Publications

Here is an overview of the publications

Tarabichi group

  • Toby M. Baker, Siqi Lai, Andrew R. Lynch, Tom Lesluyes, Haixi Yan, Huw A. Ogilvie, Annelien Verfaillie, Stefan Dentro, Amy L. Bowes, Nischalan Pillay, Adrienne M. Flanagan, Charles Swanton, Paul T. Spellman, Maxime Tarabichi, Peter Van Loo; The History of Chromosomal Instability in Genome-Doubled Tumors. Cancer Discov 2024. https://doi.org/10.1158/2159-8290.CD-23-1249
  • Salcedo, A., Tarabichi, M., Buchanan, A. et al. Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction. Nat Biotechnol (2024). https://doi.org/10.1038/s41587-024-02250-y
  • Paternot, S., Raspé, E., Meiller, C., Tarabichi, M., Assié, J.-B., Libert, F., Remmelink, M., Bisteau, X., Pauwels, P., Blum, Y., Le Stang, N., Tabone-Eglinger, S., Galateau-Sallé, F., Blanquart, C., Van Meerbeeck, J.P., Berghmans, T., Jean, D. and Roger, P.P. (2024), Preclinical evaluation of CDK4 phosphorylation predicts high sensitivity of pleural mesotheliomas to CDK4/6 inhibition. Mol Oncol, 18: 866-894. https://doi.org/10.1002/1878-0261.13351
  • Dan J. Woodcock, Atef Sahli, Ruxandra Teslo, Vinayak Bhandari, Andreas J. Gruber, Aleksandra Ziubroniewicz, Gunes Gundem, Yaobo Xu, Adam Butler, Ezequiel Anokian, Bernard J. Pope, Chol-Hee Jung, Maxime Tarabichi, Stefan C. Dentro, J. Henry R. Farmery, Peter Van Loo, Anne Y. Warren, Vincent Gnanapragasam, Freddie C. Hamdy, G. Steven Bova, Christopher S. Foster, David E. Neal, Yong-Jie Lu, Zsofia Kote-Jarai, Michael Fraser, Robert G. Bristow, Paul C. Boutros, Anthony J. Costello, Niall M. Corcoran, Christopher M. Hovens, Charlie E. Massie, Andy G. Lynch, Daniel S. Brewer, Rosalind A. Eeles, Colin S. Cooper, & David C. Wedge (2024). Genomic evolution shapes prostate cancer disease type. Cell Genomics, 4(3), 100511.
  • Baker, T.M., Waise, S., Tarabichi, M. et al. Aneuploidy and complex genomic rearrangements in cancer evolution. Nat Cancer 5, 228–239 (2024). https://doi.org/10.1038/s43018-023-00711-y
  • Jiang, Y., Montierth, M., Yu, K., Ji, S., Guo, S., Tran, Q., Liu, X., Shin, S., Cao, S., Li, R., Tang, Y., Lesluyes, T., Kopetz, S., Ajani, J., Msaouel, P., Subudhi, S., Aparicio, A., Sharma, P., Shen, J., Sood, A., Tarabichi, M., Wang, J., Kimmel, M., Van Loo, P., Zhu, H., & Wang, W. (2024). Pan-cancer subclonal mutation analysis of 7,827 tumors predicts clinical outcome. bioRxiv.
  • Tourneur, A., Rodrigues Vitoria, J., Saiselet, M., Craciun, L., Larsimont, D., Lefort, A., Libert, F., Maenhaut, C., Costagliola, S., Tarabichi, M., Romitti, M., & Detours, V. (2024). Single nuclei and spatial transcriptomes suggest a stratification of papillary and anaplastic thyroid cancer cells. bioRxiv.
  • Pita, J., Raspé, E., Coulonval, K., Decaussin-Petrucci, M., Tarabichi, M., Dom, G., Libert, F., Craciun, L., Andry, G., Wicquart, L., Leteurtre, E., Trésallet, C., Marlow, L., Copland, J., Durante, C., Maenhaut, C., Cavaco, B., Dumont, J., Costante, G., & Roger, P. (2023). CDK4 phosphorylation status and rational use for combining CDK4/6 and BRAF/MEK inhibition in advanced thyroid carcinomas. Frontiers in Endocrinology, 14.
  • Kaufmann, T.L., Petkovic, M., Watkins, T.B.K. et al. MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution. Genome Biol 23, 241 (2022). https://doi.org/10.1186/s13059-022-02794-9
  • Bowes, A.L., Tarabichi, M., Pillay, N. and Van Loo, P. (2022), Leveraging single-cell sequencing to unravel intratumour heterogeneity and tumour evolution in human cancers. J. Pathol., 257: 466-478. https://doi.org/10.1002/path.5914
  • Drews, R.M., Hernando, B., Tarabichi, M. et al. A pan-cancer compendium of chromosomal instability. Nature 606, 976–983 (2022). https://doi.org/10.1038/s41586-022-04789-9
  • Steele, C.D., Abbasi, A., Islam, S.M.A. et al. Signatures of copy number alterations in human cancer. Nature 606, 984–991 (2022). https://doi.org/10.1038/s41586-022-04738-6
  • Maxime Tarabichi, Pieter Demetter, Ligia Craciun, Carine Maenhaut, & Vincent Detours (2022). Thyroid cancer under the scope of emerging technologies. Molecular and Cellular Endocrinology, 541, 111491.
