AIMC Topic: Algorithms

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Advancing Amorphous Solid Dispersions Design: Insights into Dissolution Kinetics via Thermodynamic Descriptor and Machine Learning.

Molecular pharmaceutics
Amorphous solid dispersions (ASD) are an effective strategy for enhancing the solubility and bioavailability of poorly soluble drugs. However, designing and optimizing ASD formulations often rely on extensive dissolution experiments without sufficie...

SHARK: web server for alignment-free homology assessment for intrinsically disordered and unalignable protein regions.

Nucleic acids research
Whereas alignment has been fundamental to sequence-based assessments of protein homology, it is ineffective for intrinsically disordered regions (IDRs) due to their lowered sequence conservation and unique sequence properties. Here, we present a web ...

CGeNArateWeb: a web server for the atomistic study of the structure and dynamics of chromatin fibers.

Nucleic acids research
We present CGeNArateWeb, a new web tool for the three-dimensional simulation of naked DNA and protein-bound chromatin fibers. The server allows the user to obtain a dynamic representation of long segments of linear, circular, or protein-DNA segments ...

OntoTiger: a platform of ontology-based application tools for integrative biomedical exploration.

Nucleic acids research
Biomedical ontologies, such as Gene Ontology (GO), Disease Ontology (DO), and the Human Phenotype Ontology (HPO), have been extensively applied to characterize molecular roles and their semantic relationships in biomedical research and clinical pract...

TmDet 4.0: determining membrane orientation of transmembrane proteins from 3D structure.

Nucleic acids research
During the structural determination of transmembrane proteins, one crucial piece of information is lost: the orientation of the protein within the lipid bilayer. The TmDet algorithm was developed in the early 2000s to determine the relative position ...

Annotating neurophysiologic data at scale with optimized human input.

Journal of neural engineering
Neuroscience experiments and devices are generating unprecedented volumes of data, but analyzing and validating them presents practical challenges, particularly in annotation. While expert annotation remains the gold standard, it is time consuming to...

VBayesMM: variational Bayesian neural network to prioritize important relationships of high-dimensional microbiome multiomics data.

Briefings in bioinformatics
The analysis of high-dimensional microbiome multiomics datasets is crucial for understanding the complex interactions between microbial communities and host physiological states across health and disease conditions. Despite their importance, current ...

spaLLM: enhancing spatial domain analysis in multi-omics data through large language model integration.

Briefings in bioinformatics
Spatial multi-omics technologies provide valuable data on gene expression from various omics in the same tissue section while preserving spatial information. However, deciphering spatial domains within spatial omics data remains challenging due to th...

Iterative clustering algorithm G-DESC-E and pan-cancer key gene analysis based on single-cell sequencing data.

Briefings in bioinformatics
Single-cell sequencing technology has profoundly revolutionized the field of cancer genomics, enabling researchers to explore gene expression profiles at the resolution of individual cells. Despite its extensive applications in the study of cancer ge...

Concurrent emergence of view invariance, sensitivity to critical features, and identity face classification through visual experience: Insights from deep learning algorithms.

Journal of vision
Visual experience is known to play a critical role in face recognition. This experience is thought to enable the formation of a view-invariant representation by learning which features are critical to identify faces across views. Discovering these cr...