【1】Gang Hu, Akila Katuwawala, Kui Wang, Zhonghua Wu, Sina Ghadermarzi, Jianzhao Gao & Lukasz Kurgan
flDPnn: Accurate intrinsic disorder prediction with putative propensities of disorder functions

Nature Communications volume 12, Article number: 4438 (2021)

【2】Marco Necci, Damiano Piovesan, CAID Predictors, DisProt Curators & Silvio C. E. Tosatto
Critical assessment of protein intrinsic disorder prediction

Nature Methods, (2021)18, 472–481.

【3】Akila Katuwawala, Sina Ghadermarzi, Gang Hu, Zhonghua Wu, Lukasz Kurgan.
QUARTERplus: Accurate disorder predictions integrated with interpretable residue-level quality assessment scores

Computational and structural biotechnology journal.(2021) 19, 2597-2606

【4】Justin Lakkis, David Wang, Yuanchao Zhang, Gang Hu, Kui Wang, Huize Pan, Lyle Ungar, Muredach Reilly, Xiangjie Li, Mingyao Li.
A joint deep learning model enables simultaneous batch effect correction, denoising and clustering in single-cell transcriptomics

Genome Research, 2021, gr. 271874.120

【5】Hong Su, Zhenling Peng*, Jianyi Yang*
Recognition of small molecule-RNA binding sites using RNA sequence and structure

Bioinformatics, in press (2021).

【6】Gao J, Wei H, Cano A, Kurgan L*
PSIONplusm Server for Accurate Multi-Label Prediction of Ion Channels and Their Types

Biomolecules, 10(6):876(2020)

【7】Saisai Sun, Wenkai Wang, Zhenling Peng, Jianyi Yang*
RNA inter-nucleotide 3D closeness prediction by deep residual neural networks

Bioinformatics, in press (2021).

【8】Yajun Dai, Yang Li, Liping Wang, Zhenling Peng, Jianyi Yang*
On monomeric and multimeric structures-based protein-ligand interactions

 IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press (2020).

【9】Kui Wang, Gang Hu, Zhonghua Wu, Hong Su, Jianyi Yang, Lukasz Kurgan*
Comprehensive survey and comparative assessment of RNA-binding residue predictions with analysis by RNA type

International Journal of Molecular Sciences, 21: 6879 (2020).

【10】Aivi T Nguyen#,Kui Wang#,Gang Hu#,Xuran Wang,Zhen Miao,Joshua A Azevedo,EunRan Suh,Vivianna M Van Deerlin,David Choi,Kathryn Roeder,Mingyao Li*, Edward B Lee*
APOE and TREM2 regulate amyloid-responsive microglia in Alzheimer's disease

Acta Neuropathologica, 140：477-493(2020)

【11】Hua X#, Hu G#, Hu Q#, Chang Y, Hu Y, Gao L, Chen X, Yang PC, Zhang Y*, Li M*, Song J*.
Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis

Circulation. 142:384-400 (2020)

【12】Zongyang Du#, Shuo Pan#, Qi Wu, Zhenling Peng, Jianyi Yang*
CATHER: a novel threading algorithm with predicted contacts

Bioinformatics, 36: 2119-2125 (2020).

【13】Hong Wei, Boling Wang, Jianyi Yang, Jianzhao Gao*
RNA flexibility prediction with sequence profile and predicted solvent accessibility

IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press (2020).

【14】Qi Wu, Zhenling Peng*, Ivan Anishchenko, Qian Cong, David Baker, Jianyi Yang*
Protein contact prediction using metagenome sequence data and residual neural networks

Bioinformatics, 36: 41-48 (2020).

【15】Jianyi Yang#, Ivan Anishchenko#, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker*
Improved protein structure prediction using predicted interresidue orientations

PNAS, 117: 1496-1503 (2020)

【16】Li X, Wang K, Lyu Y, Pan H, Zhang J, Stambolian D, Susztak K, Reilly MP, Hu G*, Li M*
Deep learning enables accurate clustering with batch effect removal in single-cell RNA-seq analysis

Nat Commun. 2020 May 11;11(1):2338.

【17】Zheng W, Wuyun Q, Cheng M, Hu G, Zhang Y
Two-Level Protein Methylation Prediction using structure model-based features

Sci Rep. 2020 Apr 7;10(1):6008. 

