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Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data.
(NATURE PORTFOLIO, 2019-07-17)
Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The ...
Landscape of transcriptomic interactions between breast cancer and its microenvironment.
(NATURE PUBLISHING GROUP, 2019-07-15)
Solid tumours comprise mixtures of tumour cells (TCs) and tumour-adjacent cells (TACs), and the intricate interconnections between these diverse populations shape the tumour's microenvironment. Despite this complexity, ...
Identification of single nucleotide variants using position-specific error estimation in deep sequencing data
(2018-11-23)
<h4>Background</h4> Targeted deep sequencing is a highly effective technology to identify known and novel single nucleotide variants (SNVs) with many applications in translational medicine, disease monitoring and cancer ...
Reprogramming of Amino Acid Transporters to Support Aspartate and Glutamate Dependency Sustains Endocrine Resistance in Breast Cancer.
(CELL PRESS, 2019-07-02)
Endocrine therapy (ET) is the standard of care for estrogen receptor-positive (ER+) breast cancers. Despite its efficacy, ∼40% of women relapse with ET-resistant (ETR) disease. A global transcription analysis in ETR cells ...
The application of Hadoop in structural bioinformatics.
(Oxford University Press (OUP), 2018-11-20)
The paper reviews the use of the Hadoop platform in structural bioinformatics applications. For structural bioinformatics, Hadoop provides a new framework to analyse large fractions of the Protein Data Bank that is key for ...
Phosphorylation-mediated interactions with TOPBP1 couple 53BP1 and 9-1-1 to control the G1 DNA damage checkpoint.
(ELIFE SCIENCES PUBLICATIONS LTD, 2019-05-28)
Coordination of the cellular response to DNA damage is organised by multi-domain 'scaffold' proteins, including 53BP1 and TOPBP1, which recognise post-translational modifications such as phosphorylation, methylation and ...
Effectiveness of contrast-associated acute kidney injury prevention methods; a systematic review and network meta-analysis.
(BMC, 2018-11-13)
BACKGROUND: Different methods to prevent contrast-associated acute kidney injury (CA-AKI) have been proposed in recent years. We performed a mixed treatment comparison to evaluate and rank suggested interventions. METHODS: ...
Hypoxia-induced switch in SNAT2/SLC38A2 regulation generates endocrine resistance in breast cancer.
(NATL ACAD SCIENCES, 2019-06-18)
Tumor hypoxia is associated with poor patient outcomes in estrogen receptor-α-positive (ERα+) breast cancer. Hypoxia is known to affect tumor growth by reprogramming metabolism and regulating amino acid (AA) uptake. Here, ...
The Dandelion Dilemma Revisited for Oligoprogression: Treat the Whole Lawn or Weed Selectively?
(ELSEVIER SCIENCE LONDON, 2019-12-01)
Oligoprogressive disease is a relatively new clinical concept describing progression at only a few sites of metastasis in patients with otherwise controlled widespread disease. In the era of well-tolerated targeted treatments, ...
Integrin-Mediated Macrophage Adhesion Promotes Lymphovascular Dissemination in Breast Cancer.
(CELL PRESS, 2019-05-14)
Lymphatic vasculature is crucial for metastasis in triple-negative breast cancer (TNBC); however, cellular and molecular drivers controlling lymphovascular metastasis are poorly understood. We define a macrophage-dependent ...