胡刚｜南开大学｜学者主页

2026

Retraction Note: Targeted activation of ferroptosis in colorectal cancer via LGR4 targeting overcomes acquired drug resistance

Hao Zheng, Jinming Liu, Qi Cheng, Qianping Zhang, Yaoyao Zhang, Lingyu Jiang, Yan Huang, Wenlei Li, Yanping Zhao, Guo Chen, Yu Fan, Lei Liu, Yanjun Li, Xudong Liao, Lai Xu, Yi Xiao, Zhibo Zheng, Ming Li, Hongyi Wang, Gang Hu, Lei Du, Quan Chen

Nature Cancer

DOI

2026

flDPnn3: Fast and Accurate Prediction of Intrinsic Disorder in Protein Sequences

Kui Wang, Gang Hu, Sushmita Basu, Lukasz Kurgan

Journal of Molecular Biology

DOI

2026

RNAdetector: fast and accurate predictor of RNA type-specific binding residues in protein sequences.

Gang Hu, Kui Wang, Ajay Arya, Lukasz Kurgan

PubMed

DOI

2026

Modern resources for intrinsic disorder predictions: protein language models, deep learning, meta-servers, and databases

Kui Wang, Gang Hu, Jing Yu, Lukasz Kurgan

Cellular and Molecular Life Sciences

DOI

2025

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

Rachael C. Kretsch, Elisa Posani, Eugene F. Baulin, Janusz Marek Bujnicki, Giovanni Bussi, Thomas E. Cheatham, Shi‐Jie Chen, Arne Elofsson, Masoud Amiri Farsani, Olivia N. Fisher, M. Michael Gromiha, Ayush Gupta, Michiaki Hamada, Kannan Harini, Gang Hu, David Y. C. Huang, Junichi Iwakiri, Anika Jain, Yuki Kagaya, Daisuke Kihara, Sebastian Kmiecik, Sowmya Ramaswamy Krishnan, Ikuo Kurisaki, Olivier Languin–Cattoën, Jun Li, Shanshan Li, Karim Malekzadeh, Tsukasa Nakamura, Wentao Ni, Chandran Nithin, Michael Z. Palo, Joon Hong Park, Smita P. Pilla, Simón Poblete, Fabrizio Pucci, Pranav Punuru, Anouka Saha, Kengo Sato, Ambuj Srivastava, Genki Terashi, Emilia Tugolukova, Jacob C. Verburgt, Qiqige Wuyun, Gül H. Zerze, Kaiming Zhang, Sicheng Zhang, Wei Hui Zheng, Yuanzhe Zhou, Wah Chiu, David Andrew Case, Rhiju Das

Proteins Structure Function and Bioinformatics

DOI

2025

A comprehensive benchmarking of the AlphaFold3 for predicting biomacromolecules and their interactions

Chunxiang Peng, Wentao Ni, Quancheng Liu, Gang Hu, Wei Hui Zheng

Briefings in Bioinformatics

DOI

2025

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

Qiqige Wuyun, Quancheng Liu, Wentao Ni, Chunxiang Peng, Ziying Zhang, Xiaogen Zhou, Gang Hu, Lydia Freddolino, Wei Hui Zheng

Proteins Structure Function and Bioinformatics

DOI

2025

Empirical Assessment of Sequence-Based Predictions of Intrinsically Disordered Regions Involved in Phase Separation

Xuantai Wu, Kui Wang, Gang Hu, Lukasz Kurgan

Biomolecules

DOI

2025

PROBind: A Web Server for Prediction, Analysis and Visualization of Protein-Protein and Protein-Nucleic Acid Binding Residues

