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Items: 1 to 50 of 73

1.

Proteomics of PTI and Two ETI Immune Reactions in Potato Leaves.

Resjö S, Zahid MA, Burra DD, Lenman M, Levander F, Andreasson E.

Int J Mol Sci. 2019 Sep 24;20(19). pii: E4726. doi: 10.3390/ijms20194726.

2.

Towards a standardized bioinformatics infrastructure for N- and O-glycomics.

Rojas-Macias MA, Mariethoz J, Andersson P, Jin C, Venkatakrishnan V, Aoki NP, Shinmachi D, Ashwood C, Madunic K, Zhang T, Miller RL, Horlacher O, Struwe WB, Watanabe Y, Okuda S, Levander F, Kolarich D, Rudd PM, Wuhrer M, Kettner C, Packer NH, Aoki-Kinoshita KF, Lisacek F, Karlsson NG.

Nat Commun. 2019 Jul 22;10(1):3275. doi: 10.1038/s41467-019-11131-x. Review.

PMID:
31332201
3.

NormalyzerDE: Online Tool for Improved Normalization of Omics Expression Data and High-Sensitivity Differential Expression Analysis.

Willforss J, Chawade A, Levander F.

J Proteome Res. 2019 Feb 1;18(2):732-740. doi: 10.1021/acs.jproteome.8b00523. Epub 2018 Oct 15.

PMID:
30277078
4.

Patient-Derived Xenograft Models Reveal Intratumor Heterogeneity and Temporal Stability in Neuroblastoma.

Braekeveldt N, von Stedingk K, Fransson S, Martinez-Monleon A, Lindgren D, Axelson H, Levander F, Willforss J, Hansson K, Øra I, Backman T, Börjesson A, Beckman S, Esfandyari J, Berbegall AP, Noguera R, Karlsson J, Koster J, Martinsson T, Gisselsson D, Påhlman S, Bexell D.

Cancer Res. 2018 Oct 15;78(20):5958-5969. doi: 10.1158/0008-5472.CAN-18-0527. Epub 2018 Aug 28.

PMID:
30154149
5.

In Vitro Evolution of Antibodies Inspired by In Vivo Evolution.

Persson H, Kirik U, Thörnqvist L, Greiff L, Levander F, Ohlin M.

Front Immunol. 2018 Jun 21;9:1391. doi: 10.3389/fimmu.2018.01391. eCollection 2018.

6.

Comparative Membrane-Associated Proteomics of Three Different Immune Reactions in Potato.

Burra DD, Lenman M, Levander F, Resjö S, Andreasson E.

Int J Mol Sci. 2018 Feb 10;19(2). pii: E538. doi: 10.3390/ijms19020538.

7.

Antibody Heavy Chain Variable Domains of Different Germline Gene Origins Diversify through Different Paths.

Kirik U, Persson H, Levander F, Greiff L, Ohlin M.

Front Immunol. 2017 Nov 13;8:1433. doi: 10.3389/fimmu.2017.01433. eCollection 2017.

8.

Proteomic Analysis of Phytophthora infestans Reveals the Importance of Cell Wall Proteins in Pathogenicity.

Resjö S, Brus M, Ali A, Meijer HJG, Sandin M, Govers F, Levander F, Grenville-Briggs L, Andreasson E.

Mol Cell Proteomics. 2017 Nov;16(11):1958-1971. doi: 10.1074/mcp.M116.065656. Epub 2017 Sep 21.

9.

Data on haplotype-supported immunoglobulin germline gene inference.

Kirik U, Greiff L, Levander F, Ohlin M.

Data Brief. 2017 Jun 27;13:620-640. doi: 10.1016/j.dib.2017.06.031. eCollection 2017 Aug.

10.

A community proposal to integrate proteomics activities in ELIXIR.

