Genomic feature analysis
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Base substitution catalogues represent historical records of mutational processes that have been active in a cell. Such processes can be distinguished by various characteristics, like mutation type, sequence context, transcriptional and replicative strand bias, genomic distribution and association with (epi)-genomic features.
11p vibransone 28-03-2024 6 2 Download
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Glycosylphosphatidylinositol biosynthesis defects (GPIBDs) cause a group of phenotypically overlapping recessive syndromes with intellectual disability, for which pathogenic mutations have been described in 16 genes of the corresponding molecular pathway.
13p vibransone 28-03-2024 6 2 Download
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Genome-wide association studies (GWAS) have identified pervasive sharing of genetic architectures across multiple immune-mediated diseases (IMD). By learning the genetic basis of IMD risk from common diseases, this sharing can be exploited to enable analysis of less frequent IMD where, due to limited sample size, traditional GWAS techniques are challenging.
17p vibransone 28-03-2024 4 2 Download
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This study aims to identify microbiomic differences in paired tumor and non-tumor tissue samples in a large group of 121 patients with head and neck squamous cell carcinomas and correlate these differences with clinical-pathologic features.
10p vioraclene 31-03-2024 5 2 Download
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Medulloblastoma (MB) is a malignant tumour of the cerebellum which can be classifed into four major subgroups based on gene expression and genomic features. Single-cell transcriptome studies have defined the cellular states underlying each MB subgroup; however, the spatial organisation of these diverse cell states and how this impacts response to therapy remains to be determined.
28p vicwell 29-02-2024 3 1 Download
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Prostate cancer (PrCa) genomic heterogeneity causes resistance to therapies such as androgen dep‑ rivation. Such heterogeneity can be deciphered in the context of evolutionary principles, but current clinical trials do not include evolution as an essential feature.
15p vicwell 29-02-2024 2 2 Download
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Chronic limb-threatening ischemia (CLTI), a severe manifestation of peripheral arterial disease (PAD), is associated with a 1-year limb amputation rate of approximately 15–20% and substantial mortality. A key feature of CLTI is the compromised regenerative ability of skeletal muscle; however, the mechanisms responsible for this impairment are not yet fully understood.
20p vicwell 29-02-2024 6 2 Download
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Pituitary neuroendocrine tumors (PitNETs) are one of the most common types of intracranial tumors. Currently, the cellular characteristics of normal pituitary and various other types of PitNETs are still not completely understood.
17p vicwell 29-02-2024 3 2 Download
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Neoadjuvant chemotherapy (NAC) has become a standard treatment strategy for breast cancer (BC). However, owing to the high heterogeneity of these tumors, it is unclear which patient population most likely benefit from NAC. Multi-omics ofer an improved approach to uncovering genomic and transcriptomic changes before and after NAC in BC and to identifying molecular features associated with NAC sensitivity.
19p vicwell 29-02-2024 4 2 Download
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Extension of prostate cancer beyond the primary site by local invasion or nodal metastasis is associated with poor prognosis. Despite significant research on tumour evolution in prostate cancer metastasis, the emergence and evolution of cancer clones at this early stage of expansion and spread are poorly understood.
18p vicwell 29-02-2024 2 1 Download
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The objective of this study was to analyze the features of FtsZ proteins in the Bacillus and Lactococcus genus groups. By exploring the available genomes, we identified and characterized FtsZ proteins in 19 Bacillus and 22 Lactococcus species.
12p vigojek 02-02-2024 4 0 Download
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Endometrial carcinoma (EC) is one of the most common gynecological malignancies in China and globally, accounting for the fourth-prevalent cancer in women. Although numerous studies have confirmed prognostic value of The Cancer Genome Atlas (TCGA) molecular subgroups, it is unclear how they are combined with histological features.
13p vischultz 20-10-2023 5 2 Download
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We aimed to identify the relationship between the genomic characteristics and clinical outcomes of oligo-metastatic breast cancer. Methods Oligo-metastatic breast cancer diagnosed by pathology from January 2001 and August 2019 were reviewed and we matched the poly-metastatic patients based on the clinicopathological features of patients included.
10p vioracle 29-09-2023 3 2 Download
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Part 1 book "Equine genomics" includes content: Defining the equine genome - The nuclear genome and the mitochondrial genome, genetic linkage maps, physical and comparative maps, the Y-chromosome, unexpected structural features of the equine major histocompatibility complex, assembly and analysis of the equine genome sequence, genomic tools and resources - Development and applications of an equine SNP genotyping array, functional genomics, coat color genomics.
167p oursky04 14-09-2023 4 2 Download
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It is common that cancer patients have different molecular signatures even though they have similar clinical features, such as histology, due to the heterogeneity of tumors. To overcome this variability, we previously developed a new approach incorporating prior biological knowledge that identifies knowledge-driven genomic interactions associated with outcomes of interest.
11p visteverogers 24-06-2023 5 3 Download
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An important feature in many genomic studies is quality control and normalization. This is particularly important when analyzing epigenetic data, where the process of obtaining measurements can be bias prone.
6p vihagrid 30-01-2023 9 3 Download
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Organogenesis is crucial for proper organ formation during mammalian embryonic development. However, the similarities and shared features between different organs and the cellular heterogeneity during this process at single-cell resolution remain elusive.
20p vimichaelfaraday 25-03-2022 16 1 Download
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Previous approaches to defining subtypes of colorectal carcinoma (CRC) and other cancers based on transcriptomes have assumed the existence of discrete subtypes. We analyze gene expression patterns of colorectal tumors from a large number of patients to test this assumption and propose an approach to identify potentially a continuum of subtypes that are present across independent studies and cohorts.
14p vigalileogalilei 27-02-2022 8 1 Download
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Aging is characterized by loss of function of the adaptive immune system, but the underlying causes are poorly understood. To assess the molecular effects of aging on B cell development, we profiled gene expression and chromatin features genome-wide, including histone modifications and chromosome conformation, in bone marrow pro-B and pre-B cells from young and aged mice.
24p vigalileogalilei 27-02-2022 17 1 Download
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Genome-wide association studies (GWAS) have identified hundreds of loci associated with coronary artery disease (CAD) and blood pressure (BP) or hypertension. Many of these loci are not linked to traditional risk factors, nor do they include obvious candidate genes, complicating their functional characterization.
13p vigalileogalilei 27-02-2022 14 1 Download