Shi-Jie ( Chen - Publications

Affiliations: 
College of Engineering Montana State University, Bozeman, MT 
Area:
Industrial Engineering, Health Care Management

142 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
2021 Cheng Y, Zhang S, Xu X, Chen SJ. Vfold2D-MC: A Physics-Based Hybrid Model for Predicting RNA Secondary Structure Folding. The Journal of Physical Chemistry. B. PMID 34473508 DOI: 10.1021/acs.jpcb.1c04731  1
2021 Zhou Y, Li J, Hurst T, Chen SJ. SHAPER: A Web Server for Fast and Accurate SHAPE Reactivity Prediction. Frontiers in Molecular Biosciences. 8: 721955. PMID 34395533 DOI: 10.3389/fmolb.2021.721955  1
2021 Hurst T, Zhang D, Zhou Y, Chen SJ. A Bayes-inspired theory for optimally building an efficient coarse-grained folding force field. Communications in Information and Systems. 21: 65-83. PMID 34354546 DOI: 10.4310/cis.2021.v21.n1.a4  1
2021 Li J, Chen SJ. RNA 3D Structure Prediction Using Coarse-Grained Models. Frontiers in Molecular Biosciences. 8: 720937. PMID 34277713 DOI: 10.3389/fmolb.2021.720937  1
2021 Xiao MC, Qian H, Huang CK, Zheng BN, Yan FZ, Liu F, Zhang X, Chen SJ, Luo C, Xie WF. Imatinib inhibits the malignancy of hepatocellular carcinoma by suppressing autophagy. European Journal of Pharmacology. 174217. PMID 34087223 DOI: 10.1016/j.ejphar.2021.174217  1
2021 Xu X, Chen SJ. Predicting RNA Scaffolds with a Hybrid Method of Vfold3D and VfoldLA. Methods in Molecular Biology (Clifton, N.J.). 2323: 1-11. PMID 34086269 DOI: 10.1007/978-1-0716-1499-0_1  1
2021 Song Z, Gremminger T, Singh G, Cheng Y, Li J, Qiu L, Ji J, Lange MJ, Zuo X, Chen SJ, Zou X, Boris-Lawrie K, Heng X. The three-way junction structure of the HIV-1 PBS-segment binds host enzyme important for viral infectivity. Nucleic Acids Research. PMID 33978756 DOI: 10.1093/nar/gkab342  1
2021 Zhou XR, Li X, Liao LP, Han J, Huang J, Li JC, Tao HR, Fan SJ, Chen ZF, Li Q, Chen SJ, Ding H, Yang YX, Zhou B, Jiang HL, et al. P300/CBP inhibition sensitizes mantle cell lymphoma to PI3Kδ inhibitor idelalisib. Acta Pharmacologica Sinica. PMID 33850273 DOI: 10.1038/s41401-021-00643-2  1
2021 Hurst T, Chen SJ. Deciphering nucleotide modification-induced structure and stability changes. Rna Biology. 1-11. PMID 33586616 DOI: 10.1080/15476286.2021.1882179  1
2021 Chen SJ. Graph, pseudoknot, and SARS-CoV-2 genomic RNA: A biophysical synthesis. Biophysical Journal. PMID 33581060 DOI: 10.1016/j.bpj.2021.01.030  0.01
2021 Zhang D, Li J, Chen SJ. IsRNA1: Prediction and Blind Screening of RNA 3D Structures. Journal of Chemical Theory and Computation. PMID 33560836 DOI: 10.1021/acs.jctc.0c01148  1
2021 Jiang Y, Chen SJ. RLDOCK method for predicting RNA-small molecule binding modes. Methods (San Diego, Calif.). PMID 33549725 DOI: 10.1016/j.ymeth.2021.01.009  1
2021 Hurst T, Chen SJ. Sieving RNA 3D Structures with SHAPE and Evaluating Mechanisms Driving Sequence-Dependent Reactivity Bias. The Journal of Physical Chemistry. B. PMID 33497570 DOI: 10.1021/acs.jpcb.0c11365  1
2020 Cai LY, Chen SJ, Xiao SH, Sun QJ, Ding CH, Zheng BN, Zhu XY, Liu SQ, Yang F, Yang YX, Zhou B, Luo C, Zhang X, Xie WF. Targeting p300/CBP attenuates hepatocellular carcinoma progression through epigenetic regulation of metabolism. Cancer Research. PMID 33361394 DOI: 10.1158/0008-5472.CAN-20-1323  1
2020 Yu MC, Yang F, Ding XY, Sun NN, Jiang ZY, Huang YF, Yan YR, Zhu C, Xie Q, Chen ZF, Guo SQ, Jiang HL, Chen KX, Luo C, Luo XM, ... Chen SJ, et al. Crystallography-guided discovery of carbazole-based retinoic acid-related orphan receptor gamma-t (RORγt) modulators: insights into different protein behaviors with "short" and "long" inverse agonists. Acta Pharmacologica Sinica. PMID 33239687 DOI: 10.1038/s41401-020-00552-w  1
2020 Sun LZ, Jiang Y, Zhou Y, Chen SJ. RLDOCK: A New Method for Predicting RNA-Ligand Interactions. Journal of Chemical Theory and Computation. PMID 33095555 DOI: 10.1021/acs.jctc.0c00798  1
