Boris Noyvert
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View article: Imputation of structural variants using a multi-ancestry long-read sequencing panel enables identification of disease associations
Imputation of structural variants using a multi-ancestry long-read sequencing panel enables identification of disease associations Open
Advancements in long-read sequencing technology have accelerated the study of large structural variants (SVs). We created a curated, publicly available, multi-ancestry SV imputation panel by long-read sequencing 888 samples from the 1000 G…
View article: Imputation of structural variants using a multi-ancestry long-read sequencing panel enables identification of disease associations
Imputation of structural variants using a multi-ancestry long-read sequencing panel enables identification of disease associations Open
Advancements in long-read sequencing technology have accelerated the study of large structural variants (SVs). We created a curated, publicly available, multi-ancestry SV imputation panel by long-read sequencing 888 samples from the 1000 G…
View article: Deep representation learning for clustering longitudinal survival data from electronic health records
Deep representation learning for clustering longitudinal survival data from electronic health records Open
Precision medicine requires accurate identification of clinically relevant patient subgroups. Electronic health records provide major opportunities for leveraging machine learning approaches to uncover novel patient subgroups. However, man…
View article: Repression of CADM1 transcription by HPV type 18 is mediated by three-dimensional rearrangement of promoter-enhancer interactions
Repression of CADM1 transcription by HPV type 18 is mediated by three-dimensional rearrangement of promoter-enhancer interactions Open
Upon infection, human papillomavirus (HPV) manipulates host cell gene expression to create an environment that is supportive of a productive and persistent infection. The virus-induced changes to the host cell’s transcriptome are thought t…
View article: Repression of<i>CADM1</i>transcription by HPV type 18 is mediated by three-dimensional rearrangement of promoter-enhancer interactions
Repression of<i>CADM1</i>transcription by HPV type 18 is mediated by three-dimensional rearrangement of promoter-enhancer interactions Open
Upon infection, human papillomavirus (HPV) manipulates host cell gene expression to create an environment that is supportive of a productive and persistent infection. The virus-induced changes to the host cell’s transcriptome are thought t…
View article: The genomic landscape of 2,023 colorectal cancers
The genomic landscape of 2,023 colorectal cancers Open
View article: mARC1 in MASLD: Modulation of lipid accumulation in human hepatocytes and adipocytes
mARC1 in MASLD: Modulation of lipid accumulation in human hepatocytes and adipocytes Open
Background: Mutations in the gene MTARC1 (mitochondrial amidoxime–reducing component 1) protect carriers from metabolic dysfunction–associated steatohepatitis (MASH) and cirrhosis. MTARC1 encodes the mARC1 enzyme, which is localized to the…
View article: Deep representation learning for clustering longitudinal survival data from electronic health records
Deep representation learning for clustering longitudinal survival data from electronic health records Open
Precision medicine requires accurate identification of clinically relevant patient subgroups. Electronic health records provide major opportunities for leveraging machine learning approaches to uncover novel patient subgroups. However, man…
View article: Insights for precision oncology from the integration of genomic and clinical data of 13,880 tumors from the 100,000 Genomes Cancer Programme
Insights for precision oncology from the integration of genomic and clinical data of 13,880 tumors from the 100,000 Genomes Cancer Programme Open
View article: Imputation of structural variants using a multi-ancestry long-read sequencing panel enables identification of disease associations
Imputation of structural variants using a multi-ancestry long-read sequencing panel enables identification of disease associations Open
Advancements in long-read sequencing technology have accelerated the study of large structural variants (SVs). We created a curated, publicly available, multi-ancestry SV imputation panel by long-read sequencing 888 samples from the 1000 G…
