Thomas Sierocinski


Computational biologist




Major research activities/interests

My interests lie in biomarker development, quality control, data standardization and process automation. I work on whole genome bisulfite sequencing data which allows genome wide methylation profiling. More precisely, this involves defining relevant quality control metrics, automating our quality control procedure, data management and standardizing the data format in order to allow efficient data processing and distribution. This aims to facilitate and maximize reproducibility of downstream analysis such as, for instance, biomarker discovery or sample classification.

Selected publications

Mitra AP, Lam LL, Ghadessi M, Erho N, Vergara IA, Alshalalfa M, Haddad Z, Sierocinski T, Triche TJ, Skinner EC, Davicioni E, Daneshmand S, Black PC. A combination of genomic markers and clinical variables provides superior prognostic performances in high-risk bladder cancer following cystectomy. The Journal of Urology, Volume 191, Issue 4, e429, April 2014.

Jeffries, KM, Hinch, SG, Sierocinski, T, Pavlidis, P, Miller, KM. Transcriptomic responses to high water temperature in two species of Pacific salmon. Evolutionary Applications, Volume 7, Issue 2, pages 286-300, February 2014.

Wiseman SM, Haddad Z, Walker B, Vergara IA, Sierocinski T, Crisan A, Ghadessi M, Dao P, Zimmermann B, Triche TJ, Erho N, Davicioni E. Whole-transcriptome profiling of thyroid nodules identifies expression-based signatures for accurate thyroid cancer diagnosis. J Clin Endocrinol Metab. 2013 Oct; 98(10):4072-9. PMID: 23928671.

Karnes RJ, Bergstralh EJ, Davicioni E, Ghadessi M, Buerki C, Mitra AP, Crisan A, Erho N, Vergara IA, Lam LL, Carlson R, Thompson DJ, Haddad Z, Zimmermann B, Sierocinski T, Triche TJ, Kollmeyer T, Ballman KV, Black PC, Klee GG, Jenkins RB. Validation of a Genomic Classifier That Predicts Metastasis Following Radical Prostatectomy in an At Risk Patient Population. J Urol. 2013 Jun 11; PMID: 23770138.

Miller KM, Li S, Kaukinen KH, Ginther N, Hammill E, Curtis JM, Patterson DA, Sierocinski T, Donnison L, Pavlidis P, Hinch SG, Hruska KA, Cooke SJ, English KK, Farrell AP. Genomic signatures predict migration and spawning failure in wild Canadian salmon.Science. 2011 Jan 14;331(6014):214-7.

Sierocinski T, Théret N, Pétritis D, Fuzzy and quantum methods of information retrieval to analyse genomic data from patients at different stages of fibrosis. 2008 First International Symposium on Applied Sciences on Biomedical and Communication Technologies. p1-5. IEEE.

Sierocinski T, Le Béchec A, Théret N, Pétritis D. Semantic distillation: a method for clustering objects by their contextual specificity “Studies in computational intelligence”. Nature Inspired Cooperative Strategies for Optimization (2008). vol. 129 p431-442. Springer Berlin Heidelberg.

Petritis D, Sierocinski T. Quantum information retrieval and gene networks “IEEE Bio-inspired models of Network, Information and Computing System” (2006).