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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.


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.


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.


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.


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]


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic Experiments.

Rardin MJ, Schilling B, Cheng LY, MacLean BX, Sorensen DJ, Sahu AK, MacCoss MJ, Vitek O, Gibson BW.

Mol Cell Proteomics. 2015 Sep;14(9):2405-19. doi: 10.1074/mcp.O115.048181. Epub 2015 May 17.


Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments.

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

Bioinformatics. 2015 Jul 15;31(14):2418-20. doi: 10.1093/bioinformatics/btv146. Epub 2015 Mar 15.


Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues.

Bruderer R, Bernhardt OM, Gandhi T, Miladinović SM, Cheng LY, Messner S, Ehrenberger T, Zanotelli V, Butscheid Y, Escher C, Vitek O, Rinner O, Reiter L.

Mol Cell Proteomics. 2015 May;14(5):1400-10. doi: 10.1074/mcp.M114.044305. Epub 2015 Feb 27.


Quantitative variability of 342 plasma proteins in a human twin population.

Liu Y, Buil A, Collins BC, Gillet LC, Blum LC, Cheng LY, Vitek O, Mouritsen J, Lachance G, Spector TD, Dermitzakis ET, Aebersold R.

Mol Syst Biol. 2015 Feb 4;11(1):786. doi: 10.15252/msb.20145728.


Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry.

Selevsek N, Chang CY, Gillet LC, Navarro P, Bernhardt OM, Reiter L, Cheng LY, Vitek O, Aebersold R.

Mol Cell Proteomics. 2015 Mar;14(3):739-49. doi: 10.1074/mcp.M113.035550. Epub 2015 Jan 5.


A framework for installable external tools in Skyline.

Broudy D, Killeen T, Choi M, Shulman N, Mani DR, Abbatiello SE, Mani D, Ahmad R, Sahu AK, Schilling B, Tamura K, Boss Y, Sharma V, Gibson BW, Carr SA, Vitek O, MacCoss MJ, MacLean B.

Bioinformatics. 2014 Sep 1;30(17):2521-3. doi: 10.1093/bioinformatics/btu148. Epub 2014 May 9.


MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments.

Choi M, Chang CY, Clough T, Broudy D, Killeen T, MacLean B, Vitek O.

Bioinformatics. 2014 Sep 1;30(17):2524-6. doi: 10.1093/bioinformatics/btu305. Epub 2014 May 2.


Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach.

Carr SA, Abbatiello SE, Ackermann BL, Borchers C, Domon B, Deutsch EW, Grant RP, Hoofnagle AN, Hüttenhain R, Koomen JM, Liebler DC, Liu T, MacLean B, Mani DR, Mansfield E, Neubert H, Paulovich AG, Reiter L, Vitek O, Aebersold R, Anderson L, Bethem R, Blonder J, Boja E, Botelho J, Boyne M, Bradshaw RA, Burlingame AL, Chan D, Keshishian H, Kuhn E, Kinsinger C, Lee JS, Lee SW, Moritz R, Oses-Prieto J, Rifai N, Ritchie J, Rodriguez H, Srinivas PR, Townsend RR, Van Eyk J, Whiteley G, Wiita A, Weintraub S.

Mol Cell Proteomics. 2014 Mar;13(3):907-17. doi: 10.1074/mcp.M113.036095. Epub 2014 Jan 17.


Targeted protein quantification using sparse reference labeling.

Chang CY, Sabidó E, Aebersold R, Vitek O.

Nat Methods. 2014 Mar;11(3):301-4. doi: 10.1038/nmeth.2806. Epub 2014 Jan 19.


Leading a statistical bioinformatics lab: it's all about finding balance. Interview with Olga Vitek.

Vitek O.

PLoS Comput Biol. 2013;9(11):e1003333. doi: 10.1371/journal.pcbi.1003333. Epub 2013 Nov 7. No abstract available.