【18】Saisai Sun, Qi Wu, Zhenling Peng*, Jianyi Yang*
Enhanced prediction of RNA solvent accessibility with long short-term memory neural networks and improved sequence profiles

Bioinformatics, 35:1686-1691 (2019).

【19】Akila Katuwawala, Zhenling Peng, Jianyi Yang, Lukasz Kurgan*
Computational prediction of MoRFs, short disorder-to-order transitioning protein binding regions

Computational and Structural Biotechnology Journal, 17: 454-462 (2019).

【20】Mi P, Zhang QP, Zhang SH, Wang C, Zhang SZ, Fang YC, Gao JZ, Feng DF, Chen DY, Feng XZ
The effects of fluorene-9-bisphenol on female zebrafish (Danio rerio) reproductive and exploratory behaviors

Chemosphere, 2019 Apr 25;228:398-411. 

【21】Hong Su, Mengchen Liu, Saisai Sun, Zhenling Peng*, Jianyi Yang*
Improving the prediction of protein-nucleic acids binding residues via multiple sequence profiles and the consensus of complementary algorithms

Bioinformatics, 35:930-936 (2019).

【22】Wang J, Agarwal D, Huang M, Hu G, Zhou Z, Ye C, Zhang NR
Data denoising with transfer learning in single-cell transcriptomics

Nat Methods. 2019 Sep;16(9):875-878. 

【23】Hu G, Wu Z, Oldfield CJ, Wang C, Kurgan L
Quality assessment for the putative intrinsic disorder in proteins

Bioinformatics. 2019 May 15;35(10):1692-1700.

【24】Hu G, Kurgan L
Sequence Similarity Searching

Curr Protoc Protein Sci. 2019 Feb;95(1):e71. 

【25】Zheng W, Wuyun Q, Li Y, Mortuza SM, Zhang C, Pearce R, Ruan J, Zhang Y
Detecting distant-homology protein structures by aligning deep neural-network based contact maps

PLoS Comput Biol. 2019 Oct 17;15(10):e1007411.

【26】Wu Z, Liu W, Jin X, Ji H, Wang H, Glusman G, Robinson M, Liu L, Ruan J, Gao S
NormExpression: An R Package to Normalize Gene Expression Data Using Evaluated Methods

Front Genet. 2019 Apr 30;10:400.

【27】Xu X, Ji H, Jin X, Cheng Z, Yao X, Liu Y, Zhao Q, Zhang T, Ruan J, Bu W, Chen Z, Gao S
Using Pan RNA-Seq Analysis to Reveal the Ubiquitous Existence of 5' and 3' End Small RNAs

Front Genet.2019 Feb 14;10:105.

【28】Tan, C., Cui, W., Cui, X., Ning, K.
Strain-GeMS: optimized subspecies identification from microbiome data based on accurate variant modeling

Bioinformatics, 35(10), 1789-1791 (2019).

【29】Zhang Z, Ruan J, Gao J, Wu FX
Predicting essential proteins from protein-protein interactions using order statistics

J Theor Biol. , 480: 274-283 (2019)

【30】Gao J, Miao Z, Zhang Z, Wei H, Kurgan L
Prediction of Ion Channels and their Types from Protein Sequences: Comprehensive Review and Comparative Assessment

Curr Drug Targets. 2019;20(5):579-592.

【31】Gao J, Yang Y, Zhou Y
Grid-based prediction of torsion angle probabilities of protein backbone and its application to discrimination of protein intrinsic disorder regions and selection of model structures

BMC Bioinformatics. 2018 Feb 1;19(1):29.

【32】Gao J, Wu Z, Hu G, Wang K, Song J, Joachimiak A, Kurgan L
Survey of Predictors of Propensity for Protein Production and Crystallization with Application to Predict Resolution of Crystal Structures

Curr Protein Pept Sci. 2018;19(2):200-210.

【33】Yang Y, Gao J, Wang J, Heffernan R, Hanson J, Paliwal K, Zhou Y.
Sixty-five years of the long march in protein secondary structure prediction: the final stretch?

Brief Bioinform. 2018 May 1;19(3):482-494.

【34】Evan N. Feinberg*, Debnil Sur, Zhenqin Wu, Brooke E. Husic, Huanghao Mai, Yang Li, Saisai Sun, Jianyi Yang, Bharath Ramsundar, Vijay S. Pande*
PotentialNet for molecular property prediction

ACS Central Science, 4: 1520-1530 (2018).