Vizcaíno JA, Walzer M, Jiménez RC, Bittremieux W, Bouyssié D, Carapito C, Corrales F, Ferro M, Heck AJR, Horvatovich P, Hubalek M, Lane L, Laukens K, Levander F, Lisacek F, Novak P, Palmblad M, Piovesan D, Pühler A, Schwämmle V, Valkenborg D, van Rijswijk M, Vondrasek J, Eisenacher M, Martens L, Kohlbacher O.

F1000Res. 2017 Jun 13;6. pii: ELIXIR-875. doi: 10.12688/f1000research.11751.1. eCollection 2017.

11.

Parallel antibody germline gene and haplotype analyses support the validity of immunoglobulin germline gene inference and discovery.

Kirik U, Greiff L, Levander F, Ohlin M.

Mol Immunol. 2017 Jul;87:12-22. doi: 10.1016/j.molimm.2017.03.012. Epub 2017 Apr 4.

12.

NLK-mediated phosphorylation of HDAC1 negatively regulates Wnt signaling.

Masoumi KC, Daams R, Sime W, Siino V, Ke H, Levander F, Massoumi R.

Mol Biol Cell. 2017 Jan 15;28(2):346-355. doi: 10.1091/mbc.E16-07-0547. Epub 2016 Nov 30.

13.

Antibody-encoding repertoires of bone marrow and peripheral blood-a focus on IgE.

Levin M, Levander F, Palmason R, Greiff L, Ohlin M.

J Allergy Clin Immunol. 2017 Mar;139(3):1026-1030. doi: 10.1016/j.jaci.2016.06.040. Epub 2016 Aug 9. No abstract available.

14.

Dinosaur: A Refined Open-Source Peptide MS Feature Detector.

Teleman J, Chawade A, Sandin M, Levander F, Malmström J.

J Proteome Res. 2016 Jul 1;15(7):2143-51. doi: 10.1021/acs.jproteome.6b00016. Epub 2016 Jun 8.

15.

Aberrant activation of the PI3K/mTOR pathway promotes resistance to sorafenib in AML.

Lindblad O, Cordero E, Puissant A, Macaulay L, Ramos A, Kabir NN, Sun J, Vallon-Christersson J, Haraldsson K, Hemann MT, Borg Å, Levander F, Stegmaier K, Pietras K, Rönnstrand L, Kazi JU.

Oncogene. 2016 Sep 29;35(39):5119-31. doi: 10.1038/onc.2016.41. Epub 2016 Mar 21.

16.

Targeted Proteomics Approach for Precision Plant Breeding.

Chawade A, Alexandersson E, Bengtsson T, Andreasson E, Levander F.

J Proteome Res. 2016 Feb 5;15(2):638-46. doi: 10.1021/acs.jproteome.5b01061. Epub 2016 Jan 12.

17.

BEX1 acts as a tumor suppressor in acute myeloid leukemia.

Lindblad O, Li T, Su X, Sun J, Kabir NN, Levander F, Zhao H, Lu G, Rönnstrand L, Kazi JU.

Oncotarget. 2015 Aug 28;6(25):21395-405.

18.

Representation of selected-reaction monitoring data in the mzQuantML data standard.

Qi D, Lawless C, Teleman J, Levander F, Holman SW, Hubbard S, Jones AR.

Proteomics. 2015 Aug;15(15):2592-6. doi: 10.1002/pmic.201400281. Epub 2015 Jun 5.

19.

Is label-free LC-MS/MS ready for biomarker discovery?

Sandin M, Chawade A, Levander F.

Proteomics Clin Appl. 2015 Apr;9(3-4):289-94. doi: 10.1002/prca.201400202. Epub 2015 Mar 21. Review.

PMID:
25656266
20.

Comparative proteomic analysis of hyphae and germinating cysts of Phytophthora pisi and Phytophthora sojae.

Hosseini S, Resjö S, Liu Y, Durling M, Heyman F, Levander F, Liu Y, Elfstrand M, Funck Jensen D, Andreasson E, Karlsson M.

