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Arjan van der Vaart - Publications

Affiliations: 
2006-2009 Chemistry Arizona State University, Tempe, AZ, United States 
 2009- Chemistry University of South Florida, Tampa, FL, United States 
Area:
General Biophysics, Biochemistry
Website:
http://chemistry.usf.edu/faculty/vandervaart/
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29/104 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
2023 Orndorff PB, van der Vaart A. Register-Shifted Structures in Base-Flipped Uracil-Damaged DNA. Journal of the American Chemical Society. 145: 16350-16354. PMID 37478299 DOI: 10.1021/jacs.3c05890  0.314
2023 Orndorff PB, van der Vaart A. Systematic assessment of the flexibility of uracil damaged DNA. Journal of Biomolecular Structure & Dynamics. 1-11. PMID 37261803 DOI: 10.1080/07391102.2023.2217683  0.337
2023 Orndorff PB, Poddar S, Owens AM, Kumari N, Ugaz BT, Amin S, Van Horn WD, van der Vaart A, Levitus M. Uracil-DNA glycosylase efficiency is modulated by substrate rigidity. Scientific Reports. 13: 3915. PMID 36890276 DOI: 10.1038/s41598-023-30620-0  0.324
2017 Ma N, van der Vaart A. Free Energy Coupling between DNA Bending and Base Flipping. Journal of Chemical Information and Modeling. 57: 2020-2026. PMID 28696686 DOI: 10.1021/acs.jcim.7b00215  0.419
2017 Ma N, van der Vaart A. [KCl] Dependence of B-DNA Groove Bending Anisotropy. The Journal of Physical Chemistry. B. 121: 5322-5330. PMID 28481093 DOI: 10.1021/acs.jpcb.7b01957  0.366
2017 Peguero-Tejada A, van der Vaart A. 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. Journal of Chemical Information and Modeling. 57: 85-92. PMID 27976883 DOI: 10.1021/acs.jcim.6b00660  0.344
2016 Ma N, van der Vaart A. Anisotropy of B-DNA Groove Bending. Journal of the American Chemical Society. 138: 9951-8. PMID 27435602 DOI: 10.1021/jacs.6b05136  0.421
2016 Karolak A, van der Vaart A. Molecular Dynamics Simulations of 5-Hydroxycytosine Damaged DNA. The Journal of Physical Chemistry. B. 120: 42-8. PMID 26654566 DOI: 10.1021/acs.jpcb.5b09250  0.354
2015 Gray GM, van der Vaart A. 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. Biochemistry. 54: 4918-26. PMID 26169609 DOI: 10.1021/acs.biochem.5b00433  0.333
2015 van der Vaart A. Coupled binding-bending-folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations. Biochimica Et Biophysica Acta. 1850: 1091-8. PMID 25161164 DOI: 10.1016/j.bbagen.2014.08.009  0.44
2014 Karolak A, van der Vaart A. Enhanced sampling simulations of DNA step parameters. Journal of Computational Chemistry. 35: 2297-304. PMID 25303338 DOI: 10.1002/jcc.23751  0.359
2014 Chung YH, van der Vaart A. RevErbα preferentially deforms DNA by induced fit. Chembiochem : a European Journal of Chemical Biology. 15: 643-6. PMID 24677802 DOI: 10.1002/cbic.201300557  0.395
2014 Stennett EM, Ma N, van der Vaart A, Levitus M. Photophysical and dynamical properties of doubly linked Cy3-DNA constructs. The Journal of Physical Chemistry. B. 118: 152-63. PMID 24328104 DOI: 10.1016/J.Bpj.2013.11.448  0.355
2013 Spiriti J, van der Vaart A. DNA binding and bending by Sac7d is stepwise. Chembiochem : a European Journal of Chemical Biology. 14: 1434-7. PMID 23853062 DOI: 10.1002/Cbic.201300264  0.712
