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1. Full Text A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs
by Miao, Zhichao and Westhof, Eric
PLoS Computational Biology, ISSN 1553-734X, 2015, Volume 11, Issue 12, p. e1004639
Computational prediction of nucleic acid binding sites in proteins are necessary to disentangle functional mechanisms in most biological processes and to... 
SEQUENCE-BASED PREDICTION | DNA | SERVER | ALGORITHM | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | PROPENSITY | SVM | PROTEINS | IDENTIFICATION | RESIDUES | RNA-PUZZLES | Amino Acid Sequence | Protein Interaction Mapping - methods | Sequence Analysis, Protein - methods | Models, Chemical | Nucleic Acids - chemistry | Molecular Sequence Data | Protein Binding | Molecular Docking Simulation | Proteins - chemistry | Binding Sites | Physiological aspects | Nucleic acids | Observations | Binding sites (Biochemistry) | Datasets | Proteins | Accuracy | Bias | Deoxyribonucleic acid | Binding sites | Methods
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2. Full Text RNA Structure: Advances and Assessment of 3D Structure Prediction
by Miao, Zhichao and Westhof, Eric
Annual Review of Biophysics, ISSN 1936-122X, 5/2017, Volume 46, Issue 1, pp. 483 - 503
Biological functions of RNA molecules are dependent upon sustained specific three-dimensional (3D) structures of RNA, with or without the help of proteins.... 
prediction | structural module | evaluation metrics | three-dimensional | RNA-puzzles | RNA structure | Three-dimensional | Structural module | Evaluation metrics | Prediction | CRYSTAL-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | RIBOSWITCH | RIBOSOMAL-RNA | KISSING COMPLEX | CAD-SCORE | BIOPHYSICS | 3-DIMENSIONAL ARCHITECTURE | SEQUENCE | SECONDARY STRUCTURE | SARCIN-RICIN LOOP | WEB SERVER | Software | Base Pairing | Nucleic Acid Conformation | RNA - chemistry | Protein structure prediction | RNA | Structure | Methods
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3. Full Text A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs
: e1004639
by Zhichao Miao and Eric Westhof
PLoS Computational Biology, ISSN 1553-734X, 12/2015, Volume 11, Issue 12
  Computational prediction of nucleic acid binding sites in proteins are necessary to disentangle functional mechanisms in most biological processes and to... 
Datasets | Proteins | Accuracy | Bias | Binding sites | Deoxyribonucleic acid--DNA | Methods
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4. Full Text Quantifying side-chain conformational variations in protein structure
by Miao, Zhichao and Cao, Yang
Scientific Reports, ISSN 2045-2322, 11/2016, Volume 6, Issue 1, p. 37024
Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking... 
SYSTEM | CASP | MULTIDISCIPLINARY SCIENCES | ROTAMER LIBRARY | PACKING | BACKBONE | STRUCTURE PREDICTION | RNA-PUZZLES | Proteins | Gene polymorphism | Protein structure
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5. Full Text Evaluation of protein–ligand docking by Cyscore
by Cao, Yang and Dai, Wentao and Miao, Zhichao
Methods in Molecular Biology, ISSN 1064-3745, 2018, Volume 1762, pp. 233 - 243
Protein-ligand docking is a powerful method in drug discovery. The reliability of docking can be quantified by RMSD between a docking structure and an... 
Protein–ligand docking | Scoring function | Cyscore | Binding pocket | CurvatureSurface | Computational Biology - methods | Databases, Protein | Models, Molecular | Protein Binding | Ligands | Molecular Docking Simulation | Software | Proteins - chemistry | Binding Sites
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6. Full Text Interleukin-15 inhibits adipogenic differentiation of cattle bone marrow-derived mesenchymal stem cells via regulating the crosstalk between signal transducer and activator of transcription 5A and Akt signalling
by Shi, Mingyan and Li, Zhichao and Miao, Zhiguo and Guo, Yanjie and Yi, Li
Biochemical and Biophysical Research Communications, ISSN 0006-291X, 09/2019, Volume 517, Issue 2, pp. 346 - 352
Interleukin (IL)-15 is an important regulator of adipogenic differentiation of bone marrow-derived mesenchymal stem cells (BMSCs). This study was designed to... 
