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Owing to the complexity of higher eukaryotic cells, a complete proteome is likely to be very difficult to achieve. However, advantage can be taken of the cell compartmentalization to build organelle proteomes, which can moreover be viewed…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
Molecular and morphological characters, as important parts of biological taxonomy, are contradictory but need to be integrated. Organism's image recognition and bioinformatics are emerging and hot problems nowadays but with a gap between…
The recent development of metagenomic sequencing makes it possible to sequence microbial genomes including viruses in an environmental sample. Identifying viral sequences from metagenomic data is critical for downstream virus analyses. The…
Ancient mitochondrial DNA has been used in a wide variety of palaeontological and archaeological studies, ranging from population dynamics of extinct species to patterns of domestication. Most of these studies have traditionally been based…
Over the last years, huge resources of biological and medical data have become available for research. This data offers great chances for machine learning applications in health care, e.g. for precision medicine, but is also challenging to…
Determining cell identities in imaging sequences is an important yet challenging task. The conventional method for cell identification is via cell tracking, which is complex and can be time-consuming. In this study, we propose an innovative…
This paper presents a method for automatic segmentation, localization, and identification of vertebrae in arbitrary 3D CT images. Many previous works do not perform the three tasks simultaneously even though requiring a priori knowledge of…
Analyzing and inspecting bone marrow cell cytomorphology is a critical but highly complex and time-consuming component of hematopathology diagnosis. Recent advancements in artificial intelligence have paved the way for the application of…
MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play an important role in post-transcriptional gene regulation. However, the experimental determination of miRNA sequence and structure is both expensive and time-consuming.…
Among the different biomarkers of aging based on omics and clinical data, DNA methylation clocks stand apart providing unmatched accuracy in assessing the biological age of both humans and animal models of aging. Here, we discuss robustness…
A novel method to classify human cells is presented in this work based on the transform-domain method on DNA methylation data. DNA methylation profile variations are observed in human cells with the progression of disease stages, and the…
In recent years, several machine learning approaches have been proposed to predict gene expression and epigenetic signals from the DNA sequence alone. These models are often used to deduce, and, to some extent, assess putative new…
DNA methylation is a significant driver of cell-type heterogeneity and has been implicated in various regulatory processes ranging from cell differentiation to imprinting. As the methyl group is embedded in the DNA molecule, assessing DNA…
Motivation: Bisulphite sequencing enables the detection of cytosine methylation. The sequence of the methylation states of cytosines on any given read forms a methylation pattern that carries substantially more information than merely…
The classification of DNA sequences is a key research area in bioinformatics as it enables researchers to conduct genomic analysis and detect possible diseases. In this paper, three state-of-the-art algorithms, namely Convolutional Neural…
We develop Bayesian inference methods for a recently-emerging type of epigenetic data to study the transmission fidelity of DNA methylation patterns over cell divisions. The data consist of parent-daughter double-stranded DNA methylation…
Foundation models have made significant strides in understanding the genomic language of DNA sequences. However, previous models typically adopt the tokenization methods designed for natural language, which are unsuitable for DNA sequences…
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…
Lineage marker population frequencies can serve as one way to express evidential value in forensic genetics. However, for high-quality whole mitochondrial DNA genome sequences (mitogenomes), population data remain limited. In this paper, we…