Publications by authors named "Zhichao Miao"

35Publications

Advances in RNA 3D Structure Modeling Using Experimental Data.

Front Genet 2020 26;11:574485. Epub 2020 Oct 26.

Translational Research Institute of Brain and Brain-Like Intelligence, Department of Anesthesiology, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, China.

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http://dx.doi.org/10.3389/fgene.2020.574485DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7649352PMC
October 2020

Secondary structure of the SARS-CoV-2 5'-UTR.

RNA Biol 2020 Sep 23:1-10. Epub 2020 Sep 23.

Architecture Et Réactivité De l'ARN, Université De Strasbourg, Institut De Biologie Moléculaire Et Cellulaire Du CNRS , Strasbourg, France.

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http://dx.doi.org/10.1080/15476286.2020.1814556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7544965PMC
September 2020

Two Cases of Recessive Intellectual Disability Caused by and Variants.

Genes (Basel) 2020 Aug 31;11(9). Epub 2020 Aug 31.

Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR_S 1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), LabEx TRANSPLANTEX, Université de Strasbourg, 67085 Strasbourg, France.

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http://dx.doi.org/10.3390/genes11091021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7563614PMC
August 2020

NCKAP1L defects lead to a novel syndrome combining immunodeficiency, lymphoproliferation, and hyperinflammation.

J Exp Med 2020 Dec;217(12)

Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, Institut National de la Santé et de la Recherche Médicale UMR_S 1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg, Laboratory of Excellence TRANSPLANTEX, Université de Strasbourg, Strasbourg, France.

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http://dx.doi.org/10.1084/jem.20192275DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7526481PMC
December 2020

Putative cell type discovery from single-cell gene expression data.

Nat Methods 2020 06 18;17(6):621-628. Epub 2020 May 18.

Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom.

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http://dx.doi.org/10.1038/s41592-020-0825-9DOI Listing
June 2020

Recent Progresses in Constructing the Highly Efficient Ni Based Catalysts With Advanced Low-Temperature Activity Toward CO Methanation.

Front Chem 2020 28;8:269. Epub 2020 Apr 28.

CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences (CAS), Qingdao, China.

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http://dx.doi.org/10.3389/fchem.2020.00269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7199494PMC
April 2020

First-Principles Study of Nitrogen Adsorption and Dissociation on PuH (111) Surface.

Molecules 2020 Apr 19;25(8). Epub 2020 Apr 19.

Department of Radiochemistry, China Institute of Atomic Energy, Beijing 102413, China.

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http://dx.doi.org/10.3390/molecules25081891DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7222015PMC
April 2020

RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools.

Nucleic Acids Res 2020 01;48(2):576-588

Translational Research Institute of Brain and Brain-Like Intelligence and Department of Anesthesiology, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai 200081, China.

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http://dx.doi.org/10.1093/nar/gkz1108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145511PMC
January 2020

BBKNN: fast batch alignment of single cell transcriptomes.

Bioinformatics 2020 02;36(3):964-965

Cellular Genetics, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1093/bioinformatics/btz625DOI Listing
February 2020

Exome sequencing identifies a novel missense variant in CTSC causing nonsyndromic aggressive periodontitis.

J Hum Genet 2019 Jul 8;64(7):689-694. Epub 2019 May 8.

Laboratoire d'ImmunoRhumatologie Moléculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), LabEx TRANSPLANTEX, Université de Strasbourg, 4 rue Kirschleger, 67085, Strasbourg, France.

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http://dx.doi.org/10.1038/s10038-019-0615-3DOI Listing
July 2019

AbRSA: A robust tool for antibody numbering.

Protein Sci 2019 08 11;28(8):1524-1531. Epub 2019 May 11.

Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, People's Republic of China.

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http://dx.doi.org/10.1002/pro.3633DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6635766PMC
August 2019

Monitoring mitochondrial pH with a hemicyanine-based ratiometric fluorescent probe.

Analyst 2019 May 23;144(10):3422-3427. Epub 2019 Apr 23.