2012 Spiriti J, Kamberaj H, de Graff AM, Thorpe MF, van der Vaart A. DNA Bending through Large Angles Is Aided by Ionic Screening. Journal of Chemical Theory and Computation. 8: 2145-56. PMID 26593845 DOI: 10.1021/Ct300177R  0.717
2012 Spiriti J, van der Vaart A. DNA Bending through Roll Angles Is Independent of Adjacent Base Pairs. The Journal of Physical Chemistry Letters. 3: 3029-33. PMID 26292244 DOI: 10.1021/Jz301227Y  0.719
2012 Karolak A, van der Vaart A. Importance of local interactions for the stability of inhibitory helix 1 in apo Ets-1. Biophysical Chemistry. 165: 74-8. PMID 22494801 DOI: 10.1016/j.bpc.2012.03.007  0.301
2012 Barr D, van der Vaart A. The natural DNA bending angle in the lac repressor headpiece-O1 operator complex is determined by protein-DNA contacts and water release. Physical Chemistry Chemical Physics : Pccp. 14: 2070-7. PMID 22234444 DOI: 10.1039/C2Cp23780F  0.611
2011 Barr D, Oashi T, Burkhard K, Lucius S, Samadani R, Zhang J, Shapiro P, MacKerell AD, van der Vaart A. Importance of domain closure for the autoactivation of ERK2. Biochemistry. 50: 8038-48. PMID 21842857 DOI: 10.1021/Bi200503A  0.518
2011 Spiriti J, Binder JK, Levitus M, van der Vaart A. Cy3-DNA stacking interactions strongly depend on the identity of the terminal basepair. Biophysical Journal. 100: 1049-57. PMID 21320450 DOI: 10.1016/J.Bpj.2011.01.014  0.722
2010 Spiriti J, van der Vaart A. Mechanism of the calcium-induced trans-cis isomerization of a non-prolyl peptide bond in Clostridium histolyticum collagenase. Biochemistry. 49: 5314-20. PMID 20499930 DOI: 10.1021/Bi1007047  0.668
2009 Maragakis P, van der Vaart A, Karplus M. Gaussian-mixture umbrella sampling. The Journal of Physical Chemistry. B. 113: 4664-73. PMID 19284746 DOI: 10.1021/Jp808381S  0.397
2009 Kamberaj H, van der Vaart A. Correlated motions and interactions at the onset of the DNA-induced partial unfolding of Ets-1. Biophysical Journal. 96: 1307-17. PMID 19217849 DOI: 10.1016/j.bpj.2008.11.019  0.325
2008 Spiriti J, Bogani F, van der Vaart A, Ghirlanda G. Modulation of protein stability by O-glycosylation in a designed Gc-MAF analog. Biophysical Chemistry. 134: 157-67. PMID 18329161 DOI: 10.1016/J.Bpc.2008.02.005  0.686
2007 van der Vaart A, Karplus M. Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations. The Journal of Chemical Physics. 126: 164106. PMID 17477588 DOI: 10.1063/1.2719697  0.469
2005 Monard G, Bernal-Uruchurtu MI, van der Vaart A, Merz KM, Ruiz-López MF. Simulation of liquid water using semiempirical Hamiltonians and the divide and conquer approach. The Journal of Physical Chemistry. A. 109: 3425-32. PMID 16833679 DOI: 10.1021/Jp0459099  0.6
2005 van der Vaart A, Karplus M. Simulation of conformational transitions by the restricted perturbation-targeted molecular dynamics method. The Journal of Chemical Physics. 122: 114903. PMID 15836253 DOI: 10.1063/1.1861885  0.446
2005 Karplus M, Gao YQ, Ma J, van der Vaart A, Yang W. Protein structural transitions and their functional role. Philosophical Transactions. Series a, Mathematical, Physical, and Engineering Sciences. 363: 331-55; discussion 3. PMID 15664887 DOI: 10.1098/Rsta.2004.1496  0.494