J Proteomics. 2015 Mar 18;117:24-40. doi: 10.1016/j.jprot.2015.01.006. Epub 2015 Jan 19.

PMID:
25613045
21.

Data processing has major impact on the outcome of quantitative label-free LC-MS analysis.

Chawade A, Sandin M, Teleman J, Malmström J, Levander F.

J Proteome Res. 2015 Feb 6;14(2):676-87. doi: 10.1021/pr500665j. Epub 2014 Nov 26.

PMID:
25407311
22.

DIANA--algorithmic improvements for analysis of data-independent acquisition MS data.

Teleman J, Röst HL, Rosenberger G, Schmitt U, Malmström L, Malmström J, Levander F.

Bioinformatics. 2015 Feb 15;31(4):555-62. doi: 10.1093/bioinformatics/btu686. Epub 2014 Oct 27.

23.

Phosphite-induced changes of the transcriptome and secretome in Solanum tuberosum leading to resistance against Phytophthora infestans.

Burra DD, Berkowitz O, Hedley PE, Morris J, Resjö S, Levander F, Liljeroth E, Andreasson E, Alexandersson E.

BMC Plant Biol. 2014 Oct 1;14:254. doi: 10.1186/s12870-014-0254-y.

24.

Quantitative proteomics and transcriptomics of potato in response to Phytophthora infestans in compatible and incompatible interactions.

Ali A, Alexandersson E, Sandin M, Resjö S, Lenman M, Hedley P, Levander F, Andreasson E.

BMC Genomics. 2014 Jun 19;15:497. doi: 10.1186/1471-2164-15-497.

25.

Proteomics and transcriptomics of the BABA-induced resistance response in potato using a novel functional annotation approach.

Bengtsson T, Weighill D, Proux-Wéra E, Levander F, Resjö S, Burra DD, Moushib LI, Hedley PE, Liljeroth E, Jacobson D, Alexandersson E, Andreasson E.

BMC Genomics. 2014 Apr 28;15:315. doi: 10.1186/1471-2164-15-315.

26.

Normalyzer: a tool for rapid evaluation of normalization methods for omics data sets.

Chawade A, Alexandersson E, Levander F.

J Proteome Res. 2014 Jun 6;13(6):3114-20. doi: 10.1021/pr401264n. Epub 2014 May 2.

27.

Numerical compression schemes for proteomics mass spectrometry data.

Teleman J, Dowsey AW, Gonzalez-Galarza FF, Perkins S, Pratt B, Röst HL, Malmström L, Malmström J, Jones AR, Deutsch EW, Levander F.

Mol Cell Proteomics. 2014 Jun;13(6):1537-42. doi: 10.1074/mcp.O114.037879. Epub 2014 Mar 27.

28.

Quantitative label-free phosphoproteomics of six different life stages of the late blight pathogen Phytophthora infestans reveals abundant phosphorylation of members of the CRN effector family.

Resjö S, Ali A, Meijer HJ, Seidl MF, Snel B, Sandin M, Levander F, Govers F, Andreasson E.

J Proteome Res. 2014 Apr 4;13(4):1848-59. doi: 10.1021/pr4009095. Epub 2014 Mar 17.

PMID:
24588563
29.

Proteome of the nematode-trapping cells of the fungus Monacrosporium haptotylum.

Andersson KM, Meerupati T, Levander F, Friman E, Ahrén D, Tunlid A.

Appl Environ Microbiol. 2013 Aug;79(16):4993-5004. doi: 10.1128/AEM.01390-13. Epub 2013 Jun 14.

30.

Automated quality control system for LC-SRM setups.

Teleman J, Waldemarson S, Malmström J, Levander F.

J Proteomics. 2013 Dec 16;95:77-83. doi: 10.1016/j.jprot.2013.03.029. Epub 2013 Apr 11.

PMID:
23584149
31.

Data processing methods and quality control strategies for label-free LC-MS protein quantification.

