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Items: 1 to 50 of 340

1.

Molecular dynamics study of ACBP denaturation in alkyl sulfates demonstrates possible pathways of unfolding through fused surfactant clusters.

Poghosyan AH, Schafer NP, Lyngsø J, Shahinyan AA, Pedersen JS, Otzen DE.

Protein Eng Des Sel. 2019 Dec 2. pii: gzz037. doi: 10.1093/protein/gzz037. [Epub ahead of print]

PMID:
31788684
2.

EBADIMEX: an empirical Bayes approach to detect joint differential expression and methylation and to classify samples.

Madsen T, Świtnicki M, Juul M, Pedersen JS.

Stat Appl Genet Mol Biol. 2019 Nov 16;18(6). pii: /j/sagmb.2019.18.issue-6/sagmb-2018-0050/sagmb-2018-0050.xml. doi: 10.1515/sagmb-2018-0050.

PMID:
31734658
3.

Anisotropic Hollow Microgels That Can Adapt Their Size, Shape, and Softness.

Nickel AC, Scotti A, Houston JE, Ito T, Crassous J, Pedersen JS, Richtering W.

Nano Lett. 2019 Nov 13;19(11):8161-8170. doi: 10.1021/acs.nanolett.9b03507. Epub 2019 Oct 18.

PMID:
31613114
4.

Effect of Temperature and Ionic Strength on Micellar Aggregates of Oppositely Charged Thermoresponsive Block Copolymer Polyelectrolytes.

Fehér B, Zhu K, Nyström B, Varga I, Pedersen JS.

Langmuir. 2019 Oct 22;35(42):13614-13623. doi: 10.1021/acs.langmuir.9b01896. Epub 2019 Oct 11.

PMID:
31577150
5.

Unfolding and partial refolding of a cellulase from the SDS-denatured state: From β-sheet to α-helix and back.

Rasmussen HØ, Enghild JJ, Otzen DE, Pedersen JS.

Biochim Biophys Acta Gen Subj. 2020 Jan;1864(1):129434. doi: 10.1016/j.bbagen.2019.129434. Epub 2019 Sep 13.

PMID:
31525408
6.

Bacterial amphiphiles as amyloid inducers: Effect of Rhamnolipid and Lipopolysaccharide on FapC fibrillation.

Najarzadeh Z, Pedersen JN, Christiansen G, Shojaosadati SA, Pedersen JS, Otzen DE.

Biochim Biophys Acta Proteins Proteom. 2019 Nov;1867(11):140263. doi: 10.1016/j.bbapap.2019.140263. Epub 2019 Aug 14.

PMID:
31421227
7.

Acetaminophen toxicity induces mitochondrial complex I inhibition in human liver tissue.

Chrøis KM, Larsen S, Pedersen JS, Rygg MO, Boilsen AEB, Bendtsen F, Dela F.

Basic Clin Pharmacol Toxicol. 2019 Aug 12. doi: 10.1111/bcpt.13304. [Epub ahead of print]

PMID:
31403256
8.

Complementary substrate specificity and distinct quaternary assembly of the Escherichia coli aerobic and anaerobic β-oxidation trifunctional enzyme complexes.

Sah-Teli SK, Hynönen MJ, Schmitz W, Geraets JA, Seitsonen J, Pedersen JS, Butcher SJ, Wierenga RK, Venkatesan R.

Biochem J. 2019 Jul 15;476(13):1975-1994. doi: 10.1042/BCJ20190314.

PMID:
31235482
9.

Deficiency of nucleotide excision repair is associated with mutational signature observed in cancer.

Jager M, Blokzijl F, Kuijk E, Bertl J, Vougioukalaki M, Janssen R, Besselink N, Boymans S, de Ligt J, Pedersen JS, Hoeijmakers J, Pothof J, van Boxtel R, Cuppen E.

Genome Res. 2019 Jul;29(7):1067-1077. doi: 10.1101/gr.246223.118. Epub 2019 Jun 20.

10.

Using nutritional geometry to define the fundamental macronutrient niche of the widespread invasive ant Monomorium pharaonis.

Krabbe BA, Arnan X, Lannes P, Bergstedt CE, Larsen RS, Pedersen JS, Shik JZ.

