| Year |
Citation |
Score |
| 2024 |
Yang R, Pan M, Guo J, Huang Y, Zhang QC, Deng T, Wang J. Mapping of the influenza A virus genome RNA structure and interactions reveals essential elements of viral replication. Cell Reports. 43: 113833. PMID 38416642 DOI: 10.1016/j.celrep.2024.113833 |
0.373 |
|
| 2024 |
Huang W, Xiong T, Zhao Y, Heng J, Han G, Wang P, Zhao Z, Shi M, Li J, Wang J, Wu Y, Liu F, Xi JJ, Wang Y, Zhang QC. Computational prediction and experimental validation identify functionally conserved lncRNAs from zebrafish to human. Nature Genetics. PMID 38195860 DOI: 10.1038/s41588-023-01620-7 |
0.342 |
|
| 2023 |
Xiang Y, Huang W, Tan L, Chen T, He Y, Irving PS, Weeks KM, Zhang QC, Dong X. Pervasive downstream RNA hairpins dynamically dictate start-codon selection. Nature. PMID 37674078 DOI: 10.1038/s41586-023-06500-y |
0.332 |
|
| 2023 |
Deng P, Tan SQ, Yang QY, Fu L, Wu Y, Zhu HZ, Sun L, Bao Z, Lin Y, Zhang QC, Wang H, Wang J, Liu JG. Structural RNA components supervise the sequential DNA cleavage in R2 retrotransposon. Cell. PMID 37301196 DOI: 10.1016/j.cell.2023.05.032 |
0.338 |
|
| 2023 |
Xu Y, Zhu J, Huang W, Xu K, Yang R, Zhang QC, Sun L. PrismNet: predicting protein-RNA interaction using in vivo RNA structural information. Nucleic Acids Research. PMID 37140045 DOI: 10.1093/nar/gkad353 |
0.447 |
|
| 2022 |
Zhao J, Chow EY, Yeung PY, Zhang QC, Chan TF, Kwok CK. Enhanced transcriptome-wide RNA G-quadruplex sequencing for low RNA input samples with rG4-seq 2.0. Bmc Biology. 20: 257. PMID 36372875 DOI: 10.1186/s12915-022-01448-3 |
0.356 |
|
| 2022 |
Xiong L, Tian K, Li Y, Ning W, Gao X, Zhang QC. Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space. Nature Communications. 13: 6118. PMID 36253379 DOI: 10.1038/s41467-022-33758-z |
0.605 |
|
| 2022 |
Huang W, Zhang QC. Prediction of Dynamic RBP-RNA Interactions Using PrismNet. Methods in Molecular Biology (Clifton, N.J.). 2568: 123-132. PMID 36227565 DOI: 10.1007/978-1-0716-2687-0_8 |
0.397 |
|
| 2022 |
Zhang J, Fei Y, Sun L, Zhang QC. Advances and opportunities in RNA structure experimental determination and computational modeling. Nature Methods. 19: 1193-1207. PMID 36203019 DOI: 10.1038/s41592-022-01623-y |
0.513 |
|
| 2022 |
Yu B, Li P, Zhang QC, Hou L. Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure. Nature Communications. 13: 4227. PMID 35869080 DOI: 10.1038/s41467-022-31875-3 |
0.428 |
|
| 2022 |
Xu B, Zhu Y, Cao C, Chen H, Jin Q, Li G, Ma J, Yang SL, Zhao J, Zhu J, Ding Y, Fang X, Jin Y, Kwok CK, Ren A, ... ... Zhang QC, et al. Recent advances in RNA structurome. Science China. Life Sciences. PMID 35717434 DOI: 10.1007/s11427-021-2116-2 |
0.65 |
|
| 2022 |
Zhang B, Zhang Y, Xiong L, Li Y, Zhang Y, Zhao J, Jiang H, Li C, Liu Y, Liu X, Liu H, Ping YF, Zhang QC, Zhang Z, Bian XW, et al. CD127 imprints functional heterogeneity to diversify monocyte responses in inflammatory diseases. The Journal of Experimental Medicine. 219. PMID 35015026 DOI: 10.1084/jem.20211191 |
