AIMC Topic: Phylogeny
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Universal probabilistic programming offers a powerful approach to statistical phylogenetics.
Communications biology
Feb 24, 2021
Statistical phylogenetic analysis currently relies on complex, dedicated software packages, making it difficult for evolutionary biologists to explore new models and inference strategies. Recent years have seen more generic solutions based on probabi...
Discrimination of Malaysian stingless bee honey from different entomological origins based on physicochemical properties and volatile compound profiles using chemometrics and machine learning.
Food chemistry
Jan 15, 2021
Identification of honey origin based on specific chemical markers is important for honey authentication. This study is aimed to differentiate Malaysian stingless bee honey from different entomological origins (Heterotrigona bakeri, Geniotrigona thora...
Forest and Trees: Exploring Bacterial Virulence with Genome-wide Association Studies and Machine Learning.
Trends in microbiology
Jan 14, 2021
The advent of inexpensive and rapid sequencing technologies has allowed bacterial whole-genome sequences to be generated at an unprecedented pace. This wealth of information has revealed an unanticipated degree of strain-to-strain genetic diversity w...
Deep learning for HGT insertion sites recognition.
BMC genomics
Dec 29, 2020
BACKGROUND: Horizontal Gene Transfer (HGT) refers to the sharing of genetic materials between distant species that are not in a parent-offspring relationship. The HGT insertion sites are important to understand the HGT mechanisms. Recent studies in m...
Review of the genus Shilovia Makarchenko (Diptera: Chironomidae: Diamesinae: Boreoheptagyiini) from the mountains of Central Asia, with morphological description and DNA barcoding of known species.
Zootaxa
Dec 15, 2020
Chironomids of the genus Shilovia Makarchenko (Diamesinae, Boreoheptagyiini) from the mountains of Central Asia are revised using both morphological characters and molecular data. Illustrated descriptions of the adult male Shilovia xinhuawangi sp. no...
Ensembling of Gene Clusters Utilizing Deep Learning and Protein-Protein Interaction Information.
IEEE/ACM transactions on computational biology and bioinformatics
Dec 8, 2020
Cluster ensemble techniques aim to combine the outputs of multiple clustering algorithms to obtain a single consensus partitioning. The current paper reports about the development of a cluster ensemble based technique combining the concepts of multio...
Scalable classification of organisms into a taxonomy using hierarchical supervised learners.
Journal of bioinformatics and computational biology
Oct 29, 2020
Accurately identifying organisms based on their partially available genetic material is an important task to explore the phylogenetic diversity in an environment. Specific fragments in the DNA sequence of a living organism have been defined as DNA ba...
Improving the taxonomy of fossil pollen using convolutional neural networks and superresolution microscopy.
Proceedings of the National Academy of Sciences of the United States of America
Oct 23, 2020
Taxonomic resolution is a major challenge in palynology, largely limiting the ecological and evolutionary interpretations possible with deep-time fossil pollen data. We present an approach for fossil pollen analysis that uses optical superresolution ...
lncRNAKB, a knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA.
Scientific data
Oct 5, 2020
Long non-coding RNA Knowledgebase (lncRNAKB) is an integrated resource for exploring lncRNA biology in the context of tissue-specificity and disease association. A systematic integration of annotations from six independent databases resulted in 77,19...
Pollen analysis using multispectral imaging flow cytometry and deep learning.
The New phytologist
Sep 22, 2020
Pollen identification and quantification are crucial but challenging tasks in addressing a variety of evolutionary and ecological questions (pollination, paleobotany), but also for other fields of research (e.g. allergology, honey analysis or forensi...
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