Northeastern University

College of Science
College of Computer and Information Science
360 Huntington Ave.
Boston, Massachusetts 02115

 

Short List:

  1. E. Dogu, S. Mohammad-Taheri, S. E. Abbatiello, M. S. Bereman, B. MacLean, B. Schilling, O. Vitek. “MSstatsQC: Longitudinal system suitability monitoring and quality control for targeted proteomic experiments”. Molecular and Cellular Proteomics, M116.064774, 2017. [LINK]
  2. R. O. Ness, K. Sachs, P. Mallick, O. Vitek. “A Bayesian active learning experimental design for inferring signaling networks”. International Conference on Research in Computational Molecular Biology (RECOMB),10229:134, Springer, 2017. [LINK]
  3. K. D. Bemis, A. Harry, L. S. Eberlin, C. R. Ferreira, S. M. van de Ven, P. Mallick, M. Stolowitz, O. Vitek. “Probabilistic segmentation of mass spectrometry images helps select important ions and characterize confidence in the resulting segments”. Molecular and Cellular Proteomics, O115.053918, 2016. [LINK]
  4. K. D. Bemis, A. Harry, L. S. Eberlin, C. Ferreira, S. M. van de Ven, P. Mallick, M. Stolowitz, O. Vitek. “Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments”. Bioinformatics, 31:2418, 2015. [LINK]
  5. M. Choi, C.-Y. Chang, T. Clough, D. Broudy, T. Killeen, B. MacLean, O. Vitek. “MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments”. Bioinformatics, 30:2524, 2014. [LINK]
  6. C.-Y. Chang, E. Sabidó, R. Aebersold, O. Vitek. “Targeted protein quantification using sparse reference labeling”. Nature Methods, 11:301, 2014. [LINK]
  7. D. Yu, W. Huber, O. Vitek. “Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size”. Bioinformatics, 29:1275, 2013. [LINK]
  8. A. L. Oberg, O. Vitek. “Statistical design of quantitative mass spectrometry-based proteomic experiments”. Journal of Proteome Research, 8:2144, 2009 [LINK].

 

All publications:

  1. E. Dogu, S. Mohammad-Taheri, S. E. Abbatiello, M. S. Bereman, B. MacLean, B. Schilling, O. Vitek. “MSstatsQC: Longitudinal system suitability monitoring and quality control for targeted proteomic experiments”. Molecular and Cellular Proteomics, M116.064774, 2017. [LINK]
  2. R. O. Ness, K. Sachs, P. Mallick, O. Vitek. “A Bayesian active learning experimental design for inferring signaling networks”. International Conference on Research in Computational Molecular Biology (RECOMB),10229:134, Springer, 2017. [LINK]
  3. M. Choi, Z. F. Eren-Dogu, C. M. Colangelo, J. S. Cottrell, M. R. Hoopmann, E. A. Kapp, S. Kim, H. Lam, T. A. Neubert, M. Palmblad, B. S. Phinney, S. T. Weintraub, B. MacLean, O. Vitek. “ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of differentially abundant proteins in label-free quantitative LC-MS/MS experiments”. Journal of Proteome Research, in press, 2016.
