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@article{DBLP:journals/bioinformatics/GuoFBV23,
  author       = {Dan Guo and
                  Melanie Christine F{\"{o}}ll and
                  Kylie A. Bemis and
                  Olga Vitek},
  title        = {A noise-robust deep clustering of biomolecular ions improves interpretability
                  of mass spectrometric images},
  journal      = {Bioinform.},
  volume       = {39},
  number       = {2},
  year         = {2023}
}

@article{DBLP:journals/bioinformatics/TaheriTKRSHZV23,
  author       = {Sara Mohammad Taheri and
                  Vartika Tewari and
                  Rohan Kapre and
                  Ehsan Rahiminasab and
                  Karen Sachs and
                  Charles Tapley Hoyt and
                  Jeremy Zucker and
                  Olga Vitek},
  title        = {Optimal adjustment sets for causal query estimation in partially observed
                  biomolecular networks},
  journal      = {Bioinform.},
  volume       = {39},
  number       = {Supplement-1},
  pages        = {494--503},
  year         = {2023}
}

@article{DBLP:journals/cgf/SouthSVDB22,
  author       = {Laura South and
                  David Saffo and
                  Olga Vitek and
                  Cody Dunne and
                  Michelle A. Borkin},
  title        = {Effective Use of Likert Scales in Visualization Evaluations: {A} Systematic
                  Review},
  journal      = {Comput. Graph. Forum},
  volume       = {41},
  number       = {3},
  pages        = {43--55},
  year         = {2022}
}

@article{DBLP:journals/tbd/ZuckerPTBKBTHON21,
  author       = {Jeremy Zucker and
                  Kaushal Paneri and
                  Sara Mohammad Taheri and
                  Somya Bhargava and
                  Pallavi Kolambkar and
                  Craig Bakker and
                  Jeremy Teuton and
                  Charles Tapley Hoyt and
                  Kristie L. Oxford and
                  Robert Osazuwa Ness and
                  Olga Vitek},
  title        = {Leveraging Structured Biological Knowledge for Counterfactual Inference:
                  {A} Case Study of Viral Pathogenesis},
  journal      = {{IEEE} Trans. Big Data},
  volume       = {7},
  number       = {1},
  pages        = {25--37},
  year         = {2021}
}

@article{DBLP:journals/corr/abs-2101-05136,
  author       = {Jeremy Zucker and
                  Kaushal Paneri and
                  Sara Mohammad Taheri and
                  Somya Bhargava and
                  Pallavi Kolambkar and
                  Craig Bakker and
                  Jeremy Teuton and
                  Charles Tapley Hoyt and
                  Kristie L. Oxford and
                  Robert Osazuwa Ness and
                  Olga Vitek},
  title        = {Leveraging Structured Biological Knowledge for Counterfactual Inference:
                  a Case Study of Viral Pathogenesis},
  journal      = {CoRR},
  volume       = {abs/2101.05136},
  year         = {2021}
}

@article{DBLP:journals/corr/abs-2102-06626,
  author       = {Sara Mohammad Taheri and
                  Robert Osazuwa Ness and
                  Jeremy Zucker and
                  Olga Vitek},
  title        = {Do-calculus enables causal reasoning with latent variable models},
  journal      = {CoRR},
  volume       = {abs/2102.06626},
  year         = {2021}
}

@article{DBLP:journals/bioinformatics/GuoFVEBSV20,
  author       = {Dan Guo and
                  Melanie Christine F{\"{o}}ll and
                  Veronika Volkmann and
                  Kathrin Enderle{-}Ammour and
                  Peter Bronsert and
                  Oliver Schilling and
                  Olga Vitek},
  title        = {Deep multiple instance learning classifies subtissue locations in
                  mass spectrometry images from tissue-level annotations},
  journal      = {Bioinform.},
  volume       = {36},
  number       = {Supplement-1},
  pages        = {i300--i308},
  year         = {2020}
}

@article{DBLP:journals/corr/abs-2002-00511,
  author       = {Sara Mohammad Taheri and
                  Omkar Terse and
                  Eralp Dogu and
                  Magy Seif El{-}Nasr and
                  Olga Vitek},
  title        = {Investigating usability of MSstatsQC software},
  journal      = {CoRR},
  volume       = {abs/2002.00511},
  year         = {2020}
}

@article{DBLP:journals/bioinformatics/GuoBRAV19,
  author       = {Dan Guo and
                  Kylie A. Bemis and
                  Catherine Rawlins and
                  Jeffrey N. Agar and
                  Olga Vitek},
  title        = {Unsupervised segmentation of mass spectrometric ion images characterizes
                  morphology of tissues},
  journal      = {Bioinform.},
  volume       = {35},
  number       = {14},
  pages        = {i208--i217},
  year         = {2019}
}

