百晓学者学者目录

张阳

西南财经大学

精选作品

期刊论文

2026

自然资源资产离任审计的“双碳”治理效应

张阳，刘奕臻，彭嘉熹

《广东财经大学学报》，No. 3

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2023

高声誉子公司能够抵御母公司利益侵占行为吗？——基于资源依赖理论的视角

张阳，徐向艺

《管理评论》，Vol. 35, No. 11

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2023

母公司超额委派董事对子公司投资效率的双刃效应研究

张阳，徐向艺

《审计与经济研究》，Vol. 38, No. 6

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2022

Fast and accurate Ab Initio Protein structure prediction using deep learning potentials

Robin Pearce, Yang Li, G. Omenn, Yang Zhang

PLoS Comput. Biol.

DOI

2022

GPU-I-TASSER: a GPU accelerated I-TASSER protein structure prediction tool

Elijah MacCarthy, Chengxin Zhang, Yang Zhang, KC DukkaB

Bioinform.

DOI

2022

Accurate flexible refinement for atomic-level protein structure using cryo-EM density maps and deep learning

Biao Zhang, Dong Liu, Yang Zhang, Hong-Bin Shen, Gui-Jun Zhang

Briefings Bioinform.

DOI

2022

Predicting Protein-Ligand Binding Affinity via Joint Global-Local Interaction Modeling

Yang Zhang, Gengmo Zhou, Zhe-Wei Wei, Hong-Teng Xu

Industrial Conference on Data Mining

DOI

2021

审计师会收取并购商誉风险溢价吗?——基于代理成本和经营风险视角

张阳，徐子慧，王晓丹

《南京审计大学学报》，No. 2

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2021

Protein structure prediction using deep learning distance and hydrogen-bonding restraints in CASP14

Wei Zheng, Yang Li, Chengxin Zhang, Xiao-Gen Zhou, Robin Pearce, Eric W. Bell, Xiao-Qiang Huang, Yang Zhang

Proteins: Structure, Function, and Bioinformatics

DOI

2021

MPDB: a unified multi-domain protein structure database integrating structural analogue detection

Chunxiang Peng, Xiao-Gen Zhou, Yu-Hao Xia, Yang Zhang, Gui-Jun Zhang

bioRxiv

DOI

2021

Decoding microbiome and protein family linkage to improve protein structure prediction

Pengshuo Yang, Wei Zheng, Kang Ning, Yang Zhang

bioRxiv

DOI

2021

MMpred: a distance-assisted multimodal conformation sampling for de novo protein structure prediction

Kai-Long Zhao, Jun Liu, Xiao-Gen Zhou, Jianwen Su, Yang Zhang, Gui-Jun Zhang

bioRxiv

DOI

2021

Identification of 13 Guanidinobenzoyl- or Aminidinobenzoyl-Containing Drugs to Potentially Inhibit TMPRSS2 for COVID-19 Treatment

Xiao-Qiang Huang, Robin Pearce, G. Omenn, Yang Zhang

International Journal of Molecular Sciences

DOI

2021

Computational analysis of vertebrate myoglobins reveals aggregation resistance in aquatic birds and higher surface hydrophobicity in fish

Syed M. Rizvi, Wei Zheng, Chengxin Zhang, Yang Zhang

DOI

2021

Decoding the link of microbiome niches with homologous sequences enables accurately targeted protein structure prediction

Pengshuo Yang, Wei Zheng, K. Ning, Yang Zhang

Proceedings of the National Academy of Sciences of the United States of America

DOI

2021

TripletGO: Integrating Transcript Expression Profiles with Protein Homology Inferences for High-Accuracy Gene Function Annotations

Yi-Heng Zhu, Chengxin Zhang, Yan Liu, G. Omenn, P. Freddolino, Dong-Jun Yu, Yang Zhang

bioRxiv

DOI

2021

Protein inter-residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14

Yang Li, Chengxin Zhang, Wei Zheng, Xiao-Gen Zhou, Eric W. Bell, Dong-Jun Yu, Yang Zhang

Proteins: Structure, Function, and Bioinformatics

DOI

2021

Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome

Chengxin Zhang, Wei Zheng, Micah Cheng, G. Omenn, P. Freddolino, Yang Zhang

Journal of Proteome Research

DOI

2021

ADDRESS: A database of disease-associated human variants incorporating protein structure and folding stabilities

Jaie C. Woodard, Chengxin Zhang, Yang Zhang

Journal of Molecular Biology

DOI

2021

Deep learning techniques have significantly impacted protein structure prediction and protein design

Robin Pearce, Yang Zhang

Current Opinion in Structural Biology

DOI

2021

PEPPI: Whole-proteome protein-protein interaction prediction through structure and sequence similarity, functional association, and machine learning

Eric W. Bell, Jacob H. Schwartz, P. Freddolino, Yang Zhang

bioRxiv

DOI

2021

Toward the solution of the protein structure prediction problem

Robin Pearce, Yang Zhang

Journal of Biological Chemistry

DOI

2021

Fitting Low-Resolution Protein Structures into Cryo-EM Density Maps by Multiobjective Optimization of Global and Local Correlations.

Biao Zhang, Wen-Yi Zhang, Robin Pearce, Yang Zhang, Hong-Bin Shen

Journal of Physical Chemistry B

DOI

2021

Protein structural features predict responsiveness to pharmacological chaperone treatment for three lysosomal storage disorders

Jaie C. Woodard, Wei Zheng, Yang Zhang

bioRxiv

DOI

2021

Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions

S. Mortuza, Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Yang Zhang

Nature Communications

DOI

2021

Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations

Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang

Cell Reports Methods

DOI

2020

CEO声誉对真实盈余管理的“双刃”效应研究:“逐利争名”还是“取义舍利”

徐宁，张阳，徐向艺

《上海财经大学学报》，Vol. 22, No. 4

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2020

Genome-wide structure and function modeling of SARS-COV-2

Xiao-Qiang Huang, Robin Pearcs, Yang Zhang

DOI

2020

FASPR: an open-source tool for fast and accurate protein side-chain packing

Xiao-Qiang Huang, Robin Pearce, Yang Zhang

Bioinform.

DOI

2020

Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks

Yang Li, Chengxin Zhang, Eric W. Bell, Wei Zheng, Xiao-Gen Zhou, Dong-Jun Yu, Yang Zhang

bioRxiv

DOI

2020

Landscape of variable domain of heavy‐chain‐only antibody repertoire from alpaca

Zhui Tu, Xiao-Qiang Huang, Jin-Heng Fu, Na Hu, Wei Zheng, Yanping Li, Yang Zhang

Immunology

DOI

2020

Virtual screening of human Class-A GPCRs using ligand profiles built on multiple ligand-receptor interactions

Wallace K. B. Chan, Yang Zhang

Journal of Molecular Biology

DOI

2020

Computational design of SARS-CoV-2 spike glycoproteins to increase immunogenicity by T cell epitope engineering

E. Ong, Xiao-Qiang Huang, Robin Pearce, Yang Zhang, Y. He

Computational and Structural Biotechnology Journal

DOI

2020

FUpred: detecting protein domains through deep-learning-based contact map prediction

Wei Zheng, Xiao-Gen Zhou, Q. Wuyun, Robin Pearce, Yang Li, Yang Zhang

Bioinform.

DOI

2020

A new protocol for atomic-level protein structure modeling and refinement using low-to-medium resolution cryo-EM density maps

Biao Zhang, Xi Zhang, Robin Pearce, Hong-Bin Shen, Yang Zhang

Journal of Molecular Biology

DOI

2020

Integrating multimeric threading with high-throughput experiments for structural interactome of Escherichia coli

Weikang Gong, Aysam Guerler, Chengxin Zhang, E. Warner, Chunhua Li, Yang Zhang

bioRxiv

DOI

2020

Identifying the Zoonotic Origin of SARS-CoV-2 by Modeling the Binding Affinity Between the Spike Receptor-Binding Domain and Host ACE2

Xiao-Qiang Huang, Chengxin Zhang, Robin Pearce, G. Omenn, Yang Zhang

Journal of Proteome Research

DOI

2020

Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features

Yi-Heng Zhu, Jun-Da Hu, Fang Ge, Fuyi Li, Jiangning Song, Yang Zhang, Dong-Jun Yu

Briefings Bioinform.