Chao-Jin Wu, Fuhao Zhang, Pengzhen Jia, Jiuxiang Zhu, Min Zeng, Gang Hu, Kui Wang, Lukasz Kurgan, Min Li

bioRxiv

DOI

2024

Endothelial FUNDC1 Deficiency Drives Pulmonary Hypertension

Yandong Pei, Dongfeng Ren, Yuanhao Yin, Jiajia Shi, Qianyuan Ai, Wenxin Hao, Xiaofan Luo, Chenyue Zhang, Yanping Zhao, Chenyu Bai, Lin Zhu, Qiong Wang, Shuangling Li, Yuwei Zhang, Jiangtao Lu, Lin Liu, Lin Zhou, Yuli Wu, Yiqi Weng, Yongle Jing, Chengzhi Lu, Yujie Cui, Hao Zheng, Yanjun Li, Guo Chen, Gang Hu, Quan Chen, Xudong Liao

Circulation Research

DOI

2024

RETRACTED ARTICLE: Targeted activation of ferroptosis in colorectal cancer via LGR4 targeting overcomes acquired drug resistance

Nature Cancer

DOI

2024

flDPnn2: Accurate and Fast Predictor of Intrinsic Disorder in Proteins

Kui Wang, Gang Hu, Sushmita Basu, Lukasz Kurgan

Journal of Molecular Biology

DOI

2024

[Identification of Protein-Coding Gene Markers in Breast Invasive Carcinoma Based on Machine Learning].

Yue Wu, Kaiyuan Min, Jiang-Feng Liu, Wanfeng Liang, Yehong Yang, Gang Hu, Juntao Yang

PubMed

DOI

2024

Assessment of Disordered Linker Predictions in the CAID2 Experiment

Kui Wang, Gang Hu, Zhonghua Wu, Vladimir Nikolaevich Uversky, Lukasz Kurgan

Biomolecules

DOI

2024

Recent Progress of Protein Tertiary Structure Prediction

Qiqige Wuyun, Yihan Chen, Yifeng Shen, Yang Cao, Gang Hu, Wei Cui, Jianzhao Gao, Wei Hui Zheng

Molecules

DOI

2024

The Historical Evolution and Significance of Multiple Sequence Alignment in Molecular Structure and Function Prediction

Chenyue Zhang, Qinxin Wang, Yiyang Li, Anqi Teng, Gang Hu, Qiqige Wuyun, Wei Hui Zheng

Biomolecules

DOI

2023

DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options

Sushmita Basu, Bi Zhao, Bálint Biró, Eshel Faraggi, Jörg A. Gsponer, Gang Hu, Andrzej Kloczkowski, Nawar Malhis, Milot Mirdita, Johannes Söding, Martin Steinegger, Duolin Wang, Kui Wang, Dong He Xu, Jian Zhang, Lukasz Kurgan

Nucleic Acids Research

DOI

2023

Single-cell transcriptome analysis reveals cellular heterogeneity and highlights Fstl1-regulated alveolar myofibroblasts in mouse lung at birth

Si Zhang, Xiuxue Mo, Yueyue Jin, Zhuan Niu, Maolin Yao, Yue Zhang, Lian Li, Gang Hu, Wen Ning

Genomics

DOI

2023

CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins

Alessio Del Conte, Kamel Eddine Adel Bouhraoua, Mahta Mehdiabadi, Damiano Clementel, Alexander Miguel Monzón, CAID predictors, Alex S. Holehouse, Daniel Griffith, Ryan J. Emenecker, Ashwini Patil, Ronesh Sharma, Tatsuhiko Tsunoda, Alok K. Sharma, Yi Jun Tang, Bin Liu, Claudio Mirabello, Björn Wallner, Burkhard Rost, Dagmar Ilzhöfer, Maria Littmann, Michael Heinzinger, Lea I M Krautheimer, Michael Bernhofer, Liam James McGuffin, Isabelle Callebaut, Tristan Bitard‐Feildel, Jian Liu, Jianlin Jack Cheng, Zhiye Guo, Jinbo Xu, Sheng Wang, Nawar Malhis, Jörg A. Gsponer, Chol-Song Kim, Kun‐Sop Han, Myong-Chol Ma, Lukasz Kurgan, Sina Ghadermarzi, Akila Katuwawala, Bi Zhao, Zhenling Peng, Zhonghua Wu, Gang Hu, Kui Wang, Md Tamjidul Hoque, Md Wasi Ul Kabir, Michele Vendruscolo, Pietro Sormanni, Min Li, Fuhao Zhang, Pengzhen Jia, Yida Wang, Michail Yu. Lobanov, Oxana V. Galzitskaya, Wim Vranken, Adrián Díaz, Thomas Litfin, Yaoqi Zhou, Jack Hanson, Kuldip K. Paliwal, Zsuzsanna Dosztányi, Gábor Erdős, Silvio C. E. Tosatto, Damiano Piovesan