View article: Lineage skewing and genome instability underlie marrow failure in a zebrafish model of GATA2 deficiency
Lineage skewing and genome instability underlie marrow failure in a zebrafish model of GATA2 deficiency Open
View article: MYB insufficiency disrupts proteostasis in hematopoietic stem cells, leading to age-related neoplasia
MYB insufficiency disrupts proteostasis in hematopoietic stem cells, leading to age-related neoplasia Open
MYB plays a key role in gene regulation throughout the hematopoietic hierarchy and is critical for the maintenance of normal hematopoietic stem cells (HSC). Acquired genetic dysregulation of MYB is involved in the etiology of a number of l…
View article: Insights for precision healthcare from the 100,000 Genomes Cancer Programme
Insights for precision healthcare from the 100,000 Genomes Cancer Programme Open
The Cancer Programme of the 100,000 Genomes Project was a transformational UK government initiative that aimed to bring whole genome sequencing (WGS) to cancer patients and evaluate the opportunities for precision cancer care. Genomics Eng…
View article: Whole genome sequencing of 2,023 colorectal cancers reveals mutational landscapes, new driver genes and immune interactions
Whole genome sequencing of 2,023 colorectal cancers reveals mutational landscapes, new driver genes and immune interactions Open
To characterise the somatic alterations in colorectal cancer (CRC), we conducted whole-genome sequencing analysis of 2,023 tumours. We provide the most detailed high-resolution map to date of somatic mutations in CRC, and demonstrate assoc…
View article: Whole genome sequencing of 2,023 colorectal cancers reveals mutational landscapes, new driver genes and immune interactions
Whole genome sequencing of 2,023 colorectal cancers reveals mutational landscapes, new driver genes and immune interactions Open
To characterise the somatic alterations in colorectal cancer (CRC), we conducted whole-genome sequencing analysis of 2,023 tumours. We provide the most detailed high-resolution map to date of somatic mutations in CRC, and demonstrate assoc…
View article: Combined exome and transcriptome sequencing of non-muscle-invasive bladder cancer: associations between genomic changes, expression subtypes, and clinical outcomes
Combined exome and transcriptome sequencing of non-muscle-invasive bladder cancer: associations between genomic changes, expression subtypes, and clinical outcomes Open
Background Three-quarters of bladder cancer patients present with early-stage disease (non-muscle-invasive bladder cancer, NMIBC, UICC TNM stages Ta, T1 and Tis); however, most next-generation sequencing studies to date have concentrated o…
View article: Publisher Correction: Signatures of TOP1 transcription-associated mutagenesis in cancer and germline
Publisher Correction: Signatures of TOP1 transcription-associated mutagenesis in cancer and germline Open
View article: Germline MBD4 deficiency causes a multi-tumor predisposition syndrome
Germline MBD4 deficiency causes a multi-tumor predisposition syndrome Open
View article: Signatures of TOP1 transcription-associated mutagenesis in cancer and germline
Signatures of TOP1 transcription-associated mutagenesis in cancer and germline Open
View article: Lineage Skewing and Genome Instability Underlie Marrow Failure in a Zebrafish Model of GATA2 Deficiency
Lineage Skewing and Genome Instability Underlie Marrow Failure in a Zebrafish Model of GATA2 Deficiency Open
View article: Additional file 1 of Combined exome and transcriptome sequencing of non-muscle-invasive bladder cancer: associations between genomic changes, expression subtypes, and clinical outcomes
Additional file 1 of Combined exome and transcriptome sequencing of non-muscle-invasive bladder cancer: associations between genomic changes, expression subtypes, and clinical outcomes Open
Additional file 1: Readme. Index page for the constituent tables in this file. Table S1. Clinical phenotype for the 96 patients in the BCPP cohort. Table S2. Somatic mutations: Single Nucleotide variants (SNVs) and Insertion/ Deletions (In…
View article: The chromatin insulator CTCF regulates HPV18 transcript splicing and differentiation-dependent late gene expression
