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Items: 1 to 50 of 144

1.

LION/web: a web-based ontology enrichment tool for lipidomic data analysis.

Molenaar MR, Jeucken A, Wassenaar TA, van de Lest CHA, Brouwers JF, Helms JB.

Gigascience. 2019 Jun 1;8(6). pii: giz061. doi: 10.1093/gigascience/giz061.

2.

Associations between modifiable risk factors and white matter of the aging brain: insights from diffusion tensor imaging studies.

Wassenaar TM, Yaffe K, van der Werf YD, Sexton CE.

Neurobiol Aging. 2019 Apr 11;80:56-70. doi: 10.1016/j.neurobiolaging.2019.04.006. [Epub ahead of print]

3.

In silico Selection of Amplification Targets for Rapid Polymorphism Screening in Ebola Virus Outbreaks.

Wassenaar TM, Wanchai V, Buzard GS, Ussery DW.

Front Microbiol. 2019 Apr 26;10:857. doi: 10.3389/fmicb.2019.00857. eCollection 2019.

4.

Anti-genotoxic and anti-mutagenic activity of Escherichia coli Nissle 1917 as assessed by in vitro tests.

Janosch D, Dubbert S, Eiteljörge K, Diehl BWK, Sonnenborn U, Passchier LV, Wassenaar TM, von Bünau R.

Benef Microbes. 2019 Apr 19;10(4):449-461. doi: 10.3920/BM2018.0113. Epub 2019 Apr 8.

PMID:
30957533
5.

Effects of a programme of vigorous physical activity during secondary school physical education on academic performance, fitness, cognition, mental health and the brain of adolescents (Fit to Study): study protocol for a cluster-randomised trial.

Wassenaar TM, Wheatley CM, Beale N, Salvan P, Meaney A, Possee JB, Atherton KE, Duda JL, Dawes H, Johansen-Berg H.

Trials. 2019 Apr 2;20(1):189. doi: 10.1186/s13063-019-3279-6.

6.

Mechanisms linking preterm birth to onset of cardiovascular disease later in adulthood.

Bavineni M, Wassenaar TM, Agnihotri K, Ussery DW, Lüscher TF, Mehta JL.

Eur Heart J. 2019 Apr 7;40(14):1107-1112. doi: 10.1093/eurheartj/ehz025.

PMID:
30753448
7.

Impact of Survivorship Care Plans and Planning on Breast, Colon, and Prostate Cancer Survivors in a Community Oncology Practice.

Hua A, Sesto ME, Zhang X, Wassenaar TR, Tevaarwerk AJ.

J Cancer Educ. 2019 Jan 4. doi: 10.1007/s13187-018-1457-y. [Epub ahead of print]

PMID:
30610655
8.

Lipopolysaccharides in Food, Food Supplements, and Probiotics: Should We be Worried?

Wassenaar TM, Zimmermann K.

Eur J Microbiol Immunol (Bp). 2018 Aug 21;8(3):63-69. doi: 10.1556/1886.2018.00017. eCollection 2018 Sep 28. Review.

9.

Statistical efficiency of methods for computing free energy of hydration.

Yildirim A, Wassenaar TA, van der Spoel D.

J Chem Phys. 2018 Oct 14;149(14):144111. doi: 10.1063/1.5041835.

PMID:
30316276
10.

Case of Microcephaly after Congenital Infection with Asian Lineage Zika Virus, Thailand.

Wongsurawat T, Athipanyasilp N, Jenjaroenpun P, Jun SR, Kaewnapan B, Wassenaar TM, Leelahakorn N, Angkasekwinai N, Kantakamalakul W, Ussery DW, Sutthent R, Nookaew I, Horthongkham N.

Emerg Infect Dis. 2018 Sep;24(9). doi: 10.3201/eid2409.180416. Epub 2018 Sep 17.

11.

Lipid-Protein Interactions Are Unique Fingerprints for Membrane Proteins.

Corradi V, Mendez-Villuendas E, Ingólfsson HI, Gu RX, Siuda I, Melo MN, Moussatova A, DeGagné LJ, Sejdiu BI, Singh G, Wassenaar TA, Delgado Magnero K, Marrink SJ, Tieleman DP.

ACS Cent Sci. 2018 Jun 27;4(6):709-717. doi: 10.1021/acscentsci.8b00143. Epub 2018 Jun 13.

12.

E. coli and colorectal cancer: a complex relationship that deserves a critical mindset.

Wassenaar TM.

Crit Rev Microbiol. 2018 Sep;44(5):619-632. doi: 10.1080/1040841X.2018.1481013. Epub 2018 Jun 17. Review.

PMID:
29909724
13.

Dopamine transporter oligomerization involves the scaffold domain, but spares the bundle domain.