Nucleic Acids Research

DOI

2023

DIST: spatial transcriptomics enhancement using deep learning

Yanping Zhao, Kui Wang, Gang Hu

Briefings in Bioinformatics

DOI

2023

[Role of Eukaryotic Translation Elongation Factor 1 Family Members in the Tumorigenesis and Progression of Lung Adenocarcinoma].

Yue Wu, Jiangfeng Liu, Wanfeng Liang, Yehong Yang, Gang Hu, Juntao Yang

PubMed

DOI

2023

CXCL9+ Macrophage-targeted NIR-II aggregation-induced emission nanoprobes for the early diagnosis of myocarditis

Zhe Sun, Xiumeng Hua, Mengni Bao, Weilin Xu, Miaomiao Kang, Mo Han, Gang Hu, Guangxin Yue, Xiao Chen, Shimin Mo, Zhijun Zhang, Dong Wang, Jiangping Song

Nano Today

DOI

2023

Tutorial: a guide for the selection of fast and accurate computational tools for the prediction of intrinsic disorder in proteins

Lukasz Kurgan, Gang Hu, Kui Wang, Sina Ghadermarzi, Bi Zhao, Nawar Malhis, Gábor Erdős, Jörg A. Gsponer, Vladimir Nikolaevich Uversky, Zsuzsanna Dosztányi

Nature Protocols

DOI

2023

Correction: APOE and TREM2 regulate amyloid-responsive microglia in Alzheimer’s disease

Aivi T. Nguyen, Kui Wang, Gang Hu, Xuran Wang, Zhen Miao, Joshua A. Azevedo, EunRan R. Suh, Vivianna M. Van Deerlin, David S. Choi, Kathryn Roeder, Mingyao Li, Edward B. Lee

Acta Neuropathologica

DOI

2023

NRF1‐mediated mitochondrial biogenesis antagonizes innate antiviral immunity

Tian Zhao, Jiaojiao Zhang, Hong Lei, Yuanyuan Meng, Hongcheng Cheng, Yanping Zhao, Guangfeng Geng, Chenglong Mu, Linbo Chen, Qiangqiang Liu, Qian Luo, Chuanmei Zhang, Yijia Long, Jingyi Su, Yinhao Wang, Zhuoya Li, Jiaxing Sun, Guo Chen, Yanjun Li, Xudong Liao, Yingli Shang, Gang Hu, Quan Chen, Yushan Zhu

The EMBO Journal

DOI

2023

STING regulates the transformation of the proinflammatory macrophage phenotype by HIF1A into autoimmune myocarditis

Xiumeng Hua, Mengni Bao, Mo Han, Zhe Sun, Mengda Xu, Xiao Chen, Xiuxue Mo, Gang Hu, Menghao Tao, Jiangping Song

International Immunopharmacology

DOI

2023

Inhibition of NETosis via PAD4 alleviated inflammation in giant cell myocarditis

Hu Zhan, Xiumeng Hua, Xiuxue Mo, Yuan Chang, Xiao Chen, Zhenyu Xu, Mengtao Tao, Gang Hu, Jiangping Song

iScience

DOI

2022

Propensity score matching enables batch-effect-corrected imputation in single-cell RNA-seq analysis

Xinyi Xu, Xiaokang Yu, Gang Hu, Kui Wang, Jingxiao Zhang, Xiangjie Li

Briefings in Bioinformatics

DOI

2022

Hypoxia-induced proteasomal degradation of DBC1 by SIAH2 in breast cancer progression

