Sidi Chen - Publications

Affiliations: 
Ecology and Evolution University of Chicago, Chicago, IL 
Area:
Evolution of novelties, genome evolution and phenotypic evolution
Website:
http://home.uchicago.edu/sidichen/

16/51 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
2016 Yi S, Chen S, Zhang L, Sahni N. Signal Transduction and Regulation: Insights into Evolution. Biomed Research International. 2016: 8604245. PMID 27525280 DOI: 10.1155/2016/8604245  0.56
2015 Chen S, Sanjana NE, Zheng K, Shalem O, Lee K, Shi X, Scott DA, Song J, Pan JQ, Weissleder R, Lee H, Zhang F, Sharp PA. Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis. Cell. 160: 1246-60. PMID 25748654 DOI: 10.1016/j.cell.2015.02.038  0.56
2014 Platt RJ, Chen S, Zhou Y, Yim MJ, Swiech L, Kempton HR, Dahlman JE, Parnas O, Eisenhaure TM, Jovanovic M, Graham DB, Jhunjhunwala S, Heidenreich M, Xavier RJ, Langer R, et al. CRISPR-Cas9 knockin mice for genome editing and cancer modeling. Cell. 159: 440-55. PMID 25263330 DOI: 10.1016/j.cell.2014.09.014  0.56
2014 Xue W, Chen S, Yin H, Tammela T, Papagiannakopoulos T, Joshi NS, Cai W, Yang G, Bronson R, Crowley DG, Zhang F, Anderson DG, Sharp PA, Jacks T. CRISPR-mediated direct mutation of cancer genes in the mouse liver. Nature. 514: 380-4. PMID 25119044 DOI: 10.1038/nature13589  0.56
2014 Chen S, Xue Y, Wu X, Le C, Bhutkar A, Bell EL, Zhang F, Langer R, Sharp PA. Global microRNA depletion suppresses tumor angiogenesis. Genes & Development. 28: 1054-67. PMID 24788094 DOI: 10.1101/gad.239681.114  0.56
2014 Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD, Dadon DB, Cheng AW, Trevino AE, Konermann S, Chen S, Jaenisch R, Zhang F, Sharp PA. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nature Biotechnology. 32: 670-6. PMID 24752079 DOI: 10.1038/nbt.2889  0.56
2014 Yin H, Xue W, Chen S, Bogorad RL, Benedetti E, Grompe M, Koteliansky V, Sharp PA, Jacks T, Anderson DG. Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype. Nature Biotechnology. 32: 551-3. PMID 24681508 DOI: 10.1038/nbt.2884  0.56
2013 Long M, VanKuren NW, Chen S, Vibranovski MD. New gene evolution: little did we know. Annual Review of Genetics. 47: 307-33. PMID 24050177 DOI: 10.1146/annurev-genet-111212-133301  0.64
2013 Chen S, Krinsky BH, Long M. New genes as drivers of phenotypic evolution. Nature Reviews. Genetics. 14: 645-60. PMID 23949544 DOI: 10.1038/nrg3521  0.64
2012 Ni X, Zhang YE, Nègre N, Chen S, Long M, White KP. Adaptive evolution and the birth of CTCF binding sites in the Drosophila genome. Plos Biology. 10: e1001420. PMID 23139640 DOI: 10.1371/journal.pbio.1001420  0.56
2012 Chen S, Spletter M, Ni X, White KP, Luo L, Long M. Frequent recent origination of brain genes shaped the evolution of foraging behavior in Drosophila. Cell Reports. 1: 118-32. PMID 22832161 DOI: 10.1016/j.celrep.2011.12.010  0.56
2012 Chen S, Ni X, Krinsky BH, Zhang YE, Vibranovski MD, White KP, Long M. Reshaping of global gene expression networks and sex-biased gene expression by integration of a young gene. The Embo Journal. 31: 2798-809. PMID 22543869 DOI: 10.1038/emboj.2012.108  0.56
2011 Chen S, Yang H, Krinsky BH, Zhang A, Long M. Roles of young serine-endopeptidase genes in survival and reproduction revealed rapid evolution of phenotypic effects at adult stages. Fly. 5: 345-51. PMID 21946255 DOI: 10.4161/fly.5.4.17808  0.64
