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Items: 1 to 50 of 68

1.

Quantitative proteomic characterization of the lung extracellular matrix in chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis.

Åhrman E, Hallgren O, Malmström L, Hedström U, Malmström A, Bjermer L, Zhou XH, Westergren-Thorsson G, Malmström J.

J Proteomics. 2018 Mar 1. pii: S1874-3919(18)30084-8. doi: 10.1016/j.jprot.2018.02.027. [Epub ahead of print]

PMID:
29501846
2.

An objective comparison of cell-tracking algorithms.

Ulman V, Maška M, Magnusson KEG, Ronneberger O, Haubold C, Harder N, Matula P, Matula P, Svoboda D, Radojevic M, Smal I, Rohr K, Jaldén J, Blau HM, Dzyubachyk O, Lelieveldt B, Xiao P, Li Y, Cho SY, Dufour AC, Olivo-Marin JC, Reyes-Aldasoro CC, Solis-Lemus JA, Bensch R, Brox T, Stegmaier J, Mikut R, Wolf S, Hamprecht FA, Esteves T, Quelhas P, Demirel Ö, Malmström L, Jug F, Tomancak P, Meijering E, Muñoz-Barrutia A, Kozubek M, Ortiz-de-Solorzano C.

Nat Methods. 2017 Dec;14(12):1141-1152. doi: 10.1038/nmeth.4473. Epub 2017 Oct 30.

3.

Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS.

Rosenberger G, Liu Y, Röst HL, Ludwig C, Buil A, Bensimon A, Soste M, Spector TD, Dermitzakis ET, Collins BC, Malmström L, Aebersold R.

Nat Biotechnol. 2017 Aug;35(8):781-788. doi: 10.1038/nbt.3908. Epub 2017 Jun 12.

4.

Targeted Proteomics and Absolute Protein Quantification for the Construction of a Stoichiometric Host-Pathogen Surface Density Model.

Sjöholm K, Kilsgård O, Teleman J, Happonen L, Malmström L, Malmström J.

Mol Cell Proteomics. 2017 Apr;16(4 suppl 1):S29-S41. doi: 10.1074/mcp.M116.063966. Epub 2017 Feb 9.

5.

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research.

Wolstencroft K, Krebs O, Snoep JL, Stanford NJ, Bacall F, Golebiewski M, Kuzyakiv R, Nguyen Q, Owen S, Soiland-Reyes S, Straszewski J, van Niekerk DD, Williams AR, Malmström L, Rinn B, Müller W, Goble C.

Nucleic Acids Res. 2017 Jan 4;45(D1):D404-D407. doi: 10.1093/nar/gkw1032. Epub 2016 Nov 28.

6.

OpenMS: a flexible open-source software platform for mass spectrometry data analysis.

Röst HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walzer M, Wojnar D, Wolski WE, Schilling O, Choudhary JS, Malmström L, Aebersold R, Reinert K, Kohlbacher O.

Nat Methods. 2016 Aug 30;13(9):741-8. doi: 10.1038/nmeth.3959.

PMID:
27575624
7.

TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics.

Röst HL, Liu Y, D'Agostino G, Zanella M, Navarro P, Rosenberger G, Collins BC, Gillet L, Testa G, Malmström L, Aebersold R.

Nat Methods. 2016 Sep;13(9):777-83. doi: 10.1038/nmeth.3954. Epub 2016 Aug 1.

8.

Deciphering the Mode of Action of the Processive Polysaccharide Modifying Enzyme Dermatan Sulfate Epimerase 1 by Hydrogen-Deuterium Exchange Mass Spectrometry.

Tykesson E, Mao Y, Maccarana M, Pu Y, Gao J, Lin C, Zaia J, Westergren-Thorsson G, Ellervik U, Malmström L, Malmström A.

Chem Sci. 2016 Feb 1;7(2):1447-1456. Epub 2015 Nov 30.

9.

Large-scale inference of protein tissue origin in gram-positive sepsis plasma using quantitative targeted proteomics.

Malmström E, Kilsgård O, Hauri S, Smeds E, Herwald H, Malmström L, Malmström J.

Nat Commun. 2016 Jan 6;7:10261. doi: 10.1038/ncomms10261.