0.57 |
|
| 2021 |
Zhang S, Huang W, Ren L, Ju X, Gong M, Rao J, Sun L, Li P, Ding Q, Wang J, Zhang QC. Comparison of viral RNA-host protein interactomes across pathogenic RNA viruses informs rapid antiviral drug discovery for SARS-CoV-2. Cell Research. PMID 34737357 DOI: 10.1038/s41422-021-00581-y |
0.419 |
|
| 2021 |
Wang XW, Liu CX, Chen LL, Zhang QC. RNA structure probing uncovers RNA structure-dependent biological functions. Nature Chemical Biology. 17: 755-766. PMID 34172967 DOI: 10.1038/s41589-021-00805-7 |
0.425 |
|
| 2021 |
Luo QJ, Zhang J, Li P, Wang Q, Zhang Y, Roy-Chaudhuri B, Xu J, Kay MA, Zhang QC. RNA structure probing reveals the structural basis of Dicer binding and cleavage. Nature Communications. 12: 3397. PMID 34099665 DOI: 10.1038/s41467-021-23607-w |
0.416 |
|
| 2021 |
Sun L, Li P, Ju X, Rao J, Huang W, Ren L, Zhang S, Xiong T, Xu K, Zhou X, Gong M, Miska E, Ding Q, Wang J, Zhang QC. In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs. Cell. PMID 33636127 DOI: 10.1016/j.cell.2021.02.008 |
0.53 |
|
| 2021 |
Sun L, Xu K, Huang W, Yang YT, Li P, Tang L, Xiong T, Zhang QC. Predicting dynamic cellular protein-RNA interactions by deep learning using in vivo RNA structures. Cell Research. PMID 33623109 DOI: 10.1038/s41422-021-00476-y |
0.533 |
|
| 2021 |
Shao Y, Zhang QC. Targeting RNA structures in diseases with small molecules. Essays in Biochemistry. 64: 955-966. PMID 33078198 DOI: 10.1042/EBC20200011 |
0.385 |
|
| 2020 |
Zhang B, Zhang Y, Xiong L, Li Y, Zhang Y, Zhao J, Jiang H, Li C, Liu Y, Liu X, Liu H, Ping YF, Zhang QC, Zhang Z, Bian XW, et al. CD127 imprints functional heterogeneity to diversify monocyte responses in human inflammatory diseases. Biorxiv : the Preprint Server For Biology. PMID 33200127 DOI: 10.1101/2020.11.10.376277 |
0.573 |
|
| 2020 |
Li P, Zhou X, Xu K, Zhang QC. RASP: an atlas of transcriptome-wide RNA secondary structure probing data. Nucleic Acids Research. PMID 33068412 DOI: 10.1093/nar/gkaa880 |
0.412 |
|
| 2020 |
Xu K, Liu N, Xu J, Guo C, Zhao L, Wang HW, Zhang QC. VRmol: an Integrative Web-Based Virtual Reality System to Explore Macromolecular Structure. Bioinformatics (Oxford, England). PMID 32745209 DOI: 10.1093/Bioinformatics/Btaa696 |
0.349 |
|
| 2020 |
Shi B, Zhang J, Heng J, Gong J, Zhang T, Li P, Sun BF, Yang Y, Zhang N, Zhao YL, Wang HL, Liu F, Zhang QC, Yang YG. RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function. Genome Biology. 21: 120. PMID 32423473 DOI: 10.1186/S13059-020-02022-2 |
0.492 |
|
| 2020 |
Yin Y, Lu JY, Zhang X, Shao W, Xu Y, Li P, Hong Y, Cui L, Shan G, Tian B, Zhang QC, Shen X. U1 snRNP regulates chromatin retention of noncoding RNAs. Nature. 580: 147-150. PMID 32238924 DOI: 10.1038/S41586-020-2105-3 |
0.456 |
|
| 2020 |
Li X, Liang QX, Lin JR, Peng J, Yang JH, Yi C, Yu Y, Zhang QC, Zhou KR. Epitranscriptomic technologies and analyses. Science China. Life Sciences. PMID 32170629 DOI: 10.1007/S11427-019-1658-X |
0.401 |
|
| 2020 |