【35】Zijuan Zhao, Zhenling Peng*, Jianyi Yang*
Improving sequence-based prediction of protein-peptide binding residues by introducing intrinsic disorder and a consensus method

Journal of Chemical Information and Modeling, 58: 1459-1468 (2018).

【36】Qi Wu, Zhenling Peng*, Yang Zhang, Jianyi Yang*
COACH-D: improved protein-ligand binding site prediction with refined ligand-binding poses through molecular docking

Nucleic Acids Research, 46: W438-W442 (2018).

【37】Runze Dong#, Shuo Pan#, Zhenling Peng*, Yang Zhang, Jianyi Yang*
mTM-align: a server for fast protein structure database search and multiple protein structure alignment

Nucleic Acids Research, 46: W380-W386 (2018).

【38】Qiaozhen Meng, Zhenling Peng*, Jianyi Yang*
CoABind: a novel algorithm for Coenzyme A (CoA)- and CoA derivatives-binding residues prediction

Bioinformatics, 34: 2598-2604 (2018).

【39】Runze Dong, Zhenling Peng, Yang Zhang*, Jianyi Yang*
mTM-align: an algorithm for fast and accurate multiple protein structure alignment

Bioinformatics, 34: 1719-1725 (2018).

【40】Gao S, Tian X, Chang H, Sun Y, Wu Z, Cheng Z, Dong P, Zhao Q, Ruan J, Bu W
Two novel lncRNAs discovered in human mitochondrial DNA using PacBio full-length transcriptome data

Mitochondrion. 2018 Jan;38:41-47.

【41】Qiqige Wuyun#, Wei Zheng#, Zhenling Peng, Jianyi Yang*
A large-scale comparative assessment of methods for residue-residue contact prediction

Briefings in Bioinformatics, 19: 219-230 (2018).

【42】Mary Ashley Rimmer, Owen W. Nadeau, Jianyi Yang, Antonio Artigues, Yang Zhang, Gerald M. Carlson
The structure of the large regulatory alpha subunit of phosphorylase kinase examined by modeling and hydrogen-deuterium exchange

Protein Science, 27: 472-484 (2018).

【43】Hu G, Wang K, Song J, Uversky VN, Kurgan L
Taxonomic Landscape of the Dark Proteomes: Whole-Proteome Scale Interplay Between Structural Darkness, Intrinsic Disorder, and Crystallization Propensity

Proteomics. 2018 Nov;18(21-22):e1800243.

【44】Hu Y, Lin J, Hu J, Hu G, Wang K, Zhang H, Reilly MP, Li M
PennDiff: detecting differential alternative splicing and transcription by RNA sequencing

Bioinformatics. 2018 Jul 15;34(14):2384-2391.

【45】Groenendyk J, Paskevicius T, Urra H, Viricel C, Wang K, Barakat K, Hetz C, Kurgan L, Agellon LB, Michalak M
Cyclosporine A binding to COX-2 reveals a novel signaling pathway that activates the IRE1α unfolded protein response sensor

Sci Rep. 2018 Nov 12;8(1):16678. 

【46】Liu C, Chen Z, Hu Y, Ji H, Yu D, Shen W, Li S, Ruan J, Bu W, Gao S
Complemented Palindromic Small RNAs First Discovered from SARS Coronavirus

Genes (Basel). 2018 Sep 5;9(9). pii: E442.

【47】Li Y, Zheng W, Qiqige W, Cao S, Ruan J, Zhang Y.
A Novel Method for Drug Screen to Regulate G Protein-Coupled Receptors in the Metabolic Network of Alzheimer's Disease

Biomed Res Int. 2018 Feb 20;2018:5486403.

【48】Cheng Z, Sun Y, Niu X, Shang Y, Ruan J, Chen Z, Gao S, Zhang T
Gene expression profiling reveals U1 snRNA regulates cancer gene expression

Oncotarget. 2017 Dec 1;8(68):112867-112874. 