2011 Chen Y, Dai H, Chen S, Zhang L, Long M. Highly tissue specific expression of Sphinx supports its male courtship related role in Drosophila melanogaster. Plos One. 6: e18853. PMID 21541324 DOI: 10.1371/journal.pone.0018853  0.56
2010 Chen S, Zhang YE, Long M. New genes in Drosophila quickly become essential. Science (New York, N.Y.). 330: 1682-5. PMID 21164016 DOI: 10.1126/science.1196380  0.64
2008 Dai H, Chen Y, Chen S, Mao Q, Kennedy D, Landback P, Eyre-Walker A, Du W, Long M. The evolution of courtship behaviors through the origination of a new gene in Drosophila. Proceedings of the National Academy of Sciences of the United States of America. 105: 7478-83. PMID 18508971 DOI: 10.1073/pnas.0800693105  0.64
Low-probability matches
2013 Yang C, Wang C, Chen X, Chen S, Zhang Y, Zhi F, Wang J, Li L, Zhou X, Li N, Pan H, Zhang J, Zen K, Zhang CY, Zhang C. Identification of seven serum microRNAs from a genome-wide serum microRNA expression profile as potential noninvasive biomarkers for malignant astrocytomas. International Journal of Cancer. Journal International Du Cancer. 132: 116-27. PMID 22674182 DOI: 10.1002/ijc.27657  0.2
2019 Chen S, Pu W, Guo S, Jin L, He D, Wang J. Genome-Wide DNA Methylation Profiles Reveal Common Epigenetic Patterns of Interferon-Related Genes in Multiple Autoimmune Diseases. Frontiers in Genetics. 10: 223. PMID 31024609 DOI: 10.3389/fgene.2019.00223  0.16
2017 Pu W, Wang C, Chen S, Zhao D, Zhou Y, Ma Y, Wang Y, Li C, Huang Z, Jin L, Guo S, Wang J, Wang M. Targeted bisulfite sequencing identified a panel of DNA methylation-based biomarkers for esophageal squamous cell carcinoma (ESCC). Clinical Epigenetics. 9: 129. PMID 29270239 DOI: 10.1186/s13148-017-0430-7  0.16
2016 Pu W, Geng X, Chen S, Tan L, Tan Y, Wang A, Lu Z, Guo S, Chen X, Wang J. Aberrant methylation of CDH13 can be a diagnostic biomarker for lung adenocarcinoma. Journal of Cancer. 7: 2280-2289. PMID 27994665 DOI: 10.7150/jca.15758  0.16
2020 Chen S, Yuan B, Liu G, Zhang D. Electrochemical Sensors Based on Covalent Organic Frameworks: A Critical Review. Frontiers in Chemistry. 8: 601044. PMID 33330394 DOI: 10.3389/fchem.2020.601044  0.12
2020 Yuan S, Peng L, Park JJ, Hu Y, Devarkar SC, Dong MB, Shen Q, Wu S, Chen S, Lomakin IB, Xiong Y. Nonstructural Protein 1 of SARS-CoV-2 Is a Potent Pathogenicity Factor Redirecting Host Protein Synthesis Machinery toward Viral RNA. Molecular Cell. PMID 33188728 DOI: 10.1016/j.molcel.2020.10.034  0.12
2020 Wang G, Chow RD, Zhu L, Bai Z, Ye L, Zhang F, Renauer PA, Dong MB, Dai X, Zhang X, Du Y, Cheng Y, Niu L, Chu Z, Kim K, ... ... Chen S, et al. CRISPR-GEMM pooled mutagenic screening identifies KMT2D as a major modulator of immune checkpoint blockade. Cancer Discovery. PMID 32887696 DOI: 10.1158/2159-8290.CD-19-1448  0.12
2019 Wang G, Chow RD, Bai Z, Zhu L, Errami Y, Dai X, Dong MB, Ye L, Zhang X, Renauer PA, Park JJ, Shen L, Ye H, Fuchs CS, Chen S. Multiplexed activation of endogenous genes by CRISPRa elicits potent antitumor immunity. Nature Immunology. PMID 31611701 DOI: 10.1038/s41590-019-0500-4  0.12
2018 Wang G, Chow RD, Ye L, Guzman CD, Dai X, Dong MB, Zhang F, Sharp PA, Platt RJ, Chen S. Mapping a functional cancer genome atlas of tumor suppressors in mouse liver using AAV-CRISPR-mediated direct in vivo screening. Science Advances. 4: eaao5508. PMID 29503867 DOI: 10.1126/sciadv.aao5508  0.12
