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Items: 1 to 50 of 103

1.

Adaptive group-regularized logistic elastic net regression.

Münch MM, Peeters CFW, Van Der Vaart AW, Van De Wiel MA.

Biostatistics. 2019 Dec 30. pii: kxz062. doi: 10.1093/biostatistics/kxz062. [Epub ahead of print]

PMID:
31886488
2.

Rational discovery of antimetastatic agents targeting the intrinsically disordered region of MBD2.

Kim MY, Na I, Kim JS, Son SH, Choi S, Lee SE, Kim JH, Jang K, Alterovitz G, Chen Y, van der Vaart A, Won HS, Uversky VN, Kim CG.

Sci Adv. 2019 Nov 20;5(11):eaav9810. doi: 10.1126/sciadv.aav9810. eCollection 2019 Nov.

3.

Calculation of Conformational Free Energies with the Focused Confinement Method.

van der Vaart A, Orndorff PB, Le Phan ST.

J Chem Theory Comput. 2019 Dec 10;15(12):6760-6768. doi: 10.1021/acs.jctc.9b00590. Epub 2019 Nov 4.

PMID:
31639308
4.

Orthogonal Halogen-Bonding-Driven 3D Supramolecular Assembly of Right-Handed Synthetic Helical Peptides.

Teng P, Gray GM, Zheng M, Singh S, Li X, Wojtas L, van der Vaart A, Cai J.

Angew Chem Int Ed Engl. 2019 Jun 3;58(23):7778-7782. doi: 10.1002/anie.201903259. Epub 2019 Apr 30.

PMID:
30957356
5.

Glycogen synthase kinase 3 beta regulates ethanol consumption and is a risk factor for alcohol dependence.

van der Vaart A, Meng X, Bowers MS, Batman AM, Aliev F, Farris SP, Hill JS, Green TA, Dick D; and the COGA Consortium, Wolstenholme JT, Miles MF.

Neuropsychopharmacology. 2018 Dec;43(13):2521-2531. doi: 10.1038/s41386-018-0202-x. Epub 2018 Sep 6.

6.

De Novo Left-Handed Synthetic Peptidomimetic Foldamers.

She F, Teng P, Peguero-Tejada A, Wang M, Ma N, Odom T, Zhou M, Gjonaj E, Wojtas L, van der Vaart A, Cai J.

Angew Chem Int Ed Engl. 2018 Jul 26;57(31):9916-9920. doi: 10.1002/anie.201805184. Epub 2018 Jul 3.

7.

A novel gene expression analytics-based approach to structure aided design of rexinoids for development as next-generation cancer therapeutics.

Hanish BJ, Hackney Price JF, Kaneko I, Ma N, van der Vaart A, Wagner CE, Jurutka PW, Marshall PA.

Steroids. 2018 Jul;135:36-49. doi: 10.1016/j.steroids.2018.04.009. Epub 2018 Apr 26.

8.

Hydrogen-Bonding-Driven 3D Supramolecular Assembly of Peptidomimetic Zipper.

Teng P, Niu Z, She F, Zhou M, Sang P, Gray GM, Verma G, Wojtas L, van der Vaart A, Ma S, Cai J.

J Am Chem Soc. 2018 May 2;140(17):5661-5665. doi: 10.1021/jacs.7b11997. Epub 2018 Apr 3.

PMID:
29590526
9.

Phosphorylation induced cochaperone unfolding promotes kinase recruitment and client class-specific Hsp90 phosphorylation.

Bachman AB, Keramisanou D, Xu W, Beebe K, Moses MA, Vasantha Kumar MV, Gray G, Noor RE, van der Vaart A, Neckers L, Gelis I.

Nat Commun. 2018 Jan 17;9(1):265. doi: 10.1038/s41467-017-02711-w.

10.

One-Bead-Two-Compound Thioether Bridged Macrocyclic γ-AApeptide Screening Library against EphA2.

Shi Y, Challa S, Sang P, She F, Li C, Gray GM, Nimmagadda A, Teng P, Odom T, Wang Y, van der Vaart A, Li Q, Cai J.

J Med Chem. 2017 Nov 22;60(22):9290-9298. doi: 10.1021/acs.jmedchem.7b01280. Epub 2017 Nov 14.

11.

HIGHER ORDER ESTIMATING EQUATIONS FOR HIGH-DIMENSIONAL MODELS.

Robins J, Li L, Mukherjee R, Tchetgen ET, van der Vaart A.

Ann Stat. 2017 Oct;45(5):1951-1987. doi: 10.1214/16-AOS1515. Epub 2017 Oct 31.

12.

