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View article: Finite-State Likelihood: an Approximation for Genome Phylogeny Inference based on Generalized Gene Contents
Finite-State Likelihood: an Approximation for Genome Phylogeny Inference based on Generalized Gene Contents Open
Rapid growth of entire genome data has revolutionized the field of phylogenomics, i.e., the problem of tree of life. Substantial studies demonstrated that genome phylogeny can be inferred based upon the generalized gene content approach. T…
View article: Population Genetics of Fluctuating Selection among Individuals (FSI): a New Paradigm of Molecular Evolution
Population Genetics of Fluctuating Selection among Individuals (FSI): a New Paradigm of Molecular Evolution Open
The FSI (fluctuating selection among individuals) theory of population genetics postulates that the fitness effect of a mutation may fluctuate among individuals with the same genotype (heterozygote or homozygote), whereas the wildtype fitn…
View article: Spanve: A Statistical Method for Downstream-friendly Spatially Variable Genes in Large-scale Data
Spanve: A Statistical Method for Downstream-friendly Spatially Variable Genes in Large-scale Data Open
Depicting gene expression in a spatial context through spatial transcriptomics is beneficial for inferring cellular mechanisms. Identifying spatially variable genes is a crucial step in leveraging spatial transcriptome data to understand i…
View article: DIVERGE v4: A Platform for Large-Scale Analysis of Functional Divergence Across Multi-Gene Families
DIVERGE v4: A Platform for Large-Scale Analysis of Functional Divergence Across Multi-Gene Families Open
Gene duplication and subsequent divergence are fundamental drivers in the evolution of novel gene functions. The DIVERGE software, widely utilized for identifying amino acid residues critical to functional shifts between protein subfamilie…
View article: A chromosome-level genome assembly for Ficus carica provides genetic insights into flowerless fig fruit development, psoralen biosynthesis, and drought tolerance
A chromosome-level genome assembly for Ficus carica provides genetic insights into flowerless fig fruit development, psoralen biosynthesis, and drought tolerance Open
View article: Oxygen-Sparing Photodynamic Therapy via Dissolving Microneedles for Rheumatoid Arthritis
Oxygen-Sparing Photodynamic Therapy via Dissolving Microneedles for Rheumatoid Arthritis Open
View article: Characterization of paralogous protein families in rice
Characterization of paralogous protein families in rice Open
Background High gene numbers in plant genomes reflect polyploidy and major gene duplication events. Oryza sativa, cultivated rice, is a diploid monocotyledonous species with a ~390 Mb genome that has undergone segmental duplication of a su…
View article: Spanve: A Statistical Method for Detecting Downstream-Friendly Spatially Variable Genes in Large-Scale Spatial Transcriptomic Data
Spanve: A Statistical Method for Detecting Downstream-Friendly Spatially Variable Genes in Large-Scale Spatial Transcriptomic Data Open
View article: MATTE: a pipeline of transcriptome module alignment for anti-noise phenotype-gene-related analysis
MATTE: a pipeline of transcriptome module alignment for anti-noise phenotype-gene-related analysis Open
A phenotype may be associated with multiple genes that interact with each other in the form of a gene module or network. How to identify these relationships is one important aspect of comparative transcriptomics. However, it is still a cha…
View article: 5-aminolevulinic acid-loaded dissolving microneedle array for photodynamic therapy of rheumatoid arthritis on rats
5-aminolevulinic acid-loaded dissolving microneedle array for photodynamic therapy of rheumatoid arthritis on rats Open
Photodynamic therapy (PDT) is a noninvasive technique that can be used to treat rheumatoid arthritis (RA) by irradiating photosensitizers with specific wavelengths of light to generate reactive oxygen species (ROS), thus leading to targete…
View article: Posterior Inference of Differential Expression (DE) State and Evolutionary Distance
Posterior Inference of Differential Expression (DE) State and Evolutionary Distance Open
To address how gene regulation plays a key role in phenotypic innovations through high throughput transcriptomes, it is desirable to develop statistically-sound methods that enable researchers to study the pattern of transcriptome evolutio…
View article: Spanve: A Statistical Method for Detecting Downstream-Friendly Spatially Variable Genes in Large-Scale Spatial Transcriptomic Data
Spanve: A Statistical Method for Detecting Downstream-Friendly Spatially Variable Genes in Large-Scale Spatial Transcriptomic Data Open
Depicting gene expression in a spatial context through spatial transcriptomics would be beneficial for inferring cell function mechanisms. The identification of spatially variable genes is a crucial step in leveraging the spatial transcrip…
View article: Genome Distance and Phylogenetic Inference Accommodating Gene Duplication, Loss and New Gene Input
Genome Distance and Phylogenetic Inference Accommodating Gene Duplication, Loss and New Gene Input Open
View article: TSNAdb v2.0: The Updated Version of Tumor-Specific Neoantigen Database
TSNAdb v2.0: The Updated Version of Tumor-Specific Neoantigen Database Open
In recent years, neoantigens have been recognized as ideal targets for tumor immunotherapy. With the development of neoantigen-based tumor immunotherapy, comprehensive neoantigen databases are urgently needed to meet the growing demand for…
View article: TSNAdb v2.0: the updated version of tumor-specific neoantigen database
TSNAdb v2.0: the updated version of tumor-specific neoantigen database Open
Tumor neoantigens have been well-acknowledged as ideal targets for tumor immunotherapy in recent years. With the deepening of research on neoantigen-based tumor immunotherapy, comprehensive neoantigen databases are urgently needed to meet …
View article: [Retracted] Assembly of 97 Novel Bacterial Genomes in the Microbial Community Affiliated with Polyvinyl Alcohol in Soil of Northern China
