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Items: 38

1.

Correction to "Structure-Based in Silico Screening Identifies a Potent Ebolavirus Inhibitor from a Traditional Chinese Medicine Library".

Shaikh F, Zhao Y, Alvarez L, Iliopoulou M, Lohans C, Schofield CJ, Padilla-Parra S, Siu SWI, Fry EE, Ren J, Stuart DI.

J Med Chem. 2019 Nov 14;62(21):10004. doi: 10.1021/acs.jmedchem.9b01711. Epub 2019 Oct 28. No abstract available.

PMID:
31657917
2.

Chromatin condensation fluctuations rather than steady-state predict chromatin accessibility.

Audugé N, Padilla-Parra S, Tramier M, Borghi N, Coppey-Moisan M.

Nucleic Acids Res. 2019 Jul 9;47(12):6184-6194. doi: 10.1093/nar/gkz373.

3.

Author Correction: A dynamic three-step mechanism drives the HIV-1 pre-fusion reaction.

Iliopoulou M, Nolan R, Alvarez L, Watanabe Y, Coomer CA, Jakobsdottir GM, Bowden TA, Padilla-Parra S.

Nat Struct Mol Biol. 2019 Jun;26(6):526. doi: 10.1038/s41594-019-0244-8.

PMID:
31073171
4.

Structure-Based in Silico Screening Identifies a Potent Ebolavirus Inhibitor from a Traditional Chinese Medicine Library.

Shaikh F, Zhao Y, Alvarez L, Iliopoulou M, Lohans C, Schofield CJ, Padilla-Parra S, Siu SWI, Fry EE, Ren J, Stuart DI.

J Med Chem. 2019 Mar 28;62(6):2928-2937. doi: 10.1021/acs.jmedchem.8b01328. Epub 2019 Mar 6. Erratum in: J Med Chem. 2019 Nov 14;62(21):10004.

5.

An essential role for the Zn2+ transporter ZIP7 in B cell development.

Anzilotti C, Swan DJ, Boisson B, Deobagkar-Lele M, Oliveira C, Chabosseau P, Engelhardt KR, Xu X, Chen R, Alvarez L, Berlinguer-Palmini R, Bull KR, Cawthorne E, Cribbs AP, Crockford TL, Dang TS, Fearn A, Fenech EJ, de Jong SJ, Lagerholm BC, Ma CS, Sims D, van den Berg B, Xu Y, Cant AJ, Kleiner G, Leahy TR, de la Morena MT, Puck JM, Shapiro RS, van der Burg M, Chapman JR, Christianson JC, Davies B, McGrath JA, Przyborski S, Santibanez Koref M, Tangye SG, Werner A, Rutter GA, Padilla-Parra S, Casanova JL, Cornall RJ, Conley ME, Hambleton S.

Nat Immunol. 2019 Mar;20(3):350-361. doi: 10.1038/s41590-018-0295-8. Epub 2019 Feb 4.

6.

Improved cellular uptake of perfluorocarbon nanoparticles for in vivo murine cardiac 19F MRS/MRI and temporal tracking of progenitor cells.

Constantinides C, McNeill E, Carnicer R, Al Haj Zen A, Sainz-Urruela R, Shaw A, Patel J, Swider E, Alonaizan R, Potamiti L, Hadjisavvas A, Padilla-Parra S, Kyriacou K, Srinivas M, Carr CA.

Nanomedicine. 2019 Jun;18:391-401. doi: 10.1016/j.nano.2018.10.014. Epub 2018 Nov 16.

PMID:
30448526
7.

A dynamic three-step mechanism drives the HIV-1 pre-fusion reaction.

Iliopoulou M, Nolan R, Alvarez L, Watanabe Y, Coomer CA, Jakobsdottir GM, Bowden TA, Padilla-Parra S.

Nat Struct Mol Biol. 2018 Sep;25(9):814-822. doi: 10.1038/s41594-018-0113-x. Epub 2018 Aug 27. Erratum in: Nat Struct Mol Biol. 2019 Jun;26(6):526.

PMID:
30150645
8.

Calibration-free In Vitro Quantification of Protein Homo-oligomerization Using Commercial Instrumentation and Free, Open Source Brightness Analysis Software.

Nolan R, Alvarez LA, Griffiths SC, Elegheert J, Siebold C, Padilla-Parra S.

J Vis Exp. 2018 Jul 17;(137). doi: 10.3791/58157.

PMID:
30080195
9.

Detecting protein aggregation and interaction in live cells: A guide to number and brightness.

Nolan R, Iliopoulou M, Alvarez L, Padilla-Parra S.

Methods. 2018 May 1;140-141:172-177. doi: 10.1016/j.ymeth.2017.12.001. Epub 2017 Dec 6. Review.

PMID:
29221925
10.

nandb-number and brightness in R with a novel automatic detrending algorithm.

Nolan R, Alvarez LAJ, Elegheert J, Iliopoulou M, Jakobsdottir GM, Rodriguez-Muñoz M, Aricescu AR, Padilla-Parra S.

