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Items: 1 to 50 of 125

1.

Tailoring the Mechanical Stiffness of DNA Nanostructures Using Engineered Defects.

Lee C, Kim KS, Kim YJ, Lee JY, Kim DN.

ACS Nano. 2019 Jul 10. doi: 10.1021/acsnano.9b03770. [Epub ahead of print]

PMID:
31291091
2.

cryo_fit: Democratization of Flexible Fitting for Cryo-EM.

Kim DN, Moriarty NW, Kirmizialtin S, Afonine PV, Poon B, Sobolev OV, Adams PD, Sanbonmatsu K.

J Struct Biol. 2019 Jul 3. pii: S1047-8477(19)30128-5. doi: 10.1016/j.jsb.2019.05.012. [Epub ahead of print]

PMID:
31279069
3.

Ampk regulates IgD expression but not energy stress with B cell activation.

Waters LR, Ahsan FM, Ten Hoeve J, Hong JS, Kim DNH, Minasyan A, Braas D, Graeber TG, Zangle TA, Teitell MA.

Sci Rep. 2019 Jun 3;9(1):8176. doi: 10.1038/s41598-019-43985-y.

4.

Configurational Design of Mechanical Perturbation for Fine Control of Twisted DNA Origami Structures.

Kim YJ, Lee C, Lee JG, Kim DN.

ACS Nano. 2019 Jun 25;13(6):6348-6355. doi: 10.1021/acsnano.9b01561. Epub 2019 May 22.

PMID:
31091071
5.

Gamma Entrainment Binds Higher-Order Brain Regions and Offers Neuroprotection.

Adaikkan C, Middleton SJ, Marco A, Pao PC, Mathys H, Kim DN, Gao F, Young JZ, Suk HJ, Boyden ES, McHugh TJ, Tsai LH.

Neuron. 2019 Jun 5;102(5):929-943.e8. doi: 10.1016/j.neuron.2019.04.011. Epub 2019 May 7.

PMID:
31076275
6.

Multi-sensory Gamma Stimulation Ameliorates Alzheimer's-Associated Pathology and Improves Cognition.

Martorell AJ, Paulson AL, Suk HJ, Abdurrob F, Drummond GT, Guan W, Young JZ, Kim DN, Kritskiy O, Barker SJ, Mangena V, Prince SM, Brown EN, Chung K, Boyden ES, Singer AC, Tsai LH.

Cell. 2019 Apr 4;177(2):256-271.e22. doi: 10.1016/j.cell.2019.02.014. Epub 2019 Mar 14.

PMID:
30879788
7.

Investigating the sequence-dependent mechanical properties of DNA nicks for applications in twisted DNA nanostructure design.

Lee JY, Kim YJ, Lee C, Lee JG, Yagyu H, Tabata O, Kim DN.

Nucleic Acids Res. 2019 Jan 10;47(1):93-102. doi: 10.1093/nar/gky1189.

8.

Cross-Linked Fluorescent Supramolecular Nanoparticles for Intradermal Controlled Release of Antifungal Drug-A Therapeutic Approach for Onychomycosis.

Wang F, Yang P, Choi JS, Antovski P, Zhu Y, Xu X, Kuo TH, Lin LE, Kim DNH, Huang PC, Xu H, Lee CF, Wang C, Hsu CC, Chen K, Weiss PS, Tseng HR.

ACS Nano. 2018 Jul 24;12(7):6851-6859. doi: 10.1021/acsnano.8b02099. Epub 2018 Jun 27.

PMID:
29851454
9.

Soft lithography fabrication of index-matched microfluidic devices for reducing artifacts in fluorescence and quantitative phase imaging.

Kim DNH, Kim KT, Kim C, Teitell MA, Zangle TA.

Microfluid Nanofluidics. 2018 Jan;22. pii: 2. Epub 2017 Dec 1.

10.

Poro-elasto-capillary wicking of cellulose sponges.

Ha J, Kim J, Jung Y, Yun G, Kim DN, Kim HY.

Sci Adv. 2018 Mar 30;4(3):eaao7051. doi: 10.1126/sciadv.aao7051. eCollection 2018 Mar.

11.

Publisher Correction: Polymorphic design of DNA origami structures through mechanical control of modular components.

Lee C, Lee JY, Kim DN.

Nat Commun. 2018 Feb 7;9(1):626. doi: 10.1038/s41467-018-02948-z.

12.

Polymorphic design of DNA origami structures through mechanical control of modular components.

