AIMC Topic: Software

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ProQ3D: improved model quality assessments using deep learning.

Bioinformatics (Oxford, England)
SUMMARY: Protein quality assessment is a long-standing problem in bioinformatics. For more than a decade we have developed state-of-art predictors by carefully selecting and optimising inputs to a machine learning method. The correlation has increase...

TSSPlant: a new tool for prediction of plant Pol II promoters.

Nucleic acids research
Our current knowledge of eukaryotic promoters indicates their complex architecture that is often composed of numerous functional motifs. Most of known promoters include multiple and in some cases mutually exclusive transcription start sites (TSSs). M...

Semantic closure demonstrated by the evolution of a universal constructor architecture in an artificial chemistry.

Journal of the Royal Society, Interface
We present a novel stringmol-based artificial chemistry system modelled on the universal constructor architecture (UCA) first explored by von Neumann. In a UCA, machines interact with an abstract description of themselves to replicate by copying the ...

Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction.

Bioinformatics (Oxford, England)
MOTIVATION: Loops are often vital for protein function, however, their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of frag...

RED-ML: a novel, effective RNA editing detection method based on machine learning.

GigaScience
With the advancement of second generation sequencing techniques, our ability to detect and quantify RNA editing on a global scale has been vastly improved. As a result, RNA editing is now being studied under a growing number of biological conditions ...

What "learning" machines will mean for medicine.

CMAJ : Canadian Medical Association journal = journal de l'Association medicale canadienne

Planning bioinformatics workflows using an expert system.

Bioinformatics (Oxford, England)
MOTIVATION: Bioinformatic analyses are becoming formidably more complex due to the increasing number of steps required to process the data, as well as the proliferation of methods that can be used in each step. To alleviate this difficulty, pipelines...