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ORCIDOlga Vitek
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- affiliation: Northeastern University, Boston, MA, USA
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2020 – today
- 2023
[j24]Dan Guo, Melanie Christine Föll, Kylie A. Bemis, Olga Vitek:
A noise-robust deep clustering of biomolecular ions improves interpretability of mass spectrometric images. Bioinform. 39(2) (2023)- [j23]Sara Mohammad Taheri, Vartika Tewari, Rohan Kapre, Ehsan Rahiminasab, Karen Sachs, Charles Tapley Hoyt, Jeremy Zucker, Olga Vitek:
Optimal adjustment sets for causal query estimation in partially observed biomolecular networks. Bioinform. 39(Supplement-1): 494-503 (2023) - 2022
- [j22]Laura South
, David Saffo, Olga Vitek, Cody Dunne, Michelle A. Borkin:
Effective Use of Likert Scales in Visualization Evaluations: A Systematic Review. Comput. Graph. Forum 41(3): 43-55 (2022) - 2021
- [j21]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:
Leveraging Structured Biological Knowledge for Counterfactual Inference: A Case Study of Viral Pathogenesis. IEEE Trans. Big Data 7(1): 25-37 (2021) - [i8]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:
Leveraging Structured Biological Knowledge for Counterfactual Inference: a Case Study of Viral Pathogenesis. CoRR abs/2101.05136 (2021) - [i7]Sara Mohammad Taheri, Robert Osazuwa Ness, Jeremy Zucker, Olga Vitek:
Do-calculus enables causal reasoning with latent variable models. CoRR abs/2102.06626 (2021) - 2020
- [j20]Dan Guo, Melanie Christine Föll, Veronika Volkmann, Kathrin Enderle-Ammour, Peter Bronsert, Oliver Schilling, Olga Vitek:
Deep multiple instance learning classifies subtissue locations in mass spectrometry images from tissue-level annotations. Bioinform. 36(Supplement-1): i300-i308 (2020) - [i6]Sara Mohammad Taheri, Omkar Terse, Eralp Dogu, Magy Seif El-Nasr, Olga Vitek:
Investigating usability of MSstatsQC software. CoRR abs/2002.00511 (2020)
2010 – 2019
- 2019
- [j19]Dan Guo, Kylie A. Bemis, Catherine Rawlins, Jeffrey N. Agar, Olga Vitek:
Unsupervised segmentation of mass spectrometric ion images characterizes morphology of tissues. Bioinform. 35(14): i208-i217 (2019) - [j18]Emery D. Berger, Celeste Hollenbeck, Petr Maj, Olga Vitek, Jan Vitek:
On the Impact of Programming Languages on Code Quality: A Reproduction Study. ACM Trans. Program. Lang. Syst. 41(4): 21:1-21:24 (2019) - [c5]Michail Schwab, Sicheng Hao, Olga Vitek, James Tompkin, Jeff Huang, Michelle A. Borkin:
Evaluating Pan and Zoom Timelines and Sliders. CHI 2019: 556 - [c4]Robert Osazuwa Ness, Kaushal Paneri, Olga Vitek:
Integrating Markov processes with structural causal modeling enables counterfactual inference in complex systems. NeurIPS 2019: 14211-14221 - [i5]Emery D. Berger, Celeste Hollenbeck, Petr Maj, Olga Vitek, Jan Vitek:
On the Impact of Programming Languages on Code Quality. CoRR abs/1901.10220 (2019) - [i4]Robert Osazuwa Ness, Kaushal Paneri, Olga Vitek:
Integrating Markov processes with structural causal modeling enables counterfactual inference in complex systems. CoRR abs/1911.02175 (2019) - [i3]Emery D. Berger, Petr Maj, Olga Vitek, Jan Vitek:
FSE/CACM Rebuttal2: Correcting A Large-Scale Study of Programming Languages and Code Quality in GitHub. CoRR abs/1911.11894 (2019) - 2018
- [j17]Robert Osazuwa Ness, Karen Sachs, Parag Mallick, Olga Vitek:
A Bayesian Active Learning Experimental Design for Inferring Signaling Networks. J. Comput. Biol. 25(7): 709-725 (2018) - [c3]Cyril Galitzine, Pierre M. Jean Beltran, Ileana M. Cristea, Olga Vitek:
Statistical Inference of Peroxisome Dynamics. RECOMB 2018: 54-74 - 2017
- [j16]Kylie A. Bemis, Olga Vitek:
matter: an R package for rapid prototyping with larger-than-memory datasets on disk. Bioinform. 33(19): 3142-3144 (2017) - [c2]Robert Osazuwa Ness, Karen Sachs, Parag Mallick, Olga Vitek:
A Bayesian Active Learning Experimental Design for Inferring Signaling Networks. RECOMB 2017: 134-156 - 2015
- [j15]Andrew Palmer, Ekaterina Ovchinnikova, Mikael Thuné, Régis Lavigne, Blandine Guével, Andrey Dyatlov, Olga Vitek, Charles Pineau, Mats Borén, Theodore Alexandrov:
Using collective expert judgements to evaluate quality measures of mass spectrometry images. Bioinform. 31(12): 375-384 (2015) - [j14]Kyle D. Bemis, April Harry, Livia S. Eberlin, Christina Ferreira, Stephanie M. van de Ven, Parag Mallick, Mark L. Stolowitz, Olga Vitek:
Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments. Bioinform. 31(14): 2418-2420 (2015) - [j13]Lin-Yang Cheng, Yansheng Liu, Ching-Yun Chang, Hannes L. Röst, Ruedi Aebersold, Olga Vitek:
Statistical elimination of spectral features with large between-run variation enhances quantitative protein-level conclusions in experiments with data-independent spectral acquisition. BMC Bioinform. 16(S-2): A4 (2015) - [i2]Rudolf Aebersold, Oliver Kohlbacher, Olga Vitek:
Computational Mass Spectrometry (Dagstuhl Seminar 15351). Dagstuhl Reports 5(8): 9-33 (2015) - 2014
- [j12]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, Vagisha Sharma, Bradford W. Gibson, Steven A. Carr, Olga Vitek, Michael J. MacCoss, Brendan MacLean:
A framework for installable external tools in Skyline. Bioinform. 30(17): 2521-2523 (2014) - [j11]Meena Choi, Ching-Yun Chang, Timothy Clough, Daniel Broudy, Trevor Killeen, Brendan MacLean, Olga Vitek:
MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments. Bioinform. 30(17): 2524-2526 (2014) - 2013
- [j10]Danni Yu, Wolfgang Huber, Olga Vitek:
Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size. Bioinform. 29(10): 1275-1282 (2013) - [j9]Olga Vitek:
Leading a Statistical Bioinformatics Lab: It's All About Finding Balance. PLoS Comput. Biol. 9(11) (2013) - [i1]Ruedi Aebersold, Oliver Kohlbacher, Olga Vitek:
Computational Mass Spectrometry (Dagstuhl Seminar 13491). Dagstuhl Reports 3(12): 1-16 (2013) - 2012
- [j8]Kelvin Ma, Olga Vitek, Alexey I. Nesvizhskii:
A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet. BMC Bioinform. 13(S-16): S1 (2012) - [j7]Timothy Clough, Safia Thaminy, Susanne Ragg, Ruedi Aebersold, Olga Vitek:
Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs. BMC Bioinform. 13(S-16): S6 (2012) - [j6]Kyle D. Bemis, Livia Eberlin, Christina Ferreira, R. Cooks, Olga Vitek:
Spatial segmentation and feature selection for desi imaging mass spectrometry data with spatially-aware sparse clustering. BMC Bioinform. 13(S-18): A8 (2012) - 2011
- [j5]Cheng Zheng, Shucha Zhang, Susanne Ragg, Daniel Raftery, Olga Vitek:
Identification and quantification of metabolites in 1H NMR spectra by Bayesian model selection. Bioinform. 27(12): 1637-1644 (2011) - [j4]Danni Yu, John Danku, Ivan Baxter, Sungjin Kim, Olena K. Vatamaniuk, David E. Salt, Olga Vitek:
Noise reduction in genome-wide perturbation screens using linear mixed-effect models. Bioinform. 27(16): 2173-2180 (2011) - [j3]Lukas Käll, Olga Vitek:
Computational Mass Spectrometry-Based Proteomics. PLoS Comput. Biol. 7(12) (2011)
2000 – 2009
- 2009
- [j2]Olga Vitek:
Getting Started in Computational Mass Spectrometry-Based Proteomics. PLoS Comput. Biol. 5(5) (2009) - 2008
- [j1]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, Ruedi Aebersold, Julian D. Watts:
Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics. BMC Bioinform. 9 (2008) - 2005
- [c1]Olga Vitek, Chris Bailey-Kellogg, Bruce A. Craig, Paul Kuliniewicz, Jan Vitek:
Reconsidering complete search algorithms for protein backbone NMR assignment. ECCB/JBI 2005: 236
Coauthor Index
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