Qiangfeng C. Zhang, Ph.D. - Publications

Biochemistry and Molecular Biophysics Columbia University, New York, NY 
computational biophysics and bioinformatics

34 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  0.6
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  0.4
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  0.6
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  0.4
2019 Xiong L, Xu K, Tian K, Shao Y, Tang L, Gao G, Zhang M, Jiang T, Zhang QC. SCALE method for single-cell ATAC-seq analysis via latent feature extraction. Nature Communications. 10: 4576. PMID 31594952 DOI: 10.1038/s41467-019-12630-7  0.4
2019 Gao Y, Pei G, Li D, Li R, Shao Y, Zhang QC, Li P. Multivalent mA motifs promote phase separation of YTHDF proteins. Cell Research. PMID 31388144 DOI: 10.1038/s41422-019-0210-3  0.4
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  1
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  0.4
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  0.6
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  0.6
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  0.4
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  0.6
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  0.4
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  0.4
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2013 Yan ZY, Shen YH, Zhang QC, Zhu ZY, Lei H, Cheng GC, Lu Z, Yan Y, Wang L. A combined branched stent grafting technique to reconstruct total aortic arch in the treatment of stanford A aortic dissection. The Annals of Thoracic Surgery. 96: 1888-90. PMID 24182490 DOI: 10.1016/j.athoracsur.2013.04.112  0.6
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  0.2
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  1
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  1
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  1
2012 Shen YH, Yan ZY, Zhang QC, Lu Z, Zhu ZY, Cheng GC, Sun Y, Zheng L, Wu YJ. [Efficacy comparison between total aortic arch reconstruction with open placement of triple-branched stent graft and total aortic replacement combined with stented elephant trunk implantation for patients with Stanford A aortic dissection]. Zhonghua Xin Xue Guan Bing Za Zhi. 40: 676-80. PMID 23141013 DOI: 10.3760/cma.j.issn.0253-3758.2012.08.011  0.6
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  1
2012 Luo M, Zhang QC, Lu ZG. [An efficient high-throughput screening assay against nuclear transport]. Yi Chuan = Hereditas / Zhongguo Yi Chuan Xue Hui Bian Ji. 34: 927-34. PMID 22805220  0.52
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  1
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  1
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  1
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  1
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