Publications

Genomic evolution shapes prostate cancer disease type — 2024 — Cell Genomics (Maxime Tarabichi)

Aneuploidy and complex genomic rearrangements in cancer evolution — 2024 — Nature Cancer (Maxime Tarabichi)

Impact of the radiological morphology of the mesopancreas on the outcome after pancreatoduodenectomy for pancreatic ductal adenocarcinoma: retrospective study — 2024 — BJS Open (Oier Azurmendi Senar)

Pan-cancer subclonal mutation analysis of 7,827 tumors predicts clinical outcome — 2024 — bioRxiv (Cold Spring Harbor Laboratory) (Maxime Tarabichi)

Epitranscriptomic rRNA fingerprinting reveals tissue-of-origin and tumor-specific signatures — 2024 — Molecular Cell (Ruben Lattuca)

The History of Chromosomal Instability in Genome-Doubled Tumors — 2024 — Cancer Discovery (Maxime Tarabichi)

Cancer-Associated Fibroblasts in Pancreatic Ductal Adenocarcinoma or a Metaphor for Heterogeneity: From Single-Cell Analysis to Whole-Body Imaging — 2024 — Biomedicines (Oier Azurmendi Senar)

IDH1 R132H and TP53 R248Q Mutations Modulate Glioma Cell Migration and Adhesion on Different ECM Components — 2024 — International Journal of Molecular Sciences (Valeriia Gulaia)

Author Correction: The evolutionary history of 2,658 cancers — 2023 — Nature (Maxime Tarabichi)

Dual targeting of MAPK and PI3K pathways unlocks redifferentiation ofBraf-mutated thyroid cancer organoids — 2023 — bioRxiv (Cold Spring Harbor Laboratory) (Vincent Detours)

A Comprehensive Review of the Potential Role of Liquid Biopsy as a Diagnostic, Prognostic, and Predictive Biomarker in Pancreatic Ductal Adenocarcinoma — 2023 — Cells (Oier Azurmendi Senar)

Dual targeting of MAPK and PI3K pathways unlocks redifferentiation of Braf-mutated thyroid cancer organoids — 2023 — Oncogene (Vincent Detours)

CDK4 phosphorylation status and rational use for combining CDK4/6 and BRAF/MEK inhibition in advanced thyroid carcinomas — 2023 — Frontiers in Endocrinology (Maxime Tarabichi)

Resistance to Gemcitabine in Pancreatic Cancer Is Connected to Methylglyoxal Stress and Heat Shock Response — 2023 — Cells (Oier Azurmendi Senar)

Comprehensive clinical assays for molecular diagnostics of gliomas: the current state and future prospects — 2023 — Frontiers in Molecular Biosciences (Valeriia Gulaia)

Crowd-sourced benchmarking of single-sample tumour subclonal reconstruction — 2022 — bioRxiv (Cold Spring Harbor Laboratory) (Maxime Tarabichi)

Transplantable human thyroid organoids generated from embryonic stem cells to rescue hypothyroidism — 2022 — Nature Communications (Vincent Detours)

A pan-cancer compendium of chromosomal instability — 2022 — Nature (Maxime Tarabichi)

Single-nucleus transcriptomics of IDH1- and TP53-mutant glioma stem cells displays diversified commitment on invasive cancer progenitors — 2022 — Scientific Reports (Valeriia Gulaia)

Signatures of copy number alterations in human cancer — 2022 — Nature (Maxime Tarabichi)

Systematic mapping of rRNA 2’-O methylation during frog development and involvement of the methyltransferase Fibrillarin in eye and craniofacial development in Xenopus laevis — 2022 — PLoS Genetics (Ruben Lattuca)

Dynamic Cancer Cell Heterogeneity: Diagnostic and Therapeutic Implications — 2022 — Cancers (Vincent Detours)