DOI

2020

EDock: blind protein–ligand docking by replica-exchange monte carlo simulation

Wen-Yi Zhang, Eric W. Bell, Minghao Yin, Yang Zhang

Journal of Cheminformatics

DOI

2020

De novo design of protein peptides to block association of the SARS-CoV-2 spike protein with human ACE2

Xiao-Qiang Huang, Robin Pearce, Yang Zhang

Aging

DOI

2020

Progressive and accurate assembly of multi-domain protein structures from cryo-EM density maps

Xiao-Gen Zhou, Yang Li, Chengxin Zhang, Wei Zheng, Gui-Jun Zhang, Yang Zhang

bioRxiv

DOI

2020

Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons

Xiaoqiong Wei, Chengxin Zhang, P. Freddolino, Yang Zhang, Zhi-Yong Lu

Bioinform.

DOI

2020

Protein structure and sequence re-analysis of 2019-nCoV genome does not indicate snakes as its intermediate host or the unique similarity between its spike protein insertions and HIV-1

Chengxin Zhang, Wei Zheng, Xiao-Qiang Huang, Eric W. Bell, Xiao-Gen Zhou, Yang Zhang

bioRxiv

DOI

2020

Effects of SARS‐CoV‐2 mutations on protein structures and intraviral protein–protein interactions

Siqi Wu, C. Tian, Panpan Liu, D. Guo, Wei Zheng, Xiao-Qiang Huang, Yang Zhang, Lijun Liu

bioRxiv

DOI

2019

EvoDesign: Designing protein-protein binding interactions using evolutionary interface profiles in conjunction with an optimized physical energy function

Robin Pearce, Xiao-Qiang Huang, Dani Setiawan, Yang Zhang

Journal of Molecular Biology

DOI

2019

Artificial intelligence-based multi-objective optimization protocol for protein structure refinement

Di Wang, Ling Geng, Yu-Jun Zhao, Yang Yang, Yan Huang, Yang Zhang, Hong-Bin Shen

Bioinform.

DOI

2019

Precise modelling and interpretation of bioactivities of ligands targeting G protein-coupled receptors

Jian-Sheng Wu, Ben Liu, Wallace K. B. Chan, Weijian Wu, Tao Pang, Haifeng Hu, Shancheng Yan, Xiao-Yan Ke, Yang Zhang

Bioinform.

DOI

2019

I-TASSER gateway: A protein structure and function prediction server powered by XSEDE

Wei Zheng, Chengxin Zhang, Eric W. Bell, Yang Zhang

Future generations computer systems

DOI

2019

Interpreting the Dynamics of Binding Interactions of snRNA and U1A Using a Coarse-Grained Model.

Zhong-Jie Han, Qi Shao, Weikang Gong, Shihao Wang, Ji-Guo Su, Chunhua Li, Yang Zhang

Biophysical Journal

DOI

2019

LabCaS for Ranking Potential Calpain Substrate Cleavage Sites from Amino Acid Sequence.

Yong-Xian Fan, Xiaoyong Pan, Yang Zhang, Hong-Bin Shen

Methods in molecular biology

DOI

2019

Blinded Testing of Function Annotation for uPE1 Proteins by I-TASSER/COFACTOR Pipeline Using the 2018–2019 Additions to neXtProt and the CAFA3 Challenge

Chengxin Zhang, L. Lane, G. Omenn, Yang Zhang

Journal of Proteome Research

DOI

2019

Changing the Ap Evolutionary Pro

D. Shultis, Pralay Mitra, Design, Huang, Jarrett S. Johnson, N. A. Khattak, F. Gray, Clint Piper, Jeff Czajka, Logan Hansen, B. Wan, Krishnapriya Chinnaswamy, Liu Liu, Mi Wang, Jingxi Pan, J. Stuckey, T. Cierpicki, C. Borchers, Shaomeng Wang, M. Lei, Yang Zhang

2019

Underestimation-Assisted Global-Local Cooperative Differential Evolution and the Application to Protein Structure Prediction

Xiao-Gen Zhou, Chunxiang Peng, Jun Liu, Yang Zhang, Gui-Jun Zhang

IEEE Transactions on Evolutionary Computation

DOI

2019

SSIPe: accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function

Xiao-Qiang Huang, Wei Zheng, Robin Pearce, Yang Zhang

Bioinform.

DOI

2019

LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins

Wei Zheng, Chengxin Zhang, Q. Wuyun, Robin Pearce, Yang Li, Yang Zhang

Nucleic Acids Res.

DOI

2019

Function Prediction for G Protein-Coupled Receptors through Text Mining and Induction Matrix Completion

Jian-Sheng Wu, Qing Yin, Chengxin Zhang, Jingjing Geng, Hongjie Wu, Haifeng Hu, Xiao-Yan Ke, Yang Zhang

ACS Omega

DOI

2019

RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA

Sha Gong, Chengxin Zhang, Yang Zhang

Bioinform.

DOI

2019

Assembling multidomain protein structures through analogous global structural alignments

Xiao-Gen Zhou, Jun-Da Hu, Chengxin Zhang, Gui-Jun Zhang, Yang Zhang

Proceedings of the National Academy of Sciences of the United States of America

DOI

2019

DAMpred: Recognizing disease-associated nsSNPs through Bayes-guided neural-network model built on low-resolution structure prediction of proteins and protein-protein interactions

Li-Jun Quan, Hongjie Wu, Qiang Lyu, Yang Zhang

Journal of Molecular Biology

DOI

2019

Detecting distant-homology protein structures by aligning deep neural-network based contact maps

Wei Zheng, Q. Wuyun, Yang Li, S. Mortuza, Chengxin Zhang, Robin Pearce, J. Ruan, Yang Zhang

PLoS Comput. Biol.

DOI

2019

Changing the Ap through Evolutio

D. Shultis, Pralay Mitra, Huang, Jarrett S. Johnson, N. A. Khattak, F. Gray, Clint Piper, Jeff Czajka, Logan Hansen, B. Wan, Krishnapriya Chinnaswamy, Liu Liu, Mi Wang, Jingxi Pan, J. Stuckey, T. Cierpicki, C. Borchers, Shaomeng Wang, M. Lei, Yang Zhang

2019

gnizing Disease-Associated Bayes-Guided Neural-uilt on Low-Resolution tion of Proteins and Interactions

Li-Jun Quan, Hongjie Wu, Qiang Lyu, Yang Zhang

2019

Ensembling multiple raw coevolutionary features with deep residual neural networks for contact-map prediction in CASP13

Yang Li, Chengxin Zhang, Eric W. Bell, Dong-Jun Yu, Yang Zhang

Proteins: Structure, Function, and Bioinformatics

DOI

2019

ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks

Yang Li, Jun-Da Hu, Chengxin Zhang, Dong-Jun Yu, Yang Zhang

Bioinform.

DOI

2019

Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families

Yan Wang, Qiang Shi, Pengshuo Yang, Chengxin Zhang, S. Mortuza, Zhidong Xue, Kang Ning, Yang Zhang

Genome Biology

DOI

2019

Changing the Apoptosis Pathway through Evolutionary Protein Design

D. Shultis, Pralay Mitra, Xiao-Qiang Huang, Jarrett S. Johnson, N. A. Khattak, F. Gray, Clint Piper, Jeff Czajka, Logan Hansen, B. Wan, Krishnapriya Chinnaswamy, Liu Liu, Mi Wang, Jingxi Pan, J. Stuckey, T. Cierpicki, C. Borchers, Shaomeng Wang, M. Lei, Yang Zhang