2020 Zhao C, Zhang D, Jiang Y, Chen SJ. Modeling Loop Composition and Ion Concentration Effects in RNA Hairpin Folding Stability. Biophysical Journal. PMID 32949490 DOI: 10.1016/j.bpj.2020.07.042  1
2020 Ptacek J, Zhang D, Qiu L, Kruspe S, Motlova L, Kolenko P, Novakova Z, Shubham S, Havlinova B, Baranova P, Chen SJ, Zou X, Giangrande P, Barinka C. Structural basis of prostate-specific membrane antigen recognition by the A9g RNA aptamer. Nucleic Acids Research. PMID 32525981 DOI: 10.1093/Nar/Gkaa494  1
2020 Xu X, Chen SJ. Topological constraints of RNA pseudoknotted and loop-kissing motifs: applications to three-dimensional structure prediction. Nucleic Acids Research. PMID 32491164 DOI: 10.1093/nar/gkaa463  1
2020 Miao Z, Adamiak RW, Antczak M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Cheng Y, Chou FC, Das R, Dokholyan NV, Ding F, Geniesse C, Jiang Y, Joshi A, et al. RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers. Rna (New York, N.Y.). PMID 32371455 DOI: 10.1261/Rna.075341.120  1
2020 Chen SJ, Zhang GS, Li YJ, Li JL, Lv RJ, Wang P, Chen N, Chen X, Huang YY, Yang L, Zhao DC. Synthesis of Surfactant-Assisted C/Fe-FeVO₄ Nanostructure: Characterization and Photocatalytic Degradation of Ciprofloxacin. Journal of Nanoscience and Nanotechnology. 20: 5636-5641. PMID 32331149 DOI: 10.1166/jnn.2020.17862  1
2020 Wasala NB, Chen SJ, Duan D. Duchenne muscular dystrophy animal models for high-throughput drug discovery and precision medicine. Expert Opinion On Drug Discovery. 1-14. PMID 32000537 DOI: 10.1080/17460441.2020.1718100  1
2020 Nguyen PDM, Zheng J, Gremminger TJ, Qiu L, Zhang D, Tuske S, Lange MJ, Griffin PR, Arnold E, Chen SJ, Zou X, Heng X, Burke DH. Binding interface and impact on protease cleavage for an RNA aptamer to HIV-1 reverse transcriptase. Nucleic Acids Research. PMID 31943114 DOI: 10.1093/Nar/Gkz1224  1
2020 Zhu NW, Yin XL, Lin R, Fan XL, Chen SJ, Zhu YM, Zhao XZ. Possible mechanisms of lycopene amelioration of learning and memory impairment in rats with vascular dementia. Neural Regeneration Research. 15: 332-341. PMID 31552907 DOI: 10.4103/1673-5374.265565  0.01
2019 Chen SJ, Jiang CS, Ni X, Li XX, Hao QJ. [Effect of Plastic Film Mulching on Greenhouse Gas Emissions from Rice-Rapeseed Rotation in Cropland]. Huan Jing Ke Xue= Huanjing Kexue. 40: 4213-4220. PMID 31854887 DOI: 10.13227/j.hjkx.201901037  1
2019 Wang F, Sun LZ, Cai P, Chen SJ, Xu X. Kinetic Mechanism of RNA Helix-Terminal Basepairing-A Kinetic Minima Network Analysis. Biophysical Journal. PMID 31590890 DOI: 10.1016/j.bpj.2019.09.017  1
2019 Sun LZ, Zhou Y, Chen SJ. Predicting Monovalent Ion Correlation Effects in Nucleic Acids. Acs Omega. 4: 13435-13446. PMID 31460472 DOI: 10.1021/acsomega.9b01689  1
2019 Nance ME, Shi R, Hakim CH, Wasala NB, Yue Y, Pan X, Zhang T, Robinson CA, Duan SX, Yao G, Yang NN, Chen SJ, Wagner KR, Gersbach CA, Duan D. AAV9 Edits Muscle Stem Cells in Normal and Dystrophic Adult Mice. Molecular Therapy : the Journal of the American Society of Gene Therapy. PMID 31327755 DOI: 10.1016/J.Ymthe.2019.06.012  1
2019 Chen SJ. Minimizing off-target effects in CRISPR-Cas9 genome editing. Cell Biology and Toxicology. PMID 31317359 DOI: 10.1007/s10565-019-09486-4  0.01
2019 Xu X, Zhao C, Chen SJ. VfoldLA: a web server for loop assembly-based prediction of putative 3D RNA structures. Journal of Structural Biology. PMID 31173857 DOI: 10.1016/j.jsb.2019.06.002  1
2019 Zheng BN, Ding CH, Chen SJ, Zhu K, Shao J, Feng J, Xu WP, Cai LY, Zhu CP, Duan W, Ding J, Zhang X, Luo C, Xie WF. Targeting PRMT5 Activity Inhibits the Malignancy of Hepatocellular Carcinoma by Promoting the Transcription of HNF4α. Theranostics. 9: 2606-2617. PMID 31131056 DOI: 10.7150/thno.32344  1
2019 Chen SJ. Site-Specific Binding of Non-Site-Specific Ions. Biophysical Journal. PMID 31126585 DOI: 10.1016/j.bpj.2019.04.038  0.01