2004 van der Vaart A, Ma J, Karplus M. The unfolding action of GroEL on a protein substrate. Biophysical Journal. 87: 562-73. PMID 15240489 DOI: 10.1529/Biophysj.103.037333  0.452
Low-probability matches (unlikely to be authored by this person)
2009 Kamberaj H, van der Vaart A. Extracting the causality of correlated motions from molecular dynamics simulations. Biophysical Journal. 97: 1747-55. PMID 19751680 DOI: 10.1016/j.bpj.2009.07.019  0.296
2016 Villemot F, Capelli R, Colombo G, van der Vaart A. Balancing Accuracy and Cost of Confinement Simulations by Interpolation and Extrapolation of Confinement Energies. Journal of Chemical Theory and Computation. 12: 2779-89. PMID 27120438 DOI: 10.1021/acs.jctc.5b01183  0.288
2019 van der Vaart A, Orndorff PB, Le Phan ST. Calculation of Conformational Free Energies with the Focused Confinement Method. Journal of Chemical Theory and Computation. PMID 31639308 DOI: 10.1021/acs.jctc.9b00590  0.287
2015 Karolak A, van der Vaart A. BII stability and base step flexibility of N6-adenine methylated GATC motifs. Biophysical Chemistry. 203: 22-7. PMID 26004863 DOI: 10.1016/j.bpc.2015.05.001  0.279
2020 Orndorff PB, Le Phan ST, Li KH, van der Vaart A. Conformational free energy differences of large solvated systems with the focused confinement method. Journal of Chemical Theory and Computation. PMID 32559097 DOI: 10.1021/acs.jctc.0c00403  0.278
2017 van der Vaart A, Lorkowski A, Ma N, Gray GM. Computer Simulations of the Retinoid X Receptor: Conformational Dynamics and Allosteric Networks. Current Topics in Medicinal Chemistry. 17: 731-741. PMID 27320334  0.272
2013 Ma N, Chung YH, van der Vaart A. Free energy simulation of helical transitions. Journal of Computational Chemistry. 34: 640-5. PMID 23125002 DOI: 10.1002/jcc.23174  0.27
2016 Capelli R, Villemot F, Moroni E, Tiana G, van der Vaart A, Colombo G. Assessment of Mutational Effects on Peptide Stability through Confinement Simulations. The Journal of Physical Chemistry Letters. 7: 126-30. PMID 26678679 DOI: 10.1021/acs.jpclett.5b02221  0.269
2006 van der Vaart A. Simulation of conformational transitions Theoretical Chemistry Accounts. 116: 183-193. DOI: 10.1007/s00214-005-0004-1  0.236
2005 Raha K, van der Vaart AJ, Riley KE, Peters MB, Westerhoff LM, Kim H, Merz KM. Pairwise decomposition of residue interaction energies using semiempirical quantum mechanical methods in studies of protein-ligand interaction. Journal of the American Chemical Society. 127: 6583-94. PMID 15869279 DOI: 10.1021/Ja042666P  0.233
2007 Ababou A, van der Vaart A, Gogonea V, Merz KM. Interaction energy decomposition in protein-protein association: a quantum mechanical study of barnase-barstar complex. Biophysical Chemistry. 125: 221-36. PMID 16962699 DOI: 10.1016/J.Bpc.2006.08.003  0.227
2017 Gray GM, Ma N, Wagner CE, van der Vaart A. Molecular dynamics simulations and molecular flooding studies of the retinoid X-receptor ligand binding domain. Journal of Molecular Modeling. 23: 98. PMID 28251414 DOI: 10.1007/s00894-017-3260-9  0.225
2007 Ahmed EA, van der Vaart A, Barten A, Kal HB, Chen J, Lou Z, Minter-Dykhouse K, Bartkova J, Bartek J, de Boer P, de Rooij DG. Differences in DNA double strand breaks repair in male germ cell types: Lessons learned from a differential expression of Mdc1 and 53BP1 Dna Repair. 6: 1243-1254. PMID 17376750 DOI: 10.1016/J.Dnarep.2007.02.011  0.201
