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O. Vitek · SciRah

Researcher profile · Semantic Scholar

O. Vitek

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O. Vitek — researcher profile on SciRah

h-index: 45
Works: 132
Citations: 8,881

Most-cited papers

Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues
R. Bruderer, Oliver M. Bernhardt, Tejas Gandhi, Saša M. Miladinović +9 more
2015Molecular & Cellular Proteomics1,033 citations Open access
Semantic Scholar
MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments
Meena Choi, Ching-Yun Chang, Timothy Clough, Daniel Broudy +3 more
2014Bioinform.969 citations Open access
Semantic Scholar
Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments
Kyle D. Bemis, April Harry, L. Eberlin, C. Ferreira +4 more
2015Bioinform.267 citations Open access
Semantic Scholar
Reproducible and Consistent Quantification of the Saccharomyces cerevisiae Proteome by SWATH-mass spectrometry*
N. Selevsek, Ching-Yun Chang, Ludovic C. J. Gillet, Pedro Navarro +5 more
2015Molecular & Cellular Proteomics165 citations Open access
Semantic Scholar
Comparison of Protein Quantification in a Complex Background by DIA and TMT Workflows with Fixed Instrument Time.
J. Muntel, Joanna M. Kirkpatrick, R. Bruderer, Ting Huang +3 more
2019Journal of Proteome Research142 citations
Semantic Scholar
Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size
Danni Yu, W. Huber, O. Vitek
2013Bioinform.140 citations Open access
Semantic Scholar
Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows
D. Amodei, J. Egertson, B. MacLean, Richard S. Johnson +6 more
2019Journal of the American Society for Mass Spectrometry139 citations Open access
Semantic Scholar
MSstatsTMT: Statistical Detection of Differentially Abundant Proteins in Experiments with Isobaric Labeling and Multiple Mixtures
Ting Huang, Meena Choi, M. Tzouros, S. Golling +4 more
2020Molecular & Cellular Proteomics138 citations Open access
Semantic Scholar
Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs
Timothy Clough, S. Thaminy, S. Ragg, R. Aebersold +1 more
2012BMC Bioinformatics134 citations Open access
Semantic Scholar
A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet
Kelvin Ma, O. Vitek, A. Nesvizhskii
2012BMC Bioinformatics127 citations Open access
Semantic Scholar
MSstats Version 4.0: Statistical Analyses of Quantitative Mass Spectrometry-Based Proteomic Experiments with Chromatography-Based Quantification at Scale
Devon Kohler, M. Staniak, Tsung-Heng Tsai, Ting Huang +8 more
2023Journal of Proteome Research124 citations Open access
Semantic Scholar
Proteome-wide structural changes measured with limited proteolysis-mass spectrometry: an advanced protocol for high-throughput applications
L. Malinovska, V. Cappelletti, Devon Kohler, Ilaria Piazza +12 more
2022Nature Protocols119 citations
Semantic Scholar
MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets
Meena Choi, Jeremy J. Carver, C. Chiva, M. Tzouros +19 more
2020Nature Methods118 citations Open access
Semantic Scholar
Developmental Changes in the Metabolic Network of Snapdragon Flowers
J. Muhlemann, Hiroshi A. Maeda, Ching-Yun Chang, Phillip San Miguel +7 more
2012PLoS ONE87 citations Open access
Semantic Scholar
Prediction of colorectal cancer diagnosis based on circulating plasma proteins
S. Surinova, Meena Choi, S. Tao, P. Schüffler +14 more
2015EMBO Molecular Medicine84 citations Open access
Semantic Scholar
Infection-induced peroxisome biogenesis is a metabolic strategy for herpesvirus replication
Pierre M. Jean Beltran, Katelyn C. Cook, Yutaka Hashimoto, Cyril Galitzine +3 more
2018Cell Host and Microbe78 citations Open access
Semantic Scholar
On the Impact of Programming Languages on Code Quality
E. Berger, Celeste Hollenbeck, Petr Maj, O. Vitek +1 more
2019ACM Transactions on Programming Languages and Systems75 citations Open access
Semantic Scholar