2019 Ni X, Jiang CS, Chen SJ, Li XX, Shi XJ, Hao QJ. [Effects of Plastic Film Mulching and Nitrogen Fertilizer Application on CH Emissions from a Vegetable Field]. Huan Jing Ke Xue= Huanjing Kexue. 40: 2404-2412. PMID 31087882 DOI: 10.13227/j.hjkx.201809045  1
2019 Zhang D, Hurst T, Duan D, Chen SJ. Unified energetics analysis unravels SpCas9 cleavage activity for optimal gRNA design. Proceedings of the National Academy of Sciences of the United States of America. PMID 30988204 DOI: 10.1073/Pnas.1820523116  1
2019 Wasala NB, Hakim C, Chen SJ, Yang NN, Duan D. Questions answered and unanswered by the first CRISPR editing study in the canine model of Duchenne muscular dystrophy. Human Gene Therapy. PMID 30648435 DOI: 10.1089/Hum.2018.243  1
2019 Ni X, Hao QJ, Chen SJ, Li XX, Shi XJ, Jiang CS. [Effects of Plastic Film Mulching and Nitrogen Fertilizer Application on NO Emissions from a Vegetable Field]. Huan Jing Ke Xue= Huanjing Kexue. 40: 893-903. PMID 30628358 DOI: 10.13227/j.hjkx.201806139  1
2018 Sun LZ, Chen SJ. Predicting RNA-Metal Ion Binding with Ion Dehydration Effects. Biophysical Journal. PMID 30612712 DOI: 10.1016/j.bpj.2018.12.006  1
2018 Hakim CH, Wasala NB, Nelson CE, Wasala LP, Yue Y, Louderman JA, Lessa TB, Dai A, Zhang K, Jenkins GJ, Nance ME, Pan X, Kodippili K, Yang NN, Chen SJ, et al. AAV CRISPR editing rescues cardiac and muscle function for 18 months in dystrophic mice. Jci Insight. 3. PMID 30518686 DOI: 10.1172/Jci.Insight.124297  1
2018 Sun T, Zhao C, Chen SJ. Predicting Cotranscriptional Folding Kinetics for Riboswitch. The Journal of Physical Chemistry. B. PMID 29985608 DOI: 10.1021/acs.jpcb.8b04249  1
2018 Lu T, Hu JC, Lu WC, Han J, Ding H, Jiang H, Zhang YY, Yue LY, Chen SJ, Jiang HL, Chen KX, Chai HF, Luo C. Identification of small molecule inhibitors targeting the SMARCA2 bromodomain from a high-throughput screening assay. Acta Pharmacologica Sinica. PMID 29795359 DOI: 10.1038/aps.2017.188  1
2018 Hurst T, Xu X, Zhao P, Chen SJ. Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis. The Journal of Physical Chemistry. B. PMID 29659274 DOI: 10.1021/acs.jpcb.8b00575  1
2018 Yu T, Chen SJ. Hexahydrated MgBinding and Outer-Shell Dehydration on RNA Surface. Biophysical Journal. 114: 1274-1284. PMID 29590585 DOI: 10.1016/j.bpj.2018.01.040  1
2018 Zhang D, Chen SJ. IsRNA: An iterative simulated reference state approach to modeling correlated interactions in RNA folding. Journal of Chemical Theory and Computation. PMID 29499114 DOI: 10.1021/acs.jctc.7b01228  1
2018 Ding CH, Yin C, Chen SJ, Wen LZ, Ding K, Lei SJ, Liu JP, Wang J, Chen KX, Jiang HL, Zhang X, Luo C, Xie WF. The HNF1α-regulated lncRNA HNF1A-AS1 reverses the malignancy of hepatocellular carcinoma by enhancing the phosphatase activity of SHP-1. Molecular Cancer. 17: 63. PMID 29466992 DOI: 10.1186/s12943-018-0813-1  1
2017 Sun LZ, Heng X, Chen SJ. Theory Meets Experiment: Metal Ion Effects in HCV Genomic RNA Kissing Complex Formation. Frontiers in Molecular Biosciences. 4: 92. PMID 29312955 DOI: 10.3389/fmolb.2017.00092  1
2017 Xu X, Chen SJ. Hierarchical Assembly of RNA Three-Dimensional Structures Based on Loop Templates. The Journal of Physical Chemistry. B. PMID 29258305 DOI: 10.1021/acs.jpcb.7b10102  1
2017 Zhang X, Zhang D, Zhao C, Tian K, Shi R, Du X, Burcke AJ, Wang J, Chen SJ, Gu LQ. Nanopore electric snapshots of an RNA tertiary folding pathway. Nature Communications. 8: 1458. PMID 29133841 DOI: 10.1038/S41467-017-01588-Z  1
2017 Zhao C, Xu X, Chen SJ. Predicting RNA Structure with Vfold. Methods in Molecular Biology (Clifton, N.J.). 1654: 3-15. PMID 28986779 DOI: 10.1007/978-1-4939-7231-9_1  1
2017 Kranawetter C, Brady S, Sun L, Schroeder M, Chen SJ, Heng X. NMR study of RNA structures in the 3´-end of the Hepatitis C Virus genome. Biochemistry. PMID 28829576 DOI: 10.1021/acs.biochem.7b00573  1