2018 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. De novo Left-Handed Synthetic Peptidomimetic Foldamers. Angewandte Chemie (International Ed. in English). PMID 29889349 DOI: 10.1002/Anie.201805184  0.196
2007 Kamberaj H, van der Vaart A. Multiple scaling replica exchange for the conformational sampling of biomolecules in explicit water. The Journal of Chemical Physics. 127: 234102. PMID 18154370 DOI: 10.1063/1.2806930  0.184
2009 Kamberaj H, van der Vaart A. An optimized replica exchange molecular dynamics method. The Journal of Chemical Physics. 130: 074906. PMID 19239315 DOI: 10.1063/1.3077857  0.178
2016 Gray GM, van der Vaart A, Guo C, Jones J, Onofrei D, Cherry BR, Lewis RV, Yarger JL, Holland GP. Secondary Structure Adopted by the Gly-Gly-X Repetitive Regions of Dragline Spider Silk. International Journal of Molecular Sciences. 17. PMID 27918448 DOI: 10.3390/Ijms17122023  0.174
2013 Van De Wiel MA, Leday GG, Pardo L, Rue H, Van Der Vaart AW, Van Wieringen WN. Bayesian analysis of RNA sequencing data by estimating multiple shrinkage priors. Biostatistics (Oxford, England). 14: 113-28. PMID 22988280 DOI: 10.1093/biostatistics/kxs031  0.174
2017 Teng P, Ma N, Cerrato DC, She F, Odom T, Wang X, Ming LJ, van der Vaart A, Wojtas L, Xu H, Cai J. Right-Handed Helical Foldamers Consisting of De Novo d-AApeptides. Journal of the American Chemical Society. 139: 7363-7369. PMID 28480699 DOI: 10.1021/Jacs.7B03007  0.162
2019 Teng P, Gray GM, Zheng M, Singh S, Li X, Wojtas L, van der Vaart A, Cai J. Orthogonal Halogen Bonding Driven 3D Supramolecular Assembly of Right-Handed Synthetic Helical Peptides. Angewandte Chemie (International Ed. in English). PMID 30957356 DOI: 10.1002/Anie.201903259  0.157
2022 Gray GM, Thiessen B, van der Vaart A. Secondary structure of peptides mimicking the Gly-rich regions of major ampullate spidroin protein 1 and 2. Biophysical Chemistry. 284: 106783. PMID 35220089 DOI: 10.1016/j.bpc.2022.106783  0.156
2012 Cebollero E, van der Vaart A, Zhao M, Rieter E, Klionsky DJ, Helms JB, Reggiori F. Phosphatidylinositol-3-phosphate clearance plays a key role in autophagosome completion. Current Biology : Cb. 22: 1545-53. PMID 22771041 DOI: 10.1016/J.Cub.2012.06.029  0.146
2018 Teng P, Niu Z, She F, Zhou M, Sang P, Gray GM, Verma G, Wojtas L, van der Vaart A, Ma S, Cai J. Hydrogen-Bonding-Driven 3D Supramolecular Assembly of Peptidomimetic Zipper. Journal of the American Chemical Society. PMID 29590526 DOI: 10.1021/Jacs.7B11997  0.144
2012 Cebollero E, van der Vaart A, Reggiori F. Understanding phosphatidylinositol-3-phosphate dynamics during autophagosome biogenesis. Autophagy. 8: 1868-70. PMID 22992453 DOI: 10.4161/auto.22162  0.144
2015 van der Vaart A, Rademakers S, Jansen G. DLK-1/p38 MAP Kinase Signaling Controls Cilium Length by Regulating RAB-5 Mediated Endocytosis in Caenorhabditis elegans. Plos Genetics. 11: e1005733. PMID 26657059 DOI: 10.1371/journal.pgen.1005733  0.119
2017 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. One-Bead-Two-Compound Thioether Bridged Macrocyclic γ-AApeptide Screening Library against EphA2. Journal of Medicinal Chemistry. 60: 9290-9298. PMID 29111705 DOI: 10.1021/Acs.Jmedchem.7B01280  0.117