Adipogenic differentiation | STAT pathway | Interleukin-15 | Akt signalling | Mesenchymal stem cells | Type 2 diabetes | Interleukins | RNA | Cattle | Stem cells | Genetic transcription | Fatty acids | Protein binding
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7. Full Text Genomic variation in 3,010 diverse accessions of Asian cultivated rice
by Wang, Wensheng and Mauleon, Ramil and Hu, Zhiqiang and Chebotarov, Dmytro and Tai, Shuaishuai and Wu, Zhichao and Li, Min and Zheng, Tianqing and Fuentes, Roven Rommel and Zhang, Fan and Mansueto, Locedie and Copetti, Dario and Sanciangco, Millicent and Palis, Kevin Christian and Xu, Jianlong and Sun, Chen and Fu, Binying and Zhang, Hongliang and Gao, Yongming and Zhao, Xiuqin and Shen, Fei and Cui, Xiao and Yu, Hong and Li, Zichao and Chen, Miaolin and Detras, Jeffrey and Zhou, Yongli and Zhang, Xinyuan and Zhao, Yue and Kudrna, Dave and Wang, Chunchao and Li, Rui and Jia, Ben and Lu, Jinyuan and He, Xianchang and Dong, Zhaotong and Xu, Jiabao and Li, Yanhong and Wang, Miao and Shi, Jianxin and Li, Jing and Zhang, Dabing and Lee, Seunghee and Hu, Wushu and Poliakov, Alexander and Dubchak, Inna and Ulat, Victor Jun and Borja, Frances Nikki and Mendoza, John Robert and Ali, Jauhar and Gao, Qiang and Niu, Yongchao and Yue, Zhen and Naredo, Ma. Elizabeth B and Talag, Jayson and Wang, Xueqiang and Li, Jinjie and Fang, Xiaodong and Yin, Ye and Glaszmann, Jean-Christophe and Zhang, Jianwei and Li, Jiayang and Hamilton, Ruaraidh Sackville and Wing, Rod A and Ruan, Jue and Zhang, Gengyun and Wei, Chaochun and Alexandrov, Nickolai and McNally, Kenneth L and Li, Zhikang and Leung, Hei and Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Nature, ISSN 0028-0836, 05/2018, Volume 557, Issue 7703, pp. 43 - 49
Here we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice... 
ENCODES | ORYZA | MAJOR QTL | PROTEIN | GENE | GRAIN WIDTH | MULTIDISCIPLINARY SCIENCES | DOMESTICATION | SEQUENCING DATA | ASSOCIATION | WEB SERVER | Haplotypes | Genetics, Population | Genome, Plant - genetics | Genomics | Plant Breeding | INDEL Mutation - genetics | Phylogeny | Oryza - classification | Genetic Variation | Crops, Agricultural - classification | Oryza - genetics | Asia | Genes, Plant - genetics | Polymorphism, Single Nucleotide - genetics | Crops, Agricultural - genetics | Evolution, Molecular | Genetic aspects | Observations | Genetic variation | Rice | Subpopulations | Automation | Breeding | Genes | Grain cultivation | Domestication | Population structure | Genomes | Genetic diversity | Single-nucleotide polymorphism | Population genetics | Proteins | Plant breeding | Acids | Genetic analysis | Population | Variation | Bioinformatics | BASIC BIOLOGICAL SCIENCES
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8. Full Text A test metric for assessing single-cell RNA-seq batch correction
by Büttner, Maren and Miao, Zhichao and Wolf, F. Alexander and Teichmann, Sarah A and Theis, Fabian J
Nature Methods, ISSN 1548-7091, 01/2019, Volume 16, Issue 1, pp. 43 - 49
Single-cell transcriptomics is a versatile tool for exploring heterogeneous cell populations, but as with all genomics experiments, batch effects can hamper... 
PROGRAMS | PACKAGE | BIOCHEMICAL RESEARCH METHODS | GENE-EXPRESSION | NORMALIZATION | SEQUENCING DATA | FATE | Biological effects | Integration | Populations | Nearest-neighbor | Data integration | Variability | Peripheral blood mononuclear cells | Inspection | Data processing | Leukocytes (mononuclear) | Ribonucleic acid--RNA
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9. Full Text Fe3O4@Ti3C2 MXene hybrids with ultrahigh volumetric capacity as an anode material for lithium-ion batteries
by Wang, YS and Li, YY and Qiu, ZP and Wu, XZ and Zhou, PF and Zhou, T and Zhao, JP and Miao, ZC and Zhou, J and Zhuo, SP
JOURNAL OF MATERIALS CHEMISTRY A, ISSN 2050-7488, 06/2018, Volume 6, Issue 24, pp. 11189 - 11197
The volumetric capacity of lithium-ion batteries is becoming an increasingly important parameter restricting their practical applications in limited space,... 
