Abstract：
:Because of its clonal evolution a tumor rarely contains multiple genomic alterations in the same pathway as disrupting the pathway by one gene often is sufficient to confer the complete fitness advantage. As a result, many cancer driver genes display mutual exclusivity across tumors. However, searching for mutually exclusive gene sets requires analyzing all possible combinations of genes, leading to a problem which is typically too computationally complex to be solved without a stringent a priori filtering, restricting the mutations included in the analysis. To overcome this problem, we present SSA-ME, a network-based method to detect cancer driver genes based on independently scoring small subnetworks for mutual exclusivity using a reinforced learning approach. Because of the algorithmic efficiency, no stringent upfront filtering is required. Analysis of TCGA cancer datasets illustrates the added value of SSA-ME: well-known recurrently mutated but also rarely mutated drivers are prioritized. We show that using mutual exclusivity to detect cancer driver genes is complementary to state-of-the-art approaches. This framework, in which a large number of small subnetworks are being analyzed in order to solve a computationally complex problem (SSA), can be generically applied to any problem in which local neighborhoods in a network hold useful information.
journal_name
Sci Repjournal_title
Scientific reportsauthors
Pulido-Tamayo S,Weytjens B,De Maeyer D,Marchal Kdoi
10.1038/srep36257subject
Has Abstractpub_date
2016-11-03 00:00:00pages
36257issn
2045-2322pii
srep36257journal_volume
6pub_type
杂志文章abstract：:The current study aims to evaluate the burden of disease in Singapore by estimating the quality-adjusted life years (QALYs) lost due to mental disorders and chronic physical conditions. The second Singapore Mental Health Study (SMHS-2016) was conducted in 2016 among 6126 respondents aged 18 years and above. The World ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-59604-0
更新日期：2020-02-14 00:00:00
abstract：:Porcine circovirus 2 (PCV-2) is a virus characterized by a high evolutionary rate, promoting the potential emergence of different genotypes and strains. Despite the likely relevance in the emergence of new PCV-2 variants, the subtle evolutionary patterns of PCV-2 at the individual-host level or over short transmission...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-33849-2
更新日期：2018-10-19 00:00:00
abstract：:The aim of this study was to assess the systemic and analgesic effects of epidural dexmedetomidine in thoracic epidural anaesthesia (TEA) combined with total intravenous anaesthesia during thoracic surgery. Seventy-one patients undergoing open thoracotomy were included in this study and randomly divided into three gro...
journal_title：Scientific reports
pub_type： 杂志文章,随机对照试验
doi：10.1038/s41598-017-04382-5
更新日期：2017-06-21 00:00:00
abstract：:The spin-transfer nano-oscillator (STNO) offers the possibility of using the transfer of spin angular momentum via spin-polarized currents to generate microwave signals. However, at present STNO microwave emission mainly relies on both large drive currents and external magnetic fields. These issues hinder the implemen...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep01426
更新日期：2013-01-01 00:00:00
abstract：:Heparan sulfate (HS) is a polysaccharide known to modulate many important biological processes, including Wnt signaling. However, the biochemical interaction between HS and Wnt molecules is not well characterized largely due to the lack of suitable methods. To determine the Wnt binding domain in HS, we used a Wnt sign...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep26245
更新日期：2016-05-17 00:00:00
abstract：:Practical applications of bacteriophages in medicine and biotechnology induce a great need for technologies of phage purification. None of the popular methods offer solutions for separation of a phage from another similar phage. We used affinity chromatography combined with competitive phage display (i) to purify T4 b...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep03220
更新日期：2013-11-14 00:00:00
abstract：:Scientific Reports 7: Article number: 45816; published online: 06 April 2017; updated: 16 May 2017. The original version of this Article contained an error in Affiliation 2, which was incorrectly given as: 'Department of Biophysics, School of Life Sciences, Manipal University, Manipal, 567014, India'. ...
journal_title：Scientific reports
pub_type： 已发布勘误
doi：10.1038/srep46803
更新日期：2017-05-16 00:00:00
abstract：:Invasion of ocean surface waters by anthropogenic CO2 emitted to the atmosphere is expected to reduce surface seawater pH to 7.8 by the end of this century compromising marine calcifiers. A broad range of biological and mineralogical mechanisms allow marine calcifiers to cope with ocean acidification, however these me...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep19374
更新日期：2016-01-18 00:00:00
abstract：:An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...
journal_title：Scientific reports
pub_type： 已发布勘误
doi：10.1038/s41598-020-63126-0
更新日期：2020-04-20 00:00:00
abstract：:We previously demonstrated that ABCD4 does not localize to peroxisomes but rather, the endoplasmic reticulum (ER), because it lacks the NH2-terminal hydrophilic region required for peroxisomal targeting. It was recently reported that mutations in ABCD4 result in a failure to release vitamin B12 from lysosomes. A simil...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep30183
更新日期：2016-07-26 00:00:00
abstract：:The current theories of antimalarial mechanism of artemisinin are inadequate to fully explain the observed effects. In our study, "organism-like" formation of Schistosoma hemozoin granules by attaching to and utilizing erythrocytes to form new ones was observed. This indicates that heme iron is transferred from erythr...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep34463
更新日期：2016-10-03 00:00:00
abstract：:Globally breast cancer is the leading cause of cancer death among women. The breast consists of epithelium, stroma and a mucosal immune system that make up a complex microenvironment. Growing awareness of the role of microbes in the microenvironment recently has led to a series of findings important for human health. ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep30751
更新日期：2016-08-03 00:00:00
abstract：:There is lack of consensus regarding the prognostic significance of primary tumor location of upper tract urothelial carcinoma(UTUC). We performed a meta-analysis to evaluate the impact of primary tumor location on prognosis in patients with UTUC who had undergone radical nephroureterectomy(RNU). We included eligible ...