  • Zoumpoulidou, G., Alvarez-Mendoza, C., Mancusi, C. et al. Therapeutic vulnerability to PARP1,2 inhibition in RB1-mutant osteosarcoma. Nat Commun 12, 7064 (2021). https://doi.org/10.1038/s41467-021-27291-8
  • Tarabichi, M., Demeulemeester, J., Verfaillie, A. et al. A pan-cancer landscape of somatic mutations in non-unique regions of the human genome. Nat Biotechnol 39, 1589–1596 (2021). https://doi.org/10.1038/s41587-021-00971-y
  • Haixi Yan, Maxime Tarabichi, Nicholas McGranahan, & Peter Van Loo (2021). DeCiFering the subclonal composition of tumors. Cell Systems, 12(10), 955-957.
  • Turati, V.A., Guerra-Assunção, J.A., Potter, N.E. et al. Chemotherapy induces canalization of cell state in childhood B-cell precursor acute lymphoblastic leukemia. Nat Cancer 2, 835–852 (2021). https://doi.org/10.1038/s43018-021-00219-3
  • Tarabichi, M., Salcedo, A., Deshwar, A.G. et al. A practical guide to cancer subclonal reconstruction from DNA sequencing. Nat Methods 18, 144–155 (2021). https://doi.org/10.1038/s41592-020-01013-2
  • Fittall, M.W., Lyskjær, I., Ellery, P., Lombard, P., Ijaz, J., Strobl, A.-C., Oukrif, D., Tarabichi, M., Sill, M., Koelsche, C., Mechtersheimer, G., Demeulemeester, J., Tirabosco, R., Amary, F., Campbell, P.J., Pfister, S.M., Jones, D.T., Pillay, N., Van Loo, P., Behjati, S. and Flanagan, A.M. (2020), Drivers underpinning the malignant transformation of giant cell tumour of bone. J. Pathol., 252: 433-440. https://doi.org/10.1002/path.5537
  • Gerstung, M., Jolly, C., Leshchiner, I. et al. The evolutionary history of 2,658 cancers. Nature 578, 122–128 (2020). https://doi.org/10.1038/s41586-019-1907-7
  • The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Pan-cancer analysis of whole genomes. Nature 578, 82–93 (2020). https://doi.org/10.1038/s41586-020-1969-6
  • Salcedo, A., Tarabichi, M., Espiritu, S.M.G. et al. A community effort to create standards for evaluating tumor subclonal reconstruction. Nat Biotechnol 38, 97–107 (2020). https://doi.org/10.1038/s41587-019-0364-z
  • Perez-Rodriguez, D., Kalyva, M., Leija-Salazar, M. et al. Investigation of somatic CNVs in brains of synucleinopathy cases using targeted SNCA analysis and single cell sequencing. Acta Neuropathol Commun 7, 219 (2019). https://doi.org/10.1186/s40478-019-0873-5
  • Christopher D. Steele, Maxime Tarabichi, Dahmane Oukrif, Amy P. Webster, Hongtao Ye, Matthew Fittall, Patrick Lombard, Iñigo Martincorena, Patrick S. Tarpey, Grace Collord, Kerstin Haase, Sandra J. Strauss, Fitim Berisha, Heli Vaikkinen, Pawan Dhami, Marnix Jansen, Sam Behjati, M. Fernanda Amary, Roberto Tirabosco, Andrew Feber, Peter J. Campbell, Ludmil B. Alexandrov, Peter Van Loo, Adrienne M. Flanagan, & Nischalan Pillay (2019). Undifferentiated Sarcomas Develop through Distinct Evolutionary Pathways. Cancer Cell, 35(3), 441-456.e8.