Automated selected reaction monitoring data analysis workflow for large-scale targeted proteomic studies
S. Surinova, Ruth Hüttenhain, Ching-Yun Chang, L. Espona +2 more
2013Nature Protocols69 citations
Semantic Scholar
Computational Mass Spectrometry–Based Proteomics
L. Käll, O. Vitek
2011PLoS Comput. Biol.66 citations Open access
Semantic Scholar
Probabilistic Segmentation of Mass Spectrometry (MS) Images Helps Select Important Ions and Characterize Confidence in the Resulting Segments
Kyle D. Bemis, April Harry, L. Eberlin, C. Ferreira +4 more
2016Molecular & Cellular Proteomics65 citations Open access
Semantic Scholar
MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic Experiments
Matthew J. Rardin, B. Schilling, Lin-Yang Cheng, B. MacLean +5 more
2015Molecular & Cellular Proteomics59 citations Open access
Semantic Scholar
Combining Precursor and Fragment Information for Improved Detection of Differential Abundance in Data Independent Acquisition
Ting Huang, R. Bruderer, J. Muntel, Yue Xuan +2 more
2019Molecular & Cellular Proteomics57 citations Open access
Semantic Scholar
High-resolution genome-wide scan of genes, gene-networks and cellular systems impacting the yeast ionome
Danni Yu, John M. C. Danku, Ivan R. Baxter, Sungjin Kim +4 more
2012BMC Genomics54 citations Open access
Semantic Scholar
Non-invasive prognostic protein biomarker signatures associated with colorectal cancer
S. Surinova, L. Radová, Meena Choi, J. Srovnal +4 more
2015EMBO Molecular Medicine50 citations Open access
Semantic Scholar
Identification of a seven glycopeptide signature for malignant pleural mesothelioma in human serum by selected reaction monitoring
F. Cerciello, Meena Choi, A. Nicastri, D. Bausch-Fluck +6 more
2013Clinical Proteomics49 citations Open access
Semantic Scholar
New Guidelines for Publication of Manuscripts Describing Development and Application of Targeted Mass Spectrometry Measurements of Peptides and Proteins
Susan E. Abbatiello, B. Ackermann, C. Borchers, R. Bradshaw +16 more
2017Molecular & Cellular Proteomics46 citations Open access
Semantic Scholar
MSstatsPTM: Statistical Relative Quantification of Posttranslational Modifications in Bottom-Up Mass Spectrometry-Based Proteomics
Devon Kohler, Tsung-Heng Tsai, E. Verschueren, Ting Huang +4 more
2022bioRxiv44 citations Open access
Semantic Scholar
A Targeted Mass Spectrometry Strategy for Developing Proteomic Biomarkers: A Case Study of Epithelial Ovarian Cancer*
Ruth Hüttenhain, Meena Choi, Laura Martin de la Fuente, K. Oehl +12 more
2019Molecular & Cellular Proteomics44 citations Open access
Semantic Scholar
A Bayesian Active Learning Experimental Design for Inferring Signaling Networks
R. Ness, K. Sachs, P. Mallick, O. Vitek
2017Annual International Conference on Research in Computational Molecular Biology42 citations
Semantic Scholar
Targeted Proteomics of the Eicosanoid Biosynthetic Pathway Completes an Integrated Genomics-Proteomics-Metabolomics Picture of Cellular Metabolism*
E. Sabidó, O. Quehenberger, Qin Shen, Ching-Yun Chang +6 more
2012Molecular & Cellular Proteomics42 citations Open access
Semantic Scholar
ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC-MS/MS Experiments.
Meena Choi, Z. F. Eren-Dogu, C. Colangelo, J. Cottrell +10 more
2017Journal of Proteome Research41 citations
Semantic Scholar
Targeted proteomics reveals strain-specific changes in the mouse insulin and central metabolic pathways after a sustained high-fat diet
E. Sabidó, Yi-Bo Wu, Lucía Bautista, T. Porstmann +4 more
2013Molecular Systems Biology39 citations Open access
Semantic Scholar
A framework for installable external tools in Skyline
Daniel Broudy, T. Killeen, Meena Choi, N. Shulman +14 more
2014Bioinform.37 citations Open access
Semantic Scholar
Evaluating Pan and Zoom Timelines and Sliders
Michail Schwab, Sicheng Hao, O. Vitek, James Tompkin +2 more
2019International Conference on Human Factors in Computing Systems36 citations