PLoS One. 2019 Jun 20;14(6):e0218764. doi: 10.1371/journal.pone.0218764. eCollection 2019.

11.

Effect of a pneumococcal whole cell vaccine on influenza A-induced pneumococcal otitis media in infant mice.

Manning J, Dunne EM, Wang N, Pedersen JS, Ogier JM, Burt RA, Mulholland EK, Robins-Browne RM, Malley R, Wijburg OL, Satzke C.

Vaccine. 2019 Jun 6;37(26):3495-3504. doi: 10.1016/j.vaccine.2019.03.013. Epub 2019 May 15.

12.

Neural networks for automatic scoring of arthritis disease activity on ultrasound images.

Andersen JKH, Pedersen JS, Laursen MS, Holtz K, Grauslund J, Savarimuthu TR, Just SA.

RMD Open. 2019 Mar 30;5(1):e000891. doi: 10.1136/rmdopen-2018-000891. eCollection 2019.

13.

Mus musculus deficient for secretory antibodies show delayed growth with an altered urinary metabolome.

Simpfendorfer KR, Wang N, Tull DL, De Souza DP, Nahid A, Mu A, Hocking DM, Pedersen JS, Wijburg OLC, McConville MJ, Strugnell RA.

Mol Med. 2019 Apr 3;25(1):12. doi: 10.1186/s10020-019-0077-2.

14.

Online measurement of temperature and relative humidity as marker tools for quality changes in onion bulbs during storage.

Islam MN, Wang A, Pedersen JS, Sørensen JN, Körner O, Edelenbos M.

PLoS One. 2019 Jan 17;14(1):e0210577. doi: 10.1371/journal.pone.0210577. eCollection 2019.

15.

Regmex: a statistical tool for exploring motifs in ranked sequence lists from genomics experiments.

Nielsen MM, Tataru P, Madsen T, Hobolth A, Pedersen JS.

Algorithms Mol Biol. 2018 Dec 8;13:17. doi: 10.1186/s13015-018-0135-2. eCollection 2018.

16.

Size-Dependent Fault-Driven Relaxation and Faceting in Zincblende CdSe Colloidal Quantum Dots.

Moscheni D, Bertolotti F, Piveteau L, Protesescu L, Dirin DN, Kovalenko MV, Cervellino A, Pedersen JS, Masciocchi N, Guagliardi A.

ACS Nano. 2018 Dec 26;12(12):12558-12570. doi: 10.1021/acsnano.8b07092. Epub 2018 Dec 10.

PMID:
30517780
17.

Lysophospholipids induce fibrillation of the repeat domain of Pmel17 through intermediate core-shell structures.

Pedersen JN, Jiang Z, Christiansen G, Lee JC, Pedersen JS, Otzen DE.

Biochim Biophys Acta Proteins Proteom. 2019 May;1867(5):519-528. doi: 10.1016/j.bbapap.2018.11.007. Epub 2018 Nov 22.

PMID:
30471451
18.

Can a Charged Surfactant Unfold an Uncharged Protein?

Højgaard C, Sørensen HV, Pedersen JS, Winther JR, Otzen DE.

Biophys J. 2018 Dec 4;115(11):2081-2086. doi: 10.1016/j.bpj.2018.10.022. Epub 2018 Nov 15.

19.

Structure of Phospholipid Mixed Micelles (Bicelles) Studied by Small-Angle X-ray Scattering.

Mortensen HG, Jensen GV, Hansen SK, Vosegaard T, Pedersen JS.

Langmuir. 2018 Dec 4;34(48):14597-14607. doi: 10.1021/acs.langmuir.8b02704. Epub 2018 Nov 21.

PMID:
30383384
20.

Correction to: The introduction history of invasive garden ants in Europe: integrating genetic, chemical and behavioural approaches.

Ugelvig LV, Drijfhout FP, Kronauer DJC, Boomsma JJ, Pedersen JS, Cremer S.

BMC Biol. 2018 Oct 30;16(1):128. doi: 10.1186/s12915-018-0604-6.

21.

DNA hypermethylation and differential gene expression associated with Klinefelter syndrome.