Journal of Molecular Biology

DOI

2019

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Nai-Hui Zhou, Yuxiang Jiang, T. Bergquist, Alexandra J. Lee, B. Kacsoh, Alex Crocker, Kimberley A. Lewis, G. Georghiou, Huy N. Nguyen, Md-Nafiz Hamid, Larry Davis, Tunca Dogan, V. Atalay, A. Rifaioglu, Alperen Dalkıran, Rengul Cetin Atalay, Chengxin Zhang, R. Hurto, P. Freddolino, Yang Zhang, Prajwal Bhat, F. Supek, J. M. Fernández, Branislava Gemović, Vladimir R. Perovic, Radoslav Davidović, Neven Sumonja, Nevena Veljkovic, Ehsaneddin Asgari, M. R. Mofrad, Giuseppe Profiti, Castrense Savojardo, P. Martelli, R. Casadio, Florian Boecker, H. Schoof, Indika Kahanda, Natalie Thurlby, A. Mchardy, A. Renaux, R. Saidi, J. Gough, A. Freitas, M. Antczak, Fábio Fabris, M. Wass, Jie Hou, Jian-Lin Cheng, Zheng Wang, A. Romero, Alberto Paccanaro, Hai-Xuan Yang, T. Goldberg, Chenguang Zhao, Liisa Holm, P. Törönen, A. Medlar, Elaine Zosa, I. Borukhov, Ilya B. Novikov, A. Wilkins, O. Lichtarge, Po-Han Chi, Wei-Cheng Tseng, M. Linial, Peter W. Rose, C. Dessimoz, Vedrana Vidulin, S. Džeroski, I. Sillitoe, Sayoni Das, J. Lees, David T. Jones, Cen Wan, D. Cozzetto, Rui Fa, Mateo Torres, Alex Warwick Vesztrocy, J. Rodríguez, M. Tress, M. Frasca, M. Notaro, G. Grossi, A. Petrini, M. Ré, G. Valentini, M. Mesiti, Daniel B. Roche, Jonas Reeb, David W. Ritchie, Sabeur Aridhi, Seyed Ziaeddin Alborzi, M. Devignes, D. Koo, Richard Bonneau, V. Gligorijević, Meet Barot, Hai Fang, S. Toppo, E. Lavezzo, M. Falda, Michele Berselli, S. Tosatto, Marco Carraro, D. Piovesan, H. Rehman, Qizhong Mao, Shanshan Zhang, S. Vucetic, Gage S. Black, Dane Jo, Erica Suh, Jonathan B. Dayton, D. Larsen, Ashton R. Omdahl, L. McGuffin, D. A. Brackenridge, P. Babbitt, Jeffrey M. Yunes, P. Fontana, Feng Zhang, Shanfeng Zhu, Rong-Hui You, Zi-Han Zhang, Suyang Dai, Shuwei Yao, Weidong Tian, Renzhi Cao, Caleb M. Chandler, Miguel Amezola, Devon Johnson, Jia-Ming Chang, Wen-Hung Liao, Yi-Wei Liu, Stefano Pascarelli, Yotam Frank, R. Hoehndorf, Maxat Kulmanov, Imane Boudellioua, G. Politano, S. Di Carlo, A. Benso, Kai Hakala, F. Ginter, Farrokh Mehryary, Suwisa Kaewphan, Jari Björne, Hans Moen, M. Tolvanen, Tapio Salakoski, D. Kihara, A. Jain, T. Šmuc, A. Altenhoff, Asa Ben-Hur, B. Rost, S. Brenner, C. Orengo, C. Jeffery, G. Bosco, D. A. Hogan, M. Martin, C. O'Donovan, S. Mooney, C. Greene, P. Radivojac, I. Friedberg

Genome Biology

DOI

2019

DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins

Chengxin Zhang, Wei Zheng, S. Mortuza, Yang Li, Yang Zhang

Bioinform.

DOI

2019

CGLFold: a contact-assisted de novo protein structure prediction using global exploration and loop perturbation sampling algorithm

J. Liu, Xiao-Gen Zhou, Yang Zhang, Gui-Jun Zhang

Bioinform.

DOI

2019

Cryo-EM Density Map Fitting Driven In-Silico Structure of Human Soluble Guanylate Cyclase (hsGC) reveals functional aspects of inter-domain cross talk upon NO binding

R. Khalid, Arooma Maryam, V. E. Fadouloglou, A. R. Siddiqi, Yang Zhang

Journal of Molecular Graphics and Modelling

DOI

2019

Deep-learning contact-map guided protein structure prediction in CASP13

Wei Zheng, Yang Li, Chengxin Zhang, Robin Pearce, S. Mortuza, Yang Zhang

Proteins: Structure, Function, and Bioinformatics

DOI

2019

DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism

Eric W. Bell, Yang Zhang

Journal of Cheminformatics

DOI

2019

OP-CBIO190748 1..8

Xiao-Qiang Huang, Robin Pearce, Yang Zhang

2019

EvoEF2: accurate and fast energy function for computational protein design

Xiao-Qiang Huang, Robin Pearce, Yang Zhang

Bioinform.

DOI

2019

Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries

Xiao-Qiang Huang, Robin Pearce, Yang Zhang

Journal of Chemical Information and Modeling

DOI

2018

Recent advances in automated protein design and its future challenges

Dani Setiawan, J. Brender, Yang Zhang

Expert Opinion on Drug Discovery

DOI

2018

mTM-align: a server for fast protein structure database search and multiple protein structure alignment

Runze Dong, Shuo Pan, Zhenling Peng, Yang Zhang, Jianyi Yang

Nucleic Acids Res.

DOI

2018

ATPbind: Accurate Protein–ATP Binding Site Prediction by Combining Sequence-Profiling and Structure-Based Comparisons

Jun-Da Hu, Yang Li, Yang Zhang, Dong-Jun Yu

Journal of Chemical Information and Modeling

DOI

2018

THE-DB: a threading model database for comparative protein structure analysis of the E. coli K12 and human proteomes

J. Diamond, Yang Zhang

Database J. Biol. Databases Curation

DOI

2018

MetaGO: Predicting Gene Ontology of non-homologous proteins through low-resolution protein structure prediction and protein-protein network mapping

Chengxin Zhang, Wei Zheng, P. Freddolino, Yang Zhang

Journal of Molecular Biology

DOI

2018

MR-REX: molecular replacement by cooperative conformational search and occupancy optimization on low-accuracy protein models.

Jouko J. Virtanen, Yang Zhang

Acta Crystallographica Section D: Structural Biology

DOI

2018

WDL‐RF: predicting bioactivities of ligand molecules acting with G protein‐coupled receptors by combining weighted deep learning and random forest

Jian-Sheng Wu, Qiu-Ming Zhang, Weijian Wu, Tao Pang, Haifeng Hu, Wallace K. B. Chan, Xiao-Yan Ke, Yang Zhang, Jonathan D. Wren

Bioinform.

DOI

2018

mTM‐align: an algorithm for fast and accurate multiple protein structure alignment

Runze Dong, Zhenling Peng, Yang Zhang, Jianyi Yang

Bioinform.

DOI

2018

MetaGO : Predict Non-homologou Low-Resolution Prediction and P Network Mappin

Chengxin Zhang, Wei Zheng, G. Freddolino, Yang Zhang

2018

MetaGO : Predicting Gene Ontology of Non-hom Resolutio Protein – P

Chengxin Zhang, Wei Zheng, P. Freddolino, Yang Zhang

2018

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12

C. Keasar, L. McGuffin, B. Wallner, G. Chopra, Badri Adhikari, Debswapna Bhattacharya, Lauren Blake, L. O. Bortot, Renzhi Cao, B. Dhanasekaran, Itzhel Dimas, R. Faccioli, E. Faraggi, R. Ganzynkowicz, Sambit Ghosh, Soma Ghosh, A. Giełdoń, Lukasz Golon, Yi He, Lim Heo, Jie Hou, M. Khan, F. Khatib, George A. Khoury, C. Kieslich, David E. Kim, P. Krupa, G. Lee, Hongbo Li, Ji-Long Li, A. Lipska, A. Liwo, A. H. Maghrabi, M. Mirdita, S. Mirzaei, M. Mozolewska, Melis Onel, S. Ovchinnikov, Anand Shah, Utkarsh Shah, Tomer Sidi, A. Sieradzan, M. Ślusarz, R. Ślusarz, J. Smadbeck, P. Tamamis, Nicholas Trieber, T. Wirecki, Yanping Yin, Yang Zhang, J. Bacardit, Maciej Baranowski, Nicholas Chapman, Seth Cooper, A. Defelicibus, J. Flatten, B. Koepnick, Zoran Popovic, Bartlomiej Zaborowski, D. Baker, Jian-Lin Cheng, C. Czaplewski, A. Delbem, C. Floudas, A. Kloczkowski, S. Ołdziej, M. Levitt, H. Scheraga, Chaok Seok, J. Söding, S. Vishveshwara, Dong Xu, Ahmet Caglar, A. Coral, Alison MacMillan, Allen Lubow, Barbara Failer, Bruno Kestemont, C. Landers, Charles Robert Painter, Christophe Garnier, Claudine Sellin, Dietmar Janz, Douglas Craig Wheeler, Vera Simon, Dylan M. Flear, Emmanuel Croze, George Victor McIlvaine, Gil Beecher, Gordon Lawrie, Guy Ykman, Harald Feldmann, Heidemarie K. Fuentes, Terumasa Hosokawa, Istvan Kovanecz, James Absalom Longino, Jan Hendrik Nijland, Jasper A. Diderich, Jeffrey M. Canfield, Jesper Eriksson, Janice Slone, Joan Goldsworthy Appel, Jane M. O. Mitchell, Johnson Mitch, Jorn Loots-Boiy, June M. Brownlee, Karsten Wilson, Keith T. Clayton, Kenneth E. DeFord, Kirk J. Abbey, Larry Withers, Lin-Dan Wei, L. Ives, Lori A. Miller, L. Carpenter, Manasa G. Sharma, Manuel Ricci, Mark Stewart Binfield, Matthew John Davids, Matthias Gaebel, Michael D. Cassidy, Michael Fagiola, Michael Pfützenreuter, N. Barlow, IV PeterJohnTriggiani, Renton Braden Mathew Innes, Robert Leduc, Rodrigo Luccas Corrêa dos Santos Gomes, Rosemarie L. R. Morneau, Scott J. Zaccanelli, Susan C. Kleinfelter, T. van der Laan, Thomas Bausewein, Thomas J. George, V. Mikhail, Walter Barmettler, S. Crivelli

Scientific Reports

DOI

2018

LS‐align: an atom‐level, flexible ligand structural alignment algorithm for high‐throughput virtual screening

Jun-Da Hu, Zi Liu, Dong-Jun Yu, Yang Zhang, A. Valencia

Bioinform.