Identification of a seven glycopeptide signature for malignant pleural mesothelioma in human serum by selected reaction monitoring.

Cerciello F, Choi M, Nicastri A, Bausch-Fluck D, Ziegler A, Vitek O, Felley-Bosco E, Stahel R, Aebersold R, Wollscheid B.

Clin Proteomics. 2013 Nov 8;10(1):16. doi: 10.1186/1559-0275-10-16.


Automated selected reaction monitoring data analysis workflow for large-scale targeted proteomic studies.

Surinova S, Hüttenhain R, Chang CY, Espona L, Vitek O, Aebersold R.

Nat Protoc. 2013 Aug;8(8):1602-19. doi: 10.1038/nprot.2013.091. Epub 2013 Jul 25.


Targeted proteomics reveals strain-specific changes in the mouse insulin and central metabolic pathways after a sustained high-fat diet.

Sabidó E, Wu Y, Bautista L, Porstmann T, Chang CY, Vitek O, Stoffel M, Aebersold R.

Mol Syst Biol. 2013 Jul 16;9:681. doi: 10.1038/msb.2013.36.


Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size.

Yu D, Huber W, Vitek O.

Bioinformatics. 2013 May 15;29(10):1275-82. doi: 10.1093/bioinformatics/btt143. Epub 2013 Apr 14.


Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs.

Clough T, Thaminy S, Ragg S, Aebersold R, Vitek O.

BMC Bioinformatics. 2012;13 Suppl 16:S6. doi: 10.1186/1471-2105-13-S16-S6. Epub 2012 Nov 5.


A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet.

Ma K, Vitek O, Nesvizhskii AI.

BMC Bioinformatics. 2012;13 Suppl 16:S1. doi: 10.1186/1471-2105-13-S16-S1. Epub 2012 Nov 5.


High-resolution genome-wide scan of genes, gene-networks and cellular systems impacting the yeast ionome.

Yu D, Danku JM, Baxter I, Kim S, Vatamaniuk OK, Vitek O, Ouzzani M, Salt DE.

BMC Genomics. 2012 Nov 14;13:623. doi: 10.1186/1471-2164-13-623.


Developmental changes in the metabolic network of snapdragon flowers.

Muhlemann JK, Maeda H, Chang CY, San Miguel P, Baxter I, Cooper B, Perera MA, Nikolau BJ, Vitek O, Morgan JA, Dudareva N.

PLoS One. 2012;7(7):e40381. doi: 10.1371/journal.pone.0040381. Epub 2012 Jul 11.


Targeted proteomics of the eicosanoid biosynthetic pathway completes an integrated genomics-proteomics-metabolomics picture of cellular metabolism.

Sabidó E, Quehenberger O, Shen Q, Chang CY, Shah I, Armando AM, Andreyev A, Vitek O, Dennis EA, Aebersold R.

Mol Cell Proteomics. 2012 Jul;11(7):M111.014746. doi: 10.1074/mcp.M111.014746. Epub 2012 Feb 23.


"Add to subtract": a simple method to remove complex background signals from the 1H nuclear magnetic resonance spectra of mixtures.

Ye T, Zheng C, Zhang S, Gowda GA, Vitek O, Raftery D.

Anal Chem. 2012 Jan 17;84(2):994-1002. doi: 10.1021/ac202548n. Epub 2011 Dec 30.


Protein significance analysis in selected reaction monitoring (SRM) measurements.

Chang CY, Picotti P, Hüttenhain R, Heinzelmann-Schwarz V, Jovanovic M, Aebersold R, Vitek O.

Mol Cell Proteomics. 2012 Apr;11(4):M111.014662. doi: 10.1074/mcp.M111.014662. Epub 2011 Dec 21.


Computational mass spectrometry-based proteomics.

Käll L, Vitek O.

PLoS Comput Biol. 2011 Dec;7(12):e1002277. doi: 10.1371/journal.pcbi.1002277. Epub 2011 Dec 1. No abstract available.