10.

Reproducible quantitative proteotype data matrices for systems biology.

Röst HL, Malmström L, Aebersold R.

Mol Biol Cell. 2015 Nov 5;26(22):3926-31. doi: 10.1091/mbc.E15-07-0507.

11.

xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry.

Walzthoeni T, Joachimiak LA, Rosenberger G, Röst HL, Malmström L, Leitner A, Frydman J, Aebersold R.

Nat Methods. 2015 Dec;12(12):1185-90. doi: 10.1038/nmeth.3631. Epub 2015 Oct 26.

12.

Quantitative proteogenomics of human pathogens using DIA-MS.

Malmström L, Bakochi A, Svensson G, Kilsgård O, Lantz H, Petersson AC, Hauri S, Karlsson C, Malmström J.

J Proteomics. 2015 Nov 3;129:98-107. doi: 10.1016/j.jprot.2015.09.012. Epub 2015 Sep 14.

PMID:
26381203
13.

Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry.

Parker SJ, Rost H, Rosenberger G, Collins BC, Malmström L, Amodei D, Venkatraman V, Raedschelders K, Van Eyk JE, Aebersold R.

Mol Cell Proteomics. 2015 Oct;14(10):2800-13. doi: 10.1074/mcp.O114.042267. Epub 2015 Jul 21.

14.

A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery.

Sjöström M, Ossola R, Breslin T, Rinner O, Malmström L, Schmidt A, Aebersold R, Malmström J, Niméus E.

J Proteome Res. 2015 Jul 2;14(7):2807-18. doi: 10.1021/acs.jproteome.5b00315. Epub 2015 Jun 5.

PMID:
25944384
15.

Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry.

Röst HL, Schmitt U, Aebersold R, Malmström L.

PLoS One. 2015 Apr 30;10(4):e0125108. doi: 10.1371/journal.pone.0125108. eCollection 2015.

16.

Efficient visualization of high-throughput targeted proteomics experiments: TAPIR.

Röst HL, Rosenberger G, Aebersold R, Malmström L.

Bioinformatics. 2015 Jul 15;31(14):2415-7. doi: 10.1093/bioinformatics/btv152. Epub 2015 Mar 18.

PMID:
25788625
17.

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.

PMID:
25348213
18.

Functional and structural properties of a novel protein and virulence factor (Protein sHIP) in Streptococcus pyogenes.

Wisniewska M, Happonen L, Kahn F, Varjosalo M, Malmström L, Rosenberger G, Karlsson C, Cazzamali G, Pozdnyakova I, Frick IM, Björck L, Streicher W, Malmström J, Wikström M.

J Biol Chem. 2014 Jun 27;289(26):18175-88. doi: 10.1074/jbc.M114.565978. Epub 2014 May 13.

19.

aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data.

Rosenberger G, Ludwig C, Röst HL, Aebersold R, Malmström L.

Bioinformatics. 2014 Sep 1;30(17):2511-3. doi: 10.1093/bioinformatics/btu200. Epub 2014 Apr 20.

20.

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data.

Röst HL, Rosenberger G, Navarro P, Gillet L, Miladinović SM, Schubert OT, Wolski W, Collins BC, Malmström J, Malmström L, Aebersold R.

Nat Biotechnol. 2014 Mar;32(3):219-23. doi: 10.1038/nbt.2841. No abstract available.

PMID:
24727770
21.

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.

22.

pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library.

Röst HL, Schmitt U, Aebersold R, Malmström L.

Proteomics. 2014 Jan;14(1):74-7. doi: 10.1002/pmic.201300246.

PMID:
24420968
23.

A divergent Pseudomonas aeruginosa palmitoyltransferase essential for cystic fibrosis-specific lipid A.

Thaipisuttikul I, Hittle LE, Chandra R, Zangari D, Dixon CL, Garrett TA, Rasko DA, Dasgupta N, Moskowitz SM, Malmström L, Goodlett DR, Miller SI, Bishop RE, Ernst RK.

Mol Microbiol. 2014 Jan;91(1):158-74. doi: 10.1111/mmi.12451. Epub 2013 Nov 27.

24.

Cross-link guided molecular modeling with ROSETTA.