DOI

2018

COACH-D: improved protein–ligand binding sites prediction with refined ligand-binding poses through molecular docking

Qi Wu, Zhenling Peng, Yang Zhang, Jianyi Yang

Nucleic Acids Res.

DOI

2017

政府绩效审计技术、执行和结果应用——基于“活系统理论”的分析

张阳，蔡祺

《南京审计大学学报》，Vol. 14, No. 4

下载原文

2017

Approaches to ab initio molecular replacement of α-helical transmembrane proteins

Jens M. H. Thomas, Felix Simkovic, R. Keegan, O. Mayans, Chengxin Zhang, Yang Zhang, D. Rigden

Acta Crystallographica Section D: Structural Biology

DOI

2017

Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12

Chengxin Zhang, S. Mortuza, Bao-Ji He, Yan-Ting Wang, Yang Zhang

Proteins: Structure, Function, and Bioinformatics

DOI

2017

NeBcon: protein contact map prediction using neural network training coupled with naïve Bayes classifiers

Bao-Ji He, S. Mortuza, Yan-Ting Wang, Hong-Bin Shen, Yang Zhang

Bioinform.

DOI

2017

Protein structure prediction

Haiyou Deng, Ya Jia, Yang Zhang

International Journal of Modern Physics B

DOI

2017

Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks

Hong-Dong Li, Yang Zhang, Y. Guan, Rajasree Menon, G. Omenn

Methods in molecular biology

DOI

2017

Protein–Protein Interactions and Genetic Disease

J. Brender, Yang Zhang

DOI

2017

Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework

Gwênlyn Glusman, Peter W. Rose, A. Prlić, J. Dougherty, Jose M. Duarte, Andrew R. Hoffman, G. Barton, E. Bendixen, T. Bergquist, C. Bock, Elizabeth Brunk, M. Buljan, S. Burley, Binghuang Cai, H. Carter, Jianjiong Gao, A. Godzik, M. Heuer, Michael A Hicks, Thomas Hrabe, R. Karchin, Julia Koehler Leman, L. Lane, David L. Masica, S. Mooney, J. Moult, G. Omenn, Frances M. G. Pearl, V. Pejaver, S. Reynolds, A. Rokem, T. Schwede, Sicheng Song, H. Tilgner, Yana Valasatava, Yang Zhang, E. Deutsch

Genome Medicine

DOI

2017

COFACTOR: improved protein function prediction by combining structure, sequence and protein–protein interaction information

Chengxin Zhang, L. Freddolino, Yang Zhang

Nucleic Acids Res.

DOI

2017

An Evolution-Based Approach to De Novo Protein Design

J. Brender, D. Shultis, N. A. Khattak, Yang Zhang

Methods in molecular biology

DOI

2016

STRUM: structure-based prediction of protein stability changes upon single-point mutation

Li-Jun Quan, Q. Lv, Yang Zhang

Bioinform.

DOI

2016

Recognizing metal and acid radical ion-binding sites by integrating ab initio modeling with template-based transferals

Xiuzhen Hu, Q. Dong, Jianyi Yang, Yang Zhang

Bioinform.

DOI

2016

Approach to the unfolding and folding dynamics of add A-riboswitch upon adenine dissociation using a coarse-grained elastic network model.

Chunhua Li, Da-Shuai Lv, Lei Zhang, Feng Yang, Cun-xin Wang, Ji-Guo Su, Yang Zhang

Journal of Chemical Physics

DOI

2016

A Network of Splice Isoforms for the Mouse

Hong-Dong Li, Rajasree Menon, Ridvan Eksi, Aysam Guerler, Yang Zhang, G. Omenn, Y. Guan

Scientific Reports

DOI

2016

Modeling structure of G protein-coupled receptors in huan genome

Yang Zhang

2016

BindProfX: Assessing Mutation-Induced Binding Affinity Change by Protein Interface Profiles with Pseudo-Counts

P. Xiong, Chengxin Zhang, Wei Zheng, Yang Zhang

Journal of Molecular Biology

DOI

2016

3DRobot: automated generation of diverse and well-packed protein structure decoys

Haiyou Deng, Ya Jia, Yang Zhang

Bioinform.

DOI

2015

GPCR-I-TASSER: A hybrid approach to G protein-coupled receptor structure modeling and the application to the human genome

Jian Zhang, Jianyi Yang, Richard Jang, Yang Zhang

Structure

DOI

2015

Structural Bioinformatics Inspection of neXtProt PE5 Proteins in the Human Proteome

Q. Dong, Rajasree Menon, G. Omenn, Yang Zhang

Journal of Proteome Research

DOI

2015

Template-based protein structure prediction in CASP11 and retrospect of I-TASSER in the last decade

Jianyi Yang, Wen-Xuan Zhang, Bao-Ji He, S. Walker, Hongjiu Zhang, Brandon Govindarajoo, Jouko J. Virtanen, Zhidong Xue, Hong-Bin Shen, Yang Zhang

Proteins: Structure, Function, and Bioinformatics

DOI

2015

Integration of QUARK and I-TASSER for ab initio protein structure prediction in CASP11

Wen-Xuan Zhang, Jianyi Yang, Bao-Ji He, S. Walker, Hongjiu Zhang, Brandon Govindarajoo, Jouko J. Virtanen, Zhidong Xue, Hong-Bin Shen, Yang Zhang

Proteins: Structure, Function, and Bioinformatics

DOI

2015

Improving accuracy of protein contact prediction using balanced network deconvolution

Hai-Ping Sun, Yan Huang, Xiao-Fan Wang, Yang Zhang, Hong-Bin Shen

Proteins: Structure, Function, and Bioinformatics

DOI

2015

PCalign: a method to quantify physicochemical similarity of protein-protein interfaces

Shanshan Cheng, Yang Zhang, C. L. Iii Brooks

BMC Bioinformatics

DOI

2015

Protein Structure and Function Prediction Using I-TASSER

Jianyi Yang, Yang Zhang

Current Protocols in Bioinformatics

DOI

2015

I-TASSER server: new development for protein structure and function predictions

Jianyi Yang, Yang Zhang

Nucleic Acids Res.

DOI

2015

Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project

Hong-Dong Li, Rajasree Menon, Brandon Govindarajoo, B. Panwar, Yang Zhang, G. Omenn, Y. Guan

Journal of Proteome Research

DOI

2015

Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models

R. Keegan, Jaclyn Bibby, Jens M. H. Thomas, Dong Xu, Yang Zhang, O. Mayans, M. Winn, D. Rigden

Acta Crystallographica Section D: Biological Crystallography

DOI

2015

NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment

Richard Jang, Yan Wang, Zhidong Xue, Yang Zhang

Journal of Biomolecular NMR

DOI

2015

Accurate disulfide-bonding network predictions improve ab initio structure prediction of cysteine-rich proteins

J. Yang, Bao-Ji He, Richard Jang, Yang Zhang, Hong-Bin Shen

Bioinform.

DOI

2015

GLASS: a comprehensive database for experimentally validated GPCR-ligand associations

Wallace K. B. Chan, Hongjiu Zhang, Jianyi Yang, J. Brender, J. Hur, Arzucan Özgür, Yang Zhang

Bioinform.

DOI

2015

ResQ: An approach to unified estimation of B-factor and residue-specific error in protein structure prediction

Jianyi Yang, Yan Wang, Yang Zhang

Journal of Molecular Biology

DOI

2015

Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles

J. Brender, Yang Zhang

PLoS Comput. Biol.