Jayaraman K, Morley AN, Szöllősi D, Wassenaar TA, Sitte HH, Stockner T.

PLoS Comput Biol. 2018 Jun 6;14(6):e1006229. doi: 10.1371/journal.pcbi.1006229. eCollection 2018 Jun.

14.

Randomized Phase II Trial of Fulvestrant Plus Everolimus or Placebo in Postmenopausal Women With Hormone Receptor-Positive, Human Epidermal Growth Factor Receptor 2-Negative Metastatic Breast Cancer Resistant to Aromatase Inhibitor Therapy: Results of PrE0102.

Kornblum N, Zhao F, Manola J, Klein P, Ramaswamy B, Brufsky A, Stella PJ, Burnette B, Telli M, Makower DF, Cheema P, Truica CI, Wolff AC, Soori GS, Haley B, Wassenaar TR, Goldstein LJ, Miller KD, Sparano JA.

J Clin Oncol. 2018 Jun 1;36(16):1556-1563. doi: 10.1200/JCO.2017.76.9331. Epub 2018 Apr 17.

PMID:
29664714
15.

Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes.

Cabal A, Jun SR, Jenjaroenpun P, Wanchai V, Nookaew I, Wongsurawat T, Burgess MJ, Kothari A, Wassenaar TM, Ussery DW.

Microb Ecol. 2018 Oct;76(3):801-813. doi: 10.1007/s00248-018-1155-7. Epub 2018 Feb 14.

16.

Suggested mechanisms for Zika virus causing microcephaly: what do the genomes tell us?

Jun SR, Wassenaar TM, Wanchai V, Patumcharoenpol P, Nookaew I, Ussery DW.

BMC Bioinformatics. 2017 Dec 28;18(Suppl 14):471. doi: 10.1186/s12859-017-1894-3.

17.

eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations.

Capoferri L, van Dijk M, Rustenburg AS, Wassenaar TA, Kooi DP, Rifai EA, Vermeulen NPE, Geerke DP.

J Cheminform. 2017 Nov 21;9(1):58. doi: 10.1186/s13321-017-0243-x.

18.

A secreted antibacterial neuropeptide shapes the microbiome of Hydra.

Augustin R, Schröder K, Murillo Rincón AP, Fraune S, Anton-Erxleben F, Herbst EM, Wittlieb J, Schwentner M, Grötzinger J, Wassenaar TM, Bosch TCG.

Nat Commun. 2017 Sep 26;8(1):698. doi: 10.1038/s41467-017-00625-1.

19.

Damaged fiber tracts of the nucleus basalis of Meynert in Parkinson's disease patients with visual hallucinations.

Hepp DH, Foncke EMJ, Berendse HW, Wassenaar TM, Olde Dubbelink KTE, Groenewegen HJ, D J van de Berg W, Schoonheim MM.

Sci Rep. 2017 Aug 31;7(1):10112. doi: 10.1038/s41598-017-10146-y.

20.

Three Complete Genome Sequences of Genotype G Mumps Virus from the 2016 Outbreak in Arkansas, USA.

Alkam D, Wongsurawat T, Jenjaroenpun P, Connor S, Hobbs C, Wassenaar TM, Jun SR, Nookaew I, Ussery D.

Genome Announc. 2017 Aug 10;5(32). pii: e00555-17. doi: 10.1128/genomeA.00555-17.

21.

The mobile dso-gene-sso element in rolling-circle plasmids of staphylococci reflects the evolutionary history of its resistance gene.

Wassenaar TM, Cabal A.

Lett Appl Microbiol. 2017 Sep;65(3):192-198. doi: 10.1111/lam.12767. Epub 2017 Jul 27.

PMID:
28631335
22.

Increased default-mode network centrality in cognitively impaired multiple sclerosis patients.

Eijlers AJ, Meijer KA, Wassenaar TM, Steenwijk MD, Uitdehaag BM, Barkhof F, Wink AM, Geurts JJ, Schoonheim MM.

Neurology. 2017 Mar 7;88(10):952-960. doi: 10.1212/WNL.0000000000003689. Epub 2017 Feb 8.

PMID:
28179464
23.

Dynamic Cholesterol-Conditioned Dimerization of the G Protein Coupled Chemokine Receptor Type 4.

Pluhackova K, Gahbauer S, Kranz F, Wassenaar TA, Böckmann RA.

PLoS Comput Biol. 2016 Nov 3;12(11):e1005169. doi: 10.1371/journal.pcbi.1005169. eCollection 2016 Nov.

24.

Insights from 100 Years of Research with Probiotic E. Coli.

Wassenaar TM.

Eur J Microbiol Immunol (Bp). 2016 Sep 29;6(3):147-161. eCollection 2016 Sep 29. Review.

25.
26.