Qiangqiang Liu, Qian Luo, Jianyu Feng, Yanping Zhao, Biao Ma, Hongcheng Cheng, Tian Zhao, Hong Lei, Chenglong Mu, Linbo Chen, Yuanyuan Meng, Jiaojiao Zhang, Yijia Long, Jingyi Su, Guo Chen, Yanjun Li, Gang Hu, Xudong Liao, Quan Chen, Yushan Zhu

eLife

DOI

2022

Author response: Hypoxia-induced proteasomal degradation of DBC1 by SIAH2 in breast cancer progression

DOI

2021

Accurate Estimation of Single-Cell Differentiation Potency Based on Network Topology and Gene Ontology Information

Xinzhe Ni, Bohao Geng, Haoyu Zheng, Jiawei Shi, Gang Hu, Jianzhao Gao

IEEE Transactions on Computational Biology and Bioinformatics

DOI

2021

flDPnn: Accurate intrinsic disorder prediction with putative propensities of disorder functions

Gang Hu, Akila Katuwawala, Kui Wang, Zhonghua Wu, Sina Ghadermarzi, Jianzhao Gao, Lukasz Kurgan

Nature Communications

DOI

2021

Intrinsic Disorder in Human RNA-Binding Proteins

Bi Zhao, Akila Katuwawala, Christopher J. Oldfield, Gang Hu, Zhonghua Wu, Vladimir Nikolaevich Uversky, Lukasz Kurgan

Journal of Molecular Biology

DOI

2021

Critical assessment of protein intrinsic disorder prediction

Marco Necci, Damiano Piovesan, CAID Predictors, Md Tamjidul Hoque, Ian Walsh, Sumaiya Iqbal, Michele Vendruscolo, Pietro Sormanni, Chen Wang, Daniele Raimondi, Ronesh Sharma, Yaoqi Zhou, Thomas Litfin, Oxana V. Galzitskaya, Michail Yu. Lobanov, Wim Vranken, Björn Wallner, Claudio Mirabello, Nawar Malhis, Zsuzsanna Dosztányi, Gábor Erdős, Bálint Mészáros, Jianzhao Gao, Kui Wang, Gang Hu, Zhonghua Wu, Alok K. Sharma, Jack Hanson, Kuldip K. Paliwal, Isabelle Callebaut, Tristan Bitard‐Feildel, Gabriele Orlando, Zhenling Peng, Jinbo Xu, Sheng Wang, David T. Jones, Domenico Cozzetto, Fanchi Meng, Jing Ru Yan, Jörg A. Gsponer, Jianlin Jack Cheng, Tianqi Wu, Lukasz Kurgan, DisProt Curators, Vasilis J. Promponas, Stella Tamana, Cristina Marino‐Buslje, Elizabeth Martínez‐Pérez, Anastasia Chasapi, Christos A. Ouzounis, A. Keith Dunker, Andrey V. Kajava, Jeremy Y. Leclercq, Burcu Aykaç Fas, Matteo Lambrughi, Emiliano Maiani, Elena Papaleo, Lucia Beatriz Chemes, Lucía Álvarez, Nicolás S. González Foutel, Valentín Iglesias, Jordi Pujols, Salvador Ventura, Nicolás Palópoli, Guillermo Ignacio Benítez, Gustavo D. Parisi, Claudio Bassot, Arne Elofsson, Govindarajan Sudha, John Lamb, Marco Salvatore, András Hatos, Alexander Miguel Monzón, Martina Bevilacqua, Ivan Mičetić, Giovanni Minervini, Lisanna Paladin, Federica Quaglia, Emanuela Leonardi, Norman E. Davey, Tamás Horváth, Orsolya Panna Kovacs, Nikoletta Murvai, Rita Pancsa, Éva Schád, Beáta Szabó, Ágnes Tantos, Sandra Macedo‐Ribeiro, José A. Manso, Pedro José Barbosa Pereira, Radoslav S. Davidović, Nevena Veljković, Borbála Hajdu-Soltész, Mátyás Pajkos, Tamás Szaniszló, Mainak Guharoy, Tamás Lázár, Mauricio Macossay-Castillo, Péter Tompa, Silvio C. E. Tosatto