DOI

2014

The I-TASSER Suite: protein structure and function prediction

Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang

Nature Methods

DOI

2014

Protein structure prediction provides comparable performance to crystallographic structures in docking-based virtual screening

Hong-mei Du, J. Brender, Jian Zhang, Yang Zhang

Methods

DOI

2014

Modeling the functional relationship network at the splice isoform level through heterogeneous data integration

Hong-Dong Li, Rajasree Menon, Ridvan Eksi, Aysam Guerler, Yang Zhang, G. Omenn, Y. Guan

bioRxiv

DOI

2013

EvoDesign: de novo protein design based on structural and evolutionary profiles

Pralay Mitra, D. Shultis, Yang Zhang

Nucleic Acids Res.

DOI

2013

The illustration of random-walk ideal chain model and the relationship with real protein chain.

Jian Zhang, Yang Zhang

DOI

2013

Structure Prediction and Analysis of DNA Transposon and LINE Retrotransposon Proteins*

György Abrusán, Yang Zhang, A. Szilágyi

Journal of Biological Chemistry

DOI

2013

High-accuracy prediction of transmembrane inter-helix contacts and application to GPCR 3D structure modeling

J. Yang, Richard Jang, Yang Zhang, Hong-Bin Shen

Bioinform.

DOI

2013

Modeling, Ion Conductance, and Electrostatic Properties of the Protective Antigen Pore Structure of Anthrax Toxin

Srayanta Mukherjee, Kyu Ii Lee, Yang Zhang, M. T. Fisher, W. Im

DOI

2013

Protein Depth Calculation and the Use for Improving Accuracy of Protein Fold Recognition

Dong Xu, Hua Li, Yang Zhang

J. Comput. Biol.

DOI

2013

Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10

Yang Zhang

Proteins: Structure, Function, and Bioinformatics

DOI

2013

Turning gold into ‘junk’: transposable elements utilize central proteins of cellular networks

György Abrusán, A. Szilágyi, Yang Zhang, Balázs Papp

Nucleic Acids Research

DOI

2013

An Evolution-Based Approach to De Novo Protein Design and Case Study on Mycobacterium tuberculosis

Pralay Mitra, D. Shultis, J. Brender, Jeff Czajka, David Marsh, F. Gray, T. Cierpicki, Yang Zhang

PLoS Comput. Biol.

DOI

2013

Fast and Accurate Calculation of Protein Depth by Euclidean Distance Transform

Dong Xu, Hua Li, Yang Zhang

Annual International Conference on Research in Computational Molecular Biology

DOI

2013

A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction

Renxiang Yan, Dong Xu, Jianyi Yang, S. Walker, Yang Zhang

Scientific Reports

DOI

2013

Mapping Monomeric Threading to Protein–Protein Structure Prediction

Aysam Guerler, Brandon Govindarajoo, Yang Zhang

Journal of Chemical Information and Modeling

DOI

2013

Template-based structure modeling of protein-protein interactions

A. Szilágyi, Yang Zhang

Current Opinion in Structural Biology

DOI

2013

Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment

Jianyi Yang, Ambrish Roy, Yang Zhang

Bioinform.

DOI

2013

Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment

Dong Xu, Yang Zhang

Scientific Reports

DOI

2013

Innovations in Proteomic Profiling of Cancers: Alternative Splice Variants as a New Class of Cancer Biomarker Candidates and Bridging of Proteomics with Structural Biology

G. Omenn, Rajasree Menon, Yang Zhang

Journal of Proteomics

DOI

2013

Illustrative examples of the EBM design on M. tuberculosis proteins.

Pralay Mitra, D. Shultis, J. Brender, Jeff Czajka, David Marsh, F. Gray, T. Cierpicki, Yang Zhang

DOI

2013

Segment assembly, structure alignment and iterative simulation in protein structure prediction

Yang Zhang, J. Skolnick

BMC Biology

DOI

2012

政治关系、信任担保与独立审计需求——来自中国民营上市公司的经验证据

聂新军，张阳

《宏观经济研究》，No. 11

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2012

Protein Structure Prediction

Ambrish Roy, Yang Zhang

DOI

2012

Ab Initio Protein Structure Assembly Using Continuous Structure Fragments and Optimized Knowledge-based Force Field

Dong Xu, Yang Zhang

Proteins: Structure, Function, and Bioinformatics

DOI

2012

How Many Protein-Protein Interactions Types Exist in Nature?

L. Garma, Srayanta Mukherjee, Pralay Mitra, Yang Zhang

PLoS ONE

DOI

2012

COFACTOR: an accurate comparative algorithm for structure-based protein function annotation

Ambrish Roy, Jianyi Yang, Yang Zhang

Nucleic Acids Res.

DOI

2012

LabCaS: Labeling calpain substrate cleavage sites from amino acid sequence using conditional random fields

Yong-Xian Fan, Yang Zhang, Hong-Bin Shen

Proteins: Structure, Function, and Bioinformatics

DOI

2012

What is the best reference state for designing statistical atomic potentials in protein structure prediction?

Haiyou Deng, Ya Jia, Yan-Yu Wei, Yang Zhang

Proteins: Structure, Function, and Bioinformatics

DOI

2012

Toward optimal fragment generations for ab initio protein structure assembly

Dong Xu, Yang Zhang

Proteins: Structure, Function, and Bioinformatics

DOI

2012

Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement

Ambrish Roy, Yang Zhang

Structure

DOI

2012

BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions

Jianyi Yang, Ambrish Roy, Yang Zhang

Nucleic Acids Res.

DOI

2012

Structural homology modeling and mutant cycle analysis predict pharmacoresponsiveness of a NaV1.7 mutant channel

Yang Yang, S. Dib-Hajj, Jian Zhang, Yang Zhang, L. Tyrrell, M. Estacion, S. Waxman

Nature Communications

DOI

2011

Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement

Dong Xu, Jian Zhang, Ambrish Roy, Yang Zhang

Proteins: Structure, Function, and Bioinformatics

DOI

2011

Prediction Methods and Reports

Dong Xu, J. Zhang, Ambrish Roy, Yang Zhang

2011

BSP-SLIM: A Blind Low-Resolution Ligand-Protein Docking Approach Using Predicted Protein Structures

Hui-Sun Lee, Yang Zhang

Proteins: Structure, Function, and Bioinformatics

DOI

2011

Intra-chain 3D Segment Swapping Spawns the Evolution of New Multidomain Protein Architectures

A. Szilágyi, Yang Zhang, P. Závodszky

Journal of Molecular Biology

DOI

2011

Improving protein template recognition by using small-angle x-ray scattering profiles.

M. D. dos Reis, R. Aparício, Yang Zhang

Biophysical Journal

DOI

2011

Functional Implications of Structural Predictions for Alternative Splice Proteins Expressed in Her2/neu–Induced Breast Cancers

Rajasree Menon, Ambrish Roy, Srayanta Mukherjee, Saveliy Belkin, Yang Zhang, G. Omenn

Journal of Proteome Research

DOI

2011

PROTS: A fragment based protein thermo-stability potential

Yunqi Li, Jian Zhang, David Tai, C. Middaugh, Yang Zhang, Jianwen Fang

Proteins: Structure, Function, and Bioinformatics

DOI

2011

Protein-protein complex structure predictions by multimeric threading and template recombination

Srayanta Mukherjee, Yang Zhang

Structure

DOI

2011

Predicting nucleic acid binding interfaces from structural models of proteins

I. Dror, Shula Shazman, Srayanta Mukherjee, Yang Zhang, F. Glaser, Yael Mandel-Gutfreund

Proteins: Structure, Function, and Bioinformatics

DOI

2011

Protein Homology Analysis for Function Prediction with Parallel Sub-Graph Isomorphism

Alper Kucukural, A. Szilágyi, O. Sezerman, Yang Zhang

DOI

2011

Genome-Wide Protein Structure Prediction

Srayanta Mukherjee, A. Szilágyi, Ambrish Roy, Yang Zhang

DOI

2011

A Protocol for Computer-Based Protein Structure and Function Prediction

Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang

Journal of Visualized Experiments

DOI

2011

Parkin, A Top Level Manager in the Cell’s Sanitation Department

C. Rankin, Ambrish Roy, Yang Zhang, M. Richter

Open Biochemistry Journal

DOI

2011

Improving protein structure prediction using multiple sequence-based contact predictions

Si-Tao Wu, A. Szilágyi, Yang Zhang

Structure

DOI

2011

Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization.