【49】Wang X, Hou Y, Mao J, Zhang Y, Li Z, Zhao Y, Niu T, Yuan R, Wang Y, Cui J, Shi L, Jia X, Fan R, Lin Q, Shang H, Wang B, Wang H, Zhang B, Cui X, Soh S, Ruan J
Western medication plus Traditional Chinese Medicine preparations in patients with chronic heart failure: a prospective, single-blind, randomized, controlled, and multicenter clinical trial

J Tradit Chin Med. 2017 Dec;37(6):756-766

【50】Ferreira L, Wu Z, Kurgan LA, Uversky VN, Zaslavsky
How to manipulate partition behavior of proteins in aqueous two-phase systems: Effect of trimethylamine N-oxide (TMAO)

Fluid Phase Equilibria, 449:217-224, 2017

【51】Qi Wu, Zuguo Yu*, Jianyi Yang*
DLTree: efficient and accurate phylogeny reconstruction using the dynamical language method

Bioinformatics,33: 2214-2215. (2017).

【52】Yang Li, Jianyi Yang*
Structural and sequence similarity makes a significant impact on machine learning-based scoring functions for protein-ligand interactions

Journal of Chemical Information and Modeling, 57: 1007-1012 (2017).

【53】Jiaqi Xia, Zhenling Peng, Dawei Qi, Hongbo Mu*, Jianyi Yang*
An ensemble approach to protein fold classification by integration of template-based assignment and support vector machine classifier

Bioinformatics, 33: 863-887 (2017).

【54】Hu G, Wu Z, Uversky VN, Kurgan L
Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder-Enriched Interactions

Int J Mol Sci. 2017 Dec 19;18(12). pii: E2761. 

【55】Wu Z, Hu G, Wang K, Zaslavsky BY, Kurgan L, Uversky VN
What are the structural features that drive partitioning of proteins in aqueous two-phase systems?

Biochim Biophys Acta Proteins Proteom. 2017 Jan;1865(1):113-120. 

【56】Wu Z, Hu G, Wang K, Kurgan
Exploratory Analysis of Quality Assessment of Putative Intrinsic Disorder in Proteins

16th International Conference on Artificial Intelligence and Soft Computing (ICAISC 2017), pp 722-732

【57】Niu X, Sun Y, Chen Z, Li R, Padmanabhan C, Ruan J, Kreuze JF, Ling K, Fei Z, Gao S
Using Small RNA-seq Data to Detect siRNA Duplexes Induced by Plant Viruses

Genes (Basel). 2017 Jun 16;8(6). pii: E163.

【58】Chen Z, Sun Y, Yang X, Wu Z, Guo K, Niu X, Wang Q, Ruan J, Bu W, Gao S
Two featured series of rRNA-derived RNA fragments (rRFs) constitute a novel class of small RNAs

PLoS One. 2017 Apr 25;12(4):e0176458.

【59】Gao J, Tao XW, Zhao J, Feng YM, Cai YD, Zhang N
Computational Prediction of Protein Epsilon Lysine Acetylation Sites Based on a Feature Selection Method

Comb Chem High Throughput Screen. 2017;20(7):629-637.

【60】Wang T, Zheng W, Wuyun Q, Wu Z, Ruan J, Hu G, Gao J.
PrAS: Prediction of amidation sites using multiple feature extraction

Comput Biol Chem. 2017 Feb;66:57-62.

【61】Gao J, Yang Y, Zhou Y
Predicting the errors of predicted local backbone angles and non-local solvent-accessibilities of proteins by deep neural networks

Bioinformatics. 2016 Dec 15;32(24):3768-3773. 

【62】Gao J, Cui W, Sheng Y, Ruan J, Kurgan L.
PSIONplus: Accurate Sequence-Based Predictor of Ion Channels and Their Types

PLoS One. 2016 Apr 4;11(4):e0152964.

【63】Gao S, Ren Y, Sun Y, Wu Z, Ruan J, He B, Zhang T, Yu X, Tian X, Bu W
PacBio full-length transcriptome profiling of insect mitochondrial gene expression

RNA Biol. 2016 Sep;13(9):820-5.

【64】Wuyun Q, Zheng W, Zhang Y, Ruan J, Hu G
Improved Species-Specific Lysine Acetylation Site Prediction Based on a Large Variety of Features Set

PLoS One. 2016 May 16;11(5):e0155370.