Liu X, Wang X, Li J, Hu S, Deng Y, Yin H, Bao X, Zhang QC, Wang G, Wang B, Shi Q, Shan G. Identification of mecciRNAs and their roles in the mitochondrial entry of proteins. Science China. Life Sciences. PMID 32048164 DOI: 10.1007/S11427-020-1631-9 |
0.309 |
|
| 2020 |
Weng X, Gong J, Chen Y, Wu T, Wang F, Yang S, Yuan Y, Luo G, Chen K, Hu L, Ma H, Wang P, Zhang QC, Zhou X, He C. Keth-seq for transcriptome-wide RNA structure mapping. Nature Chemical Biology. PMID 32015521 DOI: 10.1038/S41589-019-0459-3 |
0.474 |
|
| 2019 |
Kim HK, Xu J, Chu K, Park H, Jang H, Li P, Valdmanis PN, Zhang QC, Kay MA. A tRNA-Derived Small RNA Regulates Ribosomal Protein S28 Protein Levels after Translation Initiation in Humans and Mice. Cell Reports. 29: 3816-3824.e4. PMID 31851915 DOI: 10.1016/J.Celrep.2019.11.062 |
0.436 |
|
| 2019 |
Sun L, Fazal FM, Li P, Broughton JP, Lee B, Tang L, Huang W, Kool ET, Chang HY, Zhang QC. RNA structure maps across mammalian cellular compartments. Nature Structural & Molecular Biology. PMID 30886404 DOI: 10.1038/S41594-019-0200-7 |
0.797 |
|
| 2019 |
Zhao J, Qian X, Yeung PY, Zhang QC, Kwok CK. Mapping In Vivo RNA Structures and Interactions. Trends in Biochemical Sciences. PMID 30853244 DOI: 10.1016/J.Tibs.2019.01.012 |
0.495 |
|
| 2018 |
Li P, Wei Y, Mei M, Tang L, Sun L, Huang W, Zhou J, Zou C, Zhang S, Qin CF, Jiang T, Dai J, Tan X, Zhang QC. Integrative Analysis of Zika Virus Genome RNA Structure Reveals Critical Determinants of Viral Infectivity. Cell Host & Microbe. PMID 30472207 DOI: 10.1016/J.Chom.2018.10.011 |
0.569 |
|
| 2018 |
Qian X, Zhao J, Yeung PY, Zhang QC, Kwok CK. Revealing lncRNA Structures and Interactions by Sequencing-Based Approaches. Trends in Biochemical Sciences. PMID 30459069 DOI: 10.1016/J.Tibs.2018.09.012 |
0.519 |
|
| 2018 |
Ju Y, Gong J, Yang YT, Zhang QC. Investigation of RNA-RNA Interactions Using The RISE Database. Current Protocols in Bioinformatics. e58. PMID 30408350 DOI: 10.1002/Cpbi.58 |
0.479 |
|
| 2018 |
Liu Z, Wang J, Cheng H, Ke X, Sun L, Zhang QC, Wang HW. Cryo-EM Structure of Human Dicer and Its Complexes with a Pre-miRNA Substrate. Cell. PMID 29706542 DOI: 10.1016/j.cell.2018.03.080 |
0.477 |
|
| 2018 |
Lu Z, Gong J, Zhang QC. PARIS: Psoralen Analysis of RNA Interactions and Structures with High Throughput and Resolution. Methods in Molecular Biology (Clifton, N.J.). 1649: 59-84. PMID 29130190 DOI: 10.1007/978-1-4939-7213-5_4 |
0.608 |
|
| 2018 |
Liu Z, Wang J, Cheng H, Ke X, Sun L, Zhang QC, Wang H. Cryo-EM Structure of Human Dicer and Its Complexes with a Pre-miRNA Substrate Cell. 173: 1549-1550. DOI: 10.2210/Pdb5Zam/Pdb |
0.463 |
|
| 2018 |
Gong J, Ju Y, Shao D, Zhang QC. Advances and challenges towards the study of RNA-RNA interactions in a transcriptome-wide scale Quantitative Biology. 6: 239-252. DOI: 10.1007/s40484-018-0146-5 |
0.342 |
|
| 2017 |
Kim HK, Fuchs G, Wang S, Wei W, Zhang Y, Park H, Roy-Chaudhuri B, Li P, Xu J, Chu K, Zhang F, Chua MS, So S, Zhang QC, Sarnow P, et al. A transfer-RNA-derived small RNA regulates ribosome biogenesis. Nature. 552: 57-62. PMID 29186115 DOI: 10.1038/Nature25005 |