Dong Xu, Yang Zhang

Biophysical Journal

DOI

2011

Computational Protein Design and Large-Scale Assessment by I-TASSER Structure Assembly Simulations

A. Bazzoli, A. Tettamanzi, Yang Zhang

Journal of Molecular Biology

DOI

2011

Atomic-level protein structure refinement using fragment guided molecular dynamics conformation sampling

Jian Zhang, Yu Liang, Yang Zhang

Structure

DOI

2010

法律环境、企业非标审计意见规避行为与审计师的独立性——基于我国制度背景的博弈分析

张阳，张(立见)，赵兴楣

《广东财经大学学报》，Vol. 25, No. 3

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2010

A three‐dimensional model of the U1 small nuclear ribonucleoprotein particle

Jason A. Somarelli, A. Mesa, Ambrish Roy, Yang Zhang, Rene J. Herrera

DOI

2010

How significant is a protein structure similarity with TM-score = 0.5?

Jin-Rui Xu, Yang Zhang

Bioinform.

DOI

2010

Composite Approaches to Protein Tertiary Structure Prediction: A Case-Study by I-Tasser

Ambrish Roy, Si-Tao Wu, Yang Zhang

DOI

2010

A Novel Side-Chain Orientation Dependent Potential Derived from Random-Walk Reference State for Protein Fold Selection and Structure Prediction

Jian Zhang, Yang Zhang

PLoS ONE

DOI

2010

MVP-Fit: A Convenient Tool for Flexible Fitting of Protein Domain Structures with Cryo-Electron Microscopy Density Map

Dong Xu, Yang Zhang

2010

Recognizing Protein Substructure Similarity Using Segmental Threading

Si-Tao Wu, Yang Zhang

Structure

DOI

2010

GPCRRD: G protein-coupled receptor spatial restraint database for 3D structure modeling and function annotation

Jian Zhang, Yang Zhang

Bioinform.

DOI

2009

PROTEIN STRUCTURE PREDICTION II

J. Skolnick, Yang Zhang

2009

MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming

Srayanta Mukherjee, Yang Zhang

Nucleic Acids Research

DOI

2009

Revisiting the Plasmodium falciparum RIFIN family: from comparative genomics to 3D-model prediction

E. Bultrini, Kevin Brick, Srayanta Mukherjee, Yang Zhang, F. Silvestrini, P. Alano, E. Pizzi

BMC Genomics

DOI

2009

I-TASSER: Fully automated protein structure prediction in CASP8

Yang Zhang

Proteins: Structure, Function, and Bioinformatics

DOI

2009

Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform

Dong Xu, Yang Zhang

PLoS ONE

DOI

2009

HAAD: A Quick Algorithm for Accurate Prediction of Hydrogen Atoms in Protein Structures

Yunqi Li, Ambrish Roy, Yang Zhang

PLoS ONE

DOI

2009

Protein Structure Prediction: Is It Useful?

Yang Zhang

Current Opinion in Structural Biology

DOI

2009

REMO: A New Protocol to Refine Full Atomic Protein Models from C-alpha Traces by Optimizing Hydrogen-Bonding Networks

Yunqi Li, Yang Zhang

Proteins: Structure, Function, and Bioinformatics

DOI

2008

Progress and challenges in protein structure prediction.

Yang Zhang

Current Opinion in Structural Biology

DOI

2008

ANGLOR: A Composite Machine-Learning Algorithm for Protein Backbone Torsion Angle Prediction

Si-Tao Wu, Yang Zhang

PLoS ONE

DOI

2008

MUSTER: Improving protein sequence profile–profile alignments by using multiple sources of structure information

Si-Tao Wu, Yang Zhang

Proteins: Structure, Function, and Bioinformatics

DOI

2007

从博弈看审计独立性威胁

张阳

《当代财经》，No. 4

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2007

独立性威胁、审计委员会制约有效性：理论分析与实证研究

张阳，张立民

《会计研究》，No. 10

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2007

注册会计师法律监管的有效性：美国经验与中国实践

张阳

《广东财经大学学报》，Vol. 22, No. 3

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2007

Template‐based modeling and free modeling by I‐TASSER in CASP7

Yang Zhang

Proteins: Structure, Function, and Bioinformatics

DOI

2007

Monte Carlo refinement of rigid‐body protein docking structures with backbone displacement and side‐chain optimization

Stephan Lorenzen, Yang Zhang

Protein Science

DOI

2007

LOMETS: A local meta-threading-server for protein structure prediction

Si-Tao Wu, Yang Zhang

Nucleic Acids Research

DOI

2007

Identification of near‐native structures by clustering protein docking conformations

Stephan Lorenzen, Yang Zhang

Proteins: Structure, Function, and Bioinformatics

DOI

2007

Scoring function for automated assessment of protein structure template quality

Yang Zhang, J. Skolnick

DOI

2006

Benchmarking of dimeric threading and structure refinement

Vera Grimm, Yang Zhang, J. Skolnick

Proteins: Structure, Function, and Bioinformatics

DOI

2006

Correction: Structure Modeling of All Identified G Protein–Coupled Receptors in the Human Genome

Yang Zhang, M. Devries, J. Skolnick

PLoS Comput. Biol.

DOI

2006

On the origin and highly likely completeness of single-domain protein structures.

Yang Zhang, Isaac A. Hubner, Adrian K. Arakaki, E. Shakhnovich, J. Skolnick

Proceedings of the National Academy of Sciences of the United States of America

DOI

2006

TASSER-Lite: an automated tool for protein comparative modeling.

S. Pandit, Yang Zhang, J. Skolnick

Biophysical Journal

DOI

2006

TASSER‐based refinement of NMR structures

Seung Yup Lee, Yang Zhang, J. Skolnick

Proteins: Structure, Function, and Bioinformatics

DOI

2006

Structure Modeling of All Identified G Protein–Coupled Receptors in the Human Genome

Yang Zhang, M. Devries, J. Skolnick

PLoS Comput. Biol.

DOI

2005

TM-align: a protein structure alignment algorithm based on the TM-score

Yang Zhang, J. Skolnick

Nucleic Acids Research

DOI

2005

TASSER: An automated method for the prediction of protein tertiary structures in CASP6

Yang Zhang, Adrian K. Arakaki, J. Skolnick

Proteins: Structure, Function, and Bioinformatics

DOI

2005

The protein structure prediction problem could be solved using the current PDB library.

Yang Zhang, J. Skolnick

Proceedings of the National Academy of Sciences of the United States of America

DOI

2004

国家审计的定位与中国政治民主建设——从对权力的制约和监督谈起

张立民，张阳

《中山大学学报(社会科学版)》，Vol. 44, No. 3

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2004

Application of sparse NMR restraints to large-scale protein structure prediction.

Wei Li, Yang Zhang, J. Skolnick

Biophysical Journal

DOI

2004

Automated structure prediction of weakly homologous proteins on a genomic scale.

Yang Zhang, J. Skolnick

Proceedings of the National Academy of Sciences of the United States of America

DOI

2004

Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins.

Yang Zhang, J. Skolnick

Biophysical Journal

DOI

2004

Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm

J. Skolnick, D. Kihara, Yang Zhang

Proteins: Structure, Function, and Bioinformatics

DOI

2004

SPICKER: A clustering approach to identify near‐native protein folds

Yang Zhang, J. Skolnick

Journal of Computational Chemistry

DOI

2004

Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment

Adrian K. Arakaki, Yang Zhang, J. Skolnick

Bioinform.

DOI

2003

控股股东利益导向与股利政策安排——基于用友软件“高派现”的案例分析

张阳

《当代财经》，No. 10

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2003

TOUCHSTONE II: a new approach to ab initio protein structure prediction.

