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A full list of publications and other contributions is available in my Curriculum Vitae. The name of students that work under my supervision are italicized.

Work Submitted or in Progress

  1. David Kepplinger, Joe Watson and Gabriela V. Cohen Freue. A comprehensive study of regularized instrumental variables estimators with applications to genomics. To be submitted to PLoS Computational Biology; 80% completed.

  2. Anthony Christidis and Gabriela V. Cohen Freue. Robust Multi-Model Subset Selection, 40% completed. Accompanying R package RMSS published.

  3. Anthony Christidis, Jeyshinee Pyneeandee and Gabriela V. Cohen Freue. Fast and Scalable Cellwise Robust Ensembles for High-Dimensional Data, 40% completed. Accompanying R packages robStepSplitReg and srlars published.

  4. Maggie Liu and Gabriela V. Cohen Freue. Fast Robust Covariance-Regularized Regression for High-Dimensional Data. 70% completed. Manuscript based on Maggie’s MSc thesis.

  5. Chloe You, Linbo Wang and Gabriela V. Cohen Freue. On Regularized Risk Regression for High-Dimensional Data. 70% completed. Manuscript based on Chloe’s MSc thesis.

  6. Nirupama Tamvada, Sahir Bhatnagar and Gabriela V. Cohen Freue. Penalized Competing Risks Analysis using Case-Base Sampling for High-Dimensional Data. 60% completed. Manuscript based on Nirupama’s MSc thesis.

Refereed Publications: 2012 – Present

  1. Arjun Baghela, Andy An, Peter Zhang, Erica Acton, Jeff Gauthier, Elsa Brunet-Ratnasingham, Travis Blimkie, Gabriela Cohen Freue, Daniel Kauffman, Amy Lee, Roger Levesque, Robert Hancock. Predicting severity in Covid-19 disease using sepsis blood gene expression signatures. Scientific Reports 13, 1247.

  2. Nikolas Krstic, Kevin Multani, David S. Wishart, Tom Blydt-Hansen, Gabriela Cohen Freue. (2022) The impact of methodological choices when developing a metabolomic predictive model of T cell-mediated rejection. Under review in Statistics in Medicine 41, 3511-3526.

  3. Arjun Baghela, Olga M Pena, Amy H Lee, Beverlie Baquir, Reza Falsafi, Andy An, Susan W Farmer, Andrew Hurlburt, Alvaro Mondragon-Cardona, Juan Diego Rivera, Andrew Baker, Uriel Trahtemberg, Maryam Shojaei, Carlos Eduardo, Jimenez-Canizales, Claudia C Dos Santos, Benjamin Tang, Hjalmar R Bouma, Gabriela Cohen Freue, and Robert E.W. Hancock. (2022) Predicting sepsis severity at first clinical presentation: The role of endotypes and mechanistic signatures. EBioMedicine, 103776.

  4. Daisuke Ennishi, Shannon Healy, Ali Bashashati, …, Gabriela V. Cohen Freue, Louis M. Staudt, Joseph M. Connors, Marco A. Marra, Sohrab P. Shah, Randy D. Gascoyne, David W. Scott, and Christian Steidl. (2020) TMEM30A loss-of-function mutations drive lymphomagenesis and confer therapeutically exploitable vulnerability in B-cell lymphoma. Nature Medicine 26,577-588.

  5. Gabriela V. Cohen Freue, David Kepplinger, Matias Salibian-Barrera, and Ezequiel Smucler. (2019) PENSE: a Penalized Elastic Net S-Estimator. Annals of Applied Statistics, with accompanying CRAN library pense; Authors are ordered alphabetically. pdf.

  6. Hao Luo, Gabriela V. Cohen Freue, Xin Zhao, Alexandre Bouchard-Cote, Igor Burstyn, Paul Gustafson. (2019) A new perspective on the benefits of the gene-environment independence in case-control studies. Canadian Journal of Statistics** *47, 473–486.

  7. Mohammad A Anwar*, Darlene Liying Dai*, Janet Wilson-McManus, Gordon A. Francis, Christoph H Borchers, Bruce M. McManus, John S. Hill, Gabriela V. Cohen Freue. (2019) Multiplexed LC/ESI-MRM-MS-based Assay for Identification of Coronary Artery Disease Biomarkers in Human Plasma. *Equal contributors. Proteomics-Clinical Applications. doi:10.1002/prca.201700111. Accepted version here

  8. Singh, Amrit, Shannon, Casey, Kim, Young Woong, Yang, Chen Xi, Balshaw, Robert, Cohen Freue, Gabriela, Gauvreau, Gail, FitzGerald, J Mark, Boulet, Louis-Philippe, O’Byrne, Paul, Tebbutt, Scott. (2018) Novel blood-based transcriptional biomarker panels predict the late phase asthmatic response. American Journal of Respiratory and Critical Care Medicine 197, 450-462.

  9. Nikolaus Fortelny, Christopher Overall, Paul Pavlidis, Gabriela V. Cohen Freue. (2017) Can we predict protein from mRNA levels? Nature 547, E19–E20, doi:10.1038/nature22293 Link. With accompanying Shiny Application here.

  10. David Kepplinger*, Mandeep Takhar*, Mayu Sasaki, Zsuzsanna Hollander, Derek Smith, W. Robert McMaster, Raymond T. Ng, Gabriela Cohen Freue. (2017) PGCA: A New Algorithm to Link Protein Groups Created from MS/MS Data. PLoS ONE 12(5):e0177569. Link. With accompanying Bioconductor library here. *Equal contributors.