A MoS2-Based Capacitive Displacement Sensor for DNA Sequencing.

Smolyanitsky A, Yakobson BI, Wassenaar TA, Paulechka E, Kroenlein K.

ACS Nano. 2016 Sep 27;10(9):9009-16. doi: 10.1021/acsnano.6b05274. Epub 2016 Sep 16.

PMID:
27623171
27.

Integrated MRSA-Management (IMM) with prolonged decolonization treatment after hospital discharge is effective: a single centre, non-randomised open-label trial.

Jahn B, Wassenaar TM, Stroh A.

Antimicrob Resist Infect Control. 2016 Jun 14;5:25. doi: 10.1186/s13756-016-0124-5. eCollection 2016.

28.

Nucleobase-functionalized graphene nanoribbons for accurate high-speed DNA sequencing.

Paulechka E, Wassenaar TA, Kroenlein K, Kazakov A, Smolyanitsky A.

Nanoscale. 2016 Jan 28;8(4):1861-7. doi: 10.1039/c5nr07061a.

PMID:
26731166
29.

High-Throughput Simulations of Dimer and Trimer Assembly of Membrane Proteins. The DAFT Approach.

Wassenaar TA, Pluhackova K, Moussatova A, Sengupta D, Marrink SJ, Tieleman DP, Böckmann RA.

J Chem Theory Comput. 2015 May 12;11(5):2278-91. doi: 10.1021/ct5010092. Epub 2015 Mar 26.

PMID:
26574426
30.

Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations.

Wassenaar TA, Ingólfsson HI, Böckmann RA, Tieleman DP, Marrink SJ.

J Chem Theory Comput. 2015 May 12;11(5):2144-55. doi: 10.1021/acs.jctc.5b00209. Epub 2015 Apr 24.

PMID:
26574417
31.

Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis.

Jun SR, Wassenaar TM, Nookaew I, Hauser L, Wanchai V, Land M, Timm CM, Lu TY, Schadt CW, Doktycz MJ, Pelletier DA, Ussery DW.

Appl Environ Microbiol. 2015 Oct 30;82(1):375-83. doi: 10.1128/AEM.02612-15. Print 2016 Jan 1.

32.

Synaptobrevin Transmembrane Domain Dimerization Studied by Multiscale Molecular Dynamics Simulations.

Han J, Pluhackova K, Wassenaar TA, Böckmann RA.

Biophys J. 2015 Aug 18;109(4):760-71. doi: 10.1016/j.bpj.2015.06.049.

33.

Molecular dynamics study of the effect of active site protonation on Helicobacter pylori 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase.

Tekpinar M, Yildirim A, Wassenaar TA.

Eur Biophys J. 2015 Dec;44(8):685-96. doi: 10.1007/s00249-015-1067-0. Epub 2015 Aug 8.

PMID:
26254213
34.

Ebolavirus comparative genomics.

Jun SR, Leuze MR, Nookaew I, Uberbacher EC, Land M, Zhang Q, Wanchai V, Chai J, Nielsen M, Trolle T, Lund O, Buzard GS, Pedersen TD, Wassenaar TM, Ussery DW.

FEMS Microbiol Rev. 2015 Sep;39(5):764-78. doi: 10.1093/femsre/fuv031. Epub 2015 Jul 14. Review.

35.

The prediction of virulence based on presence of virulence genes in E. coli may not always be accurate.

Wassenaar TM, Gunzer F.

Gut Pathog. 2015 Jun 19;7:15. doi: 10.1186/s13099-015-0062-4. eCollection 2015.

36.

A phase 2 study of weekly temsirolimus and bortezomib for relapsed or refractory B-cell non-Hodgkin lymphoma: A Wisconsin Oncology Network study.

Fenske TS, Shah NM, Kim KM, Saha S, Zhang C, Baim AE, Farnen JP, Onitilo AA, Blank JH, Ahuja H, Wassenaar T, Qamar R, Mansky P, Traynor AM, Mattison RJ, Kahl BS.

Cancer. 2015 Oct 1;121(19):3465-71. doi: 10.1002/cncr.29502. Epub 2015 Jun 16.

37.

Activation of the bacterial thermosensor DesK involves a serine zipper dimerization motif that is modulated by bilayer thickness.

Cybulski LE, Ballering J, Moussatova A, Inda ME, Vazquez DB, Wassenaar TA, de Mendoza D, Tieleman DP, Killian JA.

Proc Natl Acad Sci U S A. 2015 May 19;112(20):6353-8. doi: 10.1073/pnas.1422446112. Epub 2015 May 4.

38.

Virulence genes in a probiotic E. coli product with a recorded long history of safe use.

Wassenaar TM, Zschüttig A, Beimfohr C, Geske T, Auerbach C, Cook H, Zimmermann K, Gunzer F.