2017 Sun L, Kranawetter C, Heng X, Chen SJ. Predicting Ion Effects in RNA Conformational Equilibrium. The Journal of Physical Chemistry. B. PMID 28780864 DOI: 10.1021/acs.jpcb.7b03873  1
2017 Sun LZ, Chen SJ. A New Method to Predict Ion Effects in RNA Folding. Methods in Molecular Biology (Clifton, N.J.). 1632: 1-17. PMID 28730429 DOI: 10.1007/978-1-4939-7138-1_1  1
2017 Wu XL, Xiao L, Lin H, Yang M, Chen SJ, An W, Wang Y, Yao XP, Yang ZX, Tang ZZ. A Novel Capillary Electrophoresis-Based High-Throughput Multiplex Polymerase Chain Reaction System for the Simultaneous Detection of Nine Pathogens in Swine. Biomed Research International. 2017: 7243909. PMID 28691030 DOI: 10.1155/2017/7243909  1
2017 Sun L, Zhang J, Chen SJ. MCTBI: a web server for predicting metal ion effects in RNA structures. Rna (New York, N.Y.). PMID 28450533 DOI: 10.1261/rna.060947.117  1
2017 Sun LZ, Zhang D, Chen SJ. Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules. Annual Review of Biophysics. PMID 28301768 DOI: 10.1146/annurev-biophys-070816-033920  1
2017 Xu X, Duan D, Chen SJ. CRISPR-Cas9 cleavage efficiency correlates strongly with target-sgRNA folding stability: from physical mechanism to off-target assessment. Scientific Reports. 7: 143. PMID 28273945 DOI: 10.1038/S41598-017-00180-1  1
2017 Miao Z, Adamiak RW, Antczak M, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki J, Chen SJ, Cheng CY, Chou FC, Ferré-D'Amaré AR, Das R, Dawson WK, Feng D, et al. RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. Rna (New York, N.Y.). PMID 28138060 DOI: 10.1261/Rna.060368.116  1
2016 Xu X, Chen SJ. A Method to Predict the Structure and Stability of RNA/RNA Complexes. Methods in Molecular Biology (Clifton, N.J.). 1490: 63-72. PMID 27665593 DOI: 10.1007/978-1-4939-6433-8_5  1
2016 Xu X, Chen SJ. VfoldCPX Server: Predicting RNA-RNA Complex Structure and Stability. Plos One. 11: e0163454. PMID 27657918 DOI: 10.1371/journal.pone.0163454  1
2016 Yu T, Zhu Y, He Z, Chen SJ. Predicting Molecular Crowding Effects in Ion-RNA Interactions. The Journal of Physical Chemistry. B. PMID 27490487 DOI: 10.1021/acs.jpcb.6b05625  1
2016 Sun LZ, Chen SJ. Monte Carlo Tightly Bound Ion Model: Predicting Ion-Binding Properties of RNA with Ion Correlations and Fluctuations. Journal of Chemical Theory and Computation. PMID 27311366 DOI: 10.1021/acs.jctc.6b00028  1
2016 Xu X, Dickey DD, Chen SJ, Giangrande PH. Structural Computational Modeling of RNA Aptamers. Methods (San Diego, Calif.). PMID 26972787 DOI: 10.1016/J.Ymeth.2016.03.004  1
2016 Urak KT, Shore S, Rockey WM, Chen SJ, McCaffrey AP, Giangrande PH. In vitro RNA SELEX for the generation of chemically-optimized therapeutic RNA drugs. Methods (San Diego, Calif.). PMID 26972786 DOI: 10.1016/J.Ymeth.2016.03.003  1
2016 Wang WG, Chen SJ, He JS, Li JS, Zang XF. The tumor suppressive role of RASSF1A in osteosarcoma through the Wnt signaling pathway. Tumour Biology : the Journal of the International Society For Oncodevelopmental Biology and Medicine. PMID 26750098 DOI: 10.1007/s13277-015-4660-z  1
2015 Xu X, Chen SJ. Physics-based RNA structure prediction. Biophysics Reports. 1: 2-13. PMID 26942214 DOI: 10.1007/s41048-015-0001-4  1
2015 Xu X, Yu T, Chen SJ. Understanding the kinetic mechanism of RNA single base pair formation. Proceedings of the National Academy of Sciences of the United States of America. PMID 26699466 DOI: 10.1073/pnas.1517511113  1
2015 Zhao Q, Li ZY, Zhang ZP, Mo ZY, Chen SJ, Xiang SY, Zhang QS, Xue M. Polylactic-co-glycolic acid microspheres containing three neurotrophic factors promote sciatic nerve repair after injury. Neural Regeneration Research. 10: 1491-1497. PMID 26604912 DOI: 10.4103/1673-5374.165522  0.01
2015 Zhang X, Xu X, Yang Z, Burcke AJ, Gates KS, Chen SJ, Gu LQ. Vectorial unfolding of RNA pseudoknot in a protein channel. Journal of the American Chemical Society. PMID 26595106 DOI: 10.1021/Jacs.5B07910  1