Preclinical evaluation of CDK4 phosphorylation predicts high sensitivity of malignant pleural mesotheliomas to CDK4/6 inhibition — 2022 — bioRxiv (Cold Spring Harbor Laboratory) (Maxime Tarabichi)

Preclinical evaluation of CDK4 phosphorylation predicts high sensitivity of pleural mesotheliomas to CDK4/6 inhibition — 2022 — Molecular Oncology (Maxime Tarabichi)

Novel assay to measure chromosome instability identifies Punica granatum extract that elevates CIN and has a potential for tumor- suppressing therapies — 2022 — Frontiers in Bioengineering and Biotechnology (Valeriia Gulaia)

Nanomechanical and Morphological AFM Mapping of Normal Tissues and Tumors on Live Brain Slices Using Specially Designed Embedding Matrix and Laser-Shaped Cantilevers — 2022 — Biomedicines (Valeriia Gulaia)

MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution — 2022 — Genome biology (Maxime Tarabichi)

Leveraging single‐cell sequencing to unravel intratumour heterogeneity and tumour evolution in human cancers — 2022 — The Journal of Pathology (Maxime Tarabichi)

Fluorescent Multiplex Immunohistochemistry Coupled With Other State-Of-The-Art Techniques to Systematically Characterize the Tumor Immune Microenvironment — 2021 — Frontiers in Molecular Biosciences (Vincent Detours)

Systematic mapping of rRNA 2’-O methylation during frog development and involvement of the methyltransferase Fibrillarin in eye and craniofacial development in Xenopus laevis — 2021 — bioRxiv (Cold Spring Harbor Laboratory) (Ruben Lattuca)

Defucosylation of Tumor-Specific Humanized Anti-MUC1 Monoclonal Antibody Enhances NK Cell-Mediated Anti-Tumor Cell Cytotoxicity — 2021 — Cancers (Valeriia Gulaia)

A practical guide to cancer subclonal reconstruction from DNA sequencing — 2021 — Nature Methods (Maxime Tarabichi)

A pan-cancer landscape of somatic mutations in non-unique regions of the human genome — 2021 — Nature Biotechnology (Maxime Tarabichi)

Chemotherapy induces canalization of cell state in childhood B-cell precursor acute lymphoblastic leukemia — 2021 — Nature Cancer (Maxime Tarabichi)

Thyroid cancer under the scope of emerging technologies — 2021 — Molecular and Cellular Endocrinology (Maxime Tarabichi, Vincent Detours)

Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes — 2021 — Cell (Maxime Tarabichi)

Therapeutic vulnerability to PARP1,2 inhibition in RB1-mutant osteosarcoma — 2021 — Nature Communications (Maxime Tarabichi)

Common clonal origin of conventional T cells and induced regulatory T cells in breast cancer patients — 2021 — Nature Communications (Maxime Tarabichi)

Breast tumours maintain a reservoir of subclonal diversity during expansion — 2021 — Nature (Maxime Tarabichi)

The evolutionary history of 2,658 cancers — 2020 — Nature (Maxime Tarabichi)

Alkaloids of fascaplysin are promising chemotherapeutic agents for the treatment of glioblastoma: Review — 2020 — International review of neurobiology (Valeriia Gulaia)

Transcriptional output, cell-type densities, and normalization in spatial transcriptomics — 2020 — Journal of Molecular Cell Biology (Vincent Detours)

Inferring structural variant cancer cell fraction — 2020 — Nature Communications (Maxime Tarabichi)

Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig — 2020 — Nature Communications (Maxime Tarabichi)

A pan-cancer landscape of somatic substitutions in non-unique regions of the human genome — 2020 — bioRxiv (Cold Spring Harbor Laboratory) (Maxime Tarabichi)

A community effort to create standards for evaluating tumor subclonal reconstruction — 2020 — Nature Biotechnology (Maxime Tarabichi)

Drivers underpinning the malignant transformation of giant cell tumour of bone — 2020 — The Journal of Pathology (Maxime Tarabichi)