Yang Zhang, A. Kolinski, J. Skolnick

Biophysical Journal

DOI

2002

市场经济与会计制度改革——中日会计制度比较

徐文华，张阳

《财经问题研究》，No. 10

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预印本

2026

TrustLDM: Benchmarking Trustworthiness in Language Diffusion Models

Yichuan Mo, Yukun Jiang, Yanbo Shi, Mingjie Li, Michael Backes, Yang Zhang, Yisen Wang

arXiv preprint

2026

PeerCheck: Enhancing LLM-Generated Academic Reviews Towards Human-Level Quality

Zeyuan Chen, Ziqing Yang, Yihan Ma, Michael Backes, Yang Zhang

arXiv preprint

2026

Intuition-Guided Latent Reasoning for LLM-Based Recommendation

Chang Liu, Yimeng Bai, Xiaoyan Zhao, Yang Zhang, Qifan Wang, Fuli Feng, Wenge Rong

arXiv preprint

2026

BadBone: Backdoor Attacks Against Backbone Models in Visual Prompt Learning

Ziqing Yang, Rui Wen, Xinlei He, Yun Shen, Michael Backes, Yang Zhang

arXiv preprint

DOI

2026

CURE:Circuit-Aware Unlearning for LLM-based Recommendation

Ziheng Chen, Jiali Cheng, Zezhong Fan, Hadi Amiri, Yunzhi Yao, Xiangguo Sun, Yang Zhang

arXiv preprint

2026

How Well Do Agentic Skills Work in the Wild: Benchmarking LLM Skill Usage in Realistic Settings

Yujian Liu, Jiabao Ji, Li An, Tommi Jaakkola, Yang Zhang, Shiyu Chang

arXiv preprint

2026

Turning Black Box into White Box: Dataset Distillation Leaks

Huajie Chen, Tianqing Zhu, Yuchen Zhong, Yang Zhang, Shang Wang, Feng He, Lefeng Zhang, Jialiang Shen, Minghao Wang, Wanlei Zhou

arXiv preprint

2026

PERM: Psychology-grounded Empathetic Reward Modeling for Large Language Models

Chengbing Wang, Wuqiang Zheng, Yang Zhang, Fengbin Zhu, Junyi Cheng, Yi Xie, Wenjie Wang, Fuli Feng

arXiv preprint

2026

PrefReward: Learning User Preference Matrix for Personalized Text Generation

Yue Wu, Chengbing Wang, Yimeng Bai, Xiaoyan Zhao, Yang Zhang, Fuli Feng

arXiv preprint

2026

MERGE: Next-Generation Item Indexing Paradigm for Large-Scale Streaming Recommendation

Jing Yan, Yimeng Bai, Zongyu Liu, Yahui Liu, Junwei Wang, Jingze Huang, Haoda Li, Sihao Ding, Shaohui Ruan, Yang Zhang

arXiv preprint

DOI

2026

Every Wrong Answer Counts: Option-Level Psychometrics for LLM Multiple-Choice Benchmarks

Xiao Fei, Yang Zhang, Sarah Almeida Carneiro, Michalis Vazirgiannis

arXiv preprint

2026

WorldAuditBench: Interactive 3D World Auditing with Multimodal Agents

Ziyan Jiang, Jingbo Yang, Jiabao Ji, Yujian Liu, Qiucheng Wu, Tommi Jaakkola, Yang Zhang, Shiyu Chang

arXiv preprint

2026

"Nothing to See Here'': Unintended Disclosure through Revision Traces of LLM Deliverables

Yage Zhang, Yukun Jiang, Yang Zhang

arXiv preprint

2026

Write Once, Plan Many: Building Reusable Visual Planning Systems from One Scene

Ruixiao Yang, Yilun Hao, Mingxin Yu, Yang Zhang, Chuchu Fan

arXiv preprint

2026

GS-FUSE: Granger-Supervised Gated Fusion and Multi-Granularity Alignment for Event-Driven Financial Forecasting

Yang Zhang, En Chun, Ziyun Mao, Yulu Wu, Jun Wang

arXiv preprint

DOI

2025

Reinforced Strategy Optimization for Conversational Recommender Systems via Network-of-Experts

Xiaoyan Zhao, Ming Yan, Yang Zhang, Yang Deng, Jian Wang, Fengbin Zhu, Yilun Qiu, Hong Cheng, Tat-Seng Chua

arXiv preprint

2025

Defeating Cerberus: Concept-Guided Privacy-Leakage Mitigation in Multimodal Language Models

Boyang Zhang, Istemi Ekin Akkus, Ruichuan Chen, Alice Dethise, Klaus Satzke, Ivica Rimac, Yang Zhang

arXiv preprint

2025

Data-Free Model-Related Attacks: Unleashing the Potential of Generative AI

Dayong Ye, Tianqing Zhu, Shang Wang, Bo Liu, Leo Yu Zhang, Wanlei Zhou, Yang Zhang

arXiv preprint

2025

AttackPilot: Autonomous Inference Attacks Against ML Services With LLM-Based Agents

Yixin Wu, Rui Wen, Chi Cui, Michael Backes, Yang Zhang

arXiv preprint

2025

Safety at Scale: A Comprehensive Survey of Large Model and Agent Safety

Xingjun Ma, Yifeng Gao, Yixu Wang, Ruofan Wang, Xin Wang, Ye Sun, Yifan Ding, Hengyuan Xu, Yunhao Chen, Yunhan Zhao, Hanxun Huang, Yige Li, Yutao Wu, Jiaming Zhang, Xiang Zheng, Yang Bai, Zuxuan Wu, Xipeng Qiu, Jingfeng Zhang, Yiming Li, Xudong Han, Haonan Li, Jun Sun, Cong Wang, Jindong Gu, Baoyuan Wu, Siheng Chen, Tianwei Zhang, Yang Liu, Mingming Gong, Tongliang Liu, Shirui Pan, Cihang Xie, Tianyu Pang, Yinpeng Dong, Ruoxi Jia, Yang Zhang, Shiqing Ma, Xiangyu Zhang, Neil Gong, Chaowei Xiao, Sarah Erfani, Tim Baldwin, Bo Li, Masashi Sugiyama, Dacheng Tao, James Bailey, Yu-Gang Jiang

arXiv preprint

2025

Fast-Decoding Diffusion Language Models via Progress-Aware Confidence Schedules

Amr Mohamed, Yang Zhang, Michalis Vazirgiannis, Guokan Shang

arXiv preprint

2025

Matryoshka Model Learning for Improved Elastic Student Models

Chetan Verma, Aditya Srinivas Timmaraju, Cho-Jui Hsieh, Suyash Damle, Ngot Bui, Yang Zhang, Wen Chen, Xin Liu, Prateek Jain, Inderjit S Dhillon

arXiv preprint

DOI

2025

Think-While-Generating: On-the-Fly Reasoning for Personalized Long-Form Generation

Chengbing Wang, Yang Zhang, Wenjie Wang, Xiaoyan Zhao, Fuli Feng, Xiangnan He, Tat-Seng Chua

arXiv preprint

2025

Brownian Bridge Diffusion for Sequential Recommendation

Yimeng Bai, Yang Zhang, Sihao Ding, Shaohui Ruan, Han Yao, Danhui Guan, Fuli Feng, Tat-Seng Chua

arXiv preprint

2025

CARL: Criticality-Aware Agentic Reinforcement Learning

Leyang Shen, Yang Zhang, Chun Kai Ling, Xiaoyan Zhao, Tat-Seng Chua

arXiv preprint

2025

NextQuill: Causal Preference Modeling for Enhancing LLM Personalization

Xiaoyan Zhao, Juntao You, Yang Zhang, Wenjie Wang, Hong Cheng, Fuli Feng, See-Kiong Ng, Tat-Seng Chua

arXiv preprint

2025

Fairness and/or Privacy on Social Graphs

Bartlomiej Surma, Michael Backes, Yang Zhang

arXiv preprint

2025

SaLoRA: Safety-Alignment Preserved Low-Rank Adaptation

Mingjie Li, Wai Man Si, Michael Backes, Yang Zhang, Yisen Wang

arXiv preprint

2025

HAD: HAllucination Detection Language Models Based on a Comprehensive Hallucination Taxonomy

Fan Xu, Xinyu Hu, Zhenghan Yu, Li Lin, Xu Zhang, Yang Zhang, Wei Zhou, Jinjie Gu, Xiaojun Wan

arXiv preprint

2025

Adjacent Words, Divergent Intents: Jailbreaking Large Language Models via Task Concurrency

Yukun Jiang, Mingjie Li, Michael Backes, Yang Zhang

arXiv preprint

2025

GEO-Detective: Unveiling Location Privacy Risks in Images with LLM Agents

Xinyu Zhang, Yixin Wu, Boyang Zhang, Chenhao Lin, Chao Shen, Michael Backes, Yang Zhang

arXiv preprint

2025

Lost in the Mix: Evaluating LLM Understanding of Code-Switched Text

Amr Mohamed, Yang Zhang, Michalis Vazirgiannis, Guokan Shang

arXiv preprint

2025

Boosting Parameter Efficiency in LLM-Based Recommendation through Sophisticated Pruning

Shanle Zheng, Keqin Bao, Jizhi Zhang, Yang Zhang, Fuli Feng, Xiangnan He

arXiv preprint

2025

Automatic Generation of a Cryptography Misuse Taxonomy Using Large Language Models