2015 Xu X, Chen SJ. A Method to Predict the 3D Structure of an RNA Scaffold. Methods in Molecular Biology (Clifton, N.J.). 1316: 1-11. PMID 25967048 DOI: 10.1007/978-1-4939-2730-2_1  1
2015 Miao Z, Adamiak RW, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cheng C, Chojnowski G, Chou FC, Cordero P, Cruz JA, Ferré-D'Amaré AR, Das R, Ding F, Dokholyan NV, et al. RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures. Rna (New York, N.Y.). 21: 1066-84. PMID 25883046 DOI: 10.1261/Rna.049502.114  1
2015 Zhu Y, He Z, Chen SJ. TBI server: a web server for predicting ion effects in RNA folding. Plos One. 10: e0119705. PMID 25798933 DOI: 10.1371/journal.pone.0119705  1
2015 Chen SJ, Burke-Agüero DH. Preface. Methods in Enzymology. 553: xv-xvii. PMID 25726473 DOI: 10.1016/S0076-6879(15)00176-7  0.04
2014 Xu X, Zhao P, Chen SJ. Vfold: a web server for RNA structure and folding thermodynamics prediction. Plos One. 9: e107504. PMID 25215508 DOI: 10.1371/journal.pone.0107504  1
2014 Zhu Y, Chen SJ. Many-body effect in ion binding to RNA. The Journal of Chemical Physics. 141: 055101. PMID 25106614 DOI: 10.1063/1.4890656  1
2014 Cao S, Xu X, Chen SJ. Predicting structure and stability for RNA complexes with intermolecular loop-loop base-pairing. Rna (New York, N.Y.). 20: 835-45. PMID 24751648 DOI: 10.1261/rna.043976.113  1
2014 He Z, Zhu Y, Chen SJ. Exploring the electrostatic energy landscape for tetraloop-receptor docking. Physical Chemistry Chemical Physics : Pccp. 16: 6367-75. PMID 24322001 DOI: 10.1039/c3cp53655f  1
2014 Gebicki M, Mooney E, Chen SJ, Mazur LM. Evaluation of hospital medication inventory policies. Health Care Management Science. 17: 215-29. PMID 24014095 DOI: 10.1007/S10729-013-9251-1  1
2013 Wang P, Wu MC, Chen SJ, Yang Y, Lu XJ. Surgical treatment of 42 patients with cerebral schistosomiasis caused by Schistosoma japonicum. Zhongguo Xue Xi Chong Bing Fang Zhi Za Zhi = Chinese Journal of Schistosomiasis Control. 25: 379-82. PMID 24358745  1
2013 Guo L, Yang SL, Chen SJ, Zhang Z, Wang C, Hou R, Ren Y, Wen X, Cao S, Guo W, Hao Z, Quan Z, Zhang M, Yan QG. Identification of canine parvovirus with the Q370R point mutation in the VP2 gene from a giant panda (Ailuropoda melanoleuca). Virology Journal. 10: 163. PMID 23706032 DOI: 10.1186/1743-422X-10-163  1
2013 He Z, Chen SJ. Quantifying Coulombic and solvent polarization-mediated forces between DNA helices. The Journal of Physical Chemistry. B. 117: 7221-7. PMID 23701377 DOI: 10.1021/jp4010955  1
2013 Wang N, Li DS, Zhou X, Xie Y, Liang YN, Wang CD, Yu H, Chen SJ, Yan YB, Gu XB, Wang SX, Peng XR, Yang GY. A sensitive and specific PCR assay for the detection of Baylisascaris schroederi eggs in giant panda feces. Parasitology International. 62: 435-6. PMID 23688803 DOI: 10.1016/j.parint.2013.05.004  0.01
2013 Xu J, Lu XJ, Wang D, Wu MC, Chen SJ, Li JC, Wang P. [Preliminary study on establishing an animal model of neuroschistosomiasis by direct injection of Schistosoma japonicum eggs through skull]. Zhongguo Xue Xi Chong Bing Fang Zhi Za Zhi = Chinese Journal of Schistosomiasis Control. 25: 28-30. PMID 23687807  1
2013 Guo L, Yang SL, Wang CD, Hou R, Chen SJ, Yang XN, Liu J, Pan HB, Hao ZX, Zhang ML, Cao SJ, Yan QG. Phylogenetic analysis of the haemagglutinin gene of canine distemper virus strains detected from giant panda and raccoon dogs in China. Virology Journal. 10: 109. PMID 23566727 DOI: 10.1186/1743-422X-10-109  1
2013 Tian K, He Z, Wang Y, Chen SJ, Gu LQ. Designing a polycationic probe for simultaneous enrichment and detection of microRNAs in a nanopore. Acs Nano. 7: 3962-9. PMID 23550815 DOI: 10.1021/Nn305789Z  1
2012 Cao S, Chen SJ. Statistical mechanical modeling of RNA folding: from free energy landscape to tertiary structural prediction. Nucleic Acids and Molecular Biology. 27: 185-212. PMID 27293312 DOI: 10.1007/978-3-642-25740-7_10  1
