Data Analysis Challenge: a machine learning competition to predict Arabidopsis chromatin feature annotations from DNA sequences.

Recently, the prospect of applying machine learning tools for automating the process of annotation analysis of large-scale sequences from next-generat...

DeepMILO: a deep learning approach to predict the impact of non-coding sequence variants on 3D chromatin structure.

Non-coding variants have been shown to be related to disease by alteration of 3D genome structures. We propose a deep learning method, DeepMILO, to pr...