Free Energy Coupling between DNA Bending and Base Flipping.

Ma N, van der Vaart A.

J Chem Inf Model. 2017 Aug 28;57(8):2020-2026. doi: 10.1021/acs.jcim.7b00215. Epub 2017 Jul 20.

PMID:
28696686
13.

[KCl] Dependence of B-DNA Groove Bending Anisotropy.

Ma N, van der Vaart A.

J Phys Chem B. 2017 Jun 1;121(21):5322-5330. doi: 10.1021/acs.jpcb.7b01957. Epub 2017 May 17.

PMID:
28481093
14.

Right-Handed Helical Foldamers Consisting of De Novo d-AApeptides.

Teng P, Ma N, Cerrato DC, She F, Odom T, Wang X, Ming LJ, van der Vaart A, Wojtas L, Xu H, Cai J.

J Am Chem Soc. 2017 May 31;139(21):7363-7369. doi: 10.1021/jacs.7b03007. Epub 2017 May 16.

15.

Gene Network Reconstruction using Global-Local Shrinkage Priors.

Leday GG, de Gunst MC, Kpogbezan GB, van der Vaart AW, van Wieringen WN, van de Wiel MA.

Ann Appl Stat. 2017 Mar;11(1):41-68.

16.

An empirical Bayes approach to network recovery using external knowledge.

Kpogbezan GB, van der Vaart AW, van Wieringen WN, Leday GGR, van de Wiel MA.

Biom J. 2017 Sep;59(5):932-947. doi: 10.1002/bimj.201600090. Epub 2017 Apr 10.

17.

A powerful and efficient two-stage method for detecting gene-to-gene interactions in GWAS.

Pecanka J, Jonker MA; International Parkinson’S Disease Genomics Consortium (IPDGC), Bochdanovits Z, Van Der Vaart AW.

Biostatistics. 2017 Jul 1;18(3):477-494. doi: 10.1093/biostatistics/kxw060.

PMID:
28334077
18.

Molecular dynamics simulations and molecular flooding studies of the retinoid X-receptor ligand binding domain.

Gray GM, Ma N, Wagner CE, van der Vaart A.

J Mol Model. 2017 Mar;23(3):98. doi: 10.1007/s00894-017-3260-9. Epub 2017 Mar 1.

PMID:
28251414
19.

Asymptotic Normality of Quadratic Estimators.

Robins J, Li L, Tchetgen E, van der Vaart A.

Stoch Process Their Appl. 2016 Dec;126(12):3733-3759. doi: 10.1016/j.spa.2016.04.005.

20.

Biasing Simulations of DNA Base Pair Parameters with Application to Propellor Twisting in AT/AT, AA/TT, and AC/GT Steps and Their Uracil Analogs.

Peguero-Tejada A, van der Vaart A.

J Chem Inf Model. 2017 Jan 23;57(1):85-92. doi: 10.1021/acs.jcim.6b00660. Epub 2016 Dec 23.

PMID:
27976883
21.

Secondary Structure Adopted by the Gly-Gly-X Repetitive Regions of Dragline Spider Silk.

Gray GM, van der Vaart A, Guo C, Jones J, Onofrei D, Cherry BR, Lewis RV, Yarger JL, Holland GP.

Int J Mol Sci. 2016 Dec 2;17(12). pii: E2023.

22.

The allostatic impact of chronic ethanol on gene expression: A genetic analysis of chronic intermittent ethanol treatment in the BXD cohort.

van der Vaart AD, Wolstenholme JT, Smith ML, Harris GM, Lopez MF, Wolen AR, Becker HC, Williams RW, Miles MF.

Alcohol. 2017 Feb;58:93-106. doi: 10.1016/j.alcohol.2016.07.010. Epub 2016 Nov 1.

23.

Switching on regeneration.

van der Vaart A, van den Heuvel S.

Stem Cell Investig. 2016 Aug 19;3:41. doi: 10.21037/sci.2016.08.05. eCollection 2016. No abstract available.

24.

Modeling, Synthesis, and Biological Evaluation of Potential Retinoid X Receptor (RXR)-Selective Agonists: Analogues of 4-[1-(3,5,5,8,8-Pentamethyl-5,6,7,8-tetrahydro-2-naphthyl)ethynyl]benzoic Acid (Bexarotene) and 6-(Ethyl(5,5,8,8-tetrahydronaphthalen-2-yl)amino)nicotinic Acid (NEt-TMN).

Heck MC, Wagner CE, Shahani PH, MacNeill M, Grozic A, Darwaiz T, Shimabuku M, Deans DG, Robinson NM, Salama SH, Ziller JW, Ma N, van der Vaart A, Marshall PA, Jurutka PW.