Lee C, Lee JY, Kim DN.

Nat Commun. 2017 Dec 12;8(1):2067. doi: 10.1038/s41467-017-02127-6. Erratum in: Nat Commun. 2018 Feb 7;9(1):626.

13.

Rhombic-Shaped Nanostructures and Mechanical Properties of 2D DNA Origami Constructed with Different Crossover/Nick Designs.

Ma Z, Huang Y, Park S, Kawai K, Kim DN, Hirai Y, Tsuchiya T, Yamada H, Tabata O.

Small. 2018 Jan;14(1). doi: 10.1002/smll.201702028. Epub 2017 Nov 13.

PMID:
29131541
14.

Tools for the cryo-EM gold rush: going from the cryo-EM map to the atomistic model.

Kim DN, Sanbonmatsu KY.

Biosci Rep. 2017 Dec 5;37(6). pii: BSR20170072. doi: 10.1042/BSR20170072. Print 2017 Dec 22. Review.

15.

A critical assessment of finite element modeling approach for protein dynamics.

Yun G, Kim J, Kim DN.

J Comput Aided Mol Des. 2017 Jul;31(7):609-624. doi: 10.1007/s10822-017-0027-4. Epub 2017 Jun 1.

PMID:
28573346
16.

Stretchable, Transparent, and Stretch-Unresponsive Capacitive Touch Sensor Array with Selectively Patterned Silver Nanowires/Reduced Graphene Oxide Electrodes.

Choi TY, Hwang BU, Kim BY, Trung TQ, Nam YH, Kim DN, Eom K, Lee NE.

ACS Appl Mater Interfaces. 2017 May 31;9(21):18022-18030. doi: 10.1021/acsami.6b16716. Epub 2017 May 16.

PMID:
28485567
17.

Coarse-Grained Molecular Dynamics Model of Double-Stranded DNA for DNA Nanostructure Design.

Yagyu H, Lee JY, Kim DN, Tabata O.

J Phys Chem B. 2017 May 18;121(19):5033-5039. doi: 10.1021/acs.jpcb.7b03931. Epub 2017 May 10.

PMID:
28448145
18.

Early and multiple PSA bounces can occur following high-dose prostate stereotactic body radiation therapy: Subset analysis of a phase 1/2 trial.

Kim DN, Straka C, Cho LC, Lotan Y, Yan J, Kavanagh B, Raben D, Cooley S, Brindle J, Xie XJ, Pistenmaa D, Timmerman R.

Pract Radiat Oncol. 2017 Jan - Feb;7(1):e43-e49. doi: 10.1016/j.prro.2016.06.010. Epub 2016 Jun 24.

PMID:
27637137
19.

Molecular characterization of an adiponectin receptor homolog in the white leg shrimp, Litopenaeus vannamei.

Kim AR, Alam MJ, Yoon TH, Lee SR, Park H, Kim DN, An DH, Lee JB, Lee CI, Kim HW.

PeerJ. 2016 Jul 14;4:e2221. doi: 10.7717/peerj.2221. eCollection 2016.

20.

A near-zero Poisson's ratio of Si with ordered nanopores.

Yoo Y, Kim YJ, Kim DN, Lee JH.

Phys Chem Chem Phys. 2016 Aug 3;18(31):21949-53. doi: 10.1039/c6cp03248f.

PMID:
27440199
21.

Methylsulfonylmethane enhances BMP‑2‑induced osteoblast differentiation in mesenchymal stem cells.

Kim DN, Joung YH, Darvin P, Kang DY, Sp N, Byun HJ, Cho KH, Park KD, Lee HK, Yang YM.

Mol Med Rep. 2016 Jul;14(1):460-6. doi: 10.3892/mmr.2016.5274. Epub 2016 May 13.

PMID:
27175741
22.

Structural Basis for Elastic Mechanical Properties of the DNA Double Helix.

Kim YJ, Kim DN.

PLoS One. 2016 Apr 7;11(4):e0153228. doi: 10.1371/journal.pone.0153228. eCollection 2016.

23.

Boosting protein stability with the computational design of β-sheet surfaces.

Kim DN, Jacobs TM, Kuhlman B.

Protein Sci. 2016 Mar;25(3):702-10. doi: 10.1002/pro.2869. Epub 2016 Jan 13.

24.

Toward Modular Analysis of Supramolecular Protein Assemblies.

Kim J, Kim JG, Yun G, Lee PS, Kim DN.