Semantic Scholar
Protein-Based Classifier to Predict Conversion from Clinically Isolated Syndrome to Multiple Sclerosis*
E. Borràs, E. Cantó, Meena Choi, Luisa Maria Villar +6 more
2015Molecular & Cellular Proteomics36 citations Open access
Semantic Scholar
Selection of Features with Consistent Profiles Improves Relative Protein Quantification in Mass Spectrometry Experiments*
Tsung-Heng Tsai, Meena Choi, Balazs Banfai, Yan-Sheng Liu +3 more
2020Molecular & Cellular Proteomics28 citations Open access
Semantic Scholar
Deep multiple instance learning classifies subtissue locations in mass spectrometry images from tissue-level annotations
Dan Guo, M. Föll, Veronika Volkmann, K. Enderle-Ammour +3 more
2020Bioinform.26 citations Open access
Semantic Scholar
MSstatsQC: Longitudinal System Suitability Monitoring and Quality Control for Targeted Proteomic Experiments*
Eralp Doğu, Sara Mohammad-Taheri, Susan E. Abbatiello, Michael S. Bereman +3 more
2017Molecular & Cellular Proteomics25 citations Open access
Semantic Scholar
Sex Determination in Ceratopteris richardii Is Accompanied by Transcriptome Changes That Drive Epigenetic Reprogramming of the Young Gametophyte
N. Atallah, O. Vitek, Federico Gaiti, M. Tanurdžić +1 more
2018G3: Genes, Genomes, Genetics23 citations Open access
Semantic Scholar
Nonlinear Regression Improves Accuracy of Characterization of Multiplexed Mass Spectrometric Assays *
Cyril Galitzine, J. Egertson, Susan E. Abbatiello, C. M. Henderson +4 more
2018Molecular & Cellular Proteomics21 citations Open access
Semantic Scholar
From Correlation to Causality: Statistical Approaches to Learning Regulatory Relationships in Large-Scale Biomolecular Investigations.
R. Ness, K. Sachs, O. Vitek
2016Journal of Proteome Research21 citations Open access
Semantic Scholar
“Add to Subtract”: A Simple Method to Remove Complex Background Signals from the 1H Nuclear Magnetic Resonance Spectra of Mixtures
T. Ye, Cheng Zheng, Shucha Zhang, G. A. Nagana Gowda +2 more
2011Analytical Chemistry21 citations Open access
Semantic Scholar
MSstatsShiny: A GUI for Versatile, Scalable, and Reproducible Statistical Analyses of Quantitative Proteomic Experiments.
Devon Kohler, Maanasa Kaza, C. Pasi, Ting Huang +5 more
2023Journal of Proteome Research20 citations
Semantic Scholar
Leveraging Structured Biological Knowledge for Counterfactual Inference: A Case Study of Viral Pathogenesis
Jeremy Zucker, Kaushal Paneri, Sara Mohammad-Taheri, Somya Bhargava +7 more
2021IEEE Transactions on Big Data18 citations Open access
Semantic Scholar
Using collective expert judgements to evaluate quality measures of mass spectrometry images
Andrew D. Palmer, E. Ovchinnikova, Mikael Thuné, R. Lavigne +6 more
2015Bioinform.18 citations Open access
Semantic Scholar
Unsupervised segmentation of mass spectrometric ion images characterizes morphology of tissues
Dan Guo, K. Bemis, Catherine M. Rawlins, Jeffrey N. Agar +1 more
2019Bioinform.17 citations Open access
Semantic Scholar
FSE/CACM Rebuttal2: Correcting A Large-Scale Study of Programming Languages and Code Quality in GitHub
E. Berger, Petr Maj, O. Vitek, J. Vitek
2019arXiv.org15 citations
Semantic Scholar
MSstatsQC 2.0: R/Bioconductor Package for Statistical Quality Control of Mass Spectrometry-Based Proteomics Experiments.
Eralp Doğu, Sara Mohammad Taheri, R. Olivella, Florian Marty +4 more
2018Journal of Proteome Research15 citations
Semantic Scholar
New mixture models for decoy-free false discovery rate estimation in mass spectrometry proteomics
Yi-Su Peng, Shantanu Jain, Yong-Fu-Ga Li, M. Greguš +3 more
2020Bioinform.14 citations Open access
Semantic Scholar
Protein biomarkers on tissue as imaged via MALDI mass spectrometry: A systematic approach to study the limits of detection
S. M. van de Ven, Kyle D. Bemis, Kenneth Lau, Ravali Adusumilli +5 more
2016Proteomics14 citations
Semantic Scholar

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