2011 Hindriks R, Bijma F, van Dijk BW, Stam CJ, van der Werf YY, van Someren EJ, de Munck JC, van der Vaart AW. Data-driven modeling of phase interactions between spontaneous MEG oscillations. Human Brain Mapping. 32: 1161-78. PMID 21225630 DOI: 10.1002/hbm.21099  0.11
2004 Wang B, Brothers EN, van der Vaart A, Merz KM. Fast semiempirical calculations for nuclear magnetic resonance chemical shifts: a divide-and-conquer approach. The Journal of Chemical Physics. 120: 11392-400. PMID 15268173 DOI: 10.1063/1.1752877  0.108
1987 van der Vaart AJ, Savelberg HH, de Groot G, Hollander AP, Toussaint HM, van Ingen Schenau GJ. An estimation of drag in front crawl swimming. Journal of Biomechanics. 20: 543-6. PMID 3611128  0.103
2019 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. Rational discovery of antimetastatic agents targeting the intrinsically disordered region of MBD2. Science Advances. 5: eaav9810. PMID 31799386 DOI: 10.1126/Sciadv.Aav9810  0.102
2018 Hanish BJ, Hackney Price JF, Kaneko I, Ma N, van der Vaart A, Wagner CE, Jurutka PW, Marshall PA. A novel gene expression analytics-based approach to structure aided design of rexinoids for development as next-generation cancer therapeutics. Steroids. PMID 29704526 DOI: 10.1016/j.steroids.2018.04.009  0.101
2011 van Wieringen WN, van der Vaart AW. Statistical analysis of the cancer cell's molecular entropy using high-throughput data. Bioinformatics (Oxford, England). 27: 556-63. PMID 21172912 DOI: 10.1093/bioinformatics/btq704  0.098
2012 Furmick JK, Kaneko I, Walsh AN, Yang J, Bhogal JS, Gray GM, Baso JC, Browder DO, Prentice JL, Montano LA, Huynh CC, Marcus LM, Tsosie DG, Kwon JS, Quezada A, ... ... van der Vaart A, et al. Modeling, synthesis and biological evaluation of potential retinoid X receptor-selective agonists: novel halogenated analogues of 4-[1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydro-2-naphthyl)ethynyl]benzoic acid (bexarotene). Chemmedchem. 7: 1551-66. PMID 22927238 DOI: 10.1002/cmdc.201200319  0.098
2018 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. Phosphorylation induced cochaperone unfolding promotes kinase recruitment and client class-specific Hsp90 phosphorylation. Nature Communications. 9: 265. PMID 29343704 DOI: 10.1038/s41467-017-02711-w  0.097
2007 Jonker MA, van der Vaart AW. Correcting missing-data bias in historical demography. Population Studies. 61: 99-113. PMID 17365876 DOI: 10.1080/00324720601048228  0.095
2011 Li MD, van der Vaart AD. MicroRNAs in addiction: adaptation's middlemen? Molecular Psychiatry. 16: 1159-68. PMID 21606928 DOI: 10.1038/mp.2011.58  0.094
2017 Leday GG, de Gunst MC, Kpogbezan GB, van der Vaart AW, van Wieringen WN, van de Wiel MA. Gene Network Reconstruction using Global-Local Shrinkage Priors. The Annals of Applied Statistics. 11: 41-68. PMID 28408966  0.093
2015 Marshall PA, Jurutka PW, Wagner CE, van der Vaart A, Kaneko I, Chavez PI, Ma N, Bhogal JS, Shahani P, Swierski JC, MacNeill M. Analysis of differential secondary effects of novel rexinoids: select rexinoid X receptor ligands demonstrate differentiated side effect profiles. Pharmacology Research & Perspectives. 3: e00122. PMID 26038698 DOI: 10.1002/prp2.122  0.093
