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Items: 1 to 20 of 70

1.

MSstatsQC 2.0: R/Bioconductor package for statistical quality control of mass spectrometry-based proteomic experiments.

Dogu E, Mohammad Taheri S, Olivella R, Marty F, Lienert I, Reiter L, Sabidó E, Vitek O.

J Proteome Res. 2018 Nov 19. doi: 10.1021/acs.jproteome.8b00732. [Epub ahead of print]

PMID:
30450913
2.

Infection-Induced Peroxisome Biogenesis Is a Metabolic Strategy for Herpesvirus Replication.

Jean Beltran PM, Cook KC, Hashimoto Y, Galitzine C, Murray LA, Vitek O, Cristea IM.

Cell Host Microbe. 2018 Oct 10;24(4):526-541.e7. doi: 10.1016/j.chom.2018.09.002. Epub 2018 Sep 27.

PMID:
30269970
3.

Principles of Systems Biology, No. 31.

Cho H, Berger B, Peng J, Galitzine C, Vitek O, Beltran PMJ, Cristea IM, Görtler F, Solbrig S, Wettig T, Oefner PJ, Spang R, Altenbuchinger M, Basso RS, Hochbaum D, Vandin F, Silverbush D, Cristea S, Yanovich G, Geiger T, Beerenwinkel N, Sharan R, Zhou Z, Luhmann N, Alikhan NF, Achtman M.

Cell Syst. 2018 Aug 22;7(2):133-135. doi: 10.1016/j.cels.2018.08.005.

PMID:
30138580
4.

A Bayesian Active Learning Experimental Design for Inferring Signaling Networks.

Ness RO, Sachs K, Mallick P, Vitek O.

J Comput Biol. 2018 Jul;25(7):709-725. doi: 10.1089/cmb.2017.0247. Epub 2018 Jun 21.

PMID:
29927613
5.

Sex Determination in Ceratopteris richardii Is Accompanied by Transcriptome Changes That Drive Epigenetic Reprogramming of the Young Gametophyte.

Atallah NM, Vitek O, Gaiti F, Tanurdzic M, Banks JA.

G3 (Bethesda). 2018 Jul 2;8(7):2205-2214. doi: 10.1534/g3.118.200292.

6.

Nonlinear Regression Improves Accuracy of Characterization of Multiplexed Mass Spectrometric Assays.

Galitzine C, Egertson JD, Abbatiello S, Henderson CM, Pino LK, MacCoss M, Hoofnagle AN, Vitek O.

Mol Cell Proteomics. 2018 May;17(5):913-924. doi: 10.1074/mcp.RA117.000322. Epub 2018 Feb 9.

PMID:
29438992
7.

Statistical characterization of therapeutic protein modifications.

Tsai TH, Hao Z, Hong Q, Moore B, Stella C, Zhang JH, Chen Y, Kim M, Koulis T, Ryslik GA, Verschueren E, Jacobson F, Haskins WE, Vitek O.

Sci Rep. 2017 Aug 11;7(1):7896. doi: 10.1038/s41598-017-08333-y.

8.

matter: an R package for rapid prototyping with larger-than-memory datasets on disk.

Bemis KA, Vitek O.

Bioinformatics. 2017 Jun 15. doi: 10.1093/bioinformatics/btx392. [Epub ahead of print]

9.

MSstatsQC: Longitudinal System Suitability Monitoring and Quality Control for Targeted Proteomic Experiments.

Dogu E, Mohammad-Taheri S, Abbatiello SE, Bereman MS, MacLean B, Schilling B, Vitek O.

Mol Cell Proteomics. 2017 Jul;16(7):1335-1347. doi: 10.1074/mcp.M116.064774. Epub 2017 May 8.

10.

New Guidelines for Publication of Manuscripts Describing Development and Application of Targeted Mass Spectrometry Measurements of Peptides and Proteins.

Abbatiello S, Ackermann BL, Borchers C, Bradshaw RA, Carr SA, Chalkley R, Choi M, Deutsch E, Domon B, Hoofnagle AN, Keshishian H, Kuhn E, Liebler DC, MacCoss M, MacLean B, Mani DR, Neubert H, Smith D, Vitek O, Zimmerman L.

