Reconsidering complete search algorithms for protein backbone NMR assignment. - Olga Vitek; Chris Bailey-Kellogg; Bruce A. Craig; Paul Kuliniewicz; Jan Vitek (ECCB/JBI, 2005)

Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics. - Mi-Youn K. Brusniak; Bernd Bodenmiller; David S. Campbell; Kelly Cooke; James Eddes; Andrew Garbutt; Hollis Lau; Simon Letarte; Lukas N. Mueller; Vagisha Sharma; Olga Vitek; Ning Zhang; et al. (BMC Bioinform., 2008)

Getting Started in Computational Mass Spectrometry-Based Proteomics. - Olga Vitek (PLoS Comput. Biol., 2009)

Noise reduction in genome-wide perturbation screens using linear mixed-effect models. - Danni Yu; John Danku; Ivan Baxter; Sungjin Kim; Olena K. Vatamaniuk; David E. Salt; Olga Vitek (Bioinform., 2011)

Identification and quantification of metabolites in 1H NMR spectra by Bayesian model selection. - Cheng Zheng; Shucha Zhang; Susanne Ragg; Daniel Raftery; Olga Vitek (Bioinform., 2011)

Computational Mass Spectrometry-Based Proteomics. - Lukas Käll; Olga Vitek (PLoS Comput. Biol., 2011)

Spatial segmentation and feature selection for desi imaging mass spectrometry data with spatially-aware sparse clustering. - Kyle D. Bemis; Livia Eberlin; Christina Ferreira; R. Cooks; Olga Vitek (BMC Bioinform., 2012)

Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs. - Timothy Clough; Safia Thaminy; Susanne Ragg; Ruedi Aebersold; Olga Vitek (BMC Bioinform., 2012)

A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet. - Kelvin Ma; Olga Vitek; Alexey I. Nesvizhskii (BMC Bioinform., 2012)

Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size. - Danni Yu; Wolfgang Huber; Olga Vitek (Bioinform., 2013)

Computational Mass Spectrometry (Dagstuhl Seminar 13491). - Ruedi Aebersold; Oliver Kohlbacher; Olga Vitek (Dagstuhl Reports, 2013)

Leading a Statistical Bioinformatics Lab: It's All About Finding Balance. - Olga Vitek (PLoS Comput. Biol., 2013)

A framework for installable external tools in Skyline. - Daniel Broudy; Trevor Killeen; Meena Choi; Nicholas Shulman; Deepak R. Mani; Susan E. Abbatiello; Deepak Mani; Rushdy Ahmad; Alexandria K. Sahu; Birgit Schilling; Kaipo Tamura; Yuval Boss; et al. (Bioinform., 2014)

MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments. - Meena Choi; Ching-Yun Chang; Timothy Clough; Daniel Broudy; Trevor Killeen; Brendan MacLean; Olga Vitek (Bioinform., 2014)

Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments. - Kyle D. Bemis; April Harry; Livia S. Eberlin; Christina Ferreira; Stephanie M. van de Ven; Parag Mallick; Mark L. Stolowitz; Olga Vitek (Bioinform., 2015)

Using collective expert judgements to evaluate quality measures of mass spectrometry images. - Andrew Palmer; Ekaterina Ovchinnikova; Mikael Thuné; Régis Lavigne; Blandine Guével; Andrey Dyatlov; Olga Vitek; Charles Pineau; Mats Borén; Theodore Alexandrov (Bioinform., 2015)

Statistical elimination of spectral features with large between-run variation enhances quantitative protein-level conclusions in experiments with data-independent spectral acquisition. - Lin-Yang Cheng; Yansheng Liu; Ching-Yun Chang; Hannes L. Röst; Ruedi Aebersold; Olga Vitek (BMC Bioinform., 2015)

Computational Mass Spectrometry (Dagstuhl Seminar 15351). - Rudolf Aebersold; Oliver Kohlbacher; Olga Vitek (Dagstuhl Reports, 2015)

matter: an R package for rapid prototyping with larger-than-memory datasets on disk. - Kylie A. Bemis; Olga Vitek (Bioinform., 2017)

Statistical Inference of Peroxisome Dynamics. - Cyril Galitzine; Pierre M. Jean Beltran; Ileana M. Cristea; Olga Vitek (RECOMB, 2018)