【65】Wang F, Sun Y, Ruan J, Chen R, Chen X, Chen C, Kreuze JF, Fei Z, Zhu X, Gao S
Using Small RNA Deep Sequencing Data to Detect Human Viruses

Biomed Res Int. 2016;2016:2596782

【66】Xiuzhen Hu, Qiwen Dong, Jianyi Yang, Yang Zhang
Recognizing metal and acid radical ion binding sites by integrating ab initio modeling with template-based transferals

Bioinformatics, 32: 3260-3269 (2016).

【67】Jianyi Yang, Yan Wang, Yang Zhang
ResQ: An approach to unified estimation of B-factor and residue-specific error in protein structure prediction

Journal of Molecular Biology, 428: 693-701 (2016).

【68】Jianyi Yang, Wenxuan Zhang, Haoji He, Sara Elizabeth Walker, Hongjiu Zhang, Brandon Govindarajoo, Jouko Virtanen, Zhidong Xue, Hongbin Shen, Yang Zhang
Template-based protein structure prediction in CASP11 and retrospect of I-TASSER in the last decade

Proteins: Structure, Function, and Bioinformatics, 84: 233-246 (2016).

【69】Wenxuan Zhang, Jianyi Yang, Haoji He, Sara Elizabeth Walker, Hongjiu Zhang, Brandon Govindarajoo, Jouko Virtanen, Zhidong Xue, Hongbin Shen, Yang Zhang
Integration of QUARK and I-TASSER for ab initio protein structure prediction in CASP11

Proteins: Structure, Function, and Bioinformatics, 84: 76-86 (2016).

【70】Murillo, G. H., You, N., Su, X., Cui, W., Reilly, M. P., Li, M., ... & Cui, X
MultiGeMS: detection of SNVs from multiple samples using model selection on high-throughput sequencing data

Bioinformatics. 2016 May 15;32(10):1486-92.

【71】Wang C, Hu G, Wang K, Brylinski M, Xie L, Kurgan L
PDID: database of molecular-level putative protein-drug interactions in the structural human proteome.

Bioinformatics. 2016 Feb 15;32(4):579-86. 

【72】Gang Hu, Zhonghua Wu, Kui Wang, Vladimir N Uversky*, Lukasz Kurgan*
Untapped Potential of Disordered Proteins in Current Druggable Human Proteome

Curr Drug Targets. 2016;17(10):1198-205.

【73】Jianyi Yang*, Yang Zhang*
Protein structure and function prediction using I-TASSER protocol

Current Protocols in Bioinformatics, 52: 5.8.1-5.8.15 (2015).

【74】Wallace Chan, Hongjiu Zhang, Jianyi Yang, Jeffrey Brender, Junguk Hur, Arzucan Ozgur, Yang Zhang
GLASS: a comprehensive database for experimentally-validated GPCR-ligand associations

Bioinformatics, 31: 3035-3042 (2015).

【75】Jian Zhang#, Jianyi Yang#, Richard Jang, Yang Zhang
GPCR-I-TASSER: A hybrid approach to G protein-coupled receptor structure modeling and the application to the human genome

Structure, 23: 1538-1549 (2015).

【76】Jianyi Yang*, Yang Zhang*
I-TASSER server: new development for protein structure and function predictions

Nucleic Acids Research, 43: W174-W181 (2015).

【77】Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang
The I-TASSER Suite: Protein structure and function prediction

Nature Methods, 12: 7-8 (2015).

【78】Wu Z, Hu G, Yang J, Peng Z, Uversky VN, Kurgan L
In various protein complexes, disordered protomers have large per-residue surface areas and area of protein-, DNA- and RNA-binding interfaces

FEBS Lett. 2015 Sep 14;589(19 Pt A):2561-9. 

【79】Zhenling Peng, Jing Yan, Xiao Fan, Marcin J Mizianty, Bin Xue, Kui Wang, Gang Hu, Vladimir N Uversky, Lukasz Kurgan*
Exceptionally abundant exceptions: comprehensive characterization of intrinsic disorder in all domains of life

Cell Mol Life Sci. 2015 Jan;72(1):137-51

【80】Cao S, Yu L, Mao J, Wang Q, Ruan J
Uncovering the Molecular Mechanism of Actions between Pharmaceuticals and Proteins on the AD Network

PLoS One. 2015 Dec 9;10(12):e0144387. 

【81】Wu FX, Li M, Ruan J, Luo F
Systems Biology Approaches to Mining High Throughput Biological Data

Biomed Res Int. 2015;2015:504362.