Skakkebæk A, Nielsen MM, Trolle C, Vang S, Hornshøj H, Hedegaard J, Wallentin M, Bojesen A, Hertz JM, Fedder J, Østergaard JR, Pedersen JS, Gravholt CH.

Sci Rep. 2018 Sep 13;8(1):13740. doi: 10.1038/s41598-018-31780-0.

22.

Potent α-Synuclein Aggregation Inhibitors, Identified by High-Throughput Screening, Mainly Target the Monomeric State.

Kurnik M, Sahin C, Andersen CB, Lorenzen N, Giehm L, Mohammad-Beigi H, Jessen CM, Pedersen JS, Christiansen G, Petersen SV, Staal R, Krishnamurthy G, Pitts K, Reinhart PH, Mulder FAA, Mente S, Hirst WD, Otzen DE.

Cell Chem Biol. 2018 Nov 15;25(11):1389-1402.e9. doi: 10.1016/j.chembiol.2018.08.005. Epub 2018 Sep 6.

23.

No effect of rifaximin on soluble CD163, mannose receptor or type III and IV neoepitope collagen markers in decompensated cirrhosis: Results from a randomized, placebo controlled trial.

Kimer N, Gudmann NS, Pedersen JS, Møller S, Nielsen MJ, Leeming DJ, Karsdal MA, Møller HJ, Bendtsen F, Grønbæk H.

PLoS One. 2018 Sep 5;13(9):e0203200. doi: 10.1371/journal.pone.0203200. eCollection 2018.

24.

APD-Containing Cyclolipodepsipeptides Target Mitochondrial Function in Hypoxic Cancer Cells.

Jacobsen KM, Villadsen NL, Tørring T, Nielsen CB, Salomón T, Nielsen MM, Tsakos M, Sibbersen C, Scavenius C, Nielsen R, Christensen EI, Guerra PF, Bross P, Pedersen JS, Enghild JJ, Johannsen M, Frøkiær J, Overgaard J, Horsman MR, Busk M, Poulsen TB.

Cell Chem Biol. 2018 Nov 15;25(11):1337-1349.e12. doi: 10.1016/j.chembiol.2018.07.010. Epub 2018 Aug 16.

25.

Insight into the molecular mechanism behind PEG-mediated stabilization of biofluid lipases.

Pérez B, Coletta A, Pedersen JN, Petersen SV, Periole X, Pedersen JS, Sessions RB, Guo Z, Perriman A, Schiøtt B.

Sci Rep. 2018 Aug 16;8(1):12293. doi: 10.1038/s41598-018-29871-z.

26.

α-Synucleins from Animal Species Show Low Fibrillation Propensities and Weak Oligomer Membrane Disruption.

Sahin C, Kjær L, Christensen MS, N Pedersen J, Christiansen G, Pérez AW, Møller IM, Enghild JJ, Pedersen JS, Larsen K, Otzen DE.

Biochemistry. 2018 Aug 28;57(34):5145-5158. doi: 10.1021/acs.biochem.8b00627. Epub 2018 Aug 15.

PMID:
30067901
27.

Effects of Hydration on Structure and Phase Behavior of Pig Gastric Mucin Elucidated by SAXS.

Znamenskaya Falk Y, Engblom J, Pedersen JS, Arnebrant T, Kocherbitov V.

J Phys Chem B. 2018 Aug 2;122(30):7539-7546. doi: 10.1021/acs.jpcb.8b05496. Epub 2018 Jul 23.

PMID:
29989815
28.

ncdDetect2: improved models of the site-specific mutation rate in cancer and driver detection with robust significance evaluation.

Juul M, Madsen T, Guo Q, Bertl J, Hobolth A, Kellis M, Pedersen JS.

Bioinformatics. 2019 Jan 15;35(2):189-199. doi: 10.1093/bioinformatics/bty511.

29.

Time-resolved structural evolution during the collapse of responsive hydrogels: The microgel-to-particle transition.

Keidel R, Ghavami A, Lugo DM, Lotze G, Virtanen O, Beumers P, Pedersen JS, Bardow A, Winkler RG, Richtering W.

Sci Adv. 2018 Apr 6;4(4):eaao7086. doi: 10.1126/sciadv.aao7086. eCollection 2018 Apr.