School of Chemistry and Chemical Engineering, Shandong University of Technology, Zibo 255049, P. R. China.

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http://dx.doi.org/10.1039/c9an00422jDOI Listing
May 2019

A test metric for assessing single-cell RNA-seq batch correction.

Nat Methods 2019 01 20;16(1):43-49. Epub 2018 Dec 20.

Helmholtz Zentrum München-German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.

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http://www.nature.com/articles/s41592-018-0254-1
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http://dx.doi.org/10.1038/s41592-018-0254-1DOI Listing
January 2019

An efficient ordered mesoporous molybdate-zirconium oxophosphate solid acid catalyst with homogeneously dispersed active sites: Synthesis, characterization and application.

J Colloid Interface Sci 2018 Sep 30;526:145-157. Epub 2018 Apr 30.

School of Chemistry and Chemical Engineering, Shandong University of Technology, Zibo 255049, PR China. Electronic address:

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http://dx.doi.org/10.1016/j.jcis.2018.04.107DOI Listing
September 2018

Evaluation of Protein-Ligand Docking by Cyscore.

Methods Mol Biol 2018 ;1762:233-243

European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.

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http://dx.doi.org/10.1007/978-1-4939-7756-7_12DOI Listing
January 2019

RNA Structure: Advances and Assessment of 3D Structure Prediction.

Annu Rev Biophys 2017 05 30;46:483-503. Epub 2017 Mar 30.

Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67000 Strasbourg, France; email: ,

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http://dx.doi.org/10.1146/annurev-biophys-070816-034125DOI Listing
May 2017

Quantifying side-chain conformational variations in protein structure.

Sci Rep 2016 11 15;6:37024. Epub 2016 Nov 15.

Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610014, China.

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http://dx.doi.org/10.1038/srep37024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5109468PMC
November 2016

RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database.

Nucleic Acids Res 2016 07 15;44(W1):W562-7. Epub 2016 Apr 15.

Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 15 Rue Descartes 67000 Strasbourg, France

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http://dx.doi.org/10.1093/nar/gkw251DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987871PMC
July 2016

A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs.

PLoS Comput Biol 2015 Dec 17;11(12):e1004639. Epub 2015 Dec 17.

Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France.

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http://dx.doi.org/10.1371/journal.pcbi.1004639DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4683125PMC
December 2015

Prediction of nucleic acid binding probability in proteins: a neighboring residue network based score.

Nucleic Acids Res 2015 Jun 4;43(11):5340-51. Epub 2015 May 4.

Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 15 Rue Descartes, 67000 Strasbourg, France

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http://dx.doi.org/10.1093/nar/gkv446DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4477668PMC
June 2015

Mesoporous Mn-Zr composite oxides with a crystalline wall: synthesis, characterization and application.

Dalton Trans 2015 Feb;44(7):2997-3001

State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China.

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http://dx.doi.org/10.1039/c4dt03835eDOI Listing
February 2015

Modeling of protein side-chain conformations with RASP.

Methods Mol Biol 2014 ;1137:43-53

Key Lab of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

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http://dx.doi.org/10.1007/978-1-4939-0366-5_4DOI Listing
October 2014

RNA structure analysis of human spliceosomes reveals a compact 3D arrangement of snRNAs at the catalytic core.

EMBO J 2013 Oct 3;32(21):2804-18. Epub 2013 Sep 3.

Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.

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http://dx.doi.org/10.1038/emboj.2013.198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3817461PMC
October 2013

RASP: rapid modeling of protein side chain conformations.

Bioinformatics 2011 Nov 23;27(22):3117-22. Epub 2011 Sep 23.

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

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http://dx.doi.org/10.1093/bioinformatics/btr538DOI Listing
November 2011

Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation.

Bioinformatics 2011 Mar 6;27(6):785-90. Epub 2011 Jan 6.

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

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http://dx.doi.org/10.1093/bioinformatics/btr009DOI Listing
March 2011