2012 Wang P, Wu MC, Chen SJ, Xu XP, Yang Y, Cai J. Microsurgery Resection of Intrinsic Insular Tumors via Transsylvian Surgical Approach in 12 Cases. Cancer Biology & Medicine. 9: 44-7. PMID 23691454 DOI: 10.3969/j.issn.2095-3941.2012.01.008  1
2012 Liu L, Chen SJ. Coarse-grained prediction of RNA loop structures. Plos One. 7: e48460. PMID 23144887 DOI: 10.1371/journal.pone.0048460  1
2012 He Z, Chen SJ. Predicting ion-nucleic acid interactions by energy landscape-guided sampling. Journal of Chemical Theory and Computation. 8: 2095-2101. PMID 23002389 DOI: 10.1021/ct300227a  1
2012 Tan ZJ, Chen SJ. Ion-mediated RNA structural collapse: effect of spatial confinement. Biophysical Journal. 103: 827-36. PMID 22947944 DOI: 10.1016/j.bpj.2012.06.048  1
2012 Xu X, Chen SJ. Kinetic mechanism of conformational switch between bistable RNA hairpins. Journal of the American Chemical Society. 134: 12499-507. PMID 22765263 DOI: 10.1021/ja3013819  1
2012 Cao S, Chen SJ. A domain-based model for predicting large and complex pseudoknotted structures. Rna Biology. 9: 200-11. PMID 22418848 DOI: 10.4161/rna.18488  1
2012 Cruz JA, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cao S, Das R, Ding F, Dokholyan NV, Flores SC, Huang L, Lavender CA, Lisi V, Major F, Mikolajczak K, et al. RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. Rna (New York, N.Y.). 18: 610-25. PMID 22361291 DOI: 10.1261/Rna.031054.111  1
2012 Cao S, Chen SJ. Predicting kissing interactions in microRNA-target complex and assessment of microRNA activity. Nucleic Acids Research. 40: 4681-90. PMID 22307238 DOI: 10.1093/nar/gks052  1
2011 Zhao P, Zhang W, Chen SJ. Cotranscriptional folding kinetics of ribonucleic acid secondary structures. The Journal of Chemical Physics. 135: 245101. PMID 22225186 DOI: 10.1063/1.3671644  1
2011 Chen G, Chen SJ. Quantitative analysis of the ion-dependent folding stability of DNA triplexes. Physical Biology. 8: 066006. PMID 22067830 DOI: 10.1088/1478-3975/8/6/066006  1
2011 Cao S, Chen SJ. Structure and stability of RNA/RNA kissing complex: with application to HIV dimerization initiation signal. Rna (New York, N.Y.). 17: 2130-43. PMID 22028361 DOI: 10.1261/rna.026658.111  1
2011 Tan ZJ, Chen SJ. Importance of diffuse metal ion binding to RNA. Metal Ions in Life Sciences. 9: 101-24. PMID 22010269  1
2011 Rockey WM, Hernandez FJ, Huang SY, Cao S, Howell CA, Thomas GS, Liu XY, Lapteva N, Spencer DM, McNamara JO, Zou X, Chen SJ, Giangrande PH. Rational truncation of an RNA aptamer to prostate-specific membrane antigen using computational structural modeling. Nucleic Acid Therapeutics. 21: 299-314. PMID 22004414 DOI: 10.1089/Nat.2011.0313  1
2011 Stammler SN, Cao S, Chen SJ, Giedroc DP. A conserved RNA pseudoknot in a putative molecular switch domain of the 3'-untranslated region of coronaviruses is only marginally stable. Rna (New York, N.Y.). 17: 1747-59. PMID 21799029 DOI: 10.1261/Rna.2816711  1
2011 Tan ZJ, Chen SJ. Salt contribution to RNA tertiary structure folding stability. Biophysical Journal. 101: 176-87. PMID 21723828 DOI: 10.1016/j.bpj.2011.05.050  1
2011 Wang P, Wang D, Chen SJ, Wu MC, Cheng XL, Li JC, Chen TX, Zhu ZS. Establishment of a cerebral schistosomiasis experimental model in rabbits. Neuroscience Bulletin. 27: 91-8. PMID 21441970 DOI: 10.1007/s12264-011-1127-0  1
2011 Cao S, Chen SJ. Physics-based de novo prediction of RNA 3D structures. The Journal of Physical Chemistry. B. 115: 4216-26. PMID 21413701 DOI: 10.1021/jp112059y  1
2010 Li XX, Zhang MB, Lu YZ, Yan SX, Chen Q, Xing ML, Zou H, Chen SJ, He JL. [Genotoxicity of organic bentonite particles in vitro]. Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi = Zhonghua Laodong Weisheng Zhiyebing Zazhi = Chinese Journal of Industrial Hygiene and Occupational Diseases. 28: 914-7. PMID 21241602  1
2010 Cao S, Fürtig B, Schwalbe H, Chen SJ. Folding kinetics for the conformational switch between alternative RNA structures. The Journal of Physical Chemistry. B. 114: 13609-15. PMID 20886868 DOI: 10.1021/Jp107912S  1
