AIMC Topic: Species Specificity

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Mapping Atlantic rainforest degradation and regeneration history with indicator species using convolutional network.

PloS one
The Atlantic rainforest of Brazil is one of the global terrestrial hotspots of biodiversity. Despite having undergone large scale deforestation, forest cover has shown signs of increases in the last decades. Here, to understand the degradation and re...

Towards a global understanding of the drivers of marine and terrestrial biodiversity.

PloS one
Understanding the distribution of life's variety has driven naturalists and scientists for centuries, yet this has been constrained both by the available data and the models needed for their analysis. Here we compiled data for over 67,000 marine and ...

DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput.

Nature methods
We present an easy-to-use integrated software suite, DIA-NN, that exploits deep neural networks and new quantification and signal correction strategies for the processing of data-independent acquisition (DIA) proteomics experiments. DIA-NN improves t...

Artificial intelligence reveals environmental constraints on colour diversity in insects.

Nature communications
Explaining colour variation among animals at broad geographic scales remains challenging. Here we demonstrate how deep learning-a form of artificial intelligence-can reveal subtle but robust patterns of colour feature variation along an ecological gr...

Boosting phosphorylation site prediction with sequence feature-based machine learning.

Proteins
Protein phosphorylation is one of the essential posttranslation modifications playing a vital role in the regulation of many fundamental cellular processes. We propose a LightGBM-based computational approach that uses evolutionary, geometric, sequenc...

scGen predicts single-cell perturbation responses.

Nature methods
Accurately modeling cellular response to perturbations is a central goal of computational biology. While such modeling has been based on statistical, mechanistic and machine learning models in specific settings, no generalization of predictions to ph...

Insights and approaches using deep learning to classify wildlife.

Scientific reports
The implementation of intelligent software to identify and classify objects and individuals in visual fields is a technology of growing importance to operatives in many fields, including wildlife conservation and management. To non-experts, the metho...

Molecules Autoinducer 2 and cjA and Their Impact on Gene Expression in Campylobacter jejuni.

Journal of molecular microbiology and biotechnology
Quorum sensing is a widespread form of cell-to-cell communication, which is based on the production of signaling molecules known as autoinducers (AIs). The first group contains highly species-specific N-acyl homoserine lactones (N-AHLs), generally kn...

Application of convolutional neural networks for classification of adult mosquitoes in the field.

PloS one
Dengue, chikungunya and Zika are arboviruses transmitted by mosquitos of the genus Aedes and have caused several outbreaks in world over the past ten years. Morphological identification of mosquitos is currently restricted due to the small number of ...

Computational prediction of inter-species relationships through omics data analysis and machine learning.

BMC bioinformatics
BACKGROUND: Antibiotic resistance and its rapid dissemination around the world threaten the efficacy of currently-used medical treatments and call for novel, innovative approaches to manage multi-drug resistant infections. Phage therapy, i.e., the us...