Kahraman A, Herzog F, Leitner A, Rosenberger G, Aebersold R, Malmström L.

PLoS One. 2013 Sep 17;8(9):e73411. doi: 10.1371/journal.pone.0073411. eCollection 2013.

25.

Adolescents' reported hearing symptoms and attitudes toward loud music.

Landälv D, Malmström L, Widén SE.

Noise Health. 2013 Sep-Oct;15(66):347-54. doi: 10.4103/1463-1741.116584.

26.

An automated pipeline for high-throughput label-free quantitative proteomics.

Weisser H, Nahnsen S, Grossmann J, Nilse L, Quandt A, Brauer H, Sturm M, Kenar E, Kohlbacher O, Aebersold R, Malmström L.

J Proteome Res. 2013 Apr 5;12(4):1628-44. doi: 10.1021/pr300992u. Epub 2013 Feb 22.

PMID:
23391308
27.

Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes.

Karlsson C, Malmström L, Aebersold R, Malmström J.

Nat Commun. 2012;3:1301. doi: 10.1038/ncomms2297.

28.

Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometry.

Herzog F, Kahraman A, Boehringer D, Mak R, Bracher A, Walzthoeni T, Leitner A, Beck M, Hartl FU, Ban N, Malmström L, Aebersold R.

Science. 2012 Sep 14;337(6100):1348-52. doi: 10.1126/science.1221483.

29.

Bioinformatic challenges in targeted proteomics.

Reker D, Malmström L.

J Proteome Res. 2012 Sep 7;11(9):4393-402. doi: 10.1021/pr300276f. Epub 2012 Aug 23.

PMID:
22866949
30.

Splicosomal and serine and arginine-rich splicing factors as targets for TGF-β.

Hallgren O, Malmström J, Malmström L, Andersson-Sjöland A, Wildt M, Tufvesson E, Juhasz P, Marko-Varga G, Westergren-Thorsson G.

Fibrogenesis Tissue Repair. 2012 Apr 28;5(1):6. doi: 10.1186/1755-1536-5-6.

31.

A computational tool to detect and avoid redundancy in selected reaction monitoring.

Röst H, Malmström L, Aebersold R.

Mol Cell Proteomics. 2012 Aug;11(8):540-9. doi: 10.1074/mcp.M111.013045. Epub 2012 Apr 24.

32.

Automated workflow for large-scale selected reaction monitoring experiments.

Malmström L, Malmström J, Selevsek N, Rosenberger G, Aebersold R.

J Proteome Res. 2012 Mar 2;11(3):1644-53. doi: 10.1021/pr200844d. Epub 2012 Feb 10.

PMID:
22283722
33.

openBIS: a flexible framework for managing and analyzing complex data in biology research.

Bauch A, Adamczyk I, Buczek P, Elmer FJ, Enimanev K, Glyzewski P, Kohler M, Pylak T, Quandt A, Ramakrishnan C, Beisel C, Malmström L, Aebersold R, Rinn B.

BMC Bioinformatics. 2011 Dec 8;12:468. doi: 10.1186/1471-2105-12-468.

34.

Streptococcus pyogenes in human plasma: adaptive mechanisms analyzed by mass spectrometry-based proteomics.

Malmström J, Karlsson C, Nordenfelt P, Ossola R, Weisser H, Quandt A, Hansson K, Aebersold R, Malmström L, Björck L.

J Biol Chem. 2012 Jan 6;287(2):1415-25. doi: 10.1074/jbc.M111.267674. Epub 2011 Nov 23.

35.

The Proteome Folding Project: proteome-scale prediction of structure and function.

Drew K, Winters P, Butterfoss GL, Berstis V, Uplinger K, Armstrong J, Riffle M, Schweighofer E, Bovermann B, Goodlett DR, Davis TN, Shasha D, Malmström L, Bonneau R.

Genome Res. 2011 Nov;21(11):1981-94. doi: 10.1101/gr.121475.111. Epub 2011 Aug 8.

36.

Quantitative proteomics of microbes: Principles and applications to virulence.

Malmström L, Malmström J, Aebersold R.

Proteomics. 2011 Aug;11(15):2947-56. doi: 10.1002/pmic.201100088. Epub 2011 Jul 4. Review.