0.45 |
|
| 2017 |
Gong J, Shao D, Xu K, Lu Z, Lu ZJ, Yang YT, Zhang QC. RISE: a database of RNA interactome from sequencing experiments. Nucleic Acids Research. PMID 29040625 DOI: 10.1093/Nar/Gkx864 |
0.612 |
|
| 2017 |
Piao M, Sun L, Zhang QC. RNA Regulations and Functions Decoded by Transcriptome-wide RNA Structure Probing. Genomics, Proteomics & Bioinformatics. PMID 29031843 DOI: 10.1016/J.Gpb.2017.05.002 |
0.573 |
|
| 2016 |
Yu KH, Hart SN, Goldfeder R, Zhang QC, Parker SC, Snyder M. HARNESSING BIG DATA FOR PRECISION MEDICINE: INFRASTRUCTURES AND APPLICATIONS. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 22: 635-639. PMID 27897013 DOI: 10.1142/9789813207813_0058 |
0.306 |
|
| 2016 |
Wen K, Yang L, Xiong T, Di C, Ma D, Wu M, Xue Z, Zhang X, Long L, Zhang W, Zhang J, Bi X, Dai J, Zhang Q, Lu ZJ, et al. Critical roles of long noncoding RNAs in Drosophila spermatogenesis. Genome Research. PMID 27516619 DOI: 10.1101/Gr.199547.115 |
0.309 |
|
| 2016 |
Lu Z, Zhang QC, Lee B, Flynn RA, Smith MA, Robinson JT, Davidovich C, Gooding AR, Goodrich KJ, Mattick JS, Mesirov JP, Cech TR, Chang HY. RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure. Cell. PMID 27180905 DOI: 10.1016/J.Cell.2016.04.028 |
0.699 |
|
| 2016 |
Quinn JJ, Zhang QC, Georgiev P, Ilik IA, Akhtar A, Chang HY. Rapid evolutionary turnover underlies conserved lncRNA-genome interactions. Genes & Development. 30: 191-207. PMID 26773003 DOI: 10.1101/Gad.272187.115 |
0.586 |
|
| 2016 |
Flynn RA, Zhang QC, Spitale RC, Lee B, Mumbach MR, Chang HY. Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE. Nature Protocols. 11: 273-90. PMID 26766114 DOI: 10.1038/Nprot.2016.011 |
0.738 |
|
| 2015 |
Spitale RC, Flynn RA, Zhang QC, Crisalli P, Lee B, Jung JW, Kuchelmeister HY, Batista PJ, Torre EA, Kool ET, Chang HY. Erratum: Structural imprints in vivo decode RNA regulatory mechanisms. Nature. PMID 26416736 DOI: 10.1038/Nature15717 |
0.762 |
|
| 2015 |
Chu C, Zhang QC, da Rocha ST, Flynn RA, Bharadwaj M, Calabrese JM, Magnuson T, Heard E, Chang HY. Systematic discovery of Xist RNA binding proteins. Cell. 161: 404-16. PMID 25843628 DOI: 10.1016/J.Cell.2015.03.025 |
0.621 |
|
| 2015 |
Spitale RC, Flynn RA, Zhang QC, Crisalli P, Lee B, Jung JW, Kuchelmeister HY, Batista PJ, Torre EA, Kool ET, Chang HY. Structural imprints in vivo decode RNA regulatory mechanisms. Nature. 519: 486-90. PMID 25799993 DOI: 10.1038/Nature14263 |
0.806 |
|
| 2014 |
Deng L, Zhang QC, Chen Z, Meng Y, Guan J, Zhou S. PredHS: a web server for predicting protein-protein interaction hot spots by using structural neighborhood properties. Nucleic Acids Research. 42: W290-5. PMID 24852252 DOI: 10.1093/Nar/Gku437 |
0.446 |
|
| 2014 |
Wan Y, Qu K, Zhang QC, Flynn RA, Manor O, Ouyang Z, Zhang J, Spitale RC, Snyder MP, Segal E, Chang HY. Landscape and variation of RNA secondary structure across the human transcriptome. Nature. 505: 706-9. PMID 24476892 DOI: 10.1038/Nature12946 |