2017 Ding W, Pu W, Wang L, Jiang S, Zhou X, Tu W, Yu L, Zhang J, Guo S, Liu Q, Ma Y, Chen S, Wu W, Reveille J, Zou H, et al. Genome-wide DNA methylation analysis in systemic sclerosis reveals hypomethylation of interferon-associated genes in CD4+ and CD8+ T cells. The Journal of Investigative Dermatology. PMID 29248544 DOI: 10.1016/j.jid.2017.12.003  0.12
2017 Chow RD, Guzman CD, Wang G, Schmidt F, Youngblood MW, Ye L, Errami Y, Dong MB, Martinez MA, Zhang S, Renauer P, Bilguvar K, Gunel M, Sharp PA, Zhang F, ... ... Chen S, et al. AAV-mediated direct in vivo CRISPR screen identifies functional suppressors in glioblastoma. Nature Neuroscience. PMID 28805815 DOI: 10.1038/nn.4620  0.12
2013 Chen X, Liang H, Guan D, Wang C, Hu X, Cui L, Chen S, Zhang C, Zhang J, Zen K, Zhang CY. A combination of Let-7d, Let-7g and Let-7i serves as a stable reference for normalization of serum microRNAs. Plos One. 8: e79652. PMID 24223986 DOI: 10.1371/journal.pone.0079652  0.12
2020 Chow RD, Chen JS, Shen J, Chen S. A web tool for the design of prime-editing guide RNAs. Nature Biomedical Engineering. PMID 32989284 DOI: 10.1038/s41551-020-00622-8  0.08
2018 Wang C, Pu W, Zhao D, Zhou Y, Lu T, Chen S, He Z, Feng X, Wang Y, Li C, Li S, Jin L, Guo S, Wang J, Wang M. Identification of Hyper-Methylated Tumor Suppressor Genes-Based Diagnostic Panel for Esophageal Squamous Cell Carcinoma (ESCC) in a Chinese Han Population. Frontiers in Genetics. 9: 356. PMID 30233644 DOI: 10.3389/fgene.2018.00356  0.08
2013 Luo Y, Wang C, Chen X, Zhong T, Cai X, Chen S, Shi Y, Hu J, Guan X, Xia Z, Wang J, Zen K, Zhang CY, Zhang C. Increased serum and urinary microRNAs in children with idiopathic nephrotic syndrome. Clinical Chemistry. 59: 658-66. PMID 23344497 DOI: 10.1373/clinchem.2012.195297  0.08
2004 Fan K, Wei P, Feng Q, Chen S, Huang C, Ma L, Lai B, Pei J, Liu Y, Chen J, Lai L. Biosynthesis, purification, and substrate specificity of severe acute respiratory syndrome coronavirus 3C-like proteinase. The Journal of Biological Chemistry. 279: 1637-42. PMID 14561748 DOI: 10.1074/jbc.M310875200  0.08
2021 Ravindra NG, Alfajaro MM, Gasque V, Huston NC, Wan H, Szigeti-Buck K, Yasumoto Y, Greaney AM, Habet V, Chow RD, Chen JS, Wei J, Filler RB, Wang B, Wang G, ... ... Chen S, et al. Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes. Plos Biology. 19: e3001143. PMID 33730024 DOI: 10.1371/journal.pbio.3001143  0.04
2019 Ye L, Park JJ, Dong MB, Yang Q, Chow RD, Peng L, Du Y, Guo J, Dai X, Wang G, Errami Y, Chen S. In vivo CRISPR screening in CD8 T cells with AAV-Sleeping Beauty hybrid vectors identifies membrane targets for improving immunotherapy for glioblastoma. Nature Biotechnology. PMID 31548728 DOI: 10.1038/s41587-019-0246-4  0.04
2019 Chow RD, Wang G, Ye L, Codina A, Kim HR, Shen L, Dong MB, Errami Y, Chen S. In vivo profiling of metastatic double knockouts through CRISPR-Cpf1 screens. Nature Methods. PMID 30962622 DOI: 10.1038/s41592-019-0371-5  0.04
2019 Codina A, Renauer PA, Wang G, Chow RD, Park JJ, Ye H, Zhang K, Dong MB, Gassaway B, Ye L, Errami Y, Shen L, Chang A, Jain D, Herbst RS, ... ... Chen S, et al. Convergent Identification and Interrogation of Tumor-Intrinsic Factors that Modulate Cancer Immunity In Vivo. Cell Systems. PMID 30797773 DOI: 10.1016/j.cels.2019.01.004  0.04
2003 Chen X, Feng Q, Wu Z, Liu Y, Huang K, Shi R, Chen S, Lu W, Ding M, Collins RA, Fung YW, Lau LT, Yu AC, Chen J. RNA-dependent RNA polymerase gene sequence from foot-and-mouth disease virus in Hong Kong. Biochemical and Biophysical Research Communications. 308: 899-905. PMID 12927804 DOI: 10.1016/S0006-291X(03)01511-0  0.04