@article{DBLP:journals/toplas/BergerHMVV19,
  author       = {Emery D. Berger and
                  Celeste Hollenbeck and
                  Petr Maj and
                  Olga Vitek and
                  Jan Vitek},
  title        = {On the Impact of Programming Languages on Code Quality: {A} Reproduction
                  Study},
  journal      = {{ACM} Trans. Program. Lang. Syst.},
  volume       = {41},
  number       = {4},
  pages        = {21:1--21:24},
  year         = {2019}
}

@inproceedings{DBLP:conf/chi/SchwabHVT0B19,
  author       = {Michail Schwab and
                  Sicheng Hao and
                  Olga Vitek and
                  James Tompkin and
                  Jeff Huang and
                  Michelle A. Borkin},
  title        = {Evaluating Pan and Zoom Timelines and Sliders},
  booktitle    = {{CHI}},
  pages        = {556},
  publisher    = {{ACM}},
  year         = {2019}
}

@inproceedings{DBLP:conf/nips/NessPV19,
  author       = {Robert Osazuwa Ness and
                  Kaushal Paneri and
                  Olga Vitek},
  title        = {Integrating Markov processes with structural causal modeling enables
                  counterfactual inference in complex systems},
  booktitle    = {NeurIPS},
  pages        = {14211--14221},
  year         = {2019}
}

@article{DBLP:journals/corr/abs-1901-10220,
  author       = {Emery D. Berger and
                  Celeste Hollenbeck and
                  Petr Maj and
                  Olga Vitek and
                  Jan Vitek},
  title        = {On the Impact of Programming Languages on Code Quality},
  journal      = {CoRR},
  volume       = {abs/1901.10220},
  year         = {2019}
}

@article{DBLP:journals/corr/abs-1911-02175,
  author       = {Robert Osazuwa Ness and
                  Kaushal Paneri and
                  Olga Vitek},
  title        = {Integrating Markov processes with structural causal modeling enables
                  counterfactual inference in complex systems},
  journal      = {CoRR},
  volume       = {abs/1911.02175},
  year         = {2019}
}

@article{DBLP:journals/corr/abs-1911-11894,
  author       = {Emery D. Berger and
                  Petr Maj and
                  Olga Vitek and
                  Jan Vitek},
  title        = {{FSE/CACM} Rebuttal\({}^{\mbox{2}}\): Correcting {A} Large-Scale Study
                  of Programming Languages and Code Quality in GitHub},
  journal      = {CoRR},
  volume       = {abs/1911.11894},
  year         = {2019}
}

@article{DBLP:journals/jcb/NessSMV18,
  author       = {Robert Osazuwa Ness and
                  Karen Sachs and
                  Parag Mallick and
                  Olga Vitek},
  title        = {A Bayesian Active Learning Experimental Design for Inferring Signaling
                  Networks},
  journal      = {J. Comput. Biol.},
  volume       = {25},
  number       = {7},
  pages        = {709--725},
  year         = {2018}
}

@inproceedings{DBLP:conf/recomb/GalitzineBCV18,
  author       = {Cyril Galitzine and
                  Pierre M. Jean Beltran and
                  Ileana M. Cristea and
                  Olga Vitek},
  title        = {Statistical Inference of Peroxisome Dynamics},
  booktitle    = {{RECOMB}},
  series       = {Lecture Notes in Computer Science},
  volume       = {10812},
  pages        = {54--74},
  publisher    = {Springer},
  year         = {2018}
}

@article{DBLP:journals/bioinformatics/BemisV17,
  author       = {Kylie A. Bemis and
                  Olga Vitek},
  title        = {matter: an {R} package for rapid prototyping with larger-than-memory
                  datasets on disk},
  journal      = {Bioinform.},
  volume       = {33},
  number       = {19},
  pages        = {3142--3144},
  year         = {2017}
}

@inproceedings{DBLP:conf/recomb/NessSMV17,
  author       = {Robert Osazuwa Ness and
                  Karen Sachs and
                  Parag Mallick and
                  Olga Vitek},
  title        = {A Bayesian Active Learning Experimental Design for Inferring Signaling
                  Networks},
  booktitle    = {{RECOMB}},
  series       = {Lecture Notes in Computer Science},
  volume       = {10229},
  pages        = {134--156},
  year         = {2017}
}