The chromatin insulator CTCF regulates HPV18 transcript splicing and differentiation-dependent late gene expression Open
The ubiquitous host protein, CCCTC-binding factor (CTCF), is an essential regulator of cellular transcription and functions to maintain epigenetic boundaries, stabilise chromatin loops and regulate splicing of alternative exons. We have pr…
View article: Immediate Sample Fixation Increases Circulating Tumour Cell (CTC) Capture and Preserves Phenotype in Head and Neck Squamous Cell Carcinoma: Towards a Standardised Approach to Microfluidic CTC Biomarker Discovery
Immediate Sample Fixation Increases Circulating Tumour Cell (CTC) Capture and Preserves Phenotype in Head and Neck Squamous Cell Carcinoma: Towards a Standardised Approach to Microfluidic CTC Biomarker Discovery Open
Introduction: Research demonstrates strong evidence that circulating tumour cells (CTCs) can provide diagnostic and/or prognostic biomarkers in head and neck squamous cell carcinoma (HNSCC) and a potential tool for therapeutic stratificati…
View article: The chromatin insulator CTCF regulates HPV18 transcript splicing and differentiation-dependent late gene expression
The chromatin insulator CTCF regulates HPV18 transcript splicing and differentiation-dependent late gene expression Open
The ubiquitous host protein, CCCTC-binding factor (CTCF), is an essential regulator of cellular transcription and functions to maintain epigenetic boundaries, stabilise chromatin loops and regulate splicing of alternative exons. We have pr…
View article: MYB insufficiency disrupts proteostasis in hematopoietic stem cells leading to age-related neoplasia
MYB insufficiency disrupts proteostasis in hematopoietic stem cells leading to age-related neoplasia Open
The Myb transcription factor plays critical roles in normal and malignant hematopoiesis. Acquired genetic dysregulation of Myb, which plays a central role in hematopoietic stem cell (HSC) gene regulation, is involved in the etiology of a n…
View article: Gata2a maintains <i>cebpa</i> and <i>npm1a</i> in haematopoietic stem cells to sustain lineage differentiation and genome stability
Gata2a maintains <i>cebpa</i> and <i>npm1a</i> in haematopoietic stem cells to sustain lineage differentiation and genome stability Open
The transcription factor Gata2 is required to produce and maintain haematopoietic stem and progenitor cells (HSPCs) in development and adult haematopoiesis. Mutations in GATA2 lead to GATA2 deficiency syndrome and predispose patients to ac…
View article: The chromatin insulator CTCF regulates HPV18 transcript splicing and differentiation-dependent late gene expression
The chromatin insulator CTCF regulates HPV18 transcript splicing and differentiation-dependent late gene expression Open
The ubiquitous host protein, CCCTC-binding factor (CTCF), is an essential regulator of cellular transcription and functions to maintain epigenetic boundaries, stabilise chromatin loops and regulate splicing of alternative exons. We have pr…
View article: Germline loss-of-function variants in the base-excision repair gene<i>MBD4</i>cause a Mendelian recessive syndrome of adenomatous colorectal polyposis and acute myeloid leukaemia
Germline loss-of-function variants in the base-excision repair gene<i>MBD4</i>cause a Mendelian recessive syndrome of adenomatous colorectal polyposis and acute myeloid leukaemia Open
Inherited defects in base-excision repair (BER) predispose to adenomatous polyposis and colorectal cancer (CRC), yet our understanding of this important DNA repair pathway remains incomplete. By combining detailed clinical, histological an…
View article: Non-Coding Mutations in Urothelial Bladder Cancer: Biological and Clinical Relevance and Potential Utility as Biomarkers
Non-Coding Mutations in Urothelial Bladder Cancer: Biological and Clinical Relevance and Potential Utility as Biomarkers Open
BACKGROUND & OBJECTIVE: Whole genome sequencing has identified recurrent non-coding mutations that may be important in carcinogenesis. We investigate the frequency of 5 such non-coding mutation hotspots in urothelial bladder cancers (UBCs)…
View article: MDSC targeting with Gemtuzumab ozogamicin restores T cell immunity and immunotherapy against cancers
MDSC targeting with Gemtuzumab ozogamicin restores T cell immunity and immunotherapy against cancers Open