Bioinformatics. 2017 Nov 1;33(21):3508-3510. doi: 10.1093/bioinformatics/btx434.

11.

On the Whereabouts of HIV-1 Cellular Entry and Its Fusion Ports.

Jakobsdottir GM, Iliopoulou M, Nolan R, Alvarez L, Compton AA, Padilla-Parra S.

Trends Mol Med. 2017 Oct;23(10):932-944. doi: 10.1016/j.molmed.2017.08.005. Epub 2017 Sep 9. Review.

PMID:
28899754
12.

exampletestr-An easy start to unit testing R packages.

Nolan R, Padilla-Parra S.

Wellcome Open Res. 2017 Jun 21;2:31. doi: 10.12688/wellcomeopenres.11635.2. eCollection 2017.

13.

Actomyosin-generated tension on cadherin is similar between dividing and non-dividing epithelial cells in early Xenopus laevis embryos.

Herbomel G, Hatte G, Roul J, Padilla-Parra S, Tassan JP, Tramier M.

Sci Rep. 2017 Mar 22;7:45058. doi: 10.1038/srep45058.

14.

Astrocytes Resist HIV-1 Fusion but Engulf Infected Macrophage Material.

Russell RA, Chojnacki J, Jones DM, Johnson E, Do T, Eggeling C, Padilla-Parra S, Sattentau QJ.

Cell Rep. 2017 Feb 7;18(6):1473-1483. doi: 10.1016/j.celrep.2017.01.027.

15.

Multiplexing PKA and ERK1&2 kinases FRET biosensors in living cells using single excitation wavelength dual colour FLIM.

Demeautis C, Sipieter F, Roul J, Chapuis C, Padilla-Parra S, Riquet FB, Tramier M.

Sci Rep. 2017 Jan 20;7:41026. doi: 10.1038/srep41026.

16.

Dynamin-2 Stabilizes the HIV-1 Fusion Pore with a Low Oligomeric State.

Jones DM, Alvarez LA, Nolan R, Ferriz M, Sainz Urruela R, Massana-Muñoz X, Novak-Kotzer H, Dustin ML, Padilla-Parra S.

Cell Rep. 2017 Jan 10;18(2):443-453. doi: 10.1016/j.celrep.2016.12.032.

17.

The nature and nurture of cell heterogeneity: accounting for macrophage gene-environment interactions with single-cell RNA-Seq.

Wills QF, Mellado-Gomez E, Nolan R, Warner D, Sharma E, Broxholme J, Wright B, Lockstone H, James W, Lynch M, Gonzales M, West J, Leyrat A, Padilla-Parra S, Filippi S, Holmes C, Moore MD, Bowden R.

BMC Genomics. 2017 Jan 7;18(1):53. doi: 10.1186/s12864-016-3445-0.

18.

Structural Basis for Plexin Activation and Regulation.

Kong Y, Janssen BJ, Malinauskas T, Vangoor VR, Coles CH, Kaufmann R, Ni T, Gilbert RJ, Padilla-Parra S, Pasterkamp RJ, Jones EY.

Neuron. 2016 Aug 3;91(3):548-60. doi: 10.1016/j.neuron.2016.06.018. Epub 2016 Jul 7.

19.

Toremifene interacts with and destabilizes the Ebola virus glycoprotein.

Zhao Y, Ren J, Harlos K, Jones DM, Zeltina A, Bowden TA, Padilla-Parra S, Fry EE, Stuart DI.

Nature. 2016 Jul 7;535(7610):169-172. doi: 10.1038/nature18615. Epub 2016 Jun 29.

20.

The β-Lactamase Assay: Harnessing a FRET Biosensor to Analyse Viral Fusion Mechanisms.

Jones DM, Padilla-Parra S.

Sensors (Basel). 2016 Jun 23;16(7). pii: E950. doi: 10.3390/s16070950. Review.

21.

Actin Dynamics and HIV-1 Entry.

Padilla-Parra S, Dustin ML.

Trends Mol Med. 2016 May;22(5):354-356. doi: 10.1016/j.molmed.2016.03.007. Epub 2016 Apr 14.

PMID:
27151391
22.

Imaging real-time HIV-1 virion fusion with FRET-based biosensors.

Jones DM, Padilla-Parra S.

Sci Rep. 2015 Aug 24;5:13449. doi: 10.1038/srep13449.

23.

Time-domain fluorescence lifetime imaging microscopy: a quantitative method to follow transient protein-protein interactions in living cells.

Padilla-Parra S, Audugé N, Tramier M, Coppey-Moisan M.

Cold Spring Harb Protoc. 2015 Jun 1;2015(6):508-21. doi: 10.1101/pdb.top086249.

PMID:
26034312
24.

Repulsive guidance molecule is a structural bridge between neogenin and bone morphogenetic protein.

Healey EG, Bishop B, Elegheert J, Bell CH, Padilla-Parra S, Siebold C.

Nat Struct Mol Biol. 2015 Jun;22(6):458-65. doi: 10.1038/nsmb.3016. Epub 2015 May 4.