J Med Chem. 2016 Oct 13;59(19):8924-8940. Epub 2016 Sep 19.

PMID:
27592633
25.

Anisotropy of B-DNA Groove Bending.

Ma N, van der Vaart A.

J Am Chem Soc. 2016 Aug 10;138(31):9951-8. doi: 10.1021/jacs.6b05136. Epub 2016 Aug 1.

PMID:
27435602
26.

Computer Simulations of the Retinoid X Receptor: Conformational Dynamics and Allosteric Networks.

van der Vaart A, Lorkowski A, Ma N, Gray GM.

Curr Top Med Chem. 2017;17(6):731-741. Review.

PMID:
27320334
27.

Balancing Accuracy and Cost of Confinement Simulations by Interpolation and Extrapolation of Confinement Energies.

Villemot F, Capelli R, Colombo G, van der Vaart A.

J Chem Theory Comput. 2016 Jun 14;12(6):2779-89. doi: 10.1021/acs.jctc.5b01183. Epub 2016 May 6.

28.

Assessment of Mutational Effects on Peptide Stability through Confinement Simulations.

Capelli R, Villemot F, Moroni E, Tiana G, van der Vaart A, Colombo G.

J Phys Chem Lett. 2016 Jan 7;7(1):126-30. doi: 10.1021/acs.jpclett.5b02221. Epub 2015 Dec 22.

PMID:
26678679
29.

DLK-1/p38 MAP Kinase Signaling Controls Cilium Length by Regulating RAB-5 Mediated Endocytosis in Caenorhabditis elegans.

van der Vaart A, Rademakers S, Jansen G.

PLoS Genet. 2015 Dec 11;11(12):e1005733. doi: 10.1371/journal.pgen.1005733. eCollection 2015 Dec.

30.

Molecular Dynamics Simulations of 5-Hydroxycytosine Damaged DNA.

Karolak A, van der Vaart A.

J Phys Chem B. 2016 Jan 14;120(1):42-8. doi: 10.1021/acs.jpcb.5b09250. Epub 2015 Dec 22.

PMID:
26654566
31.

Integrating mRNA and miRNA Weighted Gene Co-Expression Networks with eQTLs in the Nucleus Accumbens of Subjects with Alcohol Dependence.

Mamdani M, Williamson V, McMichael GO, Blevins T, Aliev F, Adkins A, Hack L, Bigdeli T, van der Vaart AD, Web BT, Bacanu SA, Kalsi G; COGA Consortium, Kendler KS, Miles MF, Dick D, Riley BP, Dumur C, Vladimirov VI.

PLoS One. 2015 Sep 18;10(9):e0137671. doi: 10.1371/journal.pone.0137671. eCollection 2015.

32.

Transcriptomic Heterogeneity in Cancer as a Consequence of Dysregulation of the Gene-Gene Interaction Network.

van Wieringen WN, van der Vaart AW.

Bull Math Biol. 2015 Sep;77(9):1768-86. doi: 10.1007/s11538-015-0103-7. Epub 2015 Sep 16.

33.

Importance of β2-β3 Loop Motion for the Increased Binding and Decreased Selectivity of the ΔLL Mutant of the Human Papillomavirus Type 6 E2 Protein.

Gray GM, van der Vaart A.

Biochemistry. 2015 Aug 11;54(31):4918-26. doi: 10.1021/acs.biochem.5b00433. Epub 2015 Jul 30.

PMID:
26169609
34.

Analysis of differential secondary effects of novel rexinoids: select rexinoid X receptor ligands demonstrate differentiated side effect profiles.

Marshall PA, Jurutka PW, Wagner CE, van der Vaart A, Kaneko I, Chavez PI, Ma N, Bhogal JS, Shahani P, Swierski JC, MacNeill M.

Pharmacol Res Perspect. 2015 Mar;3(2):e00122. doi: 10.1002/prp2.122. Epub 2015 Mar 16.

35.

BII stability and base step flexibility of N6-adenine methylated GATC motifs.

Karolak A, van der Vaart A.

Biophys Chem. 2015 Aug-Sep;203-204:22-7. doi: 10.1016/j.bpc.2015.05.001. Epub 2015 May 12.

PMID:
26004863
36.

Autophagy competes for a common phosphatidylethanolamine pool with major cellular PE-consuming pathways in Saccharomyces cerevisiae.

Wilson-Zbinden C, dos Santos AX, Stoffel-Studer I, van der Vaart A, Hofmann K, Reggiori F, Riezman H, Kraft C, Peter M.

