Liangyun Zhang
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View article: scRGP: Prediction of Single-cell Genetic Perturbation Transcriptional Responses based on Rank in Multiple Scenarios
scRGP: Prediction of Single-cell Genetic Perturbation Transcriptional Responses based on Rank in Multiple Scenarios Open
Single-cell perturbation sequencing technologies (e.g., Perturb-seq, CROP-seq), which integrate CRISPR-based gene editing with single-cell transcriptome profiling, have revolutionized the analysis of transcriptomic changes induced by genet…
View article: AIPAMPDS: an AI platform for antimicrobial peptide design and screening
AIPAMPDS: an AI platform for antimicrobial peptide design and screening Open
Antimicrobial resistance (AMR) presents a pressing global health crisis, particularly in the post-pandemic era, underscoring the urgent need for innovative therapeutics. Antimicrobial peptides (AMPs) hold promises for combating multidrug-r…
View article: The deformation and construction of Nijenhuis paired modules
The deformation and construction of Nijenhuis paired modules Open
In this paper, we introduce the notion of Nijenhuis paired module, and give characterizations of Nijenhuis paired modules. Finally, we construct Nijenhuis paired modules from Hopf algebras, Hopf modules, dimodules and weak Hopf modules.
View article: Rota–Baxter Operators on Skew Braces
Rota–Baxter Operators on Skew Braces Open
In this paper, we introduce the concept of Rota–Baxter skew braces, and provide classifications of Rota–Baxter operators on various skew braces, such as (Z,+,∘) and (Z/(4),+,∘). We also present a necessary and sufficient condition for a sk…
View article: Hopf heap and Hopf heap module
Hopf heap and Hopf heap module Open
In this paper, we firstly give some results and properties of Hopf heaps. In addition, we get a equivalent definition of a Hopf truess by a Hopf heap. Using this equivalence definition, we construct some examples of Hopf trusses by Hopf he…
View article: Design and optimization of novel succinate dehydrogenase inhibitors against agricultural fungi based on Transformer model
Design and optimization of novel succinate dehydrogenase inhibitors against agricultural fungi based on Transformer model Open
Succinate dehydrogenase inhibitors (SDHIs) are a promising class of fungicides targeting the energy production pathway of pathogenic fungi. However, overuse has led to resistance, necessitating the development of new and effective SDHIs. T…
View article: Rota-Baxter operators on cocommutative Hopf algebras and Hopf braces
Rota-Baxter operators on cocommutative Hopf algebras and Hopf braces Open
This paper studies the relationship of Rota-Baxter operators on cocommutative Hopf algebras with Hopf braces and the Yang-Baxter equation, with emphasis on the embedding of cocommutative Hopf braces into Rota-Baxter Hopf algebras. Through …
View article: NcPath: a novel platform for visualization and enrichment analysis of human non-coding RNA and KEGG signaling pathways
NcPath: a novel platform for visualization and enrichment analysis of human non-coding RNA and KEGG signaling pathways Open
Summary Non-coding RNAs play important roles in transcriptional processes and participate in the regulation of various biological functions, in particular miRNAs and lncRNAs. Despite their importance for several biological functions, the e…
View article: Prognostic value of lymphovascular space invasion evaluated by immunohistochemistry and stratification with a semi-quantitative scoring system for early-stage endometrial cancer
Prognostic value of lymphovascular space invasion evaluated by immunohistochemistry and stratification with a semi-quantitative scoring system for early-stage endometrial cancer Open
Objective To investigate the prognostic value of lymphovascular space invasion (LVSI) evaluated by immunohistochemistry and then stratification with a semi-quantitative scoring system for early-stage endometrial cancer. Methods We retrospe…
View article: Identification and Functional Analysis of Individual-Specific Subpathways in Lung Adenocarcinoma
Identification and Functional Analysis of Individual-Specific Subpathways in Lung Adenocarcinoma Open