  • Minussi, D.C., Nicholson, M.D., Ye, H. et al. Breast tumours maintain a reservoir of subclonal diversity during expansion. Nature 592, 302–308 (2021). https://doi.org/10.1038/s41586-021-03357-x
  • Xydia, M., Rahbari, R., Ruggiero, E. et al. Common clonal origin of conventional T cells and induced regulatory T cells in breast cancer patients. Nat Commun 12, 1119 (2021). https://doi.org/10.1038/s41467-021-21297-y
  • Tarabichi, M., Detours, V., Konopka, T. (2021). Piecewise Polynomial Representations of Genomic Tracks. PLOS ONE 7(11): e48941. https://doi.org/10.1371/journal.pone.0048941
  • Tomás, G., Tarabichi, M., Gacquer, D. et al. A general method to derive robust organ-specific gene expression-based differentiation indices: application to thyroid cancer diagnostic. Oncogene 31, 4490–4498 (2012). https://doi.org/10.1038/onc.2011.626
  • Tarabichi, M., Detours, V., Konopka, T. (2012). Piecewise Polynomial Representations of Genomic Tracks. PLOS ONE 7(11): e48941. https://doi.org/10.1371/journal.pone.0048941
  • Tomás, G., Tarabichi, M., Gacquer, D. et al. A general method to derive robust organ-specific gene expression-based differentiation indices: application to thyroid cancer diagnostic. Oncogene 31, 4490–4498 (2012). https://doi.org/10.1038/onc.2011.626
  • Tarabichi, M., Antoniou, A., Saiselet, M., et al. (2012). Systems biology of cancer: entropy, disorder, and selection-driven evolution to independence, invasion and “swarm intelligence”. Cancer Metastasis Rev 32, 403–421 (2013). https://doi.org/10.1007/s10555-013-9431-y
  • Saiselet, M., Pita, J.M., Augenlicht, A., Dom, G., Tarabichi, M., Fimereli, D., Dumont, J.E., Detours, V., Maenhaut, C. miRNA expression and function in thyroid carcinomas: a comparative and critical analysis and a model for other cancers. Oncotarget. 2016 Aug 9;7(32):52475-52492. doi: 10.18632/oncotarget.9655. PMID: 27248468; PMCID: PMC5239568
  • Tarabichi, M., Detours, V. A research note regarding "Variation in cancer risk among tissues can be explained by the number of stem cell divisions". F1000Res. 2016 Aug 22;5:2044. doi: 10.12688/f1000research.9448.2. PMID: 27853514; PMCID: PMC5089134
  • Tarabichi, M., Saiselet, M., Trésallet, C. et al. Revisiting the transcriptional analysis of primary tumours and associated nodal metastases with enhanced biological and statistical controls: application to thyroid cancer. Br J Cancer 112, 1665–1674 (2015). https://doi.org/10.1038/bjc.2014.665
  • Le Pennec, S., Konopka, T., Gacquer, D., Fimereli, D., Tarabichi, M., Tomás, G., Savagner, F., Decaussin-Petrucci, M., Trésallet, C., Andry, G., Larsimont, D., Detours, V., & Maenhaut, C. (2015). Intratumor heterogeneity and clonal evolution in an aggressive papillary thyroid cancer and matched metastases. Endocrine-Related Cancer, 22(2), 205-216. https://doi.org/10.1530/ERC-14-0351
  • Verbeurgt, C., Wilkin, F., Tarabichi, M., Gregoire, F., Dumont, J.E., et al. (2014) Profiling of Olfactory Receptor Gene Expression in Whole Human Olfactory Mucosa. PLOS ONE 9(5): e96333. https://doi.org/10.1371/journal.pone.0096333
  • Tarabichi, M., Antoniou, A., Saiselet, M. et al. Systems biology of cancer: entropy, disorder, and selection-driven evolution to independence, invasion and “swarm intelligence”. Cancer Metastasis Rev 32, 403–421 (2013). https://doi.org/10.1007/s10555-013-9431-y
  • Soetkin Versteyhe, Natacha Driessens, Chiraz Ghaddhab, Maxime Tarabichi, Candice Hoste, Jacques-Emile Dumont, Françoise Miot, Bernard Corvilain, Vincent Detours. Comparative Analysis of the Thyrocytes and T Cells: Responses to H2O2 and Radiation Reveals an H2O2-Induced Antioxidant Transcriptional Program in Thyrocytes. The Journal of Clinical Endocrinology & Metabolism, Volume 98, Issue 10, 1 October 2013, Pages E1645–E1654. https://doi.org/10.1210/jc.2013-1266
  • Dom, G., Galdo, V., Tarabichi, M., Tomás, G., Hébrant, A., Andry, G., De Martelar, V., Libert, F., Leteurtre, E., Dumont, J., Maenhaut, C., & Staveren, W. (2013). 5-Aza-2′-Deoxycytidine Has Minor Effects on Differentiation in Human Thyroid Cancer Cell Lines, But Modulates Genes That Are Involved in Adaptation In Vitro. Thyroid 23(3), 317-328.
  • Saiselet, M., Floor, S., Tarabichi, M., Dom, G., Hébrant, A., Staveren, W., & Maenhaut, C. (2012). Thyroid cancer cell lines: an overview. Frontiers in Endocrinology, 3.
  • Tarabichi, M., Detours, V., Konopka, T. (2012). Piecewise Polynomial Representations of Genomic Tracks. PLOS ONE 7(11): e48941. https://doi.org/10.1371/journal.pone.0048941
  • Tomás, G., Tarabichi, M., Gacquer, D. et al. A general method to derive robust organ-specific gene expression-based differentiation indices: application to thyroid cancer diagnostic. Oncogene 31, 4490–4498 (2012). https://doi.org/10.1038/onc.2011.626
  • Dom, G., Tarabichi, M., Unger, K. et al. A gene expression signature distinguishes normal tissues of sporadic and radiation-induced papillary thyroid carcinomas. Br J Cancer 107, 994–1000 (2012). https://doi.org/10.1038/bjc.2012.302