30.

The structure of the N-terminal module of the cell wall hydrolase RipA and its role in regulating catalytic activity.

Steiner EM, Lyngsø J, Guy JE, Bourenkov G, Lindqvist Y, Schneider TR, Pedersen JS, Schneider G, Schnell R.

Proteins. 2018 Sep;86(9):912-923. doi: 10.1002/prot.25523. Epub 2018 May 31.

PMID:
29722065
31.

A site specific model and analysis of the neutral somatic mutation rate in whole-genome cancer data.

Bertl J, Guo Q, Juul M, Besenbacher S, Nielsen MM, Hornshøj H, Pedersen JS, Hobolth A.

BMC Bioinformatics. 2018 Apr 19;19(1):147. doi: 10.1186/s12859-018-2141-2.

32.

Models of the complement C1 complex.

Mortensen SA, Sander B, Jensen RK, Pedersen JS, Golas MM, Thiel S, Andersen GR.

Proc Natl Acad Sci U S A. 2018 Apr 24;115(17):E3866. doi: 10.1073/pnas.1803577115. Epub 2018 Apr 13. No abstract available.

33.

Optimized targeted sequencing of cell-free plasma DNA from bladder cancer patients.

Christensen E, Nordentoft I, Vang S, Birkenkamp-Demtröder K, Jensen JB, Agerbæk M, Pedersen JS, Dyrskjøt L.

Sci Rep. 2018 Jan 30;8(1):1917. doi: 10.1038/s41598-018-20282-8.

34.

Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival.

Hornshøj H, Nielsen MM, Sinnott-Armstrong NA, Świtnicki MP, Juul M, Madsen T, Sallari R, Kellis M, Ørntoft T, Hobolth A, Pedersen JS.

NPJ Genom Med. 2018 Jan 11;3:1. doi: 10.1038/s41525-017-0040-5. eCollection 2018.

35.

Circular RNA expression is abundant and correlated to aggressiveness in early-stage bladder cancer.

Okholm TLH, Nielsen MM, Hamilton MP, Christensen LL, Vang S, Hedegaard J, Hansen TB, Kjems J, Dyrskjøt L, Pedersen JS.

NPJ Genom Med. 2017 Nov 28;2:36. doi: 10.1038/s41525-017-0038-z. eCollection 2017.

36.

Myoglobin and α-Lactalbumin Form Smaller Complexes with the Biosurfactant Rhamnolipid Than with SDS.

Mortensen HG, Madsen JK, Andersen KK, Vosegaard T, Deen GR, Otzen DE, Pedersen JS.

Biophys J. 2017 Dec 19;113(12):2621-2633. doi: 10.1016/j.bpj.2017.10.024.

37.

Release of Solubilizate from Micelle upon Core Freezing.

Dai J, Alaei Z, Plazzotta B, Pedersen JS, Furó I.

J Phys Chem B. 2017 Nov 16;121(45):10353-10363. doi: 10.1021/acs.jpcb.7b08912. Epub 2017 Nov 1.

PMID:
29050474
38.

A novel explanation for the enhanced colloidal stability of silver nanoparticles in the presence of an oppositely charged surfactant.

Skoglund S, Blomberg E, Wallinder IO, Grillo I, Pedersen JS, Bergström LM.

Phys Chem Chem Phys. 2017 Oct 25;19(41):28037-28043. doi: 10.1039/c7cp04662f.

PMID:
28994441
39.

How glycosaminoglycans promote fibrillation of salmon calcitonin.

Malmos KG, Bjerring M, Jessen CM, Nielsen EHT, Poulsen ET, Christiansen G, Vosegaard T, Skrydstrup T, Enghild JJ, Pedersen JS, Otzen DE.

J Biol Chem. 2017 Sep 22;292(38):15992. doi: 10.1074/jbc.A116.715466. No abstract available.

40.

Construction of a Polyhedral DNA 12-Arm Junction for Self-Assembly of Wireframe DNA Lattices.

Manuguerra I, Grossi G, Thomsen RP, Lyngsø J, Pedersen JS, Kjems J, Andersen ES, Gothelf KV.