Yang Zhang, Wenyi Ouyang, Yi Zhang, Liang Cheng, Chen Wu, Wenxin Hu

arXiv preprint

2025

Reason4Rec: Deliberative User Preference Alignment of Large Language Models for Recommendation

Yi Fang, Wenjie Wang, Yang Zhang, Fengbin Zhu, Qifan Wang, Fuli Feng, Xiangnan He

arXiv preprint

2025

Bi-Level Optimization for Generative Recommendation: Bridging Tokenization and Generation

Yimeng Bai, Chang Liu, Yang Zhang, Dingxian Wang, Frank Yang, Andrew Rabinovich, Wenge Rong, Fuli Feng

arXiv preprint

DOI

2025

Privacy-Preserving Decentralized Federated Learning via Explainable Adaptive Differential Privacy

Fardin Jalil Piran, Zhiling Chen, Yang Zhang, Qianyu Zhou, Jiong Tang, Farhad Imani

arXiv preprint

2025

Reinforced Latent Reasoning for LLM-based Recommendation

Yang Zhang, Wenxin Xu, Xiaoyan Zhao, Wenjie Wang, Fuli Feng, Xiangnan He, Tat-Seng Chua

arXiv preprint

2025

CAMEF: Causal-Augmented Multi-Modality Event-Driven Financial Forecasting by Integrating Time Series Patterns and Salient Macroeconomic Announcements

Yang Zhang, Wenbo Yang, Jun Wang, Qiang Ma, Jie Xiong

arXiv preprint

DOI

2024

Large Language Models are Learnable Planners for Long-Term Recommendation

Wentao Shi, Xiangnan He, Yang Zhang, Chongming Gao, Xinyue Li, Jizhi Zhang, Qifan Wang, Fuli Feng

arXiv preprint

DOI

2024

Understanding Data Importance in Machine Learning Attacks: Does Valuable Data Pose Greater Harm?

Rui Wen, Michael Backes, Yang Zhang

arXiv preprint

2024

Decoding Matters: Addressing Amplification Bias and Homogeneity Issue for LLM-based Recommendation

Keqin Bao, Jizhi Zhang, Yang Zhang, Xinyue Huo, Chong Chen, Fuli Feng

arXiv preprint

2024

ICLGuard: Controlling In-Context Learning Behavior for Applicability Authorization

Wai Man Si, Michael Backes, Yang Zhang

arXiv preprint

2024

Voice Jailbreak Attacks Against GPT-4o

Xinyue Shen, Yixin Wu, Michael Backes, Yang Zhang

arXiv preprint

2024

Defending Large Language Models against Jailbreak Attacks via Semantic Smoothing

Jiabao Ji, Bairu Hou, Alexander Robey, George J. Pappas, Hamed Hassani, Yang Zhang, Eric Wong, Shiyu Chang

arXiv preprint

2024

PRompt Optimization in Multi-Step Tasks (PROMST): Integrating Human Feedback and Heuristic-based Sampling

Yongchao Chen, Jacob Arkin, Yilun Hao, Yang Zhang, Nicholas Roy, Chuchu Fan

arXiv preprint

2024

Planning Anything with Rigor: General-Purpose Zero-Shot Planning with LLM-based Formalized Programming

Yilun Hao, Yang Zhang, Chuchu Fan

arXiv preprint

2024

Exact and Efficient Unlearning for Large Language Model-based Recommendation

Zhiyu Hu, Yang Zhang, Minghao Xiao, Wenjie Wang, Fuli Feng, Xiangnan He

arXiv preprint

2024

Efficient Data-Free Model Stealing with Label Diversity

Yiyong Liu, Rui Wen, Michael Backes, Yang Zhang

arXiv preprint

2024

The 2nd Workshop on Recommendation with Generative Models

Wenjie Wang, Yang Zhang, Xinyu Lin, Fuli Feng, Weiwen Liu, Yong Liu, Xiangyu Zhao, Wayne Xin Zhao, Yang Song, Xiangnan He

arXiv preprint

2023

Recommendation Unlearning via Influence Function

Yang Zhang, Zhiyu Hu, Yimeng Bai, Jiancan Wu, Qifan Wang, Fuli Feng

arXiv preprint

DOI

2023

Decomposing Uncertainty for Large Language Models through Input Clarification Ensembling

Bairu Hou, Yujian Liu, Kaizhi Qian, Jacob Andreas, Shiyu Chang, Yang Zhang

arXiv preprint

2023

AutoTAMP: Autoregressive Task and Motion Planning with LLMs as Translators and Checkers

Yongchao Chen, Jacob Arkin, Charles Dawson, Yang Zhang, Nicholas Roy, Chuchu Fan

arXiv preprint

2023

Generative Watermarking Against Unauthorized Subject-Driven Image Synthesis

Yihan Ma, Zhengyu Zhao, Xinlei He, Zheng Li, Michael Backes, Yang Zhang

arXiv preprint

2023

SecurityNet: Assessing Machine Learning Vulnerabilities on Public Models

Boyang Zhang, Zheng Li, Ziqing Yang, Xinlei He, Michael Backes, Mario Fritz, Yang Zhang

arXiv preprint

2023

Two-in-One: A Model Hijacking Attack Against Text Generation Models

Wai Man Si, Michael Backes, Yang Zhang, Ahmed Salem

arXiv preprint

2023

Certified Robustness for Large Language Models with Self-Denoising

Zhen Zhang, Guanhua Zhang, Bairu Hou, Wenqi Fan, Qing Li, Sijia Liu, Yang Zhang, Shiyu Chang

arXiv preprint

2023

A Bi-Step Grounding Paradigm for Large Language Models in Recommendation Systems

Keqin Bao, Jizhi Zhang, Wenjie Wang, Yang Zhang, Zhengyi Yang, Yancheng Luo, Chong Chen, Fuli Feng, Qi Tian

arXiv preprint

2023

Test-Time Poisoning Attacks Against Test-Time Adaptation Models

Tianshuo Cong, Xinlei He, Yun Shen, Yang Zhang

arXiv preprint

2023

Comprehensive Assessment of Toxicity in ChatGPT

Boyang Zhang, Xinyue Shen, Wai Man Si, Zeyang Sha, Zeyuan Chen, Ahmed Salem, Yun Shen, Michael Backes, Yang Zhang

arXiv preprint

2022

Finding MNEMON: Reviving Memories of Node Embeddings

Yun Shen, Yufei Han, Zhikun Zhang, Min Chen, Ting Yu, Michael Backes, Yang Zhang, Gianluca Stringhini

arXiv preprint

2022

Semi-Leak: Membership Inference Attacks Against Semi-supervised Learning

Xinlei He, Hongbin Liu, Neil Zhenqiang Gong, Yang Zhang

arXiv preprint

2022

Can't Steal? Cont-Steal! Contrastive Stealing Attacks Against Image Encoders

Zeyang Sha, Xinlei He, Ning Yu, Michael Backes, Yang Zhang

arXiv preprint

2022

Rethinking Missing Data: Aleatoric Uncertainty-Aware Recommendation

Chenxu Wang, Fuli Feng, Yang Zhang, Qifan Wang, Xunhan Hu, Xiangnan He

arXiv preprint

2022

Membership Inference Attacks by Exploiting Loss Trajectory

Yiyong Liu, Zhengyu Zhao, Michael Backes, Yang Zhang

arXiv preprint

2022

Membership-Doctor: Comprehensive Assessment of Membership Inference Against Machine Learning Models

Xinlei He, Zheng Li, Weilin Xu, Cory Cornelius, Yang Zhang

arXiv preprint

2022

Adversarial Support Alignment

Shangyuan Tong, Timur Garipov, Yang Zhang, Shiyu Chang, Tommi S. Jaakkola

arXiv preprint

2021

Deep Sequence Modeling: Development and Applications in Asset Pricing

Lin William Cong, Ke Tang, Jingyuan Wang, Yang Zhang

arXiv preprint

DOI

2019

AlphaStock: A Buying-Winners-and-Selling-Losers Investment Strategy using Interpretable Deep Reinforcement Attention Networks

Jingyuan Wang, Yang Zhang, Ke Tang, Junjie Wu, Zhang Xiong

arXiv preprint

DOI

2016

Streaming Recommender Systems

Shiyu Chang, Yang Zhang, Jiliang Tang, Dawei Yin, Yi Chang, Mark A. Hasegawa-Johnson, Thomas S. Huang

arXiv preprint

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