【82】Zheng W, Ruan J, Hu G, Wang K, Hanlon M, Gao J
Analysis of Conformational B-Cell Epitopes in the Antibody-Antigen Complex Using the Depth Function and the Convex Hull

PLoS One. 2015 Aug 5;10(8):e0134835.

【83】Gao J, Kurgan L
Computational prediction of B cell epitopes from antigen sequences

Methods Mol Biol. 2014;1184:197-215.

【84】Zheng W, Zhang C, Hanlon M, Ruan J, Gao J
An ensemble method for prediction of conformational B-cell epitopes from antigen sequences.

Comput Biol Chem. 2014 Apr; 49:51-8. 

【85】Zhang Y, Xu J, Zheng W, Zhang C, Qiu X, Chen K, Ruan J
newDNA-Prot: Prediction of DNA-binding proteins by employing support vector machine and a comprehensive sequence representation

Comput Biol Chem. 2014 Oct;52:51-9. 

【86】Hu G, Wang K, Groenendyk J, Barakat K, Mizianty MJ, Ruan J, Michalak M, Kurgan L
Human structural proteome-wide characterization of Cyclosporine A targets

Bioinformatics. 2014 Dec 15;30(24):3561-6

【87】Backues SK, Chen D, Ruan J, Xie Z, Klionsky DJ
Estimating the size and number of autophagic bodies by electron microscopy

Autophagy. 2014 Jan;10(1):155-64

【88】Shu Quan, Lili Wang, Evgeniy V Petrotchenko, Karl AT Makepeace, Scott Horowitz, Jianyi Yang, Yang Zhang, Christoph H Borchers, James CA Bardwell
Super Spy variants implicate flexibility in chaperone action

eLife, 3: e01584 (2014).

【89】Irina Kufareva, Vsevolod Katritch, Participants of GPCR Dock 2013 (include Jianyi Yang), Raymond C Stevens, Ruben Abagyan
Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges

Structure, 22: 1120-1139 (2014).

【90】Derek S Borgwardt, Aaron D. Martin, Jonathan R Van Hemert, Jianyi Yang, Carol L Fischer, Erica N Recker, Prashant R Nair, Robinson Vidva, Shwetha Chandrashekaraiah, Ann Progulske-Fox, David Drake, Joseph E Cavanaugh, Shireen Vali, Yang Zhang, Kim A B
Histatin 5 binds to Porphyromonas gingivalis hemagglutinin B (HagB) and alters HagB-induced chemokine responses

Scientific Reports, 4: 3904 (2014).

【91】Gao J, Hu G, Wu Z, Ruan J, Shen S, Hanlon M, Wang K*
Improved Prediction of Protein Crystallization, Purification and Production Propensity Using Hybrid Sequence Representation

Current Bioinformatics 9(1):57-64 · January 2014

【92】Grant Holdren#, David Rosenthal#, Jianyi Yang#, Amber Bates, Carol Fischer, Yang Zhang, Nicole Brogden, Kim Brogden
Antimicrobial activity of chemokine CXCL10 for dermal and oral microorganisms

Antibiotics, 3: 527-539 (2014).

【93】Zuguo Yu, Vo Anh, Jianyi Yang, Shaoming Zhu
Fractal related methods for predicting protein structure classes and functions

Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics, Chapter16: 317-337 (2014).

【94】Jianyi Yang, Ambrish Roy, Yang Zhang
BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions

Nucleic Acids Research, 41: D1096-D1103 (2013).

【95】Jianyi Yang, Ambrish Roy, Yang Zhang
Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment

Bioinformatics, 29: 2588-2595 (2013).

【96】Renxiang Yan, Dong Xu, Jianyi Yang, Sara Walker, Yang Zhang
A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction

Scientific Reports, 3: 2619 (2013).

【97】Jiaqi Fu, Song Ling, Ying Liu, Jianyi Yang, Shirly Naveh, Margaret Hannah, Chaim Gilon, Yang Zhang, Joseph Holoshitz
A small shared epitope-mimetic compound potently accelerates osteoclast-mediated bone damage in autoimmune arthritis

The Journal of Immunology, 191: 2096-2103 (2013).

