Genetics

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.

Cancer progression involves the gradual loss of a differentiated phenotype and acquisition of progenitor and stem-cell-like features. Here, we provide novel stemness indices for assessing the degree of oncogenic dedifferentiation. We used an innovative one-class logistic regression (OCLR) machine-learning algorithm to extract transcriptomic and epigenetic feature sets derived from non-transformed ...

Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas.

Precision oncology uses genomic evidence to match patients with treatment but often fails to identify all patients who may respond. The transcriptome of these "hidden responders" may reveal responsive molecular states. We describe and evaluate a machine-learning approach to classify aberrant pathway activity in tumors, which may aid in hidden responder identification. The algorithm integrates RNA-...

microRPM: a microRNA prediction model based only on plant small RNA sequencing data.

MOTIVATION: MicroRNAs (miRNAs) are endogenous non-coding small RNAs (of about 22 nucleotides), which play an important role in the post-transcriptiona...

[Artificial Intelligence in Drug Discovery].

According to the increase of data generated from analytical instruments, application of artificial intelligence(AI)technology in medical field is indi...

High Activity Target-Site Identification Using Phenotypic Independent CRISPR-Cas9 Core Functionality.

The activity of CRISPR-Cas9 target sites can be measured experimentally through phenotypic assays or mutation rate and used to build computational mod...

Research progress in machine learning methods for gene-gene interaction detection.

Complex diseases are results of gene-gene and gene-environment interactions. However, the detection of high-dimensional gene-gene interactions is comp...

Chromatin accessibility prediction via a hybrid deep convolutional neural network.

MOTIVATION: A majority of known genetic variants associated with human-inherited diseases lie in non-coding regions that lack adequate interpretation,...

Investigating the Generalizability of the MultiFlow ® DNA Damage Assay and Several Companion Machine Learning Models With a Set of 103 Diverse Test Chemicals.

The in vitro MultiFlow DNA Damage assay multiplexes p53, γH2AX, phospho-histone H3, and polyploidization biomarkers into 1 flow cytometric analysis (B...

ICG: a wiki-driven knowledgebase of internal control genes for RT-qPCR normalization.

Real-time quantitative PCR (RT-qPCR) has become a widely used method for accurate expression profiling of targeted mRNA and ncRNA. Selection of approp...

The Reactome Pathway Knowledgebase.

The Reactome Knowledgebase (https://reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism, and other...

Gramene 2018: unifying comparative genomics and pathway resources for plant research.

Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. The current release, #...

BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery.

Single-nucleotide variation and gene expression of disease samples represent important resources for biomarker discovery. Many databases have been bui...

Annotating gene sets by mining large literature collections with protein networks.

Analysis of patient genomes and transcriptomes routinely recognizes new gene sets associated with human disease. Here we present an integrative natura...

Applications of Support Vector Machine (SVM) Learning in Cancer Genomics.

Machine learning with maximization (support) of separating margin (vector), called support vector machine (SVM) learning, is a powerful classification...

Survey of Computational Approaches for Prediction of DNA-Binding Residues on Protein Surfaces.

The increasing number of protein structures with uncharacterized function necessitates the development of in silico prediction methods for functional ...

[Construction of a High-precision Chemical Prediction System Using Human ESCs].

　Toxicity prediction based on stem cells and tissue derived from stem cells plays a very important role in the fields of biomedicine and pharmacology....

MetaVW: Large-Scale Machine Learning for Metagenomics Sequence Classification.

Metagenomics is the study of microbial community diversity, especially the uncultured microorganisms by shotgun sequencing environmental samples. As t...

Deep Forest-based Prediction of Protein Subcellular Localization.

MOTIVATION: Knowledge of the correct protein subcellular localization is necessary for understanding the function of a protein and revealing the mecha...

Spatial Analysis of Functional Enrichment (SAFE) in Large Biological Networks.

Spatial analysis of functional enrichment (SAFE) is a systematic quantitative approach for annotating large biological networks. SAFE detects network ...

Machine Learning Methods in Precision Medicine Targeting Epigenetic Diseases.

BACKGROUND: On a tide of big data, machine learning is coming to its day. Referring to huge amounts of epigenetic data coming from biological experime...