Characterizing Genetic Intra-Tumor Heterogeneity Across 2,658 Human Cancer Genomes — 2020 — SSRN Electronic Journal (Maxime Tarabichi)

Single‐cell transcriptome analysis reveals thyrocyte diversity in the zebrafish thyroid gland — 2020 — EMBO Reports (Vincent Detours)

Undifferentiated Sarcomas Develop through Distinct Evolutionary Pathways — 2019 — Cancer Cell (Maxime Tarabichi)

Dissecting the Role of Thyrotropin in the DNA Damage Response in Human Thyrocytes after 131I, γ Radiation and H2O2 — 2019 — The Journal of Clinical Endocrinology & Metabolism (Vincent Detours)

Investigation of somatic CNVs in brains of synucleinopathy cases using targeted SNCA analysis and single cell sequencing — 2019 — Acta Neuropathologica Communications (Maxime Tarabichi)

The Extracellular Matrix and Biocompatible Materials in Glioblastoma Treatment — 2019 — Frontiers in Bioengineering and Biotechnology (Valeriia Gulaia)

BRCA gene mutations do not shape the extent and organization of tumor infiltrating lymphocytes in triple negative breast cancer — 2019 — Cancer Letters (Vincent Detours)

Human-Specific NOTCH2NL Genes Expand Cortical Neurogenesis through Delta/Notch Regulation — 2018 — Cell (Vincent Detours)

Molecular Mechanisms Governing the Stem Cell’s Fate in Brain Cancer: Factors of Stemness and Quiescence — 2018 — Frontiers in Cellular Neuroscience (Valeriia Gulaia)

Neutral tumor evolution? — 2018 — Nature Genetics (Maxime Tarabichi)

Towards an advanced cell-based in vitro glioma model system — 2018 — AIMS Genetics (Valeriia Gulaia)

Recurrent rearrangements of FOS and FOSB define osteoblastoma — 2018 — Nature Communications (Maxime Tarabichi)

Undifferentiated Sarcomas Develop Through Distinct Evolutionary Pathways — 2018 — SSRN Electronic Journal (Maxime Tarabichi)

Transcriptional output, cell types densities and normalization in spatial transcriptomics — 2018 — bioRxiv (Cold Spring Harbor Laboratory) (Vincent Detours)

4 Patterns of clustered mutational processes: Pan-Cancer analysis of chromothripsis, chromoplexy and kataegis — 2018 — ESMO Open (Maxime Tarabichi)

Distinctive Desmoplastic 3D Morphology Associated With BRAFV600E in Papillary Thyroid Cancers — 2018 — The Journal of Clinical Endocrinology & Metabolism (Maxime Tarabichi, Vincent Detours)

Abstract 218: The evolutionary history of 2,658 cancers — 2018 — Cancer Research (Maxime Tarabichi)

Esophageal cancer research today and tomorrow: Lessons from algae and other perspectives — 2018 — AIMS Genetics (Valeriia Gulaia)

Genomic hotspots but few recurrent fusion genes in breast cancer — 2018 — Genes Chromosomes and Cancer (Vincent Detours)

Abstract 3000: Pervasive intra-tumour heterogeneity and subclonal selection across cancer types — 2018 — Cancer Research (Maxime Tarabichi)

Factors contributing to the resistance of the thyrocyte to hydrogen peroxide — 2018 — Molecular and Cellular Endocrinology (Vincent Detours)

Creating Standards for Evaluating Tumour Subclonal Reconstruction — 2018 — bioRxiv (Cold Spring Harbor Laboratory) (Maxime Tarabichi)

Hominin-specific NOTCH2 paralogs expand human cortical neurogenesis through regulation of Delta/Notch interactions — 2017 — bioRxiv (Cold Spring Harbor Laboratory) (Vincent Detours)