A Bayesian Active Learning Experimental Design for Inferring Signaling Networks. - Robert Osazuwa Ness; Karen Sachs; Parag Mallick; Olga Vitek (J. Comput. Biol., 2018)

Evaluating Pan and Zoom Timelines and Sliders. - Michail Schwab; Sicheng Hao; Olga Vitek; James Tompkin 001; Jeff Huang 002; Michelle A. Borkin (CHI, 2019)

Integrating Markov processes with structural causal modeling enables counterfactual inference in complex systems. - Robert Osazuwa Ness; Kaushal Paneri; Olga Vitek (NeurIPS, 2019)

Unsupervised segmentation of mass spectrometric ion images characterizes morphology of tissues. - Dan Guo; Kylie A. Bemis; Catherine Rawlins; Jeffrey N. Agar; Olga Vitek (Bioinform., 2019)

On the Impact of Programming Languages on Code Quality. - Emery D. Berger; Celeste Hollenbeck; Petr Maj; Olga Vitek; Jan Vitek (CoRR, 2019)

FSE/CACM Rebuttal2: Correcting A Large-Scale Study of Programming Languages and Code Quality in GitHub. - Emery D. Berger; Petr Maj; Olga Vitek; Jan Vitek (CoRR, 2019)

On the Impact of Programming Languages on Code Quality: A Reproduction Study. - Emery D. Berger; Celeste Hollenbeck; Petr Maj; Olga Vitek; Jan Vitek (ACM Trans. Program. Lang. Syst., 2019)

Deep multiple instance learning classifies subtissue locations in mass spectrometry images from tissue-level annotations. - Dan Guo; Melanie Christine Föll; Veronika Volkmann; Kathrin Enderle-Ammour; Peter Bronsert; Oliver Schilling; Olga Vitek (Bioinform., 2020)

New mixture models for decoy-free false discovery rate estimation in mass spectrometry proteomics. - Yisu Peng; Shantanu Jain; Yong Fuga Li; Michal Gregus; Alexander R. Ivanov; Olga Vitek; Predrag Radivojac (Bioinform., 2020)

Investigating usability of MSstatsQC software. - Sara Mohammad Taheri; Omkar Terse; Eralp Dogu; Magy Seif El-Nasr; Olga Vitek (CoRR, 2020)

Do-calculus enables causal reasoning with latent variable models. - Sara Mohammad Taheri; Robert Osazuwa Ness; Jeremy Zucker; Olga Vitek (CoRR, 2021)

Leveraging Structured Biological Knowledge for Counterfactual Inference: A Case Study of Viral Pathogenesis. - Jeremy Zucker; Kaushal Paneri; Sara Mohammad Taheri; Somya Bhargava; Pallavi Kolambkar; Craig Bakker; Jeremy Teuton; Charles Tapley Hoyt; Kristie L. Oxford; Robert Osazuwa Ness; Olga Vitek (IEEE Trans. Big Data, 2021)

Do-calculus enables estimation of causal effects in partially observed biomolecular pathways. - Sara Mohammad Taheri; Jeremy Zucker; Charles Tapley Hoyt; Karen Sachs; Vartika Tewari; Robert Osazuwa Ness; Olga Vitek (Bioinform., 2022)

Effective Use of Likert Scales in Visualization Evaluations: A Systematic Review. - Laura South; David Saffo; Olga Vitek; Cody Dunne; Michelle A. Borkin (Comput. Graph. Forum, 2022)

Optimal adjustment sets for causal query estimation in partially observed biomolecular networks. - Sara Mohammad Taheri; Vartika Tewari; Rohan Kapre; Ehsan Rahiminasab; Karen Sachs; Charles Tapley Hoyt; Jeremy Zucker; Olga Vitek (Bioinform., 2023)

A noise-robust deep clustering of biomolecular ions improves interpretability of mass spectrometric images. - Dan Guo; Melanie Christine Föll; Kylie A. Bemis; Olga Vitek (Bioinform., 2023)

Causal identification with Y0. - Charles Tapley Hoyt; Craig Bakker; Richard J. Callahan; Joseph Cottam; August George; Benjamin M. Gyori; Haley M. Hummel; Nathaniel Merrill; Sara Mohammad Taheri; Pruthvi Prakash Navada; Marc-Antoine Parent; Adam Rupe; et al. (CoRR, 2025)