Small molecular networks within complex pathways are defined as subpathways. The identification of patient-specific subpathways can reveal the etiology of cancer and guide the development of personalized therapeutic strategies. The dysfunc…
View article: NcPath: A novel tool for visualization and enrichment analysis of human non-coding RNA and KEGG signaling pathways
NcPath: A novel tool for visualization and enrichment analysis of human non-coding RNA and KEGG signaling pathways Open
Noncoding RNAs play important roles in transcriptional processes and participate in the regulation of various biological functions, in particular miRNAs and lncRNAs. Despite their importance for several biological functions, the existing s…
View article: Rota–Baxter Operators on Cocommutative Weak Hopf Algebras
Rota–Baxter Operators on Cocommutative Weak Hopf Algebras Open
In this paper, we first introduce the concept of a Rota–Baxter operator on a cocommutative weak Hopf algebra H and give some examples. We then construct Rota–Baxter operators from the normalized integral, antipode, and target map of H. Mor…
View article: Rota–Baxter paired comodules and Rota–Baxter paired Hopf modules
Rota–Baxter paired comodules and Rota–Baxter paired Hopf modules Open
We introduce the concept of Rota–Baxter paired comodules, which is dual to Rota–Baxter paired modules defined by Zheng et al. (2020). We discuss some properties of Rota–Baxter paired comodules, in particular we give a characterization of g…
View article: THE STRUCTURE THEOREM OF HOM-HOPF BIMODULES AND ITS APPLICATIONS
THE STRUCTURE THEOREM OF HOM-HOPF BIMODULES AND ITS APPLICATIONS Open
In this paper, we give the structure theorem of Hom-Hopf bimodules. Furthermore, we give the structure theorem of Hom-comodule algebras. Finally, we consider and study the structure theorems of Hom-Hopf bicomodules and Hom-module coalgebra…
View article: Peer Review #2 of "SPMLMI: predicting lncRNA–miRNA interactions in humans using a structural perturbation method (v0.2)"
Peer Review #2 of "SPMLMI: predicting lncRNA–miRNA interactions in humans using a structural perturbation method (v0.2)" Open
Long non-coding RNA (lncRNA)-microRNA (miRNA) interactions are quickly emerging as important mechanisms underlying the functions of non-coding RNAs.Accordingly, predicting lncRNA-miRNA interactions provides an important basis for understan…
View article: Peer Review #1 of "SPMLMI: predicting lncRNA–miRNA interactions in humans using a structural perturbation method (v0.2)"
Peer Review #1 of "SPMLMI: predicting lncRNA–miRNA interactions in humans using a structural perturbation method (v0.2)" Open
Long non-coding RNA (lncRNA)-microRNA (miRNA) interactions are quickly emerging as important mechanisms underlying the functions of non-coding RNAs.Accordingly, predicting lncRNA-miRNA interactions provides an important basis for understan…
View article: Peer Review #2 of "SPMLMI: predicting lncRNA–miRNA interactions in humans using a structural perturbation method (v0.1)"
Peer Review #2 of "SPMLMI: predicting lncRNA–miRNA interactions in humans using a structural perturbation method (v0.1)" Open
Long non-coding RNA (lncRNA)-microRNA (miRNA) interactions are quickly emerging as important mechanisms underlying the functions of non-coding RNAs.Accordingly, predicting lncRNA-miRNA interactions provides an important basis for understan…
View article: Peer Review #1 of "SPMLMI: predicting lncRNA–miRNA interactions in humans using a structural perturbation method (v0.1)"
Peer Review #1 of "SPMLMI: predicting lncRNA–miRNA interactions in humans using a structural perturbation method (v0.1)" Open
Long non-coding RNA (lncRNA)-microRNA (miRNA) interactions are quickly emerging as important mechanisms underlying the functions of non-coding RNAs.Accordingly, predicting lncRNA-miRNA interactions provides an important basis for understan…
View article: SPMLMI: predicting lncRNA–miRNA interactions in humans using a structural perturbation method
SPMLMI: predicting lncRNA–miRNA interactions in humans using a structural perturbation method Open
Long non-coding RNA (lncRNA)–microRNA (miRNA) interactions are quickly emerging as important mechanisms underlying the functions of non-coding RNAs. Accordingly, predicting lncRNA–miRNA interactions provides an important basis for understa…
View article: Identifying RNA N6-Methyladenine Sites in Three Species Based on a Markov Model