2010 Tan ZJ, Chen SJ. Predicting ion binding properties for RNA tertiary structures. Biophysical Journal. 99: 1565-76. PMID 20816069 DOI: 10.1016/j.bpj.2010.06.029  1
2010 Liu L, Chen SJ. Computing the conformational entropy for RNA folds. The Journal of Chemical Physics. 132: 235104. PMID 20572741 DOI: 10.1063/1.3447385  1
2010 Zhao P, Zhang WB, Chen SJ. Predicting secondary structural folding kinetics for nucleic acids. Biophysical Journal. 98: 1617-25. PMID 20409482 DOI: 10.1016/j.bpj.2009.12.4319  1
2010 Wang P, Wu MC, Chen SJ, Luo GC, Cheng XL, Zhu ZS, Zhao GR. Research development of the pathogenesis pathways for neuroschistosomiasis. Neuroscience Bulletin. 26: 168-74. PMID 20332823 DOI: 10.1007/s12264-010-0920-5  1
2010 Cao S, Giedroc DP, Chen SJ. Predicting loop-helix tertiary structural contacts in RNA pseudoknots. Rna (New York, N.Y.). 16: 538-52. PMID 20100813 DOI: 10.1261/Rna.1800210  1
2010 Chen G, Tan ZJ, Chen SJ. Salt-dependent folding energy landscape of RNA three-way junction. Biophysical Journal. 98: 111-20. PMID 20085723 DOI: 10.1016/j.bpj.2009.09.057  1
2010 Mazur LM, Chen S(. Evaluation of industrial engineering students’ competencies for process improvement in hospitals Journal of Industrial Engineering and Management. 3: 603-628. DOI: 10.3926/Jiem..V3N3.P603-628  1
2009 Tan ZJ, Chen SJ. Predicting electrostatic forces in RNA folding. Methods in Enzymology. 469: 465-87. PMID 20946803 DOI: 10.1016/S0076-6879(09)69022-4  1
2009 Mazur LM, Chen SJ. An empirical study for medication delivery improvement based on healthcare professionals' perceptions of medication delivery system. Health Care Management Science. 12: 56-66. PMID 19938442 DOI: 10.1007/S10729-008-9076-5  1
2009 Cao S, Chen SJ. A new computational approach for mechanical folding kinetics of RNA hairpins. Biophysical Journal. 96: 4024-34. PMID 19450474 DOI: 10.1016/j.bpj.2009.02.044  1
2009 Cao S, Chen SJ. Predicting structures and stabilities for H-type pseudoknots with interhelix loops. Rna (New York, N.Y.). 15: 696-706. PMID 19237463 DOI: 10.1261/rna.1429009  1
2008 Wu MC, Chen SJ, Luo GC, Xu XP, Zhang ZW, Min J, Yao Y. [Surgical treatment of patients with cerebral schistosomiasis]. Zhongguo Ji Sheng Chong Xue Yu Ji Sheng Chong Bing Za Zhi = Chinese Journal of Parasitology & Parasitic Diseases. 26: 154-5. PMID 24812823  1
2008 Lou JL, Chen ZJ, Wei J, He JL, Jin LF, Chen SJ, Zheng W, Xu SJ. Response of lymphocytes to radiation in untreated breast cancer patients as detected with three different genetic assays. Biomedical and Environmental Sciences : Bes. 21: 499-508. PMID 19263806 DOI: 10.1016/S0895-3988(09)60009-X  1
2008 Chen SJ. RNA folding: conformational statistics, folding kinetics, and ion electrostatics. Annual Review of Biophysics. 37: 197-214. PMID 18573079 DOI: 10.1146/annurev.biophys.37.032807.125957  0.01
2008 Tan ZJ, Chen SJ. Salt dependence of nucleic acid hairpin stability. Biophysical Journal. 95: 738-52. PMID 18424500 DOI: 10.1529/biophysj.108.131524  1
2008 Mazur LM, Chen SJ. Understanding and reducing the medication delivery waste via systems mapping and analysis. Health Care Management Science. 11: 55-65. PMID 18390168 DOI: 10.1007/s10729-007-9024-9  1
2008 Cao S, Chen SJ. Predicting ribosomal frameshifting efficiency. Physical Biology. 5: 016002. PMID 18367782 DOI: 10.1088/1478-3975/5/1/016002  1
2008 Tan ZJ, Chen SJ. Electrostatic free energy landscapes for DNA helix bending. Biophysical Journal. 94: 3137-49. PMID 18192348 DOI: 10.1529/biophysj.107.122366  1
2007 Wang BH, Lu DQ, Jin LF, Chen SJ, Lou JL, Zheng W, He JL. [Influence of 1.8 GHz microwave on DNA damage induced by ultraviolet C ray]. Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi = Zhonghua Laodong Weisheng Zhiyebing Zazhi = Chinese Journal of Industrial Hygiene and Occupational Diseases. 25: 470-2. PMID 17945103  1