Nature Methods

DOI

2021

QUARTERplus: Accurate disorder predictions integrated with interpretable residue-level quality assessment scores

Akila Katuwawala, Sina Ghadermarzi, Gang Hu, Zhonghua Wu, Lukasz Kurgan

Computational and Structural Biotechnology Journal

DOI

2020

Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis

Xiumeng Hua, Gang Hu, Qingtao Hu, Yuan Chang, Yiqing Hu, Linlin Gao, Xiao Chen, Ping–Chang Yang, Yu Zhang, Mingyao Li, Jiangping Song

Circulation

DOI

2020

Deep learning enables accurate clustering with batch effect removal in single-cell RNA-seq analysis

Xiangjie Li, Kui Wang, Yafei Lyu, Huize Pan, Jingxiao Zhang, Dwight E. Stambolian, Katalin Suszták, Muredach P. Reilly, Gang Hu, Mingyao Li

Nature Communications

DOI

2020

Comprehensive Survey and Comparative Assessment of RNA-Binding Residue Predictions with Analysis by RNA Type

Kui Wang, Gang Hu, Zhonghua Wu, Hong Lin Su, Jianyi Yang, Lukasz Kurgan

International Journal of Molecular Sciences

DOI

2020

APOE and TREM2 regulate amyloid-responsive microglia in Alzheimer’s disease

Aivi T. Nguyen, Kui Wang, Gang Hu, Xuran Wang, Zhen Miao, Joshua A. Azevedo, EunRan R. Suh, Vivianna M. Van Deerlin, David S. Choi, Kathryn Roeder, Mingyao Li, Edward B. Lee

Acta Neuropathologica

DOI

2020

Iterative transfer learning with neural network for clustering and cell type classification in single-cell RNA-seq analysis

Jian Hu, Xiangjie Li, Gang Hu, Yafei Lyu, Katalin Suszták, Mingyao Li

Nature Machine Intelligence

DOI

2020

Two-Level Protein Methylation Prediction using structure model-based features

Wei Hui Zheng, Qiqige Wuyun, Micah Cheng, Gang Hu, Yanping Zhang

Scientific Reports

DOI

2019

GWAS发现SNP位点在妊娠期糖尿病女性产后2型糖尿病发病风险预测价值

李卫芹，黄育北，刘慧坤，张爽，王蕾棽，李楠，李薇，胡刚，冷俊宏

《中国公共卫生》

2019

Data denoising with transfer learning in single-cell transcriptomics

Jingshu Wang, Divyansh Agarwal, Mo Chao Huang, Gang Hu, Zilu Zhou, Chengzhong Ye, Nancy Ruonan Zhang

Nature Methods

DOI

2018

Quality assessment for the putative intrinsic disorder in proteins

Gang Hu, Zhonghua Wu, Christopher J. Oldfield, Chen Wang, Lukasz Kurgan

Bioinformatics

DOI

2018

PennDiff: detecting differential alternative splicing and transcription by RNA sequencing

Yu Hu, Jennie J. Lin, Jian Hu, Gang Hu, Kui Wang, Hanrui Zhang, Muredach P. Reilly, Mingyao Li

Bioinformatics

DOI

2018

Taxonomic Landscape of the Dark Proteomes: Whole‐Proteome Scale Interplay Between Structural Darkness, Intrinsic Disorder, and Crystallization Propensity

Gang Hu, Kui Wang, Jiangning Song, Vladimir Nikolaevich Uversky, Lukasz Kurgan

PROTEOMICS

DOI

2018

Sequence Similarity Searching

Gang Hu, Lukasz Kurgan

Current Protocols in Protein Science

DOI

2017

Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder-Enriched Interactions

Gang Hu, Zhonghua Wu, Vladimir Nikolaevich Uversky, Lukasz Kurgan

International Journal of Molecular Sciences

DOI

2017

Survey of Predictors of Propensity for Protein Production and Crystallization with Application to Predict Resolution of Crystal Structures