【98】Sheng Y, Zhang C, Qiu X, Zheng W, Ruan J, Shao Y
Exploring the molecular mechanism of action between drug and RNA polymerase based on partially-resolved spatial structures

Curr Comput Aided Drug Des. 2013 Dec;9(4):547-55

【99】Wang K, Gao J, Shen S, Tuszynski JA, Ruan J, Hu G.
An accurate method for prediction of protein-ligand binding site on protein surface using SVM and statistical depth function.

Biomed Res Int. 2013;2013:409658. 

【100】Gao J, Zhang N, Ruan J
Prediction of protein modification sites of gamma-carboxylation using position specific scoring matrices based evolutionary information

Comput Biol Chem. 2013 Dec;47:215-20.

【101】Hu G, Gao J, Wang K, Mizianty MJ, Ruan J, Kurgan L
Finding protein targets for small biologically relevant ligands across fold space using inverse ligand binding predictions.

Structure. 2012 Nov 7;20(11):1815-22.

【102】Gao J, Faraggi E, Zhou Y, Ruan J, Kurgan L
BEST: improved prediction of B-cell epitopes from antigen sequences

PLoS One. 2012;7(6):e40104. 

【103】Wang K, Cui W, Hu G, Gao J, Wu Z, Qiu X, Ruan J, Feng Y, Qi Z, Shao Y, Tuszynski JA
Computable features required to evaluate the efficacy of drugs and a universal algorithm to find optimally effective drug in a drug complex.

PLoS One. 2012;7(3):e33709

【104】Cui W, Wang K, Ruan J, Qi Z, Feng Y, Shao Y, Tuszynski JA
The molecular mechanism of action of the CR6261-Azichromycin combination found through computational analysis

PLoS One. 2012;7(5):e37790. 

【105】Zhang N, Feng Y, Gao S, Ruan J, Zhang T
New insights regarding protein folding as learned from beta-sheets

EXCLI J. 2012 Aug 27;11:543-55. eCollection 2012.

【106】Ambrish Roy, Jianyi Yang, Yang Zhang
COFACTOR: An accurate comparative algorithm for structure-based protein function annotation

Nucleic Acids Research, 40: W471-W477 (2012).

【107】Heng Lian, Xin Chen, Jianyi Yang
Identification of partially linear structure in additive models with an application to gene expression prediction from sequences

Biometrics, 68: 437-445 (2012).

【108】Zhang S, Du J, Zhang L, Zeng C, Liu Q, Zhang T, Hu G
Circular Cone: a novel approach for protein ligand shape matching using modified PCA

Comput Methods Programs Biomed. 2012 Oct;108(1):168-75.

【109】Zhang H, Zhang T, Gao J, Ruan J, Shen S, Kurgan L*
Determination of protein folding kinetic types using sequence and predicted secondary structure and solvent accessibility

Amino Acids,2012; 42(1):271-83

【110】Jianyi Yang*, Xin Chen
Improving taxonomy-based protein fold recognition by using global and local features

Proteins: Structure, Function, and Bioinformatics, 79: 2053-2064 (2011).

【111】Jianyi Yang*, Xin Chen
A consensus approach to predicting protein contact map via logistic regression

Lecture Notes in Bioinformatics, Springer Verlag, 6674: 136-147 (2011).

【112】Hu G, Shen S, Wang K
On the evolution rate in mammalian mitochondrial genomes

Comput Biol Chem. 2011 Jun;35(3):137-42. 

【113】Chen K, Mizianty M, Gao J, Kurgan L*
A critical comparative assessment of predictions of protein binding sites for small organic compounds

Structure. 2011 May 11;19(5):613-21. 

【114】Zhenling Peng#, Jianyi Yang*#, Xin Chen
An improved classification of G-protein-coupled receptors using sequence-derived features

BMC Bioinformatics, 11: 420 (2010).

【115】Jianyi Yang*, Zhenling Peng, Xin Chen
Prediction of protein structural classes for low-homology sequences based on predicted secondary structure

BMC Bioinformatics, 11: S9 (2010).

【116】Xin Chen, Jianyi Yang
Constructing consensus genetic maps in comparative analysis

Journal of Computational Biology, 17: 1561-1573 (2010).

【117】Zhang T, Zhang H, Chen K, Ruan J, Shen S, Kurgan L
Analysis and prediction of RNA-binding residues using sequence, evolutionary conservation, and predicted secondary structure and solvent accessibility

Curr Protein Pept Sci. 2010 Nov;11(7):609-28.