Sandin M, Teleman J, Malmström J, Levander F.

Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):29-41. doi: 10.1016/j.bbapap.2013.03.026. Epub 2013 Apr 6. Review.

PMID:
23567904
32.

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.

Mayer G, Montecchi-Palazzi L, Ovelleiro D, Jones AR, Binz PA, Deutsch EW, Chambers M, Kallhardt M, Levander F, Shofstahl J, Orchard S, Vizcaíno JA, Hermjakob H, Stephan C, Meyer HE, Eisenacher M; HUPO-PSI Group.

Database (Oxford). 2013 Mar 12;2013:bat009. doi: 10.1093/database/bat009. Print 2013.

33.

An adaptive alignment algorithm for quality-controlled label-free LC-MS.

Sandin M, Ali A, Hansson K, Månsson O, Andreasson E, Resjö S, Levander F.

Mol Cell Proteomics. 2013 May;12(5):1407-20. doi: 10.1074/mcp.O112.021907. Epub 2013 Jan 9.

34.

Automated selected reaction monitoring software for accurate label-free protein quantification.

Teleman J, Karlsson C, Waldemarson S, Hansson K, James P, Malmström J, Levander F.

J Proteome Res. 2012 Jul 6;11(7):3766-73. doi: 10.1021/pr300256x. Epub 2012 Jun 14.

35.

Paranoid potato: phytophthora-resistant genotype shows constitutively activated defense.

Ali A, Moushib LI, Lenman M, Levander F, Olsson K, Carlson-Nilson U, Zoteyeva N, Liljeroth E, Andreasson E.

Plant Signal Behav. 2012 Mar;7(3):400-8. doi: 10.4161/psb.19149. Epub 2012 Mar 1.

36.

Multimodel pathway enrichment methods for functional evaluation of expression regulation.

Kirik U, Cifani P, Albrekt AS, Lindstedt M, Heyden A, Levander F.

J Proteome Res. 2012 May 4;11(5):2955-67. doi: 10.1021/pr300038b. Epub 2012 Apr 21.

PMID:
22471554
37.

Critical comparison of multidimensional separation methods for increasing protein expression coverage.

Antberg L, Cifani P, Sandin M, Levander F, James P.

J Proteome Res. 2012 May 4;11(5):2644-52. doi: 10.1021/pr201257y. Epub 2012 Apr 6.

PMID:
22449141
38.

TraML--a standard format for exchange of selected reaction monitoring transition lists.

Deutsch EW, Chambers M, Neumann S, Levander F, Binz PA, Shofstahl J, Campbell DS, Mendoza L, Ovelleiro D, Helsens K, Martens L, Aebersold R, Moritz RL, Brusniak MY.

Mol Cell Proteomics. 2012 Apr;11(4):R111.015040. doi: 10.1074/mcp.R111.015040. Epub 2011 Dec 12.

39.

Relative quantification of membrane proteins in wild-type and prion protein (PrP)-knockout cerebellar granule neurons.

Stella R, Cifani P, Peggion C, Hansson K, Lazzari C, Bendz M, Levander F, Sorgato MC, Bertoli A, James P.

J Proteome Res. 2012 Feb 3;11(2):523-36. doi: 10.1021/pr200759m. Epub 2011 Nov 18.

PMID:
22023170
40.

Facing challenges in Proteomics today and in the coming decade: Report of Roundtable Discussions at the 4th EuPA Scientific Meeting, Portugal, Estoril 2010.

Cox J, Heeren RM, James P, Jorrin-Novo JV, Kolker E, Levander F, Morrice N, Picotti P, Righetti PG, Sánchez JC, Turck CW, Zubarev R, Alexandre BM, Corrales FJ, Marko-Varga G, O'Donovan S, O'Neil S, Prechl J, Simões T, Weckwerth W, Penque D.

J Proteomics. 2011 Dec 10;75(1):4-17. doi: 10.1016/j.jprot.2011.04.021. Epub 2011 May 3. No abstract available.