Jianzhao Gao, Zhonghua Wu, Gang Hu, Kui Wang, Jiangning Song, A. Joachimiak, Lukasz Kurgan

Current Protein and Peptide Science

DOI

2017

Exploratory Analysis of Quality Assessment of Putative Intrinsic Disorder in Proteins

Zhonghua Wu, Gang Hu, Kui Wang, Lukasz Kurgan

Lecture notes in computer science

DOI

2017

PrAS:複数の特徴抽出を用いたアミド化部位の予測【Powered by NICT】

Tong Wang, Wei Zheng, Wuyun Qiqige, Zheng-Feng Wu, J. Ruan, Gang Hu, Jian-Zhao Gao

2016

PrAS: Prediction of amidation sites using multiple feature extraction

Tong Wang, Wei Hui Zheng, Qiqige Wuyun, Zhenfeng Wu, Jishou Ruan, Gang Hu, Jianzhao Gao

Computational Biology and Chemistry

DOI

2016

What are the structural features that drive partitioning of proteins in aqueous two-phase systems?

Zhonghua Wu, Gang Hu, Kui Wang, Boris Y. Zaslavsky, Lukasz Kurgan, Vladimir Nikolaevich Uversky

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

DOI

2016

Improved Species-Specific Lysine Acetylation Site Prediction Based on a Large Variety of Features Set

Qiqige Wuyun, Wei Hui Zheng, Yanping Zhang, Jishou Ruan, Gang Hu

PLoS ONE

DOI

2016

Untapped Potential of Disordered Proteins in Current Druggable Human Proteome.

Gang Hu, Zhonghua Wu, Kui Wang, V. Uversky, Lukasz Kurgan

Current Drug Targets

DOI

2015

PDID: database of molecular-level putative protein–drug interactions in the structural human proteome

Chen Wang, Gang Hu, Kui Wang, Michał Bryliński, Lei Xie, Lukasz Kurgan

Bioinformatics

DOI

2015

In various protein complexes, disordered protomers have large per‐residue surface areas and area of protein‐, DNA‐ and RNA‐binding interfaces

Zhonghua Wu, Gang Hu, Jianyi Yang, Zhenling Peng, Vladimir Nikolaevich Uversky, Lukasz Kurgan

FEBS Letters

DOI

2015

Analysis of Conformational B-Cell Epitopes in the Antibody-Antigen Complex Using the Depth Function and the Convex Hull

Wei Hui Zheng, Jishou Ruan, Gang Hu, Kui Wang, Michelle Hanlon, Jianzhao Gao

PLoS ONE

DOI

2014

Human structural proteome-wide characterization of Cyclosporine A targets

Gang Hu, Kui Wang, Jody Groenendyk, Khaled Barakat, Marcin J. Mizianty, Jishou Ruan, Marek Michalak, Lukasz Kurgan

Bioinformatics

DOI

2014

Exceptionally abundant exceptions: comprehensive characterization of intrinsic disorder in all domains of life

Zhenling Peng, Jing Ru Yan, Xiao Fan, Marcin J. Mizianty, Bin Xue, Kui Wang, Gang Hu, Vladimir Nikolaevich Uversky, Lukasz Kurgan

Cellular and Molecular Life Sciences

DOI

2013

An Accurate Method for Prediction of Protein-Ligand Binding Site on Protein Surface Using SVM and Statistical Depth Function

Kui Wang, Jianzhao Gao, Shiyi Shen, Jack A. Tuszyński, Jishou Ruan, Gang Hu

BioMed Research International

DOI

2013

Improved Prediction of Protein Crystallization, Purification and Production Propensity Using Hybrid Sequence Representation

Jian-Zhao Gao, Gang Hu, Zhonghua Wu, J. Ruan, Shiyi Shen, Michelle Hanlon, Kui Wang

DOI

2012

Finding Protein Targets for Small Biologically Relevant Ligands across Fold Space Using Inverse Ligand Binding Predictions

Gang Hu, Jianzhao Gao, Kui Wang, Marcin J. Mizianty, Jishou Ruan, Lukasz Kurgan

Structure

DOI

2012

Circular Cone: A novel approach for protein ligand shape matching using modified PCA