PMID:
21726054
37.

Xwalk: computing and visualizing distances in cross-linking experiments.

Kahraman A, Malmström L, Aebersold R.

Bioinformatics. 2011 Aug 1;27(15):2163-4. doi: 10.1093/bioinformatics/btr348. Epub 2011 Jun 11.

38.

Protein structure modeling.

Malmström L, Goodlett DR.

Methods Mol Biol. 2010;673:63-72. doi: 10.1007/978-1-60761-842-3_5.

PMID:
20835793
39.

Deciphering diatom biochemical pathways via whole-cell proteomics.

Nunn BL, Aker JR, Shaffer SA, Tsai S, Strzepek RF, Boyd PW, Freeman TL, Brittnacher M, Malmström L, Goodlett DR.

Aquat Microb Ecol. 2009 Jun 3;55(3):241-253.

40.

Proteomics analysis of liver pathological calcification suggests a role for the IQ motif containing GTPase activating protein 1 in myofibroblast function.

Kalantari F, Auguste P, Ziafazeli T, Tzimas G, Malmström L, Bioulac-Sage P, Boismenu D, Vali H, Chevet E.

Proteomics Clin Appl. 2009 Mar;3(3):307-21. doi: 10.1002/prca.200780133.

PMID:
26238749
41.

Identification of the active site of DS-epimerase 1 and requirement of N-glycosylation for enzyme function.

Pacheco B, Maccarana M, Goodlett DR, Malmström A, Malmström L.

J Biol Chem. 2009 Jan 16;284(3):1741-7. doi: 10.1074/jbc.M805479200. Epub 2008 Nov 11.

42.

Identification of secreted glycoproteins of human prostate and bladder stromal cells by comparative quantitative proteomics.

Goo YA, Liu AY, Ryu S, Shaffer SA, Malmström L, Page L, Nguyen LT, Doneanu CE, Goodlett DR.

Prostate. 2009 Jan 1;69(1):49-61. doi: 10.1002/pros.20853.

43.

Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home.

Das R, Qian B, Raman S, Vernon R, Thompson J, Bradley P, Khare S, Tyka MD, Bhat D, Chivian D, Kim DE, Sheffler WH, Malmström L, Wollacott AM, Wang C, Andre I, Baker D.

Proteins. 2007;69 Suppl 8:118-28.

PMID:
17894356
44.

Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology.

Malmström L, Riffle M, Strauss CE, Chivian D, Davis TN, Bonneau R, Baker D.

PLoS Biol. 2007 Apr;5(4):e76.

45.

The importance of fibroblasts in remodelling of the human uterine cervix during pregnancy and parturition.

Malmström E, Sennström M, Holmberg A, Frielingsdorf H, Eklund E, Malmström L, Tufvesson E, Gomez MF, Westergren-Thorsson G, Ekman-Ordeberg G, Malmström A.

Mol Hum Reprod. 2007 May;13(5):333-41. Epub 2007 Mar 2.

PMID:
17337476
46.

2DDB - a bioinformatics solution for analysis of quantitative proteomics data.

Malmström L, Marko-Varga G, Westergren-Thorsson G, Laurell T, Malmström J.

BMC Bioinformatics. 2006 Mar 20;7:158.

47.

[Supervision--why?].

Larsen JH, Nystrup J, Risør O, Malmstrøm L.

Ugeskr Laeger. 2005 Sep 19;167(38):3578-80. Danish.

PMID:
16219185
48.

Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM.

Kim DE, Chivian D, Malmström L, Baker D.

Proteins. 2005;61 Suppl 7:193-200.

PMID:
16187362
49.

Prediction of CASP6 structures using automated Robetta protocols.

Chivian D, Kim DE, Malmström L, Schonbrun J, Rohl CA, Baker D.

Proteins. 2005;61 Suppl 7:157-66.

PMID:
16187358
50.

Free modeling with Rosetta in CASP6.

Bradley P, Malmström L, Qian B, Schonbrun J, Chivian D, Kim DE, Meiler J, Misura KM, Baker D.

Proteins. 2005;61 Suppl 7:128-34.

PMID:
16187354

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