Genetics. 2015 Feb;199(2):475-85. doi: 10.1534/genetics.114.169797. Epub 2014 Dec 17.

37.

Enhanced sampling simulations of DNA step parameters.

Karolak A, van der Vaart A.

J Comput Chem. 2014 Dec 15;35(32):2297-304. doi: 10.1002/jcc.23751. Epub 2014 Oct 10.

PMID:
25303338
38.

Coupled binding-bending-folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations.

van der Vaart A.

Biochim Biophys Acta. 2015 May;1850(5):1091-1098. doi: 10.1016/j.bbagen.2014.08.009. Epub 2014 Aug 23. Review.

PMID:
25161164
39.
40.

RevErbα preferentially deforms DNA by induced fit.

Chung YH, van der Vaart A.

Chembiochem. 2014 Mar 21;15(5):643-6.

PMID:
24677802
41.

New statistical approaches to semiparametric regression with application to air pollution research.

Robins JM, Zhang P, Ayyagari R, Logan R, Tchetgen ET, Li L, Lumley T, van der Vaart A; HEI Health Review Committee.

Res Rep Health Eff Inst. 2013 Nov;(175):3-129. No abstract available.

PMID:
24400588
42.

Photophysical and dynamical properties of doubly linked Cy3-DNA constructs.

Stennett EM, Ma N, van der Vaart A, Levitus M.

J Phys Chem B. 2014 Jan 9;118(1):152-63. doi: 10.1021/jp410976p. Epub 2013 Dec 20.

PMID:
24328104
43.

Modeling, synthesis, and biological evaluation of potential retinoid X receptor (RXR) selective agonists: novel analogues of 4-[1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydro-2-naphthyl)ethynyl]benzoic acid (bexarotene) and (E)-3-(3-(1,2,3,4-tetrahydro-1,1,4,4,6-pentamethylnaphthalen-7-yl)-4-hydroxyphenyl)acrylic acid (CD3254).

Jurutka PW, Kaneko I, Yang J, Bhogal JS, Swierski JC, Tabacaru CR, Montano LA, Huynh CC, Jama RA, Mahelona RD, Sarnowski JT, Marcus LM, Quezada A, Lemming B, Tedesco MA, Fischer AJ, Mohamed SA, Ziller JW, Ma N, Gray GM, van der Vaart A, Marshall PA, Wagner CE.

J Med Chem. 2013 Nov 14;56(21):8432-54. doi: 10.1021/jm4008517. Epub 2013 Nov 1.

44.

Editorial introduction.

Gugushvili S, Klaassen CA, van der Vaart AW.

Math Biosci. 2013 Dec;246(2):281-2. doi: 10.1016/j.mbs.2013.07.015. Epub 2013 Jul 27. No abstract available.

PMID:
23900060
45.

DNA binding and bending by Sac7d is stepwise.

Spiriti J, van der Vaart A.

Chembiochem. 2013 Aug 19;14(12):1434-7. doi: 10.1002/cbic.201300264. Epub 2013 Jul 12.

PMID:
23853062
46.

Accurate prediction of a minimal region around a genetic association signal that contains the causal variant.

Bochdanovits Z, Simón-Sánchez J, Jonker M, Hoogendijk WJ, van der Vaart A, Heutink P.

Eur J Hum Genet. 2014 Feb;22(2):238-42. doi: 10.1038/ejhg.2013.115. Epub 2013 Jun 5.

47.

Free energy simulation of helical transitions.

Ma N, Chung YH, van der Vaart A.

J Comput Chem. 2013 Mar 30;34(8):640-5. doi: 10.1002/jcc.23174. Epub 2012 Nov 5.

PMID:
23125002
48.

DNA Bending through Roll Angles Is Independent of Adjacent Base Pairs.

Spiriti J, van der Vaart A.

J Phys Chem Lett. 2012 Oct 18;3(20):3029-33. doi: 10.1021/jz301227y. Epub 2012 Oct 4.

PMID:
26292244
49.

Understanding phosphatidylinositol-3-phosphate dynamics during autophagosome biogenesis.

Cebollero E, van der Vaart A, Reggiori F.

Autophagy. 2012 Dec;8(12):1868-70. doi: 10.4161/auto.22162. Epub 2012 Sep 19.

50.

Bayesian analysis of RNA sequencing data by estimating multiple shrinkage priors.

Van De Wiel MA, Leday GG, Pardo L, Rue H, Van Der Vaart AW, Van Wieringen WN.

Biostatistics. 2013 Jan;14(1):113-28. doi: 10.1093/biostatistics/kxs031. Epub 2012 Sep 17.

PMID:
22988280

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