Shuangjian Zhang, Jun Du, Liang Zhang, Cheng Zeng, Qiao Liu, Tao Zhang, Gang Hu

Computer Methods and Programs in Biomedicine

DOI

2012

Computable Features Required to Evaluate the Efficacy of Drugs and a Universal Algorithm to Find Optimally Effective Drug in a Drug Complex

Kui Wang, Wei Cui, Gang Hu, Jianzhao Gao, Zhonghua Wu, Xingye Qiu, Jishou Ruan, Yi Feng, Zhi Qi, Yiming Shao, Jack A. Tuszyński

PLoS ONE

DOI

2011

On the evolution rate in mammalian mitochondrial genomes

Gang Hu, Shiyi Shen, Kui Wang

Computational Biology and Chemistry

DOI

2009

Using dihedral angle series of protein for protein structure comparison

Jian-Zhao Gao, Gang Hu, Kui Wang, Jia-Feng Cui

2007

Analysis of Protein Three-Dimension Structure Using Amino Acids Depths

Shiyi Shen, Gang Hu, Jack A. Tuszyński

The Protein Journal

DOI

2006

On the Alignment Space and its applications

Shiyi Shen, Kui Wang, Gang Hu, Shu‐Tao Xia

DOI

2005

SMA: An Efficient Tool for Large-Scale Multiple Alignment

Shiyi Shen, Liuhuan Dong, Kui Wang, Gang Hu

DOI

2005

On the Alignment Space

Shiyi Shen, Kui Wang, Gang Hu, Lusheng Chen, Hua Zhang, Shu‐Tao Xia

DOI

精选作品

期刊论文

Retraction Note: Targeted activation of ferroptosis in colorectal cancer via LGR4 targeting overcomes acquired drug resistance

flDPnn3: Fast and Accurate Prediction of Intrinsic Disorder in Protein Sequences

RNAdetector: fast and accurate predictor of RNA type-specific binding residues in protein sequences.

Modern resources for intrinsic disorder predictions: protein language models, deep learning, meta-servers, and databases

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

A comprehensive benchmarking of the AlphaFold3 for predicting biomacromolecules and their interactions

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

Empirical Assessment of Sequence-Based Predictions of Intrinsically Disordered Regions Involved in Phase Separation

PROBind: A Web Server for Prediction, Analysis and Visualization of Protein-Protein and Protein-Nucleic Acid Binding Residues

Endothelial FUNDC1 Deficiency Drives Pulmonary Hypertension

RETRACTED ARTICLE: Targeted activation of ferroptosis in colorectal cancer via LGR4 targeting overcomes acquired drug resistance

flDPnn2: Accurate and Fast Predictor of Intrinsic Disorder in Proteins

[Identification of Protein-Coding Gene Markers in Breast Invasive Carcinoma Based on Machine Learning].

Assessment of Disordered Linker Predictions in the CAID2 Experiment

Recent Progress of Protein Tertiary Structure Prediction

The Historical Evolution and Significance of Multiple Sequence Alignment in Molecular Structure and Function Prediction

DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options

Single-cell transcriptome analysis reveals cellular heterogeneity and highlights Fstl1-regulated alveolar myofibroblasts in mouse lung at birth

CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins

DIST: spatial transcriptomics enhancement using deep learning

[Role of Eukaryotic Translation Elongation Factor 1 Family Members in the Tumorigenesis and Progression of Lung Adenocarcinoma].