2008 van der Vaart A, Mari M, Reggiori F. A picky eater: exploring the mechanisms of selective autophagy in human pathologies. Traffic (Copenhagen, Denmark). 9: 281-9. PMID 17988219 DOI: 10.1111/j.1600-0854.2007.00674.x  0.093
2015 Wilson-Zbinden C, dos Santos AX, Stoffel-Studer I, van der Vaart A, Hofmann K, Reggiori F, Riezman H, Kraft C, Peter M. Autophagy competes for a common phosphatidylethanolamine pool with major cellular PE-consuming pathways in Saccharomyces cerevisiae. Genetics. 199: 475-85. PMID 25519895 DOI: 10.1534/Genetics.114.169797  0.092
2011 Hindriks R, Jansen R, Bijma F, Mansvelder HD, de Gunst MC, van der Vaart AW. Unbiased estimation of Langevin dynamics from time series with application to hippocampal field potentials in vitro. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 84: 021133. PMID 21928975 DOI: 10.1103/PhysRevE.84.021133  0.086
2001 Gogonea V, Suárez D, Van der Vaart A, Merz J. New developments in applying quantum mechanics to proteins Current Opinion in Structural Biology. 11: 217-223. PMID 11297931 DOI: 10.1016/S0959-440X(00)00193-7  0.082
2009 Wagner CE, Jurutka PW, Marshall PA, Groy TL, van der Vaart A, Ziller JW, Furmick JK, Graeber ME, Matro E, Miguel BV, Tran IT, Kwon J, Tedeschi JN, Moosavi S, Danishyar A, et al. 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). Journal of Medicinal Chemistry. 52: 5950-66. PMID 19791803 DOI: 10.1021/Jm900496B  0.081
2006 van den Berg SM, Setiawan A, Bartels M, Polderman TJ, van der Vaart AW, Boomsma DI. Individual differences in puberty onset in girls: Bayesian estimation of heritabilities and genetic correlations. Behavior Genetics. 36: 261-70. PMID 16408250 DOI: 10.1007/s10519-005-9022-y  0.08
2003 Mesina CT, Boellaard R, Jongbloed G, van der Vaart AW, Lammertsma AA. Experimental evaluation of iterative reconstruction versus filtered back projection for 3D [15O]water PET activation studies using statistical parametric mapping analysis. Neuroimage. 19: 1170-9. PMID 12880842 DOI: 10.1016/S1053-8119(03)00075-2  0.077
2010 van der Vaart A, Griffith J, Reggiori F. Exit from the Golgi is required for the expansion of the autophagosomal phagophore in yeast Saccharomyces cerevisiae. Molecular Biology of the Cell. 21: 2270-84. PMID 20444982 DOI: 10.1091/mbc.E09-04-0345  0.077
2008 Bochdanovits Z, Heutink P, van der Vaart A. Empirical assessment of the validity of the 'fundamental theorem of the HapMap' in the light of 'cryptic' tagging of multiple susceptibility loci. European Journal of Human Genetics : Ejhg. 16: 525-9. PMID 18197195 DOI: 10.1038/sj.ejhg.5201984  0.077
2017 Kpogbezan GB, van der Vaart AW, van Wieringen WN, Leday GG, van de Wiel MA. An empirical Bayes approach to network recovery using external knowledge. Biometrical Journal. Biometrische Zeitschrift. PMID 28393396 DOI: 10.1002/bimj.201600090  0.075
2009 van der Vaart A, Wellner JA. A note on bounds for VC dimensions. Institute of Mathematical Statistics Collections. 5: 103-107. PMID 20729995 DOI: 10.1214/09-IMSCOLL508  0.072
2011 Hindriks R, Bijma F, van Dijk BW, van der Werf YD, van Someren EJ, van der Vaart AW. Dynamics underlying spontaneous human alpha oscillations: a data-driven approach. Neuroimage. 57: 440-51. PMID 21558008 DOI: 10.1016/j.neuroimage.2011.04.043  0.072