【118】Zhang N, Duan G, Gao S, Ruan J, Zhang T
Prediction of the parallel/antiparallel orientation of beta-strands using amino acid pairing preferences and support vector machines

J Theor Biol. 2010 Apr 7;263(3):360-8.

【119】Gao J, Zhang T, Zhang H, Shen S, Ruan J, Kurgan L
Accurate prediction of protein folding rates from sequence and sequence-derived residue flexibility and solvent accessibility

Proteins. 2010 Jul;78(9):2114-30. 

【120】Zhang N, Ruan J, Duan G, Gao S, Zhang T
The interstrand amino acid pairs play a significant role in determining the parallel or antiparallel orientation of beta-strands

Biochem Biophys Res Commun. 2009 Aug 28;386(3):537-43. 

【121】Zhang H, Zhang T, Chen K, Shen S, Ruan J, Kurgan L
On the relation between residue flexibility and local solvent accessibility in proteins

Proteins. 2009 Aug 15;76(3):617-36.

【122】Jianyi Yang*#, Zhenling Peng#, Zuguo Yu, Ruijie Zhang, Vo Anh, Desheng Wang
Prediction of protein structural classes by recurrence quantification analysis based on chaos game representation

Journal of Theoretical Biology, 257: 618-626 (2009).

【123】Jianyi Yang, Zuguo Yu, Vo Anh
Clustering structures of large proteins using multifractal analyses based on 6-letters model and hydrophobicity scale of amino acids

Chaos, Solitons & Fractals, 40: 607-620 (2009).

【124】Zhang H, Zhang T, Chen K, Shen S, Ruan J, Kurgan L
Sequence based residue depth prediction using evolutionary information and predicted secondary structure

BMC Bioinformatics. 2008 Sep 20;9:388.

【125】Zhang T, Zhang H, Chen K, Shen S, Ruan J, Kurgan L
Accurate sequence-based prediction of catalytic residues

Bioinformatics. 2008 Oct 15;24(20):2329-38.

【126】Jianyi Yang, Zuguo Yu, Vo Anh
Protein structure classification based on chaos game representation and multifractal analysis

Proceedings of the 2008 Fourth International Conference on Natural Computation (ICNC'08), 665-669 (2008).

【127】 Jianyi Yang, Yu Zhou, Zuguo Yu, Vo Anh, Liqian Zhou
Human Pol II promoter recognition based on primary sequences and free energy of dinucleotides

BMC Bioinformatics, 9: 113 (2008).

【128】Hu G, Shen S, Ruan J.
SGA: a grammar-based alignment algorithm

Comput Methods Programs Biomed. 2007 Apr;86(1):17-20.

【129】Shen S, Hu G, Tuszynski JA
Analysis of protein three-dimension structure using amino acids depths

Protein J. 2007 Apr;26(3):183-92.

【130】Jianyi Yang, Zuguo Yu, Vo Anh
Correlations between designability and various structural characteristics of protein lattice models

Journal of Chemical Physics, 126: 195101 (2007).

【131】Shen S, Kai B, Ruan J, Torin Huzil J, Carpenter E, Tuszynski JA
Probabilistic analysis of the frequencies of amino acid pairs within characterized protein sequences

Physica A. 2006 Oct 15;370(2):651-662.

【132】Ruan J, Chen K, Tuszynski JA, Kurgan LA
Quantitative analysis of the conservation of the tertiary structure of protein segments

Protein J. 2006 Jul;25(5):301-15.

【133】Chen K, Ruan J, Kurgan LA
Prediction of three dimensional structure of calmodulin

Protein J. 2006 Jan;25(1):57-70.

【134】Shen SY, Wang K, Hu G, Chen LS, Zhang H, Xia ST
On the alignment space

Conf Proc IEEE Eng Med Biol Soc. 2005;2006:244-7.

【135】Shen S, Dong L, Wang K, Hu G
SMA: An Efficient Tool for Large-Scale Multiple Alignment

Conf Proc IEEE Eng Med Biol Soc. 2005;2005:2836-8.

【136】Ruan J, Wang K, Yang J, Kurgan LA, Cios K
Highly accurate and consistent method for prediction of helix and strand content from primary protein sequences

Artif Intell Med. 2005 Sep-Oct;35(1-2):19-35