Abstract Information theory (IT) addresses the analysis of communication systems and has
been widely applied in molecular biology. In particular, alignment-free sequence analysis …

Biological sequences are composed of long strings of alphabetic letters rather than arrays of
numerical values. Lack of a natural underlying metric for comparing such alphabetic data …

Pretrained embedding representations of biological sequences which capture meaningful
properties can alleviate many problems associated with supervised learning in biology. We …

The GATA-binding transcription factors comprise a protein family whose members contain
either one or two highly conserved zinc finger DNA-binding domains. Members of this group …

Quantitative analyses were carried out on a large number of proteins that contain the highly
conserved basic helix–loop–helix domain. Measures derived from information theory were …

An information theoretic approach is used to examine the magnitude and origin of
associations among amino acid sites in the basic helix-loop-helix (bHLH) family of …

Mainstream research on information theory within the field of living systems involves the
application of analytical tools to understand a broad range of life processes. This paper is …

Data-driven machine learning, especially deep learning technology, is becoming an
important tool for handling big data issues in bioinformatics. In machine learning, DNA …

Antibodies are critical components of adaptive immunity, binding with high affinity to
pathogenic epitopes. Antibodies undergo rigorous selection to achieve this high affinity, yet …

The transcriptome is a set of genes transcribed in a given tissue under specific conditions
and can be characterized by a list of genes with their corresponding frequencies of …