CXCL9+ Macrophage-targeted NIR-II aggregation-induced emission nanoprobes for the early diagnosis of myocarditis

Tutorial: a guide for the selection of fast and accurate computational tools for the prediction of intrinsic disorder in proteins

Correction: APOE and TREM2 regulate amyloid-responsive microglia in Alzheimer’s disease

NRF1‐mediated mitochondrial biogenesis antagonizes innate antiviral immunity

STING regulates the transformation of the proinflammatory macrophage phenotype by HIF1A into autoimmune myocarditis

Inhibition of NETosis via PAD4 alleviated inflammation in giant cell myocarditis

Propensity score matching enables batch-effect-corrected imputation in single-cell RNA-seq analysis

Hypoxia-induced proteasomal degradation of DBC1 by SIAH2 in breast cancer progression

Author response: Hypoxia-induced proteasomal degradation of DBC1 by SIAH2 in breast cancer progression

Accurate Estimation of Single-Cell Differentiation Potency Based on Network Topology and Gene Ontology Information

flDPnn: Accurate intrinsic disorder prediction with putative propensities of disorder functions

Intrinsic Disorder in Human RNA-Binding Proteins

Critical assessment of protein intrinsic disorder prediction

QUARTERplus: Accurate disorder predictions integrated with interpretable residue-level quality assessment scores

Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis

Deep learning enables accurate clustering with batch effect removal in single-cell RNA-seq analysis

Comprehensive Survey and Comparative Assessment of RNA-Binding Residue Predictions with Analysis by RNA Type

APOE and TREM2 regulate amyloid-responsive microglia in Alzheimer’s disease

Iterative transfer learning with neural network for clustering and cell type classification in single-cell RNA-seq analysis

Two-Level Protein Methylation Prediction using structure model-based features

GWAS发现SNP位点在妊娠期糖尿病女性产后2型糖尿病发病风险预测价值

Data denoising with transfer learning in single-cell transcriptomics

Quality assessment for the putative intrinsic disorder in proteins

PennDiff: detecting differential alternative splicing and transcription by RNA sequencing

Taxonomic Landscape of the Dark Proteomes: Whole‐Proteome Scale Interplay Between Structural Darkness, Intrinsic Disorder, and Crystallization Propensity

Sequence Similarity Searching

Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder-Enriched Interactions

Survey of Predictors of Propensity for Protein Production and Crystallization with Application to Predict Resolution of Crystal Structures

Exploratory Analysis of Quality Assessment of Putative Intrinsic Disorder in Proteins

PrAS:複数の特徴抽出を用いたアミド化部位の予測【Powered by NICT】

PrAS: Prediction of amidation sites using multiple feature extraction

What are the structural features that drive partitioning of proteins in aqueous two-phase systems?

Improved Species-Specific Lysine Acetylation Site Prediction Based on a Large Variety of Features Set

Untapped Potential of Disordered Proteins in Current Druggable Human Proteome.

PDID: database of molecular-level putative protein–drug interactions in the structural human proteome

In various protein complexes, disordered protomers have large per‐residue surface areas and area of protein‐, DNA‐ and RNA‐binding interfaces

Analysis of Conformational B-Cell Epitopes in the Antibody-Antigen Complex Using the Depth Function and the Convex Hull

Human structural proteome-wide characterization of Cyclosporine A targets

Exceptionally abundant exceptions: comprehensive characterization of intrinsic disorder in all domains of life

An Accurate Method for Prediction of Protein-Ligand Binding Site on Protein Surface Using SVM and Statistical Depth Function

Improved Prediction of Protein Crystallization, Purification and Production Propensity Using Hybrid Sequence Representation

Finding Protein Targets for Small Biologically Relevant Ligands across Fold Space Using Inverse Ligand Binding Predictions

Circular Cone: A novel approach for protein ligand shape matching using modified PCA

Computable Features Required to Evaluate the Efficacy of Drugs and a Universal Algorithm to Find Optimally Effective Drug in a Drug Complex

On the evolution rate in mammalian mitochondrial genomes

Using dihedral angle series of protein for protein structure comparison

Analysis of Protein Three-Dimension Structure Using Amino Acids Depths

On the Alignment Space and its applications

SMA: An Efficient Tool for Large-Scale Multiple Alignment

On the Alignment Space

会议论文

PPCinter:an improved method for prediction of protein crystallization

Application of the information dynamic function on protein structure

Application of the information dynamic function in prediction of protein folding rate

The analysis and applications of protein structure

预印本

A Joint Deep Learning Model for Simultaneous Batch Effect Correction, Denoising and Clustering in Single-Cell Transcriptomics