2007 Jong K, Marchiori E, van der Vaart A, Chin SF, Carvalho B, Tijssen M, Eijk PP, van den Ijssel P, Grabsch H, Quirke P, Oudejans JJ, Meijer GA, Caldas C, Ylstra B. Cross-platform array comparative genomic hybridization meta-analysis separates hematopoietic and mesenchymal from epithelial tumors. Oncogene. 26: 1499-506. PMID 16936777 DOI: 10.1038/Sj.Onc.1209919  0.07
2014 Bochdanovits Z, Simón-Sánchez J, Jonker M, Hoogendijk WJ, van der Vaart A, Heutink P. Accurate prediction of a minimal region around a genetic association signal that contains the causal variant. European Journal of Human Genetics : Ejhg. 22: 238-42. PMID 23736218 DOI: 10.1038/ejhg.2013.115  0.07
2016 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. 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). Journal of Medicinal Chemistry. 59: 8924-8940. PMID 27592633 DOI: 10.1021/Acs.Jmedchem.6B00812  0.069
2010 van der Vaart A, Reggiori F. The Golgi complex as a source for yeast autophagosomal membranes. Autophagy. 6: 800-1. PMID 20714226 DOI: 10.1091/mbc.E09-04-0345  0.068
2012 Yoon D, Kim YJ, Cui WY, Van Der Vaart A, Cho YS, Lee JY, Ma JZ, Payne TJ, Li MD, Park T. Large-scale genome-wide association study of Asian population reveals genetic factors in FRMD4A and other loci influencing smoking initiation and nicotine dependence Human Genetics. 131: 1009-1021. PMID 22006218 DOI: 10.1007/S00439-011-1102-X  0.068
2013 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, ... ... van der Vaart A, et al. 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). Journal of Medicinal Chemistry. 56: 8432-54. PMID 24180745 DOI: 10.1021/Jm4008517  0.064
2011 van der Vaart A, Wellner JA. A local maximal inequality under uniform entropy. Electronic Journal of Statistics. 5: 192-203. PMID 22423315 DOI: 10.1214/11-Ejs605  0.063
2015 van Wieringen WN, van der Vaart AW. Transcriptomic Heterogeneity in Cancer as a Consequence of Dysregulation of the Gene-Gene Interaction Network. Bulletin of Mathematical Biology. 77: 1768-86. PMID 26376888 DOI: 10.1007/s11538-015-0103-7  0.058
2003 Mesina CT, Boellaard R, van den Heuvel OA, Veltman DJ, Jongbloed G, van der Vaart AW, Lammertsma AA. Effects of attenuation correction and reconstruction method on PET activation studies. Neuroimage. 20: 898-908. PMID 14568460 DOI: 10.1016/S1053-8119(03)00379-3  0.056
2009 Robins J, Li L, Tchetgen E, van der Vaart AW. Quadratic semiparametric Von Mises calculus. Metrika. 69: 227-247. PMID 23087487 DOI: 10.1007/s00184-008-0214-3  0.05
2016 Robins J, Li L, Tchetgen E, van der Vaart A. Asymptotic Normality of Quadratic Estimators. Stochastic Processes and Their Applications. 126: 3733-3759. PMID 28090132 DOI: 10.1016/j.spa.2016.04.005  0.046
2014 Jonker M, Van der Vaart A. On the correction of the asymptotic distribution of the likelihood ratio statistic if nuisance parameters are estimated based on an external source. The International Journal of Biostatistics. 10: 123-42. PMID 24837490 DOI: 10.1515/ijb-2013-0063  0.045
2011 Chen J, Brunzell DH, Jackson K, van der Vaart A, Ma JZ, Payne TJ, Sherva R, Farrer LA, Gejman P, Levinson DF, Holmans P, Aggen SH, Damaj I, Kuo PH, Webb BT, et al. ACSL6 is associated with the number of cigarettes smoked and its expression is altered by chronic nicotine exposure. Plos One. 6: e28790. PMID 22205969 DOI: 10.1371/Journal.Pone.0028790  0.044