@article{DBLP:journals/bioinformatics/BemisHEFVMSV15,
  author       = {Kyle D. Bemis and
                  April Harry and
                  Livia S. Eberlin and
                  Christina Ferreira and
                  Stephanie M. van de Ven and
                  Parag Mallick and
                  Mark L. Stolowitz and
                  Olga Vitek},
  title        = {\emph{Cardinal}: an {R} package for statistical analysis of mass spectrometry-based
                  imaging experiments},
  journal      = {Bioinform.},
  volume       = {31},
  number       = {14},
  pages        = {2418--2420},
  year         = {2015}
}

@article{DBLP:journals/bioinformatics/PalmerOTLGDVPBA15,
  author       = {Andrew Palmer and
                  Ekaterina Ovchinnikova and
                  Mikael Thun{\'{e}} and
                  R{\'{e}}gis Lavigne and
                  Blandine Gu{\'{e}}vel and
                  Andrey Dyatlov and
                  Olga Vitek and
                  Charles Pineau and
                  Mats Bor{\'{e}}n and
                  Theodore Alexandrov},
  title        = {Using collective expert judgements to evaluate quality measures of
                  mass spectrometry images},
  journal      = {Bioinform.},
  volume       = {31},
  number       = {12},
  pages        = {375--384},
  year         = {2015}
}

@article{DBLP:journals/bmcbi/ChengLCRAV15,
  author       = {Lin{-}Yang Cheng and
                  Yansheng Liu and
                  Ching{-}Yun Chang and
                  Hannes L. R{\"{o}}st and
                  Ruedi Aebersold and
                  Olga Vitek},
  title        = {Statistical elimination of spectral features with large between-run
                  variation enhances quantitative protein-level conclusions in experiments
                  with data-independent spectral acquisition},
  journal      = {{BMC} Bioinform.},
  volume       = {16},
  number       = {{S-2}},
  pages        = {A4},
  year         = {2015}
}

@article{DBLP:journals/dagstuhl-reports/AebersoldKV15,
  author       = {Rudolf Aebersold and
                  Oliver Kohlbacher and
                  Olga Vitek},
  title        = {Computational Mass Spectrometry (Dagstuhl Seminar 15351)},
  journal      = {Dagstuhl Reports},
  volume       = {5},
  number       = {8},
  pages        = {9--33},
  year         = {2015}
}

@article{DBLP:journals/bioinformatics/BroudyKCSMAMASSTBSGCVMM14,
  author       = {Daniel Broudy and
                  Trevor Killeen and
                  Meena Choi and
                  Nicholas Shulman and
                  Deepak R. Mani and
                  Susan E. Abbatiello and
                  Deepak Mani and
                  Rushdy Ahmad and
                  Alexandria K. Sahu and
                  Birgit Schilling and
                  Kaipo Tamura and
                  Yuval Boss and
                  Vagisha Sharma and
                  Bradford W. Gibson and
                  Steven A. Carr and
                  Olga Vitek and
                  Michael J. MacCoss and
                  Brendan MacLean},
  title        = {A framework for installable external tools in Skyline},
  journal      = {Bioinform.},
  volume       = {30},
  number       = {17},
  pages        = {2521--2523},
  year         = {2014}
}

@article{DBLP:journals/bioinformatics/ChoiCCBKMV14,
  author       = {Meena Choi and
                  Ching{-}Yun Chang and
                  Timothy Clough and
                  Daniel Broudy and
                  Trevor Killeen and
                  Brendan MacLean and
                  Olga Vitek},
  title        = {MSstats: an {R} package for statistical analysis of quantitative mass
                  spectrometry-based proteomic experiments},
  journal      = {Bioinform.},
  volume       = {30},
  number       = {17},
  pages        = {2524--2526},
  year         = {2014}
}

@article{DBLP:journals/bioinformatics/YuHV13,
  author       = {Danni Yu and
                  Wolfgang Huber and
                  Olga Vitek},
  title        = {Shrinkage estimation of dispersion in Negative Binomial models for
                  RNA-seq experiments with small sample size},
  journal      = {Bioinform.},
  volume       = {29},
  number       = {10},
  pages        = {1275--1282},
  year         = {2013}
}

@article{DBLP:journals/ploscb/Vitek13,
  author       = {Olga Vitek},
  title        = {Leading a Statistical Bioinformatics Lab: It's All About Finding Balance},
  journal      = {PLoS Comput. Biol.},
  volume       = {9},
  number       = {11},
  year         = {2013}
}