J Chem Theory Comput. 2015 Sep 8;11(9):4260-72. doi: 10.1021/acs.jctc.5b00329. Epub 2015 Aug 27.

PMID:
26575921
25.

X-ray and optical stereo-based 3D sensor fusion system for image-guided neurosurgery.

Kim DN, Chae YS, Kim MY.

Int J Comput Assist Radiol Surg. 2016 Apr;11(4):529-41. doi: 10.1007/s11548-015-1290-2. Epub 2015 Sep 26.

PMID:
26410838
26.
27.

Hybrid random walk-linear discriminant analysis method for unwrapping quantitative phase microscopy images of biological samples.

Kim DN, Teitell MA, Reed J, Zangle TA.

J Biomed Opt. 2015;20(11):111211. doi: 10.1117/1.JBO.20.11.111211.

28.

Long-term Outcome of Prostate Cancer Patients Who Exhibit Biochemical Failure Despite Salvage Radiation Therapy After Radical Prostatectomy.

Ying J, Wang CJ, Yan J, Liauw SL, Straka C, Pistenmaa D, Xie XJ, Lotan Y, Roehrborn C, Kim DN.

Am J Clin Oncol. 2017 Dec;40(6):612-620. doi: 10.1097/COC.0000000000000207.

PMID:
26165416
29.

The combination of methylsulfonylmethane and tamoxifen inhibits the Jak2/STAT5b pathway and synergistically inhibits tumor growth and metastasis in ER-positive breast cancer xenografts.

S P N, Darvin P, Yoo YB, Joung YH, Kang DY, Kim DN, Hwang TS, Kim SY, Kim WS, Lee HK, Cho BW, Kim HS, Park KD, Park JH, Chang SH, Yang YM.

BMC Cancer. 2015 Jun 19;15:474. doi: 10.1186/s12885-015-1445-0.

30.

Selective Efficacy of Temsirolimus on Bone Metastases in Chromophobe Renal Cell Carcinoma.

Huelsmann L, Kim DNW, Hannan R, Watumull LM, Brugarolas J.

Clin Genitourin Cancer. 2015 Aug;13(4):e321-e323. doi: 10.1016/j.clgc.2014.12.007. Epub 2014 Dec 20. No abstract available.

PMID:
25620636
31.

Lattice-free prediction of three-dimensional structure of programmed DNA assemblies.

Pan K, Kim DN, Zhang F, Adendorff MR, Yan H, Bathe M.

Nat Commun. 2014 Dec 3;5:5578. doi: 10.1038/ncomms6578.

32.

Amphritea ceti sp. nov., isolated from faeces of Beluga whale (Delphinapterus leucas).

Kim YO, Park S, Kim DN, Nam BH, Won SM, An du H, Yoon JH.

Int J Syst Evol Microbiol. 2014 Dec;64(Pt 12):4068-72. doi: 10.1099/ijs.0.067405-0. Epub 2014 Sep 18.

PMID:
25237149
33.

Hepatoprotective role of Sestrin2 against chronic ER stress.

Park HW, Park H, Ro SH, Jang I, Semple IA, Kim DN, Kim M, Nam M, Zhang D, Yin L, Lee JH.

Nat Commun. 2014 Jun 20;5:4233. doi: 10.1038/ncomms5233.

34.

Computational approaches to understanding protein aggregation in neurodegeneration.

Redler RL, Shirvanyants D, Dagliyan O, Ding F, Kim DN, Kota P, Proctor EA, Ramachandran S, Tandon A, Dokholyan NV.

J Mol Cell Biol. 2014 Apr;6(2):104-15. doi: 10.1093/jmcb/mju007. Epub 2014 Mar 11. Review.

35.

Super-resolution fingerprinting detects chemical reactions and idiosyncrasies of single DNA pegboards.

Johnson-Buck A, Nangreave J, Kim DN, Bathe M, Yan H, Walter NG.

Nano Lett. 2013 Feb 13;13(2):728-33. doi: 10.1021/nl304415b. Epub 2013 Jan 31.

PMID:
23356935
36.

DAB2IP regulates autophagy in prostate cancer in response to combined treatment of radiation and a DNA-PKcs inhibitor.

Yu L, Tumati V, Tseng SF, Hsu FM, Kim DN, Hong D, Hsieh JT, Jacobs C, Kapur P, Saha D.

Neoplasia. 2012 Dec;14(12):1203-12.

37.

Characterization of naturally Epstein-Barr virus-infected gastric carcinoma cell line YCCEL1.