2007 Tan ZJ, Chen SJ. RNA helix stability in mixed Na+/Mg2+ solution. Biophysical Journal. 92: 3615-32. PMID 17325014 DOI: 10.1529/biophysj.106.100388  1
2007 Cao S, Chen SJ. Biphasic folding kinetics of RNA pseudoknots and telomerase RNA activity. Journal of Molecular Biology. 367: 909-24. PMID 17276459 DOI: 10.1016/j.jmb.2007.01.006  1
2007 Chen SJ, Huang E. A systematic approach for supply chain improvement using design structure matrix Journal of Intelligent Manufacturing. 18: 285-299. DOI: 10.1007/s10845-007-0022-z  1
2006 Tsai TR, Chen SJ, Chang CF, Hsu SH, Lin TY, Chi CC. Terahertz response of GaN thin films. Optics Express. 14: 4898-907. PMID 19516648  0.01
2006 Tan ZJ, Chen SJ. Electrostatic free energy landscapes for nucleic acid helix assembly. Nucleic Acids Research. 34: 6629-39. PMID 17145719 DOI: 10.1093/nar/gkl810  1
2006 Cao S, Chen SJ. Predicting RNA pseudoknot folding thermodynamics. Nucleic Acids Research. 34: 2634-52. PMID 16709732 DOI: 10.1093/nar/gkl346  1
2006 Kopeikin Z, Chen SJ. Folding thermodynamics of pseudoknotted chain conformations. The Journal of Chemical Physics. 124: 154903. PMID 16674261 DOI: 10.1063/1.2188940  1
2006 Tan ZJ, Chen SJ. Ion-mediated nucleic acid helix-helix interactions. Biophysical Journal. 91: 518-36. PMID 16648172 DOI: 10.1529/biophysj.106.084285  1
2006 Cao S, Chen SJ. Free energy landscapes of RNA/RNA complexes: with applications to snRNA complexes in spliceosomes. Journal of Molecular Biology. 357: 292-312. PMID 16413034 DOI: 10.1016/j.jmb.2005.12.014  1
2006 Tan ZJ, Chen SJ. Nucleic acid helix stability: effects of salt concentration, cation valence and size, and chain length. Biophysical Journal. 90: 1175-90. PMID 16299077 DOI: 10.1529/biophysj.105.070904  1
2006 Zhang W, Chen SJ. Exploring the complex folding kinetics of RNA hairpins: I. General folding kinetics analysis. Biophysical Journal. 90: 765-77. PMID 16272440 DOI: 10.1529/biophysj.105.062935  1
2006 Zhang W, Chen SJ. Exploring the complex folding kinetics of RNA hairpins: II. Effect of sequence, length, and misfolded states. Biophysical Journal. 90: 778-87. PMID 16272439 DOI: 10.1529/biophysj.105.062950  1
2006 Huang E, Chen SJ. Estimation of project completion time and factors analysis for concurrent engineering project management: A simulation approach Concurrent Engineering Research and Applications. 14: 329-341. DOI: 10.1177/1063293X06072482  1
2005 Cao S, Chen SJ. Predicting RNA folding thermodynamics with a reduced chain representation model. Rna (New York, N.Y.). 11: 1884-97. PMID 16251382 DOI: 10.1261/rna.2109105  1
2005 Kopeikin Z, Chen SJ. Statistical thermodynamics for chain molecules with simple RNA tertiary contacts. The Journal of Chemical Physics. 122: 094909. PMID 15836183 DOI: 10.1063/1.1857831  1
2005 Tan ZJ, Chen SJ. Electrostatic correlations and fluctuations for ion binding to a finite length polyelectrolyte. The Journal of Chemical Physics. 122: 44903. PMID 15740294 DOI: 10.1063/1.1842059  1
2003 Zhang W, Chen SJ. Analyzing the biopolymer folding rates and pathways using kinetic cluster method. The Journal of Chemical Physics. 119: 8716-8729. PMID 19079645 DOI: 10.1063/1.1613255  1
2003 Zhang W, Chen SJ. Master equation approach to finding the rate-limiting steps in biopolymer folding. The Journal of Chemical Physics. 118: 3413-3420. PMID 19079644 DOI: 10.1063/1.1538596  1
2003 Chen SJ, Li XY, Zhou LF. [Quantitative study by grey system on the latent period of lung cancer induced by air pollutants]. Zhonghua Liu Xing Bing Xue Za Zhi = Zhonghua Liuxingbingxue Zazhi. 24: 233-5. PMID 12816720  0.01
2002 Zhang W, Chen SJ. RNA hairpin-folding kinetics. Proceedings of the National Academy of Sciences of the United States of America. 99: 1931-6. PMID 11842187 DOI: 10.1073/pnas.032443099  1
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