25.

Lysosome sorting of β-glucocerebrosidase by LIMP-2 is targeted by the mannose 6-phosphate receptor.

Zhao Y, Ren J, Padilla-Parra S, Fry EE, Stuart DI.

Nat Commun. 2014 Jul 14;5:4321. doi: 10.1038/ncomms5321.

26.

Pinpointing retrovirus entry sites in cells expressing alternatively spliced receptor isoforms by single virus imaging.

Padilla-Parra S, Marin M, Kondo N, Melikyan GB.

Retrovirology. 2014 Jun 16;11:47. doi: 10.1186/1742-4690-11-47.

27.

Quantitative study of protein-protein interactions in live cell by dual-color fluorescence correlation spectroscopy.

Padilla-Parra S, Audugé N, Coppey-Moisan M, Tramier M.

Methods Mol Biol. 2014;1076:683-98. doi: 10.1007/978-1-62703-649-8_31.

PMID:
24108650
28.

Fusion of mature HIV-1 particles leads to complete release of a gag-GFP-based content marker and raises the intraviral pH.

Padilla-Parra S, Marin M, Gahlaut N, Suter R, Kondo N, Melikyan GB.

PLoS One. 2013 Aug 9;8(8):e71002. doi: 10.1371/journal.pone.0071002. eCollection 2013.

29.

Spatio-Temporal Quantification of FRET in living cells by fast time-domain FLIM: a comparative study of non-fitting methods [corrected].

Leray A, Padilla-Parra S, Roul J, Héliot L, Tramier M.

PLoS One. 2013 Jul 18;8(7):e69335. doi: 10.1371/journal.pone.0069335. Print 2013. Erratum in: PLoS One. 2013;8(8). doi:10.1371/annotation/75f99136-45ec-4078-932e-07ed1242a73e.

30.

Quantitative imaging of endosome acidification and single retrovirus fusion with distinct pools of early endosomes.

Padilla-Parra S, Matos PM, Kondo N, Marin M, Santos NC, Melikyan GB.

Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17627-32. doi: 10.1073/pnas.1211714109. Epub 2012 Oct 9.

31.

Multifaceted mechanisms of HIV-1 entry inhibition by human α-defensin.

Demirkhanyan LH, Marin M, Padilla-Parra S, Zhan C, Miyauchi K, Jean-Baptiste M, Novitskiy G, Lu W, Melikyan GB.

J Biol Chem. 2012 Aug 17;287(34):28821-38. doi: 10.1074/jbc.M112.375949. Epub 2012 Jun 25.

32.

Synchronized retrovirus fusion in cells expressing alternative receptor isoforms releases the viral core into distinct sub-cellular compartments.

Padilla-Parra S, Marin M, Kondo N, Melikyan GB.

PLoS Pathog. 2012;8(5):e1002694. doi: 10.1371/journal.ppat.1002694. Epub 2012 May 10.

33.

FRET microscopy in the living cell: different approaches, strengths and weaknesses.

Padilla-Parra S, Tramier M.

Bioessays. 2012 May;34(5):369-76. doi: 10.1002/bies.201100086. Epub 2012 Mar 13. Review.

PMID:
22415767
34.

Non fitting based FRET-FLIM analysis approaches applied to quantify protein-protein interactions in live cells.

Padilla-Parra S, Auduge N, Coppey-Moisan M, Tramier M.

Biophys Rev. 2011 Jun;3(2):63-70. doi: 10.1007/s12551-011-0047-6. Epub 2011 May 17. Review.

35.

Dual-color fluorescence lifetime correlation spectroscopy to quantify protein-protein interactions in live cell.

Padilla-Parra S, Audugé N, Coppey-Moisan M, Tramier M.

Microsc Res Tech. 2011 Aug;74(8):788-93. doi: 10.1002/jemt.21015. Epub 2011 May 26.

36.

Quantitative comparison of different fluorescent protein couples for fast FRET-FLIM acquisition.

Padilla-Parra S, Audugé N, Lalucque H, Mevel JC, Coppey-Moisan M, Tramier M.

Biophys J. 2009 Oct 21;97(8):2368-76. doi: 10.1016/j.bpj.2009.07.044.

37.

Dynamic interaction of amphiphysin with N-WASP regulates actin assembly.

Yamada H, Padilla-Parra S, Park SJ, Itoh T, Chaineau M, Monaldi I, Cremona O, Benfenati F, De Camilli P, Coppey-Moisan M, Tramier M, Galli T, Takei K.

J Biol Chem. 2009 Dec 4;284(49):34244-56. doi: 10.1074/jbc.M109.064204. Epub 2009 Sep 16.

38.

Quantitative FRET analysis by fast acquisition time domain FLIM at high spatial resolution in living cells.

Padilla-Parra S, Audugé N, Coppey-Moisan M, Tramier M.

Biophys J. 2008 Sep 15;95(6):2976-88. doi: 10.1529/biophysj.108.131276. Epub 2008 Jun 6.

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