PMID:
21571109
41.

Generic workflow for quality assessment of quantitative label-free LC-MS analysis.

Sandin M, Krogh M, Hansson K, Levander F.

Proteomics. 2011 Mar;11(6):1114-24. doi: 10.1002/pmic.201000493. Epub 2011 Feb 7.

PMID:
21298787
42.

Hunting for protein markers of hypoxia by combining plasma membrane enrichment with a new approach to membrane protein analysis.

Cifani P, Bendz M, Wårell K, Hansson K, Levander F, Sandin M, Krogh M, Ovenberger M, Fredlund E, Vaapil M, Pietras A, Påhlman S, James P.

J Proteome Res. 2011 Apr 1;10(4):1645-56. doi: 10.1021/pr100982j. Epub 2011 Feb 23.

PMID:
21235201
43.

Laboratory data and sample management for proteomics.

Häkkinen J, Levander F.

Methods Mol Biol. 2011;696:79-92. doi: 10.1007/978-1-60761-987-1_5.

PMID:
21063942
44.

mzML--a community standard for mass spectrometry data.

Martens L, Chambers M, Sturm M, Kessner D, Levander F, Shofstahl J, Tang WH, Römpp A, Neumann S, Pizarro AD, Montecchi-Palazzi L, Tasman N, Coleman M, Reisinger F, Souda P, Hermjakob H, Binz PA, Deutsch EW.

Mol Cell Proteomics. 2011 Jan;10(1):R110.000133. doi: 10.1074/mcp.R110.000133. Epub 2010 Aug 17.

45.

Improved label-free LC-MS analysis by wavelet-based noise rejection.

Cappadona S, Nanni P, Benevento M, Levander F, Versura P, Roda A, Cerutti S, Pattini L.

J Biomed Biotechnol. 2010;2010:131505. doi: 10.1155/2010/131505. Epub 2010 Jan 28.

46.

Quantification of membrane proteins using nonspecific protease digestions.

Bendz M, Möller MC, Arrigoni G, Wåhlander A, Stella R, Cappadona S, Levander F, Hederstedt L, James P.

J Proteome Res. 2009 Dec;8(12):5666-73. doi: 10.1021/pr900741t.

PMID:
19845334
47.

A label-free nano-liquid chromatography-mass spectrometry approach for quantitative serum peptidomics in Crohn's disease patients.

Nanni P, Levander F, Roda G, Caponi A, James P, Roda A.

J Chromatogr B Analyt Technol Biomed Life Sci. 2009 Oct 1;877(27):3127-36. doi: 10.1016/j.jchromb.2009.08.003. Epub 2009 Aug 7.

PMID:
19683480
48.

Getting a grip on proteomics data - Proteomics Data Collection (ProDaC).

Eisenacher M, Martens L, Hardt T, Kohl M, Barsnes H, Helsens K, Häkkinen J, Levander F, Aebersold R, Vandekerckhove J, Dunn MJ, Lisacek F, Siepen JA, Hubbard SJ, Binz PA, Blüggel M, Thiele H, Cottrell J, Meyer HE, Apweiler R, Stephan C.

Proteomics. 2009 Aug;9(15):3928-33. doi: 10.1002/pmic.200900247.

PMID:
19637238
49.

Proteome analysis of the xylose-fermenting mutant yeast strain TMB 3400.

Karhumaa K, Påhlman AK, Hahn-Hägerdal B, Levander F, Gorwa-Grauslund MF.

Yeast. 2009 Jul;26(7):371-82. doi: 10.1002/yea.1673.

50.

The proteios software environment: an extensible multiuser platform for management and analysis of proteomics data.

Häkkinen J, Vincic G, Månsson O, Wårell K, Levander F.

J Proteome Res. 2009 Jun;8(6):3037-43. doi: 10.1021/pr900189c.

PMID:
19354269

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