  4. C. Terfve, E. Sabidó, Y. Wu, E. Gonçalves, M. Choi, S. Vaga, O. Vitek, J. Saez-Rodriguez, R. Aebersold. “System-wide quantitative proteomics of the metabolic syndrome in mice: genotypic and dietary effects”. Journal of Proteome Research, 16:831, 2017. [LINK]
  5. S. van de Ven, K. Bemis, K. Lau, R. Adusumilli, U. Kota, M. Stolowitz, O. Vitek, P. Mallick, S. Gambhir. “Protein biomarkers on tissue as imaged via MALDI mass spectrometry: A systematic approach to study the limits of detection”. Proteomics, 16:1660, 2016.[LINK]
  6. K. D. Bemis, A. Harry, L. S. Eberlin, C. R. Ferreira, S. M. van de Ven, P. Mallick, M. Stolowitz, O. Vitek. “Probabilistic segmentation of mass spectrometry images helps select important ions and characterize confidence in the resulting segments”. Molecular and Cellular Proteomics, O115.053918, 2016. [LINK]
  7. R. Ness, K. Sachs, O. Vitek. “From correlation to causality: statistical approaches to learning regulatory relationships in large-scale biomolecular investigations”. Journal of Proteome Research, 15:683, 2016. [LINK]
  8. E. Borràs, E. Cantó, M. Choi, L. M. Villar, J. C. Álvarez-Cermeño, C. Chiva, X. Montalban, O. Vitek, M. Comabella, E. Sabidó. “Protein-based classifier to predict conversion from clinically isolated syndrome to multiple sclerosis”. Molecular and Cellular Proteomics, M115.053256, 2016. [LINK]
  9. S. Surinova, M. Choi, S. Tao, P. J. Schüffler, C.-Y. Chang, T. Clough, K. Vysloužil, M. Khoylou, J. Srovnal, Y. Liu, M. Matondo, R. Hüttenhain, H. Weisser, J. M. Buhmann, M. Hajdúch, H. Brenner, O. Vitek, R. Aebersold. “Prediction of colorectal cancer diagnosis based on circulating plasma proteins”. EMBO Molecular Medicine, 8:1361, 2015. [LINK]
  10. S. Surinova, L. Radová, M. Choi, J. Srovnal, H. Brenner, O. Vitek, M. Hajdúch, R. Aebersold. “Non-invasive prognostic protein biomarker signatures associated with colorectal cancer”. EMBO Molecular Medicine, 7:1153, 2015. [LINK]
  11. M. J. Rardin, B. Schilling, Lin.-Y. Cheng, B. X. MacLean, D. J. Sorenson, A. K. Sahu, M. J. MacCoss, O. Vitek and B. W. Gibson. “MS1 peptide ion intensity chromatograms in MS2 (SWATH) data independent acquisitions: Improving post acquisition analysis of proteomic experiments”. Molecular and Cellular Proteomics, O115.048181, 2015. [LINK]
  12. A. Palmer, E. Ovchinnikova, M. Thune, R. Lavigne, B. Guevel, A. Dyatlov, O. Vitek, C. Pineau, M. Boren, T. Alexandrov. “Using collective expert judgements to evaluate quality measures of mass spectrometry images”. Bioinformatics 31:i375, 2015. [LINK]
  13. K. D. Bemis, A. Harry, L. S. Eberlin, C. Ferreira, S. M. van de Ven, P. Mallick, M. Stolowitz, O. Vitek. “Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments”. Bioinformatics, 31:2418, 2015. [LINK]
  14. R. Bruderer, O. M. Bernhardt, T. Gandhi, S. M. Miladinovic, L.-Y. Cheng, S. Messner, T. Ehrenberger, V. Zanotelli, Y. Butscheid, C. Escher, O. Vitek, O. Rinner, L. Reiter. “Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen treated 3D liver microtissues”. Molecular and Cellular Proteomics, M114.044305, 2015. [LINK]
  15. Y. Liu, A. Buil, B. C. Collins, L. C. J. Gillet, L. C. Blum, L.‐Y. Cheng, O. Vitek, J. Mouritsen, G. Lachance, T. D. Spector, E. T. Dermitzakis, R. Aebersold. “Quantitative variability of 342 plasma proteins in a human twin population”. Molecular Systems Biology, 11:786, 2015. [LINK]
  16. N. Selevsek, C.-Y. Chang, L. C. Gillet, P. Navarro, O. M. Bernhardt, L. Reiter, L.-Y. Cheng, O. Vitek, R. Aebersold. “Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-MS”. Molecular and Cellular Proteomics, M113.035550, 2015. [LINK]
  17. M. Choi, C.-Y. Chang, T. Clough, D. Broudy, T. Killeen, B. MacLean, O. Vitek. “MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments”. Bioinformatics, 30:2524, 2014. [LINK]