Immune Checkpoint Molecules on Tumor-Infiltrating Lymphocytes and Their Association with Tertiary Lymphoid Structures in Human Breast Cancer — 2017 — Frontiers in Immunology (Vincent Detours)

The human bitter taste receptor T2R38 is broadly tuned for bacterial compounds — 2017 — PLoS ONE (Maxime Tarabichi)

miRNA expression and function in thyroid carcinomas: a comparative and critical analysis and a model for other cancers — 2016 — Oncotarget (Maxime Tarabichi, Vincent Detours)

Gene signature of the post-Chernobyl papillary thyroid cancer — 2016 — European Journal of Nuclear Medicine and Molecular Imaging (Vincent Detours)

Intratumor heterogeneity and clonal evolution in an aggressive papillary thyroid cancer and matched metastases — 2015 — Endocrine Related Cancer (Maxime Tarabichi, Vincent Detours)

No significant viral transcription detected in whole breast cancer transcriptomes — 2015 — BMC Cancer (Vincent Detours)

Revisiting the transcriptional analysis of primary tumours and associated nodal metastases with enhanced biological and statistical controls: application to thyroid cancer — 2015 — British Journal of Cancer (Maxime Tarabichi, Vincent Detours)

Comment on "Variation in cancer risk among tissues can be explained by the number of stem cell divisions" — 2015 — bioRxiv (Cold Spring Harbor Laboratory) (Maxime Tarabichi, Vincent Detours)

Principles Governing A-to-I RNA Editing in the Breast Cancer Transcriptome — 2015 — Cell Reports (Vincent Detours)

New global analysis of the microRNA transcriptome of primary tumors and lymph node metastases of papillary thyroid cancer — 2015 — BMC Genomics (Vincent Detours)

Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology — 2014 — BMC Genomics (Vincent Detours)

Principles governing A-to-I RNA editing in the breast cancer transcriptome — 2014 — bioRxiv (Cold Spring Harbor Laboratory) (Vincent Detours)

Profiling of Olfactory Receptor Gene Expression in Whole Human Olfactory Mucosa — 2014 — PLoS ONE (Maxime Tarabichi)

Systems biology of cancer: entropy, disorder, and selection-driven evolution to independence, invasion and “swarm intelligence” — 2013 — Cancer and Metastasis Reviews (Maxime Tarabichi, Vincent Detours)

Comparative Analysis of the Thyrocytes and T Cells: Responses to H2O2 and Radiation Reveals an H2O2-Induced Antioxidant Transcriptional Program in Thyrocytes — 2013 — The Journal of Clinical Endocrinology & Metabolism (Maxime Tarabichi, Vincent Detours)

TriageTools: tools for partitioning and prioritizing analysis of high-throughput sequencing data — 2013 — Nucleic Acids Research (Vincent Detours)

Thyroid cancer cell lines: an overview — 2012 — Frontiers in Endocrinology (Maxime Tarabichi)

Piecewise Polynomial Representations of Genomic Tracks — 2012 — PLoS ONE (Maxime Tarabichi, Vincent Detours)

A Measure of the Signal-to-Noise Ratio of Microarray Samples and Studies Using Gene Correlations — 2012 — PLoS ONE (Vincent Detours)

InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor — 2012 — Genome biology (Vincent Detours)

A general method to derive robust organ-specific gene expression-based differentiation indices: application to thyroid cancer diagnostic — 2012 — Oncogene (Maxime Tarabichi, Vincent Detours)

A gene expression signature distinguishes normal tissues of sporadic and radiation-induced papillary thyroid carcinomas — 2012 — British Journal of Cancer (Maxime Tarabichi, Vincent Detours)

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 — 2012 — Thyroid (Maxime Tarabichi)

Genes Expressed in Specific Areas of the Human Fetal Cerebral Cortex Display Distinct Patterns of Evolution — 2011 — PLoS ONE (Vincent Detours)

Gene Expression Profiles for Radiation-induced Thyroid Cancer — 2011 — Clinical Oncology (Vincent Detours)