2009 Jonker MA, Bhulai S, Boomsma DI, Ligthart RS, Posthuma D, Van der Vaart AW. Gamma frailty model for linkage analysis with application to interval-censored migraine data. Biostatistics (Oxford, England). 10: 187-200. PMID 18714083 DOI: 10.1093/Biostatistics/Kxn027  0.044
2008 Tchetgen E, Li L, Robins J, van der Vaart A. Minimax estimation of the integral of a power of a density. Statistics & Probability Letters. 78: 3307-3311. PMID 28979056 DOI: 10.1016/j.spl.2008.07.001  0.043
2011 Li L, Tchetgen ET, van der Vaart A, Robins JM. Higher Order Inference On A Treatment Effect Under Low Regularity Conditions. Statistics & Probability Letters. 81: 821-828. PMID 21552339 DOI: 10.1016/j.spl.2011.02.030  0.043
2004 Van Dommelen P, De Gunst MCM, Van Der Vaart AW, Van Buuren S, Boomsma DI. Growth charts for height, weight and body-mass index of twins during infancy | Groeidiagrammen voor lengte, gewicht en 'body mass index' van tweelingen in de peutertijd Nederlands Tijdschrift Voor Geneeskunde. 148: 1345-1350. PMID 15283027  0.037
2016 van der Vaart AD, Wolstenholme JT, Smith ML, Harris GM, Lopez MF, Wolen AR, Becker HC, Williams RW, Miles MF. The allostatic impact of chronic ethanol on gene expression: A genetic analysis of chronic intermittent ethanol treatment in the BXD cohort. Alcohol (Fayetteville, N.Y.). PMID 27838001 DOI: 10.1016/J.Alcohol.2016.07.010  0.036
2004 Van Dommelen P, De Gunst MCM, Van Der Vaart AW, Boomsma DI. Genetic study of the height and weight process during infancy Twin Research. 7: 607-616. PMID 15607012 DOI: 10.1375/1369052042663805  0.035
2017 Pecanka J, Jonker MA, Bochdanovits Z, Van Der Vaart AW. A powerful and efficient two-stage method for detecting gene-to-gene interactions in GWAS. Biostatistics (Oxford, England). PMID 28334077 DOI: 10.1093/biostatistics/kxw060  0.022
2013 Gugushvili S, Klaassen CA, van der Vaart AW. Editorial introduction. Mathematical Biosciences. 246: 281-2. PMID 23900060 DOI: 10.1016/j.mbs.2013.07.015  0.021
2008 van Dommelen P, de Gunst M, van der Vaart A, van Buuren S, Boomsma D. Growth references for height, weight and body mass index of twins aged 0-2.5 years Acta Paediatrica (Oslo, Norway : 1992). 97: 1099-1104. PMID 18460042 DOI: 10.1111/J.1651-2227.2008.00853.X  0.021
2013 Robins JM, Zhang P, Ayyagari R, Logan R, Tchetgen ET, Li L, Lumley T, van der Vaart A. New statistical approaches to semiparametric regression with application to air pollution research. Research Report (Health Effects Institute). 3-129. PMID 24400588  0.02
2011 Adank MA, Jonker MA, Kluijt I, van Mil SE, Oldenburg RA, Mooi WJ, Hogervorst FB, van den Ouweland AM, Gille JJ, Schmidt MK, van der Vaart AW, Meijers-Heijboer H, Waisfisz Q. CHEK2*1100delC homozygosity is associated with a high breast cancer risk in women. Journal of Medical Genetics. 48: 860-3. PMID 22058428 DOI: 10.1136/jmedgenet-2011-100380  0.014
2016 van der Vaart A, van den Heuvel S. Switching on regeneration. Stem Cell Investigation. 3: 41. PMID 27668248 DOI: 10.21037/sci.2016.08.05  0.01
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