  18. D. Broudy, T. Killeen, M. Choi, N. Shulman, D. R. Mani, S. E. Abbatiello, D. Mani, R. Ahmad, A. K. Sahu, B. Schilling, K. Tamura, Y. Boss, V. Sharma, B. W. Gibson, S. A. Carr, O. Vitek, M. J. MacCoss, B. MacLean. “A framework for installable external tools in Skyline”. Bioinformatics, 30:2521, 2014. [LINK]
  19. C.-Y. Chang, E. Sabidó,R. Aebersold, O. Vitek. “Targeted protein quantification using sparse reference labeling”. Nature Methods, 11:301, 2014. [LINK]
  20. S. Carr, S. E. Abbatiello. B. L. Ackermann, C. Borchers, B. Domon, E. W. Deutsch, R. P. Grant, A. N. Hoofnagle, R. Hüttenhain, J. M. Koomen, D. C. Liebler, T. Liu, B. MacLean, D. R. Mani, E. Mansfield, H. Neubert, A. G. Paulovich, L. Reiter, O. Vitek, R. Aebersold, L. Anderson, R. Bethem, J. Blonder, E. Boja, J. Botelho, M. Boyne, R. A. Bradshaw, A. L. Burlingame, D. Chan, H. Keshishian, E. Kuhn, C. Kinsinger, J. Lee, S.-W. Lee, R. Moritz, J. Oses-Prieto, N. Rifai, J. Ritchie, H. Rodriguez, P. R. Srinivas, R.R. Townsend, J. Van Eyk, G. Whiteley, A. Wiita, S. Weintraub. “Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach”. Molecular and Cellular Proteomics, M113.036095, 2014. [LINK]
  21. F. Cerciello, M. Choi, A. Nicastri, D. Bausch-Fluck, A. Ziegler, O. Vitek, E. Felley-Bosco, R. Stahel, R. Aebersold, B. Wollscheid. “Identification of a seven glycopeptide signature for malignant pleural mesothelioma in human serum by selected reaction monitoring”. Clinical Proteomics, 10:16, 2013. [LINK]
  22. S. Surinova, R. Hüttenhain, C.-Y. Chang, L. Espona, O. Vitek, R. Aebersold. “Automated selected reaction monitoring data analysis workflow for large-scale targeted proteomic studies”. Nature Protocols, 8:1602, 2013. [LINK]
  23. E. Sabidó, Y. Wu, L. Bautista, T. Porstmann, C.-Y. Chang, O. Vitek, M. Stoffel, R. Aebersold. “Targeted proteomics reveals strain-specific changes in the mouse insulin and central metabolic pathways after a sustained high-fat diet”. Molecular Systems Biology, 9:681, 2013. [LINK]
  24. D. Yu, W. Huber, O. Vitek. “Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size”. Bioinformatics, 29:1275, 2013. [LINK]
  25. D. Yu, J. M. C. Danku, I. Baxter, S. Kim, O. K. Vatamaniuk, O. Vitek, D. E. Salt. “High-resolution genome-wide scan of genes, gene-networks and cellular systems impacting the yeast ionome”. BMC Genomics, 13:623, 2012. [LINK]
  26. T. Clough, S. Thaminy, S. Ragg, R. Aebersold, O. Vitek. “Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs”. BMC Bioinformatics, 13:S16, 2012. [LINK]
  27. K. Ma, O. Vitek, A. I. Nesvizhskii. “A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet”. BMC Bioinformatics, 13:S16, 2012. [LINK]
  28. J. K. Muhlemann, H. Maeda, C.-Y. Chang, P. San Miguel, I. Baxter, B. Cooper, M. A. Perera, B. J. Nikolau, O. Vitek, J. A. Morgan, N. Dudareva. “Developmental changes in the metabolic network of snapdragon flowers”. PLoS One, 7(7):e40381, 2012. [LINK]
  29. E. Sabidó, O. Quehenberger, Q. Shen, C.-Y. Chang, I. Shah, A. M. Armando, A. Andreyev, O. Vitek, E. A. Dennis, R. Aebersold. “Targeted proteomics of the Eicosanoid biosynthetic pathway completes an integrated genomics-proteomics-metabolomics picture of cellular metabolism”. Molecular and Cellular Proteomics, 11:M111.014746, 2012. [LINK]
  30. C.-Y. Chang, P. Picotti, R. Hüttenhain, V. Heinzelmann-Schwarz, M. Jovanovic, R. Aebersold, O. Vitek. “Protein significance analysis in selected reaction monitoring (SRM) measurements”. Molecular and Cellular Proteomics, 11:M111.014662, 2012. [LINK]
  31. T. Ye, C. Zheng, S. Zhang, G. A. N. Gowda, O. Vitek, D. Raftery. “Add to Subtract: A simple method to remove complex background signals from the 1H nuclear magnetic resonance spectra of mixtures”. Analytical Chemistry, 84:994, 2012. [LINK,NEWS]
  32. L. Käll, O. Vitek. “Computational mass spectrometry-based proteomics”. PLoS Computational Biology, 7:e1002277, 2011. [LINK]
  33. L. S. Riter, P. K. Jensen, J. M. Ballam, E. Urbanczyk-Wochniak, T. Clough, O. Vitek, J. Sutton, M. Athanas, M. F. Lopez, S. MacIsaac. “Evaluation of label-free quantitative proteomics in a plant matrix: A case study of the night-to-day transition in corn leaf”. Analytical Methods, 3:2733, 2011. [LINK]
  34. D. Yu, J. Danku, I. Baxter, S. Kim, O. K. Vatamaniuk, D. E. Salt, O. Vitek. “Noise reduction in genome-wide perturbation screens using linear mixed-effect models”. Bioinformatics, 27:2173, 2011. [LINK]
  35. T. Clough, S. Braun, V. Fokin, I. Ott, S. Ragg, G. Schadow, O. Vitek. “Statistical design and analysis of label-free LC-MS proteomic experiments: A case study of coronary artery disease”. Methods in Molecular Biology, 728:293, 2011. [LINK]
  36. C. Zheng, S. Zhang, S. Ragg, D. Raftery, O. Vitek. “Identification and quantification of metabolites in 1H NMR spectra by Bayesian model selection”. Bioinformatics, 27:1637, 2011. [LINK]
  37. A. L. Dill, L. S. Eberlin, A. B. Costa, C. Zheng, D. R. Ifa, L. Cheng, T. A. Masterson, M. O. Koch, O. Vitek, R. G. Cooks. “Multivariate statistical identification of human bladder carcinomas using ambient ionization imaging mass spectrometry”. Chemistry: A European Journal, 11:2897, 2011. [LINK]
  38. B. Bodenmiller, S. Wanka, C. Kraft, J. Urban, D. Campbell, P. Pedrioli, B. Gerrits,  P. Picotti, H. Lam, O. Vitek, M.-Y. Brusniak, B. Roschitzki, C. Zhang, R. Schlapbach, K. Shokat, A. Colman-Lerner, A. Nesvizhskii, M. Peter, R. Loewith, C. von Mering and R. Aebersold.”Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast”. Science Signaling, 3:rs4, 2010. [LINK]
  39. I. Baxter, J. N. Brazelton, D. Yu, Y. S. Huang, B. Lahner, E. Yakubova, Y. Li, J. Bergelson, J. O. Borevitz, M. Nordborg, O. Vitek, D. E. Salt. “A coastal cline in sodium accumulation in Arabidopsis thaliana is driven by natural variation of the sodium transporter AtHKT1;1″. PLoS Genetics, 6:e1001193, 2010. [LINK,NEWS]
  40. A. L. Dill, L. S. Eberlin, C. Zheng, A. B. Costa, D. R. Ifa, L. Cheng, T. A. Masterson, M. O. Koch, O. Vitek and R. G. Cooks. “Multivariate statistical differentiation of renal cell carcinomas based on lipidomic analysis by ambient ionization imaging mass spectrometry”. Analytical and Bioanalytical Chemistry, 398:2969, 2010. [LINK]
  41. T. Clough, M. Key, I. Ott, S. Ragg, G. Schadow, O. Vitek. “Protein quantification in label-free LC-MS experiments”. Journal of Proteome Research, 8:5275, 2009. [LINK]
  42. C. Sherwood, A. Eastham, L. W. Lee, J. Risler, O. Vitek, D. B. Martin. “Correlation between y-type ions observed in ion trap and triple quadrupole mass spectrometers”. Journal of Proteome Research, 8:4243, 2009. [LINK]
  43. S. Zhang, C. Zheng, I. R. Lanza, K. S. Nair, D. Raftery, O. Vitek. “Interdependence of signal processing and analysis of urine 1H NMR spectra for metabolic profiling”. Analytical Chemistry, 81:6080, 2009. [LINK]
  44. O. Vitek. “Getting started in computational mass spectrometry-based proteomics”. PLoS Computational Biology, 5:e1000366, 2009. [LINK]
  45. A. L. Oberg, O. Vitek. “Statistical design of quantitative mass spectrometry-based proteomic experiments”. Journal of Proteome Research, 8:2144, 2009 [LINK].
  46. M.-Y. Brusniak, B. Bodenmiller, D. Campbell, K. Cooke, J. Eddes, A. Garbutt, H. Lau, S. Letarte, L. N. Mueller, V. Sharma, O. Vitek, N. Zhang, R. Aebersold, J. D. Watts. “Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics”. BMC Bioinformatics, 9:542, 2008 [LINK]
  47. S. Letarte, M.-Y. Brusniak, D. Campbell, J. Eddes, C. J. Kemp, H. Lau, L. Mueller, A. Schmidt, P. Shannon, K. S. Kelly-Spratt, O. Vitek, H. Zhang, R. Aebersold and J. D. Watts. “Differential plasma glycoproteome of p19ARF skin cancer mouse model using the Corra label-free LC-MS proteomics platform”. Proteomics: Clinical Applications, 4:105, 2008 [LINK].
  48. I. R. Baxter, O. Vitek, B. Lahner, B. Muthukumar, M. Borghi, J. Morrissey, M. L. Guerinot, D. E. Salt. “The leaf ionome as a multivariable system to detect a plant’s physiological status”. Proceedings of the National Academy of Sciences, 105:12081, 2008 [LINK].
  49. L. Hohmann, J. Eng, A. Gemmill, J. Klimek, O. Vitek, G. Reid, D. Martin. “Quantification of the compositional information provided by immonium ions on a quadrupole-TOF mass spectrometer”. Analytical Chemistry, 80:5596, 2008. [LINK]
  50. A. Nesvizhskii, O. Vitek, R. Aebersold. “Analysis and validation of proteomic data generated by tandem mass spectrometry”. Nature Methods, 4:787, 2007. [LINK]
  51. L. N. Mueller, O. Rinner, A. Schmidt, S. Letarte, B. Bodenmiller, M.-Y. Brusniak, O. Vitek, R. Aebersold, M. Muller. “SuperHirn – a novel tool for high resolution LC-MS based peptide/protein profiling”. Proteomics, 7:3470, 2007. [LINK]
  52. O. Vitek, C. Bailey-Kellogg, B. A. Craig, J. Vitek. “Inferential backbone assignment for sparse data”. Journal of Biomolecular NMR, 31:187, 2006. [LINK]
  53. Z. Yi, O. Vitek, M. A. Qasim, S. M. Lu, W. Lu, M. Ranjbar, J. Li, M. C. Laskowski, C. Bailey-Kellogg, M. Laskowski. “Functional evolution within protein superfamilies”. Proteins, 63:697, 2006. [LINK]
  54. O. Vitek, C. Bailey-Kellogg, B. A. Craig, P. Kuliniewicz, J. Vitek. “Reconsidering complete search algorithms for protein backbone NMR assignment”. Bioinformatics, 21:ii230, 2005. [LINK]
  55. L. S. Riter, O. Vitek, K. M. Gooding, B. D. Hodge, R. K. Julian, Jr. “Statistical design of experiments as a tool in mass spectrometry”. Journal of Mass Spectrometry, 40:565, 2005. [LINK]
  56. O. Vitek, J. Vitek, B. A. Craig, C. Bailey-Kellogg. “Model-based assignment and inference of protein backbone nuclear magnetic resonances”. Statistical Applications in Genetics and Molecular Biology, 3:Article 6, 2004. [LINK]
  57. J. C. Fleet, L. Wang, O. Vitek, B. A. Craig, H. J. Edenberg. “Gene expression profiling of Caco-2 BBe cells suggests a role for specific signaling pathways during intestinal differentiation”. Physiological Genomics, 13:57, 2003. [LINK]
  58. T. V. Perneger, A.-C. Rae, J.-M. Gaspoz, F. Borst, O. Vitek, C. Heliot. “Screening for pressure ulcer risk in an acute care hospital: Development of a brief bedside scale”. Journal of Clinical Epidemiology, 55:498, 2002.
  59. B. A. Craig, O. Vitek, M. A. Black, M. Tanurdzic, R. W. Doerge. “Designing microarrays”. InProceedings of Applied Statistics in Agriculture, Kansas State University, edited by George Milliken, p.159, 2001.
  60. S. Beer-Borst, A. Morabia, S. Hercberg, O. Vitek, M. S. Bernstein, P. Galan, R. Galasso, S. Giampaoli, S. Houterman, E. McCrum, S. Panico, F. Pannozzo, P. Preziosi, L. Ribas, L. Serra-Majem, W. M. M. Verschuren, J. Yarnell, M. E. Northridge. “Obesity and other health determinants across Europe: The Euralim Project”. Journal of Epidemiology and Community Health, 54:424, 2000.
  61. S. Beer-Borst, S. Hercberg, A. Morabia, M. S. Bernstein, P. Galan, R. Galasso, S. Giampaoli, E. McCrum, S. Panico, P. Preziosi, L. Ribas, L. Serra-Majem, M. F. Vescio, O. Vitek, J. Yarnell, M. E. Northridge. “Dietary patterns in six European populations: results from Euralim, a collaborative European data harmonization and information campaign”. European Journal of Clinical Nutrition, 54:253, 2000.