[Retracted] Assembly of 97 Novel Bacterial Genomes in the Microbial Community Affiliated with Polyvinyl Alcohol in Soil of Northern China Open
Background . Undeveloped ecosystems belong to rich source of microbial population, of which resources remain unearthed. A kind of polymeric compound system with high polyvinyl alcohol (PVA) content has been reported and named Taisui . Mark…
View article: Random Penetrance of Mutations Among Individuals: A New Type of Genetic Drift in Molecular Evolution
Random Penetrance of Mutations Among Individuals: A New Type of Genetic Drift in Molecular Evolution Open
View article: TSNAD v2.0: A one-stop software solution for tumor-specific neoantigen detection
TSNAD v2.0: A one-stop software solution for tumor-specific neoantigen detection Open
TSNAD is a one-stop software solution for predicting neoantigens from the whole genome/exome sequencing data of tumor-normal pairs. Here we present TSNAD v2.0 which provides several new features such as the function of RNA-Seq analysis inc…
View article: The Impact of DNA Methylation Dynamics on the Mutation Rate During Human Germline Development
The Impact of DNA Methylation Dynamics on the Mutation Rate During Human Germline Development Open
DNA methylation is a dynamic epigenetic modification found in most eukaryotic genomes. It is known to lead to a high CpG to TpG mutation rate. However, the relationship between the methylation dynamics in germline development and the germl…
View article: Evolutionary Transcriptome Analysis Based on Differentially Expressed (DE) Genes
Evolutionary Transcriptome Analysis Based on Differentially Expressed (DE) Genes Open
To address how gene regulation plays a key role in phenotypic innovations through high throughput transcriptomes, it is desirable to develop statistically-sound methods that enable researchers to study the pattern of transcriptome evolutio…
View article: A Statistical Framework for Evolutionary Analysis of Recurrent Somatic Mutations in Cancers
A Statistical Framework for Evolutionary Analysis of Recurrent Somatic Mutations in Cancers Open
Current cancer genomics databases have accumulated millions of somatic mutations that remain to be further explored, faciltating enormous high throuput analyses to explore the underlying mechanisms that may contribute to malignant initiati…
View article: Distinguish between Duplication of Essential Genes and Duplication of Dispensable Genes
Distinguish between Duplication of Essential Genes and Duplication of Dispensable Genes Open
When a dispensable gene is duplicated (ancestral dispensability), genetic buffering and duplicate compensation together maintain the gene dispensability, whereas duplicate compensation is the only mechanism when an essential gene is duplic…
View article: Evolutionary Distance of Gene-Gene Interactions: Estimation under Statistical Uncertainty
Evolutionary Distance of Gene-Gene Interactions: Estimation under Statistical Uncertainty Open
Consider the functional interaction of gene A to an interaction subject X ; for instance, it is the gene-gene interaction if X represents for a gene, or gene-tissue interaction (expression status) if X for a tissue. In the simplest case, t…
View article: <i>Δ</i>-<i>d</i><sub><i>N</i></sub>/<i>d</i><sub><i>S</i></sub>: A New Criteria to Distinguish among Different Selection Modes in Gene Evolution
<i>Δ</i>-<i>d</i><sub><i>N</i></sub>/<i>d</i><sub><i>S</i></sub>: A New Criteria to Distinguish among Different Selection Modes in Gene Evolution Open
One of the most widely-used measures for protein evolution is the ratio of nonsynonymous distance ( d N ) to synonymous distance ( d S ). Under the assumption that synonymous substitutions in the coding region are selectively neutral, the …
View article: Tracing Evolutionary Ages of Cancer-Driving Sites by Cancer Somatic Mutations
Tracing Evolutionary Ages of Cancer-Driving Sites by Cancer Somatic Mutations Open
Evolutionary understanding of cancer genes may provide insights on the nature and evolution of complex life and the origin of multicellularity. In this study, we focus on the evolutionary ages of cancer-driving sites, and try to explore to…
View article: DeepHLApan: A Deep Learning Approach for Neoantigen Prediction Considering Both HLA-Peptide Binding and Immunogenicity
DeepHLApan: A Deep Learning Approach for Neoantigen Prediction Considering Both HLA-Peptide Binding and Immunogenicity Open
Neoantigens play important roles in cancer immunotherapy. Current methods used for neoantigen prediction focus on the binding between human leukocyte antigens (HLAs) and peptides, which is insufficient for high-confidence neoantigen predic…
View article: TreeExp2: An Integrated Framework for Phylogenetic Transcriptome Analysis
TreeExp2: An Integrated Framework for Phylogenetic Transcriptome Analysis Open
Recent innovations of next-generation sequencing such as RNA-seq have generated an enormous amount of comparative transcriptome data, which have shed lights on our understanding of the complexity of transcriptional regulatory systems. Desp…
View article: Comparative Transcriptome Analyses Reveal the Role of Conserved Function in Electric Organ Convergence Across Electric Fishes
Comparative Transcriptome Analyses Reveal the Role of Conserved Function in Electric Organ Convergence Across Electric Fishes Open
The independent origins of multiple electric organs (EOs) of fish are fascinating examples of convergent evolution. However, comparative transcriptomics of different electric fish lineages are scarce. In this study, we found that the gene …
View article: Integrative Analysis of Somatic Mutations in Non-coding Regions Altering RNA Secondary Structures in Cancer Genomes
Integrative Analysis of Somatic Mutations in Non-coding Regions Altering RNA Secondary Structures in Cancer Genomes Open
View article: TIR-Learner, a New Ensemble Method for TIR Transposable Element Annotation, Provides Evidence for Abundant New Transposable Elements in the Maize Genome
TIR-Learner, a New Ensemble Method for TIR Transposable Element Annotation, Provides Evidence for Abundant New Transposable Elements in the Maize Genome Open