2021 Chow RD, Majety M, Chen S. The aging transcriptome and cellular landscape of the human lung in relation to SARS-CoV-2. Nature Communications. 12: 4. PMID 33397975 DOI: 10.1038/s41467-020-20323-9  0.01
2019 Craig M, Kaveh K, Woosley A, Brown AS, Goldman D, Eton E, Mehta RM, Dhawan A, Arai K, Rahman MM, Chen S, Nowak MA, Goldman A. Cooperative adaptation to therapy (CAT) confers resistance in heterogeneous non-small cell lung cancer. Plos Computational Biology. 15: e1007278. PMID 31449515 DOI: 10.1371/journal.pcbi.1007278  0.01
2019 Dong MB, Wang G, Chow RD, Ye L, Zhu L, Dai X, Park JJ, Kim HR, Errami Y, Guzman CD, Zhou X, Chen KY, Renauer PA, Du Y, Shen J, ... Chen S, et al. Systematic Immunotherapy Target Discovery Using Genome-Scale In Vivo CRISPR Screens in CD8 T Cells. Cell. 178: 1189-1204.e23. PMID 31442407 DOI: 10.1016/j.cell.2019.07.044  0.01
2019 Dai X, Park JJ, Du Y, Kim HR, Wang G, Errami Y, Chen S. One-step generation of modular CAR-T cells with AAV-Cpf1. Nature Methods. PMID 30804551 DOI: 10.1038/s41592-019-0329-7  0.01
2018 Chow RD, Chen S. Sno-derived RNAs are prevalent molecular markers of cancer immunity. Oncogene. PMID 30072739 DOI: 10.1038/s41388-018-0420-z  0.01
2018 Ye L, Wang C, Hong L, Sun N, Chen D, Chen S, Han F. Programmable DNA repair with CRISPRa/i enhanced homology-directed repair efficiency with a single Cas9. Cell Discovery. 4: 46. PMID 30062046 DOI: 10.1038/s41421-018-0049-7  0.16
2018 Chow RD, Kim HR, Chen S. Programmable sequential mutagenesis by inducible Cpf1 crRNA array inversion. Nature Communications. 9: 1903. PMID 29765043 DOI: 10.1038/s41467-018-04158-z  0.01
2018 Chow RD, Chen S. Cancer CRISPR Screens In Vivo. Trends in Cancer. 4: 349-358. PMID 29709259 DOI: 10.1016/j.trecan.2018.03.002  0.01
2017 Pyzocha NK, Chen S. Diverse Class 2 CRISPR-Cas Effector Proteins for Genome Engineering Applications. Acs Chemical Biology. PMID 29121460 DOI: 10.1021/acschembio.7b00800  0.01
2016 Geng X, Pu W, Tan Y, Lu Z, Wang A, Tan L, Chen S, Guo S, Wang J, Chen X. Quantitative assessment of the diagnostic role of FHIT promoter methylation in non-small cell lung cancer. Oncotarget. PMID 28036263 DOI: 10.18632/oncotarget.14256  0.12
2015 Wang C, Ding M, Xia M, Chen S, Van Le A, Soto-Gil R, Shen Y, Wang N, Wang J, Gu W, Wang X, Zhang Y, Zen K, Chen X, Zhang C, et al. A Five-miRNA Panel Identified From a Multicentric Case-control Study Serves as a Novel Diagnostic Tool for Ethnically Diverse Non-small-cell Lung Cancer Patients. Ebiomedicine. 2: 1377-85. PMID 26629532 DOI: 10.1016/j.ebiom.2015.07.034  0.12
2015 Chu H, Wu T, Wu W, Tu W, Jiang S, Chen S, Ma Y, Liu Q, Zhou X, Jin L, Wang J. Involvement of collagen-binding heat shock protein 47 in scleroderma-associated fibrosis. Protein & Cell. PMID 26091621 DOI: 10.1007/s13238-015-0171-3  0.12
2015 Ma DK, Li Z, Lu AY, Sun F, Chen S, Rothe M, Menzel R, Sun F, Horvitz HR. Acyl-CoA Dehydrogenase Drives Heat Adaptation by Sequestering Fatty Acids. Cell. 161: 1152-63. PMID 25981666 DOI: 10.1016/j.cell.2015.04.026  0.01
2014 Yin H, Xue W, Chen S, Bogorad RL, Benedetti E, Grompe M, Koteliansky V, Sharp PA, Jacks T, Anderson DG. Erratum: Corrigendum: Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype Nature Biotechnology. 32: 952-952. DOI: 10.1038/NBT0914-952D  0.01
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