WMRCA + : a weighted majority rule-based clustering method for cancer subtype prediction using metabolic gene sets.

Accurate classification of cancer subtypes plays a pivotal role in advancing precision medicine. In this study, we introduce WMRCA + , a novel clustering approach based on a weighted majority rule that integrates multi-omics data and incorporates metabolic gene sets to robustly determine the optimal number of clusters for tumor subtype identification. WMRCA + evaluates clustering performance using ten internal metrics and offers comprehensive functionalities for data preprocessing and visualization.

FPCAM: A Weighted Dictionary-Driven Model for Single-Cell Annotation in Pulmonary Fibrosis.

The groundbreaking development of scRNA-seq has significantly improved cellular resolution. However, accurate cell-type annotation remains a major challenge. Existing annotation tools are often limited by their reliance on reference datasets, the heterogeneity of marker genes, and subjective biases introduced through manual intervention, all of which impact annotation accuracy and reliability.

Cancer type and survival prediction based on transcriptomic feature map.

This study achieved cancer type and survival time prediction by transforming transcriptomic features into feature maps and employing deep learning models. Using transcriptomic data from 27 cancer types and survival data from 10 types in the TCGA database, a pan-cancer transcriptomic feature map was constructed through data cleaning, feature extraction, and visualization. Using Inception network and gated convolutional modules yielded a pan-cancer classification accuracy of 91.

Deciphering Sequence Determinants of Zygotic Genome Activation Genes: Insights From Machine Learning and the ZGAExplorer Platform.

The mammalian life cycle initiates with the transition of genetic control from the maternal to the embryonic genome during zygotic genome activation (ZGA), which becomes pivotal for development. Nevertheless, understanding the conservation of genes and transcription factors (TFs) that underlie mammalian ZGA remains limited. Here, we compiled a comprehensive set of ZGA genes from mice, humans, pigs, bovines and goats, including Nr5a2 and TPRX1/2.

Alternative splicing dynamics during gastrulation in mouse embryo.

Alternative splicing (AS) plays an essential role in development, differentiation and carcinogenesis. However, the mechanisms underlying splicing regulation during mouse embryo gastrulation remain unclear. Based on spatial-temporal transcriptome and epigenome data, we detected the dynamics of AS and revealed its regulatory mechanisms across primary germ layers during mouse gastrulation, spanning developmental stages from E6.

The Metal-binding Protein Atlas (MbPA): An Integrated Database for Curating Metalloproteins in All Aspects.

Metal-binding proteins are essential for the vital activities and engage in their roles by acting in concert with metal cations. MbPA (The Metal-binding Protein Atlas) is the most comprehensive resource up to now dedicated to curating metal-binding proteins. Currently, it contains 106,373 entries and 440,187 sites related to 54 metals and 8169 species.

A cost-effective machine learning-based method for preeclampsia risk assessment and driver genes discovery.

Background: The placenta, as a unique exchange organ between mother and fetus, is essential for successful human pregnancy and fetal health. Preeclampsia (PE) caused by placental dysfunction contributes to both maternal and infant morbidity and mortality. Accurate identification of PE patients plays a vital role in the formulation of treatment plans.

EmAtlas: a comprehensive atlas for exploring spatiotemporal activation in mammalian embryogenesis.

The emerging importance of embryonic development research rapidly increases the volume for a professional resource related to multi-omics data. However, the lack of global embryogenesis repository and systematic analysis tools limits the preceding in stem cell research, human congenital diseases and assisted reproduction. Here, we developed the EmAtlas, which collects the most comprehensive multi-omics data and provides multi-scale tools to explore spatiotemporal activation during mammalian embryogenesis.

Temporal Dynamic Analysis of Alternative Splicing During Embryonic Development in Zebrafish.

Alternative splicing is pervasive in mammalian genomes and involved in embryo development, whereas research on crosstalk of alternative splicing and embryo development was largely restricted to mouse and human and the alternative splicing regulation during embryogenesis in zebrafish remained unclear. We constructed the alternative splicing atlas at 18 time-course stages covering maternal-to-zygotic transition, gastrulation, somitogenesis, pharyngula stages, and post-fertilization in zebrafish. The differential alternative splicing events between different developmental stages were detected.

RaacFold: a webserver for 3D visualization and analysis of protein structure by using reduced amino acid alphabets.

Protein structure exhibits greater complexity and diversity than DNA structure, and usually affects the interpretation of the function, interactions and biological annotations. Reduced amino acid alphabets (Raaa) exhibit a powerful ability to decrease protein complexity and identify functional conserved regions, which motivated us to create RaacFold. The RaacFold provides 687 reduced amino acid clusters (Raac) based on 58 reduction methods and offers three analysis tools: Protein Analysis, Align Analysis, and Multi Analysis.

Nucleosome Assembly and Disassembly Are Governed by Chemical Kinetic Principles.

As the elementary unit of eukaryotic chromatin, nucleosomes are highly dynamic in many biological processes, such as DNA replication, repair, recombination, or transcription, to allow the necessary factors to gain access to their substrate. The dynamic mechanism of nucleosome assembly and disassembly has not been well described thus far. We proposed a chemical kinetic model of nucleosome assembly and disassembly .

