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Items: 26

1.

Bighead is a Wnt antagonist secreted by the Xenopus Spemann organizer that promotes Lrp6 endocytosis.

Ding Y, Colozza G, Sosa EA, Moriyama Y, Rundle S, Salwinski L, De Robertis EM.

Proc Natl Acad Sci U S A. 2018 Sep 25;115(39):E9135-E9144. doi: 10.1073/pnas.1812117115. Epub 2018 Sep 12.

2.

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.

Sivade Dumousseau M, Alonso-López D, Ammari M, Bradley G, Campbell NH, Ceol A, Cesareni G, Combe C, De Las Rivas J, Del-Toro N, Heimbach J, Hermjakob H, Jurisica I, Koch M, Licata L, Lovering RC, Lynn DJ, Meldal BHM, Micklem G, Panni S, Porras P, Ricard-Blum S, Roechert B, Salwinski L, Shrivastava A, Sullivan J, Thierry-Mieg N, Yehudi Y, Van Roey K, Orchard S.

BMC Bioinformatics. 2018 Apr 11;19(1):134. doi: 10.1186/s12859-018-2118-1.

3.

Inhibition by small-molecule ligands of formation of amyloid fibrils of an immunoglobulin light chain variable domain.

Brumshtein B, Esswein SR, Salwinski L, Phillips ML, Ly AT, Cascio D, Sawaya MR, Eisenberg DS.

Elife. 2015 Nov 18;4:e10935. doi: 10.7554/eLife.10935.

4.

A new reference implementation of the PSICQUIC web service.

del-Toro N, Dumousseau M, Orchard S, Jimenez RC, Galeota E, Launay G, Goll J, Breuer K, Ono K, Salwinski L, Hermjakob H.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W601-6. doi: 10.1093/nar/gkt392. Epub 2013 May 13.

5.

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium.

Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S, Bridge A, Briganti L, Brinkman FS, Cesareni G, Chatr-aryamontri A, Chautard E, Chen C, Dumousseau M, Goll J, Hancock RE, Hannick LI, Jurisica I, Khadake J, Lynn DJ, Mahadevan U, Perfetto L, Raghunath A, Ricard-Blum S, Roechert B, Salwinski L, Stümpflen V, Tyers M, Uetz P, Xenarios I, Hermjakob H.

Nat Methods. 2012 Apr;9(4):345-50. doi: 10.1038/nmeth.1931. Erratum in: Nat Methods. 2012 Jun;9(6):626. Brinkman, Fiona [corrected to Brinkman, Fiona S L]; Hancock, Robert [corrected to Hancock, Robert E W].

6.

An integrated approach to elucidate the intra-viral and viral-cellular protein interaction networks of a gamma-herpesvirus.

Lee S, Salwinski L, Zhang C, Chu D, Sampankanpanich C, Reyes NA, Vangeloff A, Xing F, Li X, Wu TT, Sahasrabudhe S, Deng H, Lacount DJ, Sun R.

PLoS Pathog. 2011 Oct;7(10):e1002297. doi: 10.1371/journal.ppat.1002297. Epub 2011 Oct 20.

7.

PSICQUIC and PSISCORE: accessing and scoring molecular interactions.

Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H.

Nat Methods. 2011 Jun 29;8(7):528-9. doi: 10.1038/nmeth.1637. No abstract available.

8.

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.

Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita KF, Yamamoto Y, Yamaguchi A, Kawashima S, Chun HW, Aerts J, Aranda B, Barboza LH, Bonnal RJ, Bruskiewich R, Bryne JC, Fernández JM, Funahashi A, Gordon PM, Goto N, Groscurth A, Gutteridge A, Holland R, Kano Y, Kawas EA, Kerhornou A, Kibukawa E, Kinjo AR, Kuhn M, Lapp H, Lehvaslaiho H, Nakamura H, Nakamura Y, Nishizawa T, Nobata C, Noguchi T, Oinn TM, Okamoto S, Owen S, Pafilis E, Pocock M, Prins P, Ranzinger R, Reisinger F, Salwinski L, Schreiber M, Senger M, Shigemoto Y, Standley DM, Sugawara H, Tashiro T, Trelles O, Vos RA, Wilkinson MD, York W, Zmasek CM, Asai K, Takagi T.

J Biomed Semantics. 2010 Aug 21;1(1):8. doi: 10.1186/2041-1480-1-8.

9.

Recurated protein interaction datasets.

Salwinski L, Licata L, Winter A, Thorneycroft D, Khadake J, Ceol A, Aryamontri AC, Oughtred R, Livstone M, Boucher L, Botstein D, Dolinski K, Berardini T, Huala E, Tyers M, Eisenberg D, Cesareni G, Hermjakob H.

Nat Methods. 2009 Dec;6(12):860-1. doi: 10.1038/nmeth1209-860. No abstract available.

PMID:
19935838
10.

Robust discrimination between self and non-self neurites requires thousands of Dscam1 isoforms.

Hattori D, Chen Y, Matthews BJ, Salwinski L, Sabatti C, Grueber WB, Zipursky SL.

Nature. 2009 Oct 1;461(7264):644-8. doi: 10.1038/nature08431.

11.

Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.

Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H.

BMC Biol. 2007 Oct 9;5:44.

12.

Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition.

Orchard S, Kerrien S, Jones P, Ceol A, Chatr-Aryamontri A, Salwinski L, Nerothin J, Hermjakob H.

Proteomics. 2007 Sep;7 Suppl 1:28-34.

PMID:
17893861
13.

The minimum information required for reporting a molecular interaction experiment (MIMIx).

Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stümpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, De Las Rivas J, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H.

Nat Biotechnol. 2007 Aug;25(8):894-8. Review.

PMID:
17687370
14.

The MiSink Plugin: Cytoscape as a graphical interface to the Database of Interacting Proteins.

Salwinski L, Eisenberg D.

Bioinformatics. 2007 Aug 15;23(16):2193-5. Epub 2007 Jun 6.

PMID:
17553858
15.

In silico simulation of biological network dynamics.

Salwinski L, Eisenberg D.

Nat Biotechnol. 2004 Aug;22(8):1017-9. Epub 2004 Jul 4.

PMID:
15235611
16.

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.

Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R.

Nat Biotechnol. 2004 Feb;22(2):177-83.

PMID:
14755292
17.

The Database of Interacting Proteins: 2004 update.

Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D449-51.

18.

Computational methods of analysis of protein-protein interactions.

Salwinski L, Eisenberg D.

Curr Opin Struct Biol. 2003 Jun;13(3):377-82. Review.

PMID:
12831890
19.

Protein interactions: two methods for assessment of the reliability of high throughput observations.

Deane CM, Salwiński Ł, Xenarios I, Eisenberg D.

Mol Cell Proteomics. 2002 May;1(5):349-56.

20.

DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions.

Xenarios I, Salwínski L, Duan XJ, Higney P, Kim SM, Eisenberg D.

Nucleic Acids Res. 2002 Jan 1;30(1):303-5.

21.

Motif-based fold assignment.

Salwinski L, Eisenberg D.

Protein Sci. 2001 Dec;10(12):2460-9.

22.

DIP: The Database of Interacting Proteins: 2001 update.

Xenarios I, Fernandez E, Salwinski L, Duan XJ, Thompson MJ, Marcotte EM, Eisenberg D.

Nucleic Acids Res. 2001 Jan 1;29(1):239-41.

23.

DIP: the database of interacting proteins.

Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D.

Nucleic Acids Res. 2000 Jan 1;28(1):289-91.

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