Qiqige Wuyun

DisoNuc: Disordered Nucleic Acid Regions Database

Qiqige Wuyun, Lukasz Kurgan

The format of the CSV download file is as follows: ID: Starts with "DN", followed by 5-digits number, e.g., DN00001. Length: Disordered DNA/RNA sequence length. Sequence: Disordered DNA/RNA sequence. Type: Type of nucleic acid, i.e., DNA or RNA. PDB Sources: The corresponding …

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DisoNuc: Disordered Nucleic Acid Regions Database

Qiqige Wuyun, Lukasz Kurgan

The format of the CSV download file is as follows: ID: Starts with "DN", followed by 5-digits number, e.g., DN00001. Length: Disordered DNA/RNA sequence length. Sequence: Disordered DNA/RNA sequence. Type: Type of nucleic acid, i.e., DNA or RNA. PDB Sources: The corresponding …

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Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16

Rachael C. Kretsch, Elisa Posani, Eugene F. Baulin, Janusz Marek Bujnicki et autres

Biomolecules rely on water and ions for stable folding, but these interactions are often transient, dynamic, or disordered and thus hidden from experiments and evaluation challenges that represent biomolecules as single, ordered structures. Here, we compare blindly predicted ensembles of water and …

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Graph convolution network based on meta-paths and mutual information for drug-target interaction prediction

Shujuan Cao, Binying Cai, Tiantian Chang, Qiqige Wuyun et autres

BACKGROUND: Predicting drug-target interactions (DTIs) plays a pivotal role in accelerating drug repositioning by prioritizing candidate drugs and reducing experimental costs. Despite advancements in deep learning, several challenges still require further exploration, including sparsity and inadequate representation of feature relationships. RESULTS: We …

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Blind prediction of complex water and ion ensembles around RNA in CASP16

Rachael C. Kretsch, Elisa Posani, Eugene F. Baulin, Janusz Marek Bujnicki et autres

Abstract Biomolecules rely on water and ions for stable folding, but these interactions are often transient, dynamic, or disordered and thus hidden from experiments and evaluation challenges that represent biomolecules as single, ordered structures. Here, we compare blindly predicted ensembles of water …

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Author response for "Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16 "

Rachael C. Kretsch, Elisa Posani, Eugene F. Baulin, Janusz Marek Bujnicki et autres

Alternative Conformation Prediction Using Deep Learning With Multi‐ MSA Strategy and Structural Clustering in CASP16

Qiqige Wuyun, Quancheng Liu, Weiyi Ni, Chunxiang Peng et autres

We report the results from the "MIEnsembles-Server" and "Zheng" groups for structure ensemble predictions in CASP16, both of which employed the EnsembleFold pipeline. Initially, multiple sequence alignments (MSAs) were generated using DeepMSA2 for proteins and rMSA for RNA targets. These MSAs were …

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Figure 6 in 16S rDNA-based detection technology: use in lambs infected with Nematodirus oiratianus to analyze changes in intestinal flora

Si-Yao Li, Bin Hou, Qiqige Wuyun, Zhula Eerdeni et autres

Figure 6. β-Diversity analysis. (A) Principal Coordinates Analysis (PCoA) according to the Unweighted UniFrac distance; (B) Clustering analysis according to the Unweighted pair-group method with arithmetic means.

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Figure 10 in 16S rDNA-based detection technology: use in lambs infected with Nematodirus oiratianus to analyze changes in intestinal flora

Si-Yao Li, Bin Hou, Qiqige Wuyun, Zhula Eerdeni et autres

Figure 10. Linear discriminant analysis (LDA) effect size (LEfSe) analysis to screen specific dominant bacterial taxa of the two groups (a, Control Group; b, Infection Group). Distribution histogram based on LDA analysis (LDA score> 2 and p <0.05). The abscissa represents the …

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Figure 7 in 16S rDNA-based detection technology: use in lambs infected with Nematodirus oiratianus to analyze changes in intestinal flora

Si-Yao Li, Bin Hou, Qiqige Wuyun, Zhula Eerdeni et autres

Figure 7. Analysis of intestinal flora composition at the phylum level. (A) Community structure of bacteria from different treatment groups in phylum level; (B) Comparison of key species differences; a, Control Group; b, Infection Group. ***, p Ý 0.001; **, p Ý …

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Figure 10 in 16S rDNA-based detection technology: use in lambs infected with Nematodirus oiratianus to analyze changes in intestinal flora

Si-Yao Li, Bin Hou, Qiqige Wuyun, Zhula Eerdeni et autres

Figure 10. Linear discriminant analysis (LDA) effect size (LEfSe) analysis to screen specific dominant bacterial taxa of the two groups (a, Control Group; b, Infection Group). Distribution histogram based on LDA analysis (LDA score> 2 and p <0.05). The abscissa represents the …

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Figure 5 in 16S rDNA-based detection technology: use in lambs infected with Nematodirus oiratianus to analyze changes in intestinal flora

Si-Yao Li, Bin Hou, Qiqige Wuyun, Zhula Eerdeni et autres

Figure 5. α-Diversity analysis. (A) Chao index; (B) ACE index; (C) Shannon index; (D) Simpson index; a, Control Group; b, Infection Group. ***p Ý 0.001.

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