A Genome-Wide Analysis of the Gene Expression and Alternative Splicing Events in a Whole-Body Hypoxic Preconditioning Mouse Model.

Exposure to specific doses of hypoxia can trigger endogenous neuroprotective and neuroplastic mechanisms of the central nervous system. These molecular mechanisms, together referred to as hypoxic preconditioning (HPC), remain poorly understood. In the present study, we applied RNA sequencing and bioinformatics analyses to study HPC in a whole-body HPC mouse model.

A deformation energy model reveals sequence-dependent property of nucleosome positioning.

We present a deformation energy model for predicting nucleosome positioning, in which a position-dependent structural parameter set derived from crystal structures of nucleosomes was used to calculate the DNA deformation energy. The model is successful in predicting nucleosome occupancy genome-wide in budding yeast, nucleosome free energy, and rotational positioning of nucleosomes. Our model also indicates that the genomic regions underlying the MNase-sensitive nucleosomes in budding yeast have high deformation energy and, consequently, low nucleosome-forming ability, while the MNase-sensitive non-histone particles are characterized by much lower DNA deformation energy and high nucleosome preference.

Deform-nu: A DNA Deformation Energy-Based Predictor for Nucleosome Positioning.

The structure and function of chromatin can be regulated through positioning patterns of nucleosomes. DNA-based processes are regulated via nucleosomes. Therefore, it is significant to determine nucleosome positions in DNA-based processes.

Transcriptome profile analysis reveals a silica-induced immune response and fibrosis in a silicosis rat model.

Silicosis is a type of pneumoconiosis caused by the inhalation of silica dust. It is characterized by inflammation and fibrosis of the lung. Although many studies have reported that crystalline silica-inhalation into the lung initiates the immune response, activating effector cells and triggering the inflammatory cascade with subsequent elaboration of the extracellular matrix and fibrosis, the mechanism of silicosis pathogenesis remains unclear.

Dynamic Alternative Splicing During Mouse Preimplantation Embryo Development.

The mechanism of alternative pre-mRNA splicing (AS) during preimplantation development is largely unknown. In order to capture the dynamic changes of AS occurring during embryogenesis, we carried out bioinformatics analysis based on scRNA-seq data over the time-course preimplantation development in mouse. We detected numerous previously-unreported differentially expressed genes at specific developmental stages and investigated the nature of AS at both minor and major zygotic genome activation (ZGA).

The affinity of DNA sequences containing R5Y5 motif and TA repeats with 10.5-bp periodicity to histone octamer in vitro.

Nucleosome positioning along the genome is partially determined by the intrinsic DNA sequence preferences on histone. RRRRRYYYYY (R5Y5, R = Purine and Y = Pyrimidine) motif in nucleosome DNA, which was presented based on several theoretical models by Trifonov et al., might be a facilitating sequence pattern for nucleosome assembly.

The implication of DNA bending energy for nucleosome positioning and sliding.

Nucleosome not only directly affects cellular processes, such as DNA replication, recombination, and transcription, but also severs as a fundamentally important target of epigenetic modifications. Our previous study indicated that the bending property of DNA is important in nucleosome formation, particularly in predicting the dyad positions of nucleosomes on a DNA segment. Here, we investigated the role of bending energy in nucleosome positioning and sliding in depth to decipher sequence-directed mechanism.

MiasDB: A Database of Molecular Interactions Associated with Alternative Splicing of Human Pre-mRNAs.

Alternative splicing (AS) is pervasive in human multi-exon genes and is a major contributor to expansion of the transcriptome and proteome diversity. The accurate recognition of alternative splice sites is regulated by information contained in networks of protein-protein and protein-RNA interactions. However, the mechanisms leading to splice site selection are not fully understood.

A deformation energy-based model for predicting nucleosome dyads and occupancy.

Nucleosome plays an essential role in various cellular processes, such as DNA replication, recombination, and transcription. Hence, it is important to decode the mechanism of nucleosome positioning and identify nucleosome positions in the genome. In this paper, we present a model for predicting nucleosome positioning based on DNA deformation, in which both bending and shearing of the nucleosomal DNA are considered.

Using weighted features to predict recombination hotspots in Saccharomyces cerevisiae.

Characterization and accurate prediction of recombination hotspots and coldspots have crucial implications for the mechanism of recombination. Several models have predicted recombination hot/cold spots successfully, but there is still much room for improvement. We present a novel classifier in which k-mer frequency, physical and thermodynamic properties of DNA sequences are incorporated in the form of weighted features.

GAA triplet-repeats cause nucleosome depletion in the human genome.

Although there have been many investigations into how trinucleotide repeats affect nucleosome formation and local chromatin structure, the nucleosome positioning of GAA triplet-repeats in the human genome has remained elusive. In this work, the nucleosome occupancy around GAA triplet-repeats across the human genome was computed statistically. The results showed a nucleosome-depleted region in the vicinity of GAA triplet-repeats in activated and resting CD4(+) T cells.