@article{DBLP:journals/dagstuhl-reports/AebersoldKV13,
  author       = {Ruedi Aebersold and
                  Oliver Kohlbacher and
                  Olga Vitek},
  title        = {Computational Mass Spectrometry (Dagstuhl Seminar 13491)},
  journal      = {Dagstuhl Reports},
  volume       = {3},
  number       = {12},
  pages        = {1--16},
  year         = {2013}
}

@article{DBLP:journals/bmcbi/BemisEFCV12,
  author       = {Kyle D. Bemis and
                  Livia Eberlin and
                  Christina Ferreira and
                  R. Cooks and
                  Olga Vitek},
  title        = {Spatial segmentation and feature selection for desi imaging mass spectrometry
                  data with spatially-aware sparse clustering},
  journal      = {{BMC} Bioinform.},
  volume       = {13},
  number       = {{S-18}},
  pages        = {A8},
  year         = {2012}
}

@article{DBLP:journals/bmcbi/CloughTRAV12,
  author       = {Timothy Clough and
                  Safia Thaminy and
                  Susanne Ragg and
                  Ruedi Aebersold and
                  Olga Vitek},
  title        = {Statistical protein quantification and significance analysis in label-free
                  {LC-MS} experiments with complex designs},
  journal      = {{BMC} Bioinform.},
  volume       = {13},
  number       = {{S-16}},
  pages        = {S6},
  year         = {2012}
}

@article{DBLP:journals/bmcbi/MaVN12,
  author       = {Kelvin Ma and
                  Olga Vitek and
                  Alexey I. Nesvizhskii},
  title        = {A statistical model-building perspective to identification of {MS/MS}
                  spectra with PeptideProphet},
  journal      = {{BMC} Bioinform.},
  volume       = {13},
  number       = {{S-16}},
  pages        = {S1},
  year         = {2012}
}

@article{DBLP:journals/bioinformatics/YuDBKVSV11,
  author       = {Danni Yu and
                  John Danku and
                  Ivan Baxter and
                  Sungjin Kim and
                  Olena K. Vatamaniuk and
                  David E. Salt and
                  Olga Vitek},
  title        = {Noise reduction in genome-wide perturbation screens using linear mixed-effect
                  models},
  journal      = {Bioinform.},
  volume       = {27},
  number       = {16},
  pages        = {2173--2180},
  year         = {2011}
}

@article{DBLP:journals/bioinformatics/ZhengZRRV11,
  author       = {Cheng Zheng and
                  Shucha Zhang and
                  Susanne Ragg and
                  Daniel Raftery and
                  Olga Vitek},
  title        = {Identification and quantification of metabolites in \({}^{\mbox{1}}\)H
                  {NMR} spectra by Bayesian model selection},
  journal      = {Bioinform.},
  volume       = {27},
  number       = {12},
  pages        = {1637--1644},
  year         = {2011}
}

@article{DBLP:journals/ploscb/KallV11,
  author       = {Lukas K{\"{a}}ll and
                  Olga Vitek},
  title        = {Computational Mass Spectrometry-Based Proteomics},
  journal      = {PLoS Comput. Biol.},
  volume       = {7},
  number       = {12},
  year         = {2011}
}

@article{DBLP:journals/ploscb/Vitek09,
  author       = {Olga Vitek},
  title        = {Getting Started in Computational Mass Spectrometry-Based Proteomics},
  journal      = {PLoS Comput. Biol.},
  volume       = {5},
  number       = {5},
  year         = {2009}
}

@article{DBLP:journals/bmcbi/BrusniakBCCEGLLMSVZAW08,
  author       = {Mi{-}Youn K. Brusniak and
                  Bernd Bodenmiller and
                  David S. Campbell and
                  Kelly Cooke and
                  James Eddes and
                  Andrew Garbutt and
                  Hollis Lau and
                  Simon Letarte and
                  Lukas N. Mueller and
                  Vagisha Sharma and
                  Olga Vitek and
                  Ning Zhang and
                  Ruedi Aebersold and
                  Julian D. Watts},
  title        = {Corra: Computational framework and tools for {LC-MS} discovery and
                  targeted mass spectrometry-based proteomics},
  journal      = {{BMC} Bioinform.},
  volume       = {9},
  year         = {2008}
}

@inproceedings{DBLP:conf/eccb/VitekBCKV05,
  author       = {Olga Vitek and
                  Chris Bailey{-}Kellogg and
                  Bruce A. Craig and
                  Paul Kuliniewicz and
                  Jan Vitek},
  title        = {Reconsidering complete search algorithms for protein backbone {NMR}
                  assignment},
  booktitle    = {{ECCB/JBI}},
  pages        = {236},
  year         = {2005}
}