journal_title：Scientific reports
pub_type： 杂志文章,meta分析
doi：10.1038/srep06361
更新日期：2014-09-15 00:00:00
abstract：:The bacterial flagellar motor is a unique supramolecular complex which converts ion flow into rotational force. Many biological devices mainly use two types of ions, proton and sodium ion. This is probably because of the fact that life originated in seawater, which is rich in protons and sodium ions. The polar flagell...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-46038-6
更新日期：2019-08-02 00:00:00
abstract：:Recent clinical trials have investigated the benefit of combining tyrosine kinase inhibitors (TKIs) and cytoreductive nephrectomy (CN) in patients with metastatic renal cell carcinoma. Our goal is to determine whether the perioperative use of TKIs increases the postoperative morbidity following CN in renal cell carcin...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-51548-4
更新日期：2019-10-24 00:00:00
abstract：:The Langendorff-perfused heart technique has become the model of choice for multiparametric optical mapping of cardiac function and electrophysiology. However, photon scattering in tissues represents a significant drawback of the optical imaging approach, fundamentally limiting its mapping capacity to the heart surfac...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-32317-1
更新日期：2018-09-20 00:00:00
abstract：:Graphite-coated magnetic cobalt nanoparticles (CoNPs) decorated with hindered phenolic antioxidant analogues of 2,6-di-tert-butyl-4-methylphenol (BHT, E321) provided easily removable nanoantioxidants capable of preventing the autoxidation of organic solvents as tetrahydrofuran (THF). ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-53531-5
更新日期：2019-11-20 00:00:00
abstract：:Cytometric studies utilizing flow cytometry or multi-well culture plate fluorometry are often limited by a deficit in temporal resolution and a lack of single cell consideration. Unfortunately, many cellular processes, including signaling, motility, and molecular transport, occur transiently over relatively short peri...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep05117
更新日期：2014-05-30 00:00:00
abstract：:Elucidating arbuscular mycorrhizal (AM) fungal responses to elevation changes is critical to improve understanding of microbial function in ecosystems under global asymmetrical climate change scenarios. Here we examined AM fungal community in a two-year reciprocal translocation of vegetation-intact soil blocks along a...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep36606
更新日期：2016-11-09 00:00:00
abstract：:Sesame is prized for its oil. Genetic improvement of sesame can be enhanced through marker-assisted breeding. However, few simple sequence repeat (SSR) markers and SSR-based genetic maps were available in sesame. In this study, 7,357 SSR markers were developed from the sesame genome and transcriptomes, and a genetic m...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-08858-2
更新日期：2017-08-21 00:00:00
abstract：:Cancer-specific promoter driven replication of oncolytic adenovirus (Ad) is cancer-specific, but shows low transcriptional activity. Thus, we generated several chimeric α-fetoprotein (AFP) promoter variants, containing reconstituted enhancer and silencer regions, to preferentially drive Ad replication in hepatocellula...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-20268-6
更新日期：2018-02-02 00:00:00
abstract：:Amazonian wildfires in 2019 have raised awareness about rainforest burning due to increased emissions of particulate matter and carbon. In the context of these emissions, by-products of lignin thermal degradation (i.e. methoxyphenols) are often neglected. Methoxyphenols entering the atmosphere may form intermediates w...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-021-81789-1
更新日期：2021-01-28 00:00:00
abstract：:Sea level rise (SLR) will cause shoreline retreat of sandy coasts in the absence of sand supply mechanisms. These coasts have high touristic and ecological value and provide protection of valuable infrastructures and buildings to storm impacts. So far, large-scale assessments of shoreline retreat use specific datasets...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-68576-0
更新日期：2020-07-17 00:00:00
abstract：:Although copy number variation (CNV) and presence-absence variation (PAV) have been discovered in selected gene families in most crop species, the global prevalence of these polymorphisms in most complex genomes is still unclear and their influence on quantitatively inherited agronomic traits is still largely unknown....
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-61228-3
更新日期：2020-03-05 00:00:00
abstract：:Droplet microfluidics has attracted significant interests in functional microcapsule synthesis, pharmaceuticals, fine chemicals, cosmetics and biomedical research. The low variability of performing chemical reactions inside droplets could benefit from improved homogeneity and reproducibility. Therefore, accurate and c...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-28270-8
更新日期：2018-07-02 00:00:00
abstract：:Multiple sclerosis (MS) is a neurodegenerative autoimmune disease, where chronic inflammation plays an essential role in its pathology. A feature of MS is the production of autoantibodies stimulated by an altered-peptide-ligand response and epitope spreading, resulting in loss of tolerance for self-proteins. The invol...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-25391-y
更新日期：2018-05-04 00:00:00
abstract：:Children with autistic spectrum disorders (ASD) experience persistent disrupted coordination in interpersonal synchronisation that is thought to be associated with deficits in neural connectivity. Robotic interventions have been explored for use with ASD children worldwide revealing that robots encourage one-to-one so...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-74438-6
更新日期：2020-10-15 00:00:00
abstract：:Tract tracing with neuronal tracers not only represents a straightforward approach to identify axonal projection connection between regions of the nervous system at distance but also provides compelling evidence for axonal regeneration. An ideal neuronal tracer meets certain criteria including high labeling efficacy, ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-46285-7
更新日期：2019-07-09