AIMC Topic: Species Specificity

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A Computational Framework Based on Ensemble Deep Neural Networks for Essential Genes Identification.

International journal of molecular sciences
Essential genes contain key information of genomes that could be the key to a comprehensive understanding of life and evolution. Because of their importance, studies of essential genes have been considered a crucial problem in computational biology. ...

Poly(A)-DG: A deep-learning-based domain generalization method to identify cross-species Poly(A) signal without prior knowledge from target species.

PLoS computational biology
In eukaryotes, polyadenylation (poly(A)) is an essential process during mRNA maturation. Identifying the cis-determinants of poly(A) signal (PAS) on the DNA sequence is the key to understand the mechanism of translation regulation and mRNA metabolism...

Performance vs. competence in human-machine comparisons.

Proceedings of the National Academy of Sciences of the United States of America
Does the human mind resemble the machines that can behave like it? Biologically inspired machine-learning systems approach "human-level" accuracy in an astounding variety of domains, and even predict human brain activity-raising the exciting possibil...

HybridSucc: A Hybrid-learning Architecture for General and Species-specific Succinylation Site Prediction.

Genomics, proteomics & bioinformatics
As an important protein acylation modification, lysine succinylation (Ksucc) is involved in diverse biological processes, and participates in human tumorigenesis. Here, we collected 26,243 non-redundant known Ksucc sites from 13 species as the benchm...

Experimentally revealed stochastic preferences for multicomponent choice options.

Journal of experimental psychology. Animal learning and cognition
Realistic, everyday rewards contain multiple components. An apple has taste and size. However, we choose in single dimensions, simply preferring some apples to others. How can such single-dimensional preference relationships refer to multicomponent c...

Cross-species regulatory sequence activity prediction.

PLoS computational biology
Machine learning algorithms trained to predict the regulatory activity of nucleic acid sequences have revealed principles of gene regulation and guided genetic variation analysis. While the human genome has been extensively annotated and studied, mod...

A supervised learning framework for chromatin loop detection in genome-wide contact maps.

Nature communications
Accurately predicting chromatin loops from genome-wide interaction matrices such as Hi-C data is critical to deepening our understanding of proper gene regulation. Current approaches are mainly focused on searching for statistically enriched dots on ...

The proteome landscape of the kingdoms of life.

Nature
Proteins carry out the vast majority of functions in all biological domains, but for technological reasons their large-scale investigation has lagged behind the study of genomes. Since the first essentially complete eukaryotic proteome was reported, ...

Accurate prediction of species-specific 2-hydroxyisobutyrylation sites based on machine learning frameworks.

Analytical biochemistry
Lysine 2-hydroxyisobutyrylation (K) is a newly discovered post-translational modification (PTM) across eukaryotes and prokaryotes in recent years, which plays a significant role in diverse cellular functions. Accurate prediction of K sites is a first...

Deep learning based prediction of species-specific protein S-glutathionylation sites.

Biochimica et biophysica acta. Proteins and proteomics
As a widespread and reversible post-translational modification of proteins, S-glutathionylation specifically generates the mixed disulfides between cysteine residues and glutathione, which regulates various biological processes including oxidative st...