The impacts of road and walking trails upon adjacent vegetation: effects of road building materials on species composition in a nutrient poor environment.

Müllerová J, Vítková M, Vítek O.

Sci Total Environ. 2011 Sep 1;409(19):3839-49. doi: 10.1016/j.scitotenv.2011.06.056. Epub 2011 Jul 19.


Noise reduction in genome-wide perturbation screens using linear mixed-effect models.

Yu D, Danku J, Baxter I, Kim S, Vatamaniuk OK, Salt DE, Vitek O.

Bioinformatics. 2011 Aug 15;27(16):2173-80. doi: 10.1093/bioinformatics/btr359. Epub 2011 Jun 17.


Statistical design and analysis of label-free LC-MS proteomic experiments: a case study of coronary artery disease.

Clough T, Braun S, Fokin V, Ott I, Ragg S, Schadow G, Vitek O.

Methods Mol Biol. 2011;728:293-319. doi: 10.1007/978-1-61779-068-3_20.


Identification and quantification of metabolites in (1)H NMR spectra by Bayesian model selection.

Zheng C, Zhang S, Ragg S, Raftery D, Vitek O.

Bioinformatics. 2011 Jun 15;27(12):1637-44. doi: 10.1093/bioinformatics/btr118. Epub 2011 Mar 12.


Multivariate statistical identification of human bladder carcinomas using ambient ionization imaging mass spectrometry.

Dill AL, Eberlin LS, Costa AB, Zheng C, Ifa DR, Cheng L, Masterson TA, Koch MO, Vitek O, Cooks RG.

Chemistry. 2011 Mar 1;17(10):2897-902. doi: 10.1002/chem.201001692. Epub 2011 Jan 31.


Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.

Bodenmiller B, Wanka S, Kraft C, Urban J, Campbell D, Pedrioli PG, Gerrits B, Picotti P, Lam H, Vitek O, Brusniak MY, Roschitzki B, Zhang C, Shokat KM, Schlapbach R, Colman-Lerner A, Nolan GP, Nesvizhskii AI, Peter M, Loewith R, von Mering C, Aebersold R.

Sci Signal. 2010 Dec 21;3(153):rs4. doi: 10.1126/scisignal.2001182.


A coastal cline in sodium accumulation in Arabidopsis thaliana is driven by natural variation of the sodium transporter AtHKT1;1.

Baxter I, Brazelton JN, Yu D, Huang YS, Lahner B, Yakubova E, Li Y, Bergelson J, Borevitz JO, Nordborg M, Vitek O, Salt DE.

PLoS Genet. 2010 Nov 11;6(11):e1001193. doi: 10.1371/journal.pgen.1001193.


Multivariate statistical differentiation of renal cell carcinomas based on lipidomic analysis by ambient ionization imaging mass spectrometry.

Dill AL, Eberlin LS, Zheng C, Costa AB, Ifa DR, Cheng L, Masterson TA, Koch MO, Vitek O, Cooks RG.

Anal Bioanal Chem. 2010 Dec;398(7-8):2969-78. doi: 10.1007/s00216-010-4259-6. Epub 2010 Oct 15.


Interdependence of signal processing and analysis of urine 1H NMR spectra for metabolic profiling.

Zhang S, Zheng C, Lanza IR, Nair KS, Raftery D, Vitek O.

Anal Chem. 2009 Aug 1;81(15):6080-8. doi: 10.1021/ac900424c.


Protein quantification in label-free LC-MS experiments.

Clough T, Key M, Ott I, Ragg S, Schadow G, Vitek O.

J Proteome Res. 2009 Nov;8(11):5275-84. doi: 10.1021/pr900610q.


Correlation between y-type ions observed in ion trap and triple quadrupole mass spectrometers.

Sherwood CA, Eastham A, Lee LW, Risler J, Vitek O, Martin DB.

J Proteome Res. 2009 Sep;8(9):4243-51. doi: 10.1021/pr900298b.

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