AIMC Topic: Software

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Nm-Nano: a machine learning framework for transcriptome-wide single-molecule mapping of 2´-O-methylation (Nm) sites in nanopore direct RNA sequencing datasets.

RNA biology
2´-O-methylation (Nm) is one of the most abundant modifications found in both mRNAs and noncoding RNAs. It contributes to many biological processes, such as the normal functioning of tRNA, the protection of mRNA against degradation by the decapping a...

A guide to artificial intelligence for cancer researchers.

Nature reviews. Cancer
Artificial intelligence (AI) has been commoditized. It has evolved from a specialty resource to a readily accessible tool for cancer researchers. AI-based tools can boost research productivity in daily workflows, but can also extract hidden informati...

SCLpred-ECL: Subcellular Localization Prediction by Deep N-to-1 Convolutional Neural Networks.

International journal of molecular sciences
The subcellular location of a protein provides valuable insights to bioinformaticians in terms of drug designs and discovery, genomics, and various other aspects of medical research. Experimental methods for protein subcellular localization determina...

MONAI Label: A framework for AI-assisted interactive labeling of 3D medical images.

Medical image analysis
The lack of annotated datasets is a major bottleneck for training new task-specific supervised machine learning models, considering that manual annotation is extremely expensive and time-consuming. To address this problem, we present MONAI Label, a f...

Python tools for structural tasks in chemistry.

Molecular diversity
In recent decades, the use of computational approaches and artificial intelligence in the scientific environment has become more widespread. In this regard, the popular and versatile programming language Python has attracted considerable attention fr...

Use of Artificial Intelligence Software to Detect Intracranial Aneurysms: A Comprehensive Stroke Center Experience.

World neurosurgery
OBJECTIVE: To evaluate variability in aneurysm detection and the potential of artificial intelligence (AI) software as a screening tool by comparing conventional computed tomography angiography (CTA) images (standard care) with AI software.

Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF.

Nature communications
Immunopeptidomics is crucial for immunotherapy and vaccine development. Because the generation of immunopeptides from their parent proteins does not adhere to clear-cut rules, rather than being able to use known digestion patterns, every possible pro...

Introducing AnatomyGPT: A customized artificial intelligence application for anatomical sciences education.

Clinical anatomy (New York, N.Y.)
Artificial intelligence (AI) technologies are poised to become an increasingly important part of education in the anatomical sciences. OpenAI has also introduced generative pretrained transformers (GPTs), which are customizable versions of the standa...

CancerGATE: Prediction of cancer-driver genes using graph attention autoencoders.

Computers in biology and medicine
Discovery of the cancer type specific-driver genes is important for understanding the molecular mechanisms of each cancer type and for providing proper treatment. Recently, graph deep learning methods became widely used in finding cancer-driver genes...

Accurate structure prediction of biomolecular interactions with AlphaFold 3.

Nature
The introduction of AlphaFold 2 has spurred a revolution in modelling the structure of proteins and their interactions, enabling a huge range of applications in protein modelling and design. Here we describe our AlphaFold 3 model with a substantially...