0.799 |
|
| 2013 |
Kasowski M, Kyriazopoulou-Panagiotopoulou S, Grubert F, Zaugg JB, Kundaje A, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, Li J, Xie D, Olarerin-George A, Steinmetz LM, Hogenesch JB, et al. Extensive variation in chromatin states across humans. Science (New York, N.Y.). 342: 750-2. PMID 24136358 DOI: 10.1126/Science.1242510 |
0.693 |
|
| 2013 |
Deng L, Guan J, Wei X, Yi Y, Zhang QC, Zhou S. Boosting prediction performance of protein-protein interaction hot spots by using structural neighborhood properties. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 878-91. PMID 24134392 DOI: 10.1089/Cmb.2013.0083 |
0.393 |
|
| 2013 |
Dey F, Zhang QC, Petrey D, Honig B. Toward a "structural BLAST": Using structural relationships to infer function Protein Science. 22: 359-366. PMID 23349097 DOI: 10.1002/Pro.2225 |
0.769 |
|
| 2013 |
Zhang QC, Petrey D, Garzón JI, Deng L, Honig B. PrePPI: a structure-informed database of protein-protein interactions. Nucleic Acids Research. 41: D828-33. PMID 23193263 DOI: 10.1093/Nar/Gks1231 |
0.756 |
|
| 2013 |
Zhang QC, Petrey D, Honig B. 180 Integrating structural and systems biology: structure-based prediction of protein–protein interactions on a genome-wide scale Journal of Biomolecular Structure and Dynamics. 31: 116-116. DOI: 10.1080/07391102.2013.786422 |
0.77 |
|
| 2013 |
Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, Honig B. Correction: Corrigendum: Structure-based prediction of protein–protein interactions on a genome-wide scale Nature. 495: 127-127. DOI: 10.1038/Nature11977 |
0.734 |
|
| 2012 |
Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, Honig B. Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature. 490: 556-60. PMID 23023127 DOI: 10.1038/Nature11503 |
0.769 |
|
| 2012 |
Eletsky A, Petrey D, Zhang QC, Lee HW, Acton TB, Xiao R, Everett JK, Prestegard JH, Honig B, Montelione GT, Szyperski T. Solution NMR structures reveal unique homodimer formation by a winged helix-turn-helix motif and provide first structures for protein domain family PF10771. Journal of Structural and Functional Genomics. 13: 1-7. PMID 22223187 DOI: 10.1007/S10969-011-9121-3 |
0.735 |
|
| 2011 |
Fischer M, Zhang QC, Dey F, Chen BY, Honig B, Petrey D. MarkUs: a server to navigate sequence-structure-function space. Nucleic Acids Research. 39: W357-61. PMID 21672961 DOI: 10.1093/Nar/Gkr468 |
0.737 |
|
| 2011 |
Zhang QC, Deng L, Fisher M, Guan J, Honig B, Petrey D. PredUs: a web server for predicting protein interfaces using structural neighbors. Nucleic Acids Research. 39: W283-7. PMID 21609948 DOI: 10.1093/Nar/Gkr311 |
0.744 |
|
| 2010 |
Zhang QC, Petrey D, Norel R, Honig BH. Protein interface conservation across structure space. Proceedings of the National Academy of Sciences of the United States of America. 107: 10896-901. PMID 20534496 DOI: 10.1073/Pnas.1005894107 |
0.76 |
|
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