Eur J Microbiol Immunol (Bp). 2015 Mar;5(1):81-93. doi: 10.1556/EUJMI-D-14-00039. Epub 2015 Mar 26.

39.

Review and phylogenetic analysis of qac genes that reduce susceptibility to quaternary ammonium compounds in Staphylococcus species.

Wassenaar TM, Ussery D, Nielsen LN, Ingmer H.

Eur J Microbiol Immunol (Bp). 2015 Mar;5(1):44-61. doi: 10.1556/EUJMI-D-14-00038. Epub 2015 Mar 26. Review.

40.

Characterization of thylakoid lipid membranes from cyanobacteria and higher plants by molecular dynamics simulations.

van Eerden FJ, de Jong DH, de Vries AH, Wassenaar TA, Marrink SJ.

Biochim Biophys Acta. 2015 Jun;1848(6):1319-30. doi: 10.1016/j.bbamem.2015.02.025. Epub 2015 Mar 5.

41.

Complete Sequence of Probiotic Symbioflor 2 Escherichia coli Strain G3/10 and Draft Sequences of Symbioflor 2 E. coli Strains G1/2, G4/9, G5, G6/7, and G8.

Zschüttig A, Auerbach C, Meltke S, Eichhorn C, Brandt M, Blom J, Goesmann A, Jarek M, Scharfe M, Zimmermann K, Wassenaar TM, Gunzer F.

Genome Announc. 2015 Mar 5;3(2). pii: e01330-14. doi: 10.1128/genomeA.01330-14.

42.

Method comparison for enhanced recovery, isolation and qualitative detection of C. jejuni and C. coli from wastewater effluent samples.

Ugarte-Ruiz M, Florez-Cuadrado D, Wassenaar TM, Porrero MC, Domínguez L.

Int J Environ Res Public Health. 2015 Mar 2;12(3):2749-64. doi: 10.3390/ijerph120302749.

43.

Insights from 20 years of bacterial genome sequencing.

Land M, Hauser L, Jun SR, Nookaew I, Leuze MR, Ahn TH, Karpinets T, Lund O, Kora G, Wassenaar T, Poudel S, Ussery DW.

Funct Integr Genomics. 2015 Mar;15(2):141-61. doi: 10.1007/s10142-015-0433-4. Epub 2015 Feb 27. Review.

44.

Spontaneous adsorption of coiled-coil model peptides K and E to a mixed lipid bilayer.

Pluhackova K, Wassenaar TA, Kirsch S, Böckmann RA.

J Phys Chem B. 2015 Mar 26;119(12):4396-408. doi: 10.1021/acs.jpcb.5b00434. Epub 2015 Mar 12.

PMID:
25719673
45.

Probing binding sites and mechanisms of action of an I(Ks) activator by computations and experiments.

Xu Y, Wang Y, Zhang M, Jiang M, Rosenhouse-Dantsker A, Wassenaar T, Tseng GN.

Biophys J. 2015 Jan 6;108(1):62-75. doi: 10.1016/j.bpj.2014.10.059.

46.

Thermodynamic and kinetic characterization of transmembrane helix association.

Pawar AB, Deshpande SA, Gopal SM, Wassenaar TA, Athale CA, Sengupta D.

Phys Chem Chem Phys. 2015 Jan 14;17(2):1390-8. doi: 10.1039/c4cp03732d. Epub 2014 Nov 26.

PMID:
25427292
47.

Is a foetus developing in a sterile environment?

Wassenaar TM, Panigrahi P.

Lett Appl Microbiol. 2014 Dec;59(6):572-9. doi: 10.1111/lam.12334. Epub 2014 Oct 27. Review.

48.

Ex-ante fate assessment of trace organic contaminants for decision making: a post-normal estimation for sludge recycling in Reunion.

Wassenaar T, Bravin MN, Dumoulin F, Doelsch E.

J Environ Manage. 2015 Jan 1;147:140-51. doi: 10.1016/j.jenvman.2014.09.015. Epub 2014 Sep 29.

PMID:
25265554
49.

Lipid organization of the plasma membrane.

Ingólfsson HI, Melo MN, van Eerden FJ, Arnarez C, Lopez CA, Wassenaar TA, Periole X, de Vries AH, Tieleman DP, Marrink SJ.

J Am Chem Soc. 2014 Oct 15;136(41):14554-9. doi: 10.1021/ja507832e. Epub 2014 Oct 1.

50.

Voluntarily exposure to a single, high dose of probiotic Escherichia coli results in prolonged colonisation.

Wassenaar TM, Beimfohr C, Geske T, Zimmermann K.

Benef Microbes. 2014 Dec;5(4):367-75. doi: 10.3920/BM2013.0087.

PMID:
24985025

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