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Signatures of positive selection reveal a universal role of chromatin modifiers as cancer driver genes.
(NATURE PORTFOLIO, 2017-10-13)Tumors are composed of an evolving population of cells subjected to tissue-specific selection, which fuels tumor heterogeneity and ultimately complicates cancer driver gene identification. Here, we integrate cancer cell ... -
Signatures of TOP1 transcription-associated mutagenesis in cancer and germline.
(NATURE PORTFOLIO, 2022-02-24)The mutational landscape is shaped by many processes. Genic regions are vulnerable to mutation but are preferentially protected by transcription-coupled repair1. In microorganisms, transcription has been demonstrated to ... -
SiGNet: A signaling network data simulator to enable signaling network inference.
(PUBLIC LIBRARY SCIENCE, 2017-05-17)Network models are widely used to describe complex signaling systems. Cellular wiring varies in different cellular contexts and numerous inference techniques have been developed to infer the structure of a network from ... -
Similarity and diversity of the tumor microenvironment in multiple metastases: critical implications for overall and progression-free survival of high-grade serous ovarian cancer.
(IMPACT JOURNALS LLC, 2016-11-01)The tumor microenvironment is pivotal in influencing cancer progression and metastasis. Different cells co-exist with high spatial diversity within a patient, yet their combinatorial effects are poorly understood. We ... -
SimPLIT: Simplified Sample Preparation for Large-Scale Isobaric Tagging Proteomics.
(AMER CHEMICAL SOC, 2022-08-05)Large scale proteomic profiling of cell lines can reveal molecular signatures attributed to variable genotypes or induced perturbations, enabling proteogenomic associations and elucidation of pharmacological mechanisms of ... -
Simulation Learning: Effectiveness and Stressfulness in Medical Student Teaching
(F1000 Research Ltd, 2020-07-09)<ns4:p>This article was migrated. The article was not marked as recommended. Introduction: The aims of this study were to assess the effectiveness of different modalities of simulation learning in medical students and the ... -
Simulation of a radiobiology facility for the Centre for the Clinical Application of Particles.
(ELSEVIER SCI LTD, 2019-09-01)The Centre for the Clinical Application of Particles' Laser-hybrid Accelerator for Radiobiological Applications (LhARA) facility is being studied and requires simulation of novel accelerator components (such as the Gabor ... -
Simulation of Patient-Specific Deformable Ultrasound Imaging in Real Time
(SPRINGER INTERNATIONAL PUBLISHING AG, 2017-01-01) -
Simulations of DNA topoisomerase 1B bound to supercoiled DNA reveal changes in the flexibility pattern of the enzyme and a secondary protein–DNA binding site
(Oxford University Press (OUP), 2014-08-18)Human topoisomerase 1B has been simulated covalently bound to a negatively supercoiled DNA minicircle, and its behavior compared to the enzyme bound to a simple linear DNA duplex. The presence of the more realistic supercoiled ... -
Single cell analysis of clonal architecture in acute myeloid leukaemia.
(NATURE PUBLISHING GROUP, 2019-05-01)We used single cell Q-PCR on a micro-fluidic platform (Fluidigm) to analyse clonal, genetic architecture and phylogeny in acute myeloid leukaemia (AML) using selected mutations. Ten cases of NPM1c mutant AML were screened ... -
Single dose prostate radiotherapy - a step too far?
(2021-04-21) -
Single-Cell Analyses of Prostate Cancer Liquid Biopsies Acquired by Apheresis.
(AMER ASSOC CANCER RESEARCH, 2018-11-15)Purpose: Circulating tumor cells (CTCs) have clinical relevance, but their study has been limited by their low frequency.Experimental Design: We evaluated liquid biopsies by apheresis to increase CTC yield from patients ... -
Single-Cell Dynamics Determines Response to CDK4/6 Inhibition in Triple-Negative Breast Cancer.
(AMER ASSOC CANCER RESEARCH, 2017-09-15)Purpose: Triple-negative breast cancer (TNBC) is a heterogeneous subgroup of breast cancer that is associated with a poor prognosis. We evaluated the activity of CDK4/6 inhibitors across the TNBC subtypes and investigated ... -
Single-cell genetic analysis of clonal dynamics in colorectal adenomas indicates CDX2 gain as a predictor of recurrence.
(WILEY, 2019-04-01)Colorectal adenomas are common precancerous lesions with the potential for malignant transformation to colorectal adenocarcinoma. Endoscopic polypectomy provides an opportunity for cancer prevention; however, recurrence ... -
Single-cell transcriptomics identifies an effectorness gradient shaping the response of CD4+ T cells to cytokines.
(NATURE RESEARCH, 2020-04-14)Naïve CD4+ T cells coordinate the immune response by acquiring an effector phenotype in response to cytokines. However, the cytokine responses in memory T cells remain largely understudied. Here we use quantitative proteomics, ... -
siRNA Knockdown of Ribosomal Protein Gene RPL19 Abrogates the Aggressive Phenotype of Human Prostate Cancer
(PUBLIC LIBRARY SCIENCE, 2011-07-22)We provide novel functional data that posttranscriptional silencing of gene RPL19 using RNAi not only abrogates the malignant phenotype of PC-3M prostate cancer cells but is selective with respect to transcription and ... -
Sirolimus for patients with progressive epithelioid hemangioendothelioma.
(WILEY, 2020-10-27)Epithelioid hemangioendothelioma is an ultrarare soft tissue sarcoma with limited literature to guide treatment. The results from a robust retrospective cohort study support the use of sirolimus for patients who have ... -
SIRT3 controls brown fat thermogenesis by deacetylation regulation of pathways upstream of UCP1.
(ELSEVIER SCIENCE BV, 2019-07-01)OBJECTIVE: Brown adipose tissue (BAT) is important for thermoregulation in many mammals. Uncoupling protein 1 (UCP1) is the critical regulator of thermogenesis in BAT. Here we aimed to investigate the deacetylation control ... -
Sirtuin inhibition is synthetic lethal with BRCA1 or BRCA2 deficiency.
(NATURE PORTFOLIO, 2021-11-08)PARP enzymes utilise NAD+ as a co-substrate for their enzymatic activity. Inhibition of PARP1 is synthetic lethal with defects in either BRCA1 or BRCA2. In order to assess whether other genes implicated in NAD+ metabolism ...