Identifying RNA N6-Methyladenine Sites in Three Species Based on a Markov Model Open
N6-methyladenosine (m6A), the most common posttranscriptional modification in eukaryotic mRNAs, plays an important role in mRNA splicing, editing, stability, degradation, etc. Since the methylation state is dynamic, methylation sequencing …
View article: Deep6mA: A deep learning framework for exploring similar patterns in DNA N6-methyladenine sites across different species
Deep6mA: A deep learning framework for exploring similar patterns in DNA N6-methyladenine sites across different species Open
N6-methyladenine (6mA) is an important DNA modification form associated with a wide range of biological processes. Identifying accurately 6mA sites on a genomic scale is crucial for under-standing of 6mA’s biological functions. However, th…
View article: EpiMOGA: An Epistasis Detection Method Based on a Multi-Objective Genetic Algorithm
EpiMOGA: An Epistasis Detection Method Based on a Multi-Objective Genetic Algorithm Open
In genome-wide association studies, detecting high-order epistasis is important for analyzing the occurrence of complex human diseases and explaining missing heritability. However, there are various challenges in the actual high-order epis…
View article: Mining influential genes based on deep learning
Mining influential genes based on deep learning Open
Background Currently, large-scale gene expression profiling has been successfully applied to the discovery of functional connections among diseases, genetic perturbation, and drug action. To address the cost of an ever-expanding gene expre…
View article: Mining influential genes based on deep learning
Mining influential genes based on deep learning Open
Background: Currently, large-scale gene expression profiling has been successfully applied to the discovery of functional connections among diseases, genetic perturbation, and drug action. To address the cost of an ever-expanding gene expr…
View article: Additional file 1 of Mining influential genes based on deep learning
Additional file 1 of Mining influential genes based on deep learning Open
Additional file 1. A file in TXT format including a list of genes sorted based on contribution scores.
View article: Revealing Prognosis-Related Pathways at the Individual Level by a Comprehensive Analysis of Different Cancer Transcription Data
Revealing Prognosis-Related Pathways at the Individual Level by a Comprehensive Analysis of Different Cancer Transcription Data Open
Identifying perturbed pathways at an individual level is important to discover the causes of cancer and develop individualized custom therapeutic strategies. Though prognostic gene lists have had success in prognosis prediction, using sing…
View article: Rota-Bater paried comodule and Rota-Bater paired Hopf module
Rota-Bater paried comodule and Rota-Bater paired Hopf module Open
In this paper, we introduce the conception of Rota-Baxter paired comodules, which is dual to Rota-Baxter paired modules in [14]. We mainly discuss some properties of Rota-Baxter paired comodules, especially we give the characterization of …
View article: Mining influential genes based on deep learning
Mining influential genes based on deep learning Open
Background: Currently, large-scale gene expression profiling has been successfully applied to the discovery of functional connections among diseases, genetic perturbation, and drug action. To address the cost of an ever-expanding gene expr…
View article: Hopf-Galois algebras and their Poisson structures
Hopf-Galois algebras and their Poisson structures Open
As is known to all, Hopf-Galois objects have a significant research value for analyzing tensor categories of comodules and classification questions of pointed Hopf algebras, and are natural generalizations of Hopf algebras with a Galois-th…
View article: Deep6mA: a deep learning framework for exploring similar patterns in DNA N6-methyladenine sites across different species
Deep6mA: a deep learning framework for exploring similar patterns in DNA N6-methyladenine sites across different species Open
N6-methyladenin(6mA) is an important DNA modification form associated with a wide range of biological processes. Identifying accurately 6mA sites on a genomic scale is crucial for understanding of 6mA’s biological functions. In this paper,…