Mol Cell Proteomics. 2017 Mar;16(3):327-328. doi: 10.1074/mcp.E117.067801. Epub 2017 Feb 9. No abstract available.

11.

ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC-MS/MS Experiments.

Choi M, Eren-Dogu ZF, Colangelo C, Cottrell J, Hoopmann MR, Kapp EA, Kim S, Lam H, Neubert TA, Palmblad M, Phinney BS, Weintraub ST, MacLean B, Vitek O.

J Proteome Res. 2017 Feb 3;16(2):945-957. doi: 10.1021/acs.jproteome.6b00881. Epub 2017 Jan 3.

PMID:
27990823
12.

System-Wide Quantitative Proteomics of the Metabolic Syndrome in Mice: Genotypic and Dietary Effects.

Terfve C, Sabidó E, Wu Y, Gonçalves E, Choi M, Vaga S, Vitek O, Saez-Rodriguez J, Aebersold R.

J Proteome Res. 2017 Feb 3;16(2):831-841. doi: 10.1021/acs.jproteome.6b00815. Epub 2017 Jan 10.

PMID:
27936760
13.

Protein biomarkers on tissue as imaged via MALDI mass spectrometry: A systematic approach to study the limits of detection.

van de Ven SM, Bemis KD, Lau K, Adusumilli R, Kota U, Stolowitz M, Vitek O, Mallick P, Gambhir SS.

Proteomics. 2016 Jun;16(11-12):1660-9. doi: 10.1002/pmic.201500515. Epub 2016 May 11.

PMID:
26970438
14.

Challenges in Large-Scale Computational Mass Spectrometry and Multiomics.

Kohlbacher O, Vitek O, Weintraub ST.

J Proteome Res. 2016 Mar 4;15(3):681-2. doi: 10.1021/acs.jproteome.6b00067. No abstract available.

PMID:
26939758
15.

Probabilistic Segmentation of Mass Spectrometry (MS) Images Helps Select Important Ions and Characterize Confidence in the Resulting Segments.

Bemis KD, Harry A, Eberlin LS, Ferreira CR, van de Ven SM, Mallick P, Stolowitz M, Vitek O.

Mol Cell Proteomics. 2016 May;15(5):1761-72. doi: 10.1074/mcp.O115.053918. Epub 2016 Jan 21.

16.

From Correlation to Causality: Statistical Approaches to Learning Regulatory Relationships in Large-Scale Biomolecular Investigations.

Ness RO, Sachs K, Vitek O.

J Proteome Res. 2016 Mar 4;15(3):683-90. doi: 10.1021/acs.jproteome.5b00911. Epub 2016 Jan 12.

PMID:
26731284
17.

Protein-Based Classifier to Predict Conversion from Clinically Isolated Syndrome to Multiple Sclerosis.

Borràs E, Cantó E, Choi M, Maria Villar L, Álvarez-Cermeño JC, Chiva C, Montalban X, Vitek O, Comabella M, Sabidó E.

Mol Cell Proteomics. 2016 Jan;15(1):318-28. doi: 10.1074/mcp.M115.053256. Epub 2015 Nov 9.

18.

Prediction of colorectal cancer diagnosis based on circulating plasma proteins.

Surinova S, Choi M, Tao S, Schüffler PJ, Chang CY, Clough T, Vysloužil K, Khoylou M, Srovnal J, Liu Y, Matondo M, Hüttenhain R, Weisser H, Buhmann JM, Hajdúch M, Brenner H, Vitek O, Aebersold R.

EMBO Mol Med. 2015 Sep;7(9):1166-78. doi: 10.15252/emmm.201404873.

19.

Non-invasive prognostic protein biomarker signatures associated with colorectal cancer.

Surinova S, Radová L, Choi M, Srovnal J, Brenner H, Vitek O, Hajdúch M, Aebersold R.

EMBO Mol Med. 2015 Sep;7(9):1153-65. doi: 10.15252/emmm.201404874.

20.

Using collective expert judgements to evaluate quality measures of mass spectrometry images.

Palmer A, Ovchinnikova E, Thuné M, Lavigne R, Guével B, Dyatlov A, Vitek O, Pineau C, Borén M, Alexandrov T.

Bioinformatics. 2015 Jun 15;31(12):i375-84. doi: 10.1093/bioinformatics/btv266.

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