Kim DN, Seo MK, Choi H, Kim SY, Shin HJ, Yoon AR, Tao Q, Rha SY, Lee SK.

J Gen Virol. 2013 Mar;94(Pt 3):497-506. doi: 10.1099/vir.0.045237-0. Epub 2012 Nov 21.

PMID:
23175241
38.

Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence.

Bansal T, Kim DN, Slininger T, Wood TK, Jayaraman A.

FEMS Immunol Med Microbiol. 2012 Dec;66(3):399-410. doi: 10.1111/1574-695X.12004.

39.

Personalized Combined Modality Therapy for Locally Advanced Non-small Cell Lung Cancer.

Kim DN, Nam TK, Choe KS, Choy H.

Cancer Res Treat. 2012 Jun;44(2):74-84. doi: 10.4143/crt.2012.44.2.74. Epub 2012 Jun 30.

40.

Role of postmastectomy radiation after neoadjuvant chemotherapy in stage II-III breast cancer.

Fowble BL, Einck JP, Kim DN, McCloskey S, Mayadev J, Yashar C, Chen SL, Hwang ES; Athena Breast Health Network.

Int J Radiat Oncol Biol Phys. 2012 Jun 1;83(2):494-503. doi: 10.1016/j.ijrobp.2012.01.068. Review.

PMID:
22579377
41.

Biogenesis of Epstein-Barr virus microRNAs.

Kim DN, Lee SK.

Mol Cell Biochem. 2012 Jun;365(1-2):203-10. doi: 10.1007/s11010-012-1261-7. Epub 2012 Feb 18.

PMID:
22350759
42.

Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures.

Kim DN, Kilchherr F, Dietz H, Bathe M.

Nucleic Acids Res. 2012 Apr;40(7):2862-8. doi: 10.1093/nar/gkr1173. Epub 2011 Dec 10.

43.

Shewanella upenei sp. nov., a lipolytic bacterium isolated from bensasi goatfish Upeneus bensasi.

Kim KK, Kim YO, Park S, Kang SJ, Nam BH, Kim DN, Oh TK, Yoon JH.

J Microbiol. 2011 Jun;49(3):381-6. doi: 10.1007/s12275-011-0175-5. Epub 2011 Jun 30.

PMID:
21717322
44.

The role of promoter methylation in Epstein-Barr virus (EBV) microRNA expression in EBV-infected B cell lines.

Kim DN, Song YJ, Lee SK.

Exp Mol Med. 2011 Jul 30;43(7):401-10. doi: 10.3858/emm.2011.43.7.044.

45.

Association between Epstein-Barr virus infection and chemoresistance to docetaxel in gastric carcinoma.

Shin HJ, Kim DN, Lee SK.

Mol Cells. 2011 Aug;32(2):173-9. doi: 10.1007/s10059-011-0066-y. Epub 2011 May 27.

46.

A primer to scaffolded DNA origami.

Castro CE, Kilchherr F, Kim DN, Shiao EL, Wauer T, Wortmann P, Bathe M, Dietz H.

Nat Methods. 2011 Mar;8(3):221-9. doi: 10.1038/nmeth.1570.

PMID:
21358626
47.

Micropatterning of a nanoporous alumina membrane with poly(ethylene glycol) hydrogel to create cellular micropatterns on nanotopographic substrates.

Lee HJ, Kim DN, Park S, Lee Y, Koh WG.

Acta Biomater. 2011 Mar;7(3):1281-9. doi: 10.1016/j.actbio.2010.11.006. Epub 2010 Nov 5.

PMID:
21056702
48.

Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies.

Kim DN, Altschuler J, Strong C, McGill G, Bathe M.

Nucleic Acids Res. 2011 Jan;39(Database issue):D451-5. doi: 10.1093/nar/gkq1088. Epub 2010 Nov 3.

49.

Conformational dynamics of supramolecular protein assemblies.

Kim DN, Nguyen CT, Bathe M.

J Struct Biol. 2011 Feb;173(2):261-70. doi: 10.1016/j.jsb.2010.09.015. Epub 2010 Sep 18.

PMID:
20854912
50.

EaMEAD: Activation energy prediction of cytochrome P450 mediated metabolism with effective atomic descriptors.

Kim DN, Cho KH, Oh WS, Lee CJ, Lee SK, Jung J, No KT.

J Chem Inf Model. 2009 Jul;49(7):1643-54. doi: 10.1021/ci900011g.

PMID:
19545128

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