Centre for Cancer Genomics & Computational Biology
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Recent Submissions
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The role of colorectal cancer plasticity in metastasis and treatment: an interview with Mirjana Efremova
(Future Science Group, 2023-12-01) -
scMoMaT jointly performs single cell mosaic integration and multi-modal bio-marker detection
(Nature Research, 2023-01-24)Single cell data integration methods aim to integrate cells across data batches and modalities, and data integration tasks can be categorized into horizontal, vertical, diagonal, and mosaic integration, where mosaic ... -
Reflected stemness as a potential driver of the tumour microenvironment
(2022-12)A fundamental requirement for cancer initiation is the activation of developmental programmes by mutant cells. Oncogenic signals often confer an undifferentiated, stem cell-like phenotype that supports the long-term ... -
Approaching Cancer Evolution from Different Angles
(Cell Press, 2020-10-22)Dr Francesca Ciccarelli (The Francis Crick Institute, UK) and Dr James De Gregori (University of Colorado, USA) interview 3 top scientists in clinical (Dr Charles Swanton, The Francis Crick Institute, UK), molecular (Dr ... -
Mechanistic insights into the interactions between cancer drivers and the tumour immune microenvironment.
(2023-06-05)BACKGROUND: The crosstalk between cancer and the tumour immune microenvironment (TIME) has attracted significant interest in the latest years because of its impact on cancer evolution and response to treatment. Despite ... -
Comparative assessment of genes driving cancer and somatic evolution in non-cancer tissues: an update of the Network of Cancer Genes (NCG) resource.
(2022-01-26)BACKGROUND: Genetic alterations of somatic cells can drive non-malignant clone formation and promote cancer initiation. However, the link between these processes remains unclear and hampers our understanding of tissue ... -
A SIMPLI (Single-cell Identification from MultiPLexed Images) approach for spatially-resolved tissue phenotyping at single-cell resolution.
(2022-02-09)Multiplexed imaging technologies enable the study of biological tissues at single-cell resolution while preserving spatial information. Currently, high-dimension imaging data analysis is technology-specific and requires ... -
Mutational signature dynamics shaping the evolution of oesophageal adenocarcinoma.
(2023-07-15)A variety of mutational processes drive cancer development, but their dynamics across the entire disease spectrum from pre-cancerous to advanced neoplasia are poorly understood. We explore the mutagenic processes shaping ... -
The transcriptional landscape of endogenous retroelements delineates esophageal adenocarcinoma subtypes.
(2023-09)Most cancer types exhibit aberrant transcriptional activity, including derepression of retrotransposable elements (RTEs). However, the degree, specificity and potential consequences of RTE transcriptional activation may ... -
Pan-cancer detection of driver genes at the single-patient resolution.
(2021-02-01)BACKGROUND: Identifying the complete repertoire of genes that drive cancer in individual patients is crucial for precision oncology. Most established methods identify driver genes that are recurrently altered across patient ... -
Rearrangement processes and structural variations show evidence of selection in oesophageal adenocarcinomas.
(2022-04-08)Oesophageal adenocarcinoma (OAC) provides an ideal case study to characterize large-scale rearrangements. Using whole genome short-read sequencing of 383 cases, for which 214 had matched whole transcriptomes, we observed ... -
Immunogenomics of Colorectal Cancer Response to Checkpoint Blockade: Analysis of the KEYNOTE 177 Trial and Validation Cohorts.
(2021-10)BACKGROUND & AIMS: Colorectal cancer (CRC) shows variable response to immune checkpoint blockade, which can only partially be explained by high tumor mutational burden (TMB). We conducted an integrated study of the cancer ... -
Apoptosis in mesenchymal stromal cells activates an immunosuppressive secretome predicting clinical response in Crohn's disease.
(2023-12-06)In vivo apoptosis of human mesenchymal stromal cells (MSCs) plays a critical role in delivering immunomodulation. Yet, caspase activity not only mediates the dying process but also death-independent functions that may shape ... -
Exome sequencing of hepatocellular carcinoma in lemurs identifies potential cancer drivers: A pilot study
(Oxford University Press, 2022-04-29)BACKGROUND AND OBJECTIVES: Hepatocellular carcinoma occurs frequently in prosimians, but the cause of these liver cancers in this group is unknown. Characterizing the genetic changes associated with hepatocellular carcinoma ... -
Rarity: Discovering rare cell populations from single-cell imaging data
(Oxford University Press, 2023-12-13)MOTIVATION: Cell type identification plays an important role in the analysis and interpretation of single-cell data and can be carried out via supervised or unsupervised clustering approaches. Supervised methods are best ...