Most Random Gene Expression Signatures Are Significantly Associated with Breast Cancer Outcome — 2011 — PLoS Computational Biology (Vincent Detours)

Human cancer cell lines: Experimental models for cancer cells in situ? For cancer stem cells? — 2009 — Biochimica et Biophysica Acta (BBA) - Reviews on Cancer (Vincent Detours)

Gene Expression in RET/PTC3 and E7 Transgenic Mouse Thyroids: RET/PTC3 But Not E7 Tumors Are Partial and Transient Models of Human Papillary Thyroid Cancers — 2008 — Endocrinology (Vincent Detours)

Editorial comment should accompany hot papers online — 2008 — Nature (Vincent Detours)

Gene expression profiles of post-Chernobyl thyroid cancers — 2008 — Current Opinion in Endocrinology Diabetes and Obesity (Vincent Detours)

Genome-wide gene expression profiling suggests distinct radiation susceptibilities in sporadic and post-Chernobyl papillary thyroid cancers — 2007 — British Journal of Cancer (Vincent Detours)

Roles of Hydrogen Peroxide in Thyroid Physiology and Disease — 2007 — The Journal of Clinical Endocrinology & Metabolism (Vincent Detours)

Human Thyroid Tumor Cell Lines Derived from Different Tumor Types Present a Common Dedifferentiated Phenotype — 2007 — Cancer Research (Vincent Detours)

Gene expression and the biological phenotype of papillary thyroid carcinomas — 2007 — Oncogene (Vincent Detours)

Negative Feedbacks in Normal Cell Growth and Their Suppression in Tumorigenesis — 2006 — Cell Cycle (Vincent Detours)

Gene expression in thyroid autonomous adenomas provides insight into their physiopathology — 2005 — Oncogene (Vincent Detours)

Gene expression in human thyrocytes and autonomous adenomas reveals suppression of negative feedbacks in tumorigenesis — 2005 — Proceedings of the National Academy of Sciences (Vincent Detours)

Absence of a specific radiation signature in post-Chernobyl thyroid cancers — 2005 — British Journal of Cancer (Vincent Detours)

Integration and cross‐validation of high‐throughput gene expression data: comparing heterogeneous data sets — 2003 — FEBS Letters (Vincent Detours)

Clustering Patterns of Cytotoxic T-Lymphocyte Epitopes in Human Immunodeficiency Virus Type 1 (HIV-1) Proteins Reveal Imprints of Immune Evasion on HIV-1 Global Variation — 2002 — Journal of Virology (Vincent Detours)

Prediction of proteasome cleavage motifs by neural networks — 2002 — Protein Engineering Design and Selection (Vincent Detours)

Evolutionary and immunological implications of contemporary HIV-1 variation — 2001 — British Medical Bulletin (Vincent Detours)

The paradox of alloreactivity and self MHC restriction: Quantitative analysis and statistics — 2000 — Proceedings of the National Academy of Sciences (Vincent Detours)

Deriving Quantitative Constraints on T Cell Selection from Data on the Mature T Cell Repertoire — 2000 — The Journal of Immunology (Vincent Detours)

Explaining high alloreactivity as a quantitative consequence of affinity-driven thymocyte selection — 1999 — Proceedings of the National Academy of Sciences (Vincent Detours)

A Quantitative Theory of Affinity-driven T Cell Repertoire Selection — 1999 — Journal of Theoretical Biology (Vincent Detours)

Size and Connectivity of the Idiotypic Network Are Independent of the Discreteness of the Affinity Distribution — 1996 — Journal of Theoretical Biology (Vincent Detours)

Asynchrony Induces Stability in Cellular Automata Based Models — 1994 — The MIT Press eBooks (Vincent Detours)

Development of an Idiotypic Network in Shape Space — 1994 — Journal of Theoretical Biology (Vincent Detours)

Computational Biology Labs @ IRIBHM