AIMC Topic: Software

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Mastering the game of Go without human knowledge.

Nature
A long-standing goal of artificial intelligence is an algorithm that learns, tabula rasa, superhuman proficiency in challenging domains. Recently, AlphaGo became the first program to defeat a world champion in the game of Go. The tree search in Alpha...

Epigenomic annotation-based interpretation of genomic data: from enrichment analysis to machine learning.

Bioinformatics (Oxford, England)
MOTIVATION: One of the goals of functional genomics is to understand the regulatory implications of experimentally obtained genomic regions of interest (ROIs). Most sequencing technologies now generate ROIs distributed across the whole genome. The in...

Partitioned learning of deep Boltzmann machines for SNP data.

Bioinformatics (Oxford, England)
MOTIVATION: Learning the joint distributions of measurements, and in particular identification of an appropriate low-dimensional manifold, has been found to be a powerful ingredient of deep leaning approaches. Yet, such approaches have hardly been ap...

DOMINO: Using Machine Learning to Predict Genes Associated with Dominant Disorders.

American journal of human genetics
In contrast to recessive conditions with biallelic inheritance, identification of dominant (monoallelic) mutations for Mendelian disorders is more difficult, because of the abundance of benign heterozygous variants that act as massive background nois...

How good are publicly available web services that predict bioactivity profiles for drug repurposing?

SAR and QSAR in environmental research
Drug repurposing provides a non-laborious and less expensive way for finding new human medicines. Computational assessment of bioactivity profiles shed light on the hidden pharmacological potential of the launched drugs. Currently, several freely ava...

OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets.

Proteomics
The availability of user-friendly software to annotate biological datasets and experimental details is becoming essential in data management practices, both in local storage systems and in public databases. The Ontology Lookup Service (OLS, http://ww...

DeepSite: protein-binding site predictor using 3D-convolutional neural networks.

Bioinformatics (Oxford, England)
MOTIVATION: An important step in structure-based drug design consists in the prediction of druggable binding sites. Several algorithms for detecting binding cavities, those likely to bind to a small drug compound, have been developed over the years b...

DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding.

Bioinformatics (Oxford, England)
MOTIVATION: Transcription factors (TFs) bind to specific DNA sequence motifs. Several lines of evidence suggest that TF-DNA binding is mediated in part by properties of the local DNA shape: the width of the minor groove, the relative orientations of ...

DIRECTION: a machine learning framework for predicting and characterizing DNA methylation and hydroxymethylation in mammalian genomes.

Bioinformatics (Oxford, England)
MOTIVATION: 5-Methylcytosine and 5-Hydroxymethylcytosine in DNA are major epigenetic modifications known to significantly alter mammalian gene expression. High-throughput assays to detect these modifications are expensive, labor-intensive, unfeasible...