ACS Nano. 2017 Sep 26;11(9):9041-9047. doi: 10.1021/acsnano.7b03538. Epub 2017 Aug 22.

PMID:
28806061
41.

The royal free hospital cirrhosis glomerular filtration rate: Validation in a danish cohort.

Pedersen JS, Kimer N, Henriksen JH, Bendtsen F, Møller S.

Hepatology. 2017 Oct;66(4):1360-1361. doi: 10.1002/hep.29386. Epub 2017 Aug 26. No abstract available.

PMID:
28727168
42.

Glycolipid Biosurfactants Activate, Dimerize, and Stabilize Thermomyces lanuginosus Lipase in a pH-Dependent Fashion.

Madsen JK, Kaspersen JD, Andersen CB, Nedergaard Pedersen J, Andersen KK, Pedersen JS, Otzen DE.

Biochemistry. 2017 Aug 15;56(32):4256-4268. doi: 10.1021/acs.biochem.7b00420. Epub 2017 Aug 7.

PMID:
28726390
43.

Reply to Arlaud et al.: Structure of the C1 complex and the unbound C1r2s2 tetramer.

Mortensen SA, Sander B, Jensen RK, Pedersen JS, Golas M, Jensenius JC, Hansen AG, Thiel S, Andersen GR.

Proc Natl Acad Sci U S A. 2017 Jul 18;114(29):E5768-E5770. doi: 10.1073/pnas.1704353114. Epub 2017 Jul 12. No abstract available.

44.

NKG2D ligand expression in Crohn's disease and NKG2D-dependent stimulation of CD8+ T cell migration.

Vadstrup K, Galsgaard ED, Jensen H, Lanier LL, Ryan JC, Chen SY, Nolan GP, Vester-Andersen MK, Pedersen JS, Gerwien J, Jensen T, Bendtsen F.

Exp Mol Pathol. 2017 Aug;103(1):56-70. doi: 10.1016/j.yexmp.2017.06.010. Epub 2017 Jul 3.

45.

Rifaximin has minor effects on bacterial composition, inflammation, and bacterial translocation in cirrhosis: A randomized trial.

Kimer N, Pedersen JS, Tavenier J, Christensen JE, Busk TM, Hobolth L, Krag A, Al-Soud WA, Mortensen MS, Sørensen SJ, Møller S, Bendtsen F; members of the CoRif study group.

J Gastroenterol Hepatol. 2018 Jan;33(1):307-314. doi: 10.1111/jgh.13852.

PMID:
28671712
46.

Refolding of SDS-Unfolded Proteins by Nonionic Surfactants.

Kaspersen JD, Søndergaard A, Madsen DJ, Otzen DE, Pedersen JS.

Biophys J. 2017 Apr 25;112(8):1609-1620. doi: 10.1016/j.bpj.2017.03.013.

47.

Coherent Nanotwins and Dynamic Disorder in Cesium Lead Halide Perovskite Nanocrystals.

Bertolotti F, Protesescu L, Kovalenko MV, Yakunin S, Cervellino A, Billinge SJL, Terban MW, Pedersen JS, Masciocchi N, Guagliardi A.

ACS Nano. 2017 Apr 25;11(4):3819-3831. doi: 10.1021/acsnano.7b00017. Epub 2017 Apr 14.

48.

Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate.

Juul M, Bertl J, Guo Q, Nielsen MM, Świtnicki M, Hornshøj H, Madsen T, Hobolth A, Pedersen JS.

Elife. 2017 Mar 31;6. pii: e21778. doi: 10.7554/eLife.21778.

49.

Significance evaluation in factor graphs.

Madsen T, Hobolth A, Jensen JL, Pedersen JS.

BMC Bioinformatics. 2017 Mar 31;18(1):199. doi: 10.1186/s12859-017-1614-z.

50.

Tailoring thermal treatment to form liprotide complexes between oleic acid and different proteins.

Sørensen HV, Pedersen JN, Pedersen JS, Otzen DE.

Biochim Biophys Acta Proteins Proteom. 2017 Jun;1865(6):682-693. doi: 10.1016/j.bbapap.2017.03.011. Epub 2017 Mar 27.

PMID:
28351690

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