DELAMINATION | METAL CARBIDES | ELECTROCHEMICAL PROPERTIES | CARBON | FE3O4 NANOPARTICLES | ENERGY & FUELS | PERFORMANCE | MATERIALS SCIENCE, MULTIDISCIPLINARY | CHEMISTRY, PHYSICAL | COMPOSITES | 2-DIMENSIONAL TITANIUM CARBIDE | BINDER-FREE ANODE | ENERGY-STORAGE | Scanning electron microscopy | Hybrids | Electrical conductivity | Conductivity | X-ray diffraction | Transition metal oxides | Oxides | Lithium | Rechargeable batteries | Lithium-ion batteries | Nanoparticles | Electrodes | Multilayers | Electrode materials | Diffusion barriers | Electrical resistivity | Electric vehicles | Iron oxides | Anodes
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10. Full Text RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database
by Miao, Zhichao and Westhof, Eric
Nucleic acids research, ISSN 0305-1048, 07/2016, Volume 44, Issue 1, pp. W562 - W567
RBscore&NBench combines a web server, RBscore and a database, NBench. RBscore predicts RNA/DNA-binding residues in proteins and visualizes the prediction... 
RNA | DATA-BANK | DNA | BIOCHEMISTRY & MOLECULAR BIOLOGY | SEQUENCE | SITES | GENERATION | ELECTROSTATICS | PROTEINS | SIDE-CHAIN CONFORMATIONS | FEATURES | DNA - chemistry | Datasets as Topic | Probability | Benchmarking | Software | Internet | Proteins - chemistry | RNA - chemistry | Binding Sites | Databases, Factual | Life Sciences | Molecular biology | Biochemistry, Molecular Biology | Web Server issue
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11. Full Text Prediction of nucleic acid binding probability in proteins: A neighboring residue network based score
by Miao, Zhichao and Westhof, Eric
Nucleic Acids Research, ISSN 0305-1048, 04/2015, Volume 43, Issue 11, pp. 5340 - 5351
We describe a general binding score for predicting the nucleic acid binding probability in proteins. The score is directly derived from physicochemical and... 
DOCKING BENCHMARK | RNA-BINDING | DNA | SERVER | BIOCHEMISTRY & MOLECULAR BIOLOGY | HIGH-RESOLUTION | SEQUENCE | SITES | ELECTROSTATICS | ACCURATE PREDICTION | FEATURES | RNA-Binding Proteins - chemistry | Support Vector Machine | RNA - chemistry | Static Electricity | DNA-Binding Proteins - chemistry | DNA-Binding Proteins - metabolism | Sequence Analysis, Protein | Protein Binding | Software | Structural Homology, Protein | Binding Sites | RNA-Binding Proteins - metabolism | RNA - metabolism | Computational Biology
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12. Full Text miR-140-5p regulates T cell differentiation and attenuates experimental autoimmune encephalomyelitis by affecting CD4+T cell metabolism and DNA methylation
by Zhu, Shang and Zhang, Xiaorong and Guan, Hongbing and Huang, Liwen and Huang, Feng and Wu, Lihong and Hou, Dan and Zheng, Zhichao and Yu, Miao and Ge, Linhu
International Immunopharmacology, ISSN 1567-5769, 10/2019, Volume 75, p. 105778
We previously demonstrated that decreased expression of miR-140-5p was associated with the progression of multiple sclerosis (MS) and miR-140-5p targeted STAT1... 
miR-140-5p | Multiple sclerosis | Experimental autoimmune encephalomyelitis | miRNA | Th1 | Methylation | Metabolism | Encephalomyelitis | Differentiation (biology) | Lymphocytes T | Mitochondrial DNA | Blockage | Electron transport chain | Demethylation | Cell activation | Lymphocytes | DNA methylation | Remission | Inhibition | Stat1 protein | Deoxyribonucleic acid--DNA | Cell differentiation | Gene expression | Experimental allergic encephalomyelitis | CD4 antigen | γ-Interferon | GATA-3 protein | Glycolysis | Electron transport
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13. Full Text RNA structure analysis of human spliceosomes reveals a compact 3D arrangement of snRNAs at the catalytic core
by Anokhina, Maria and Bessonov, Sergey and Miao, Zhichao and Westhof, Eric and Hartmuth, Klaus and Lührmann, Reinhard
The EMBO Journal, ISSN 0261-4189, 10/2013, Volume 32, Issue 21, pp. 2804 - 2818
Although U snRNAs play essential roles in splicing, little is known about the 3D arrangement of U2, U6, and U5 snRNAs and the pre‐mRNA in active spliceosomes.... 
3‐way junction | spliceosome | RNA structure | RNA modelling | U2–U6 duplex | 3-way junction | U2-U6 duplex | GROUP-II INTRON | ACTIVE-SITE | CRYSTAL-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | U6 SNRNA | PRE-MESSENGER-RNA | CELL BIOLOGY | FUNCTIONAL ASSOCIATION | SPLICING INVITRO | U5 SNRNA | U2 SNRNP | SMALL NUCLEAR RNAS | Spliceosomes - chemistry | Cross-Linking Reagents - chemistry | Ficusin - chemistry | Spliceosomes - genetics | Humans | Molecular Conformation | Models, Molecular | RNA, Small Nuclear - chemistry | Ribonucleic acid--RNA | Molecular biology | Catalysis
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