  11. Tremlett H, Dai DLY, Hollander Z, Kapanen A, Aziz T, Wilson-McManus JE, Tebbutt SJ, Borchers CH, Oger J, Cohen Freue GV. (2015) Serum proteomics in multiple sclerosis disease progression, Journal of Proteomics 118, 2-11. PubMed

  12. Hollander Z, Lazarova M, Lam KKY, Ignaszewski A, Oudit GY, Dyck J, Schreiner G, Pauwels J, Chen V, Cohen Freue GV, Ng RT, Wilson-McManus J, Balshaw R, Tebbutt S, McMaster R, Keown PA, McManus BM. (2014) Proteomic Biomarkers of Recovered Heart Function. Eur J Heart Fail. 5, 551-559. PubMed

  13. Gabriela Cohen Freue, Hernan Ortiz Molina, and Ruben H. Zamar. (2013) A Natural Robustification of the Ordinary Instrumental Variables Estimator. Biometrics 69, 641-650. PubMed

  14. Gabriela V. Cohen Freue, Anna Meredith, Derek Smith, Axel Bergman, Mayu Sasaki, Karen K.Y. Lam, Zsuzsanna Hollander, Nina Opushneva, Mandeep Takhar, David Lin, Janet Wilson-McManus, Robert Balshaw, Paul Kewon, Christoph H. Borchers, Bruce McManus, Raymond T. Ng, W. Robert McMaster. (2013) Computational biomarker pipeline from discovery to clinical implementation: plasma proteomic biomarkers for cardiac transplantation. PLoS Computational Biology 9(4): e1002963. PubMed

  15. Lin D*, Cohen Freue G*, Hollander Z, Mancini GBJ, Sasaki M, Mui A, Wilson-McManus J, Ignaszewski A, Imai C, Meredith A, Balshaw R, Ng RT, Keown PA, McMaster R, Carere R, Webb JG, McManus BM. (2013) Plasma protein biosignatures for detection of cardiac allograft vasculopathy. The Journal of Heart and Lung Transplantation 7, 723-733. *Equal contributors. PubMed

  16. Hollander Z, Chen V, Lin D, Ng R.T., Balshaw R, Cohen Freue G, Ignaszewski A, Imai C, Kaan A, Wilson-McManus J, McMaster R, Keown P, McManus BM. (2013) Predicting acute cardiac allograft rejection using donor and recipient gene expression. J Heart Lung Transplant 32, 259-65. PubMed

  17. Oliver P. Günther, Virginia Chen, Gabriela Cohen Freue, Robert F. Balshaw, Scott. J. Tebbutt, Zsuzsanna Hollander, Mandeep Takhar, W. Robert McMaster, Bruce M. McManus, Paul A. Keown, Raymond T. Ng. (2012) A computational pipeline for the development of multi-marker biosignature panels and ensemble classifiers. BMC Bioinformatics 13:326. BioMed

  18. Singh, Amrit; Cohen-Freue, Gabriela; Oosthuizen, Jean; Kam, Sarah; Ruan, Jian; Takhar, Mandeep; Gauvreau, Gail; O’Byrne, Paul; Fitzgerald, Mark; Boulet, Louis-Philippe; Borchers, Christoph; Tebbutt, Scott. (2012) Plasma proteomics can discriminate isolated early from dual responses in asthmatic individuals undergoing an allergen inhalation challenge. Proteomics Clinical Applications 6, 476-485. PubMed

  19. Domanski D, Percy AJ, Yang J, Chambers AG, Hill JS, Freue GV, Borchers CH. (2012) MRM-based Multiplexed Quantitation of 67 Putative Cardiovascular Disease Biomarkers in Human Plasma. Proteomics 12, 1222-1243. PubMed

  20. Dominik Domanski*, Gabriela V. Cohen Freue*, Luis Sojo, Michael A. Kuzyk, Leslie Ratkay, Carol E. Parker, Y. Paul Goldberg, and Christoph H. Borchers. (2012) The Use of Multiplexed MRM for the Discovery of Biomarkers to Differentiate Iron-deficiency Anemia from Anemia of Inflammation. Journal of Proteomics JPROT-D-11-00502.*Equal contributors. PubMed

  21. Gabriela V. Cohen Freue and Christoph H. Borchers. (2012) Multiple Reaction Monitoring (MRM) – Principles and Application to Coronary Artery Disease. Circulation: Cardiovascular Genetics 5, 378. PubMed

Selected Publications before 2012

Freue GV, Sasaki M, Meredith A, Günther OP, Bergman A, Takhar M, Mui A, Balshaw RF, Ng RT, Opushneva N, Hollander Z, Li G, Borchers CH, Wilson-McManus J, McManus BM, Keown PA, McMaster WR (2010) Proteomic signatures in plasma during early acute renal allograft rejection. Mol Cell Proteomics 9 1954-1967. PubMed

Cohen Freue GV, Hollander Z, Shen E, Zamar RH, Balshaw R, Scherer A, McManus B, Keown P, McMaster WR, Ng RT. (2007) MDQC: a new quality assessment method for microarrays based on quality control reports. Bioinformatics 23, 3162-3169. PubMed

Gabriela V. Cohen Freue. (2007) The Pitman Estimator of the Cauchy Location Parameter. Journal of Statistical Planning and Inference 137 1900-1913. link

Cohen-Freue, G; Holzer, TR; Forney, JD; McMaster, WR. (2007) Global Gene Expression in Leishmania. International Journal for Parasitology 37 1077-1086. PubMed

Leifso, K; Cohen-Freue, G; Dogra, N; Murray, A; McMaster, WR. (2007) Genomic and Proteomic Expression Analysis of Leishmania Promastigote and Amastigote Life Stages: The Leishmania Genome is Constitutively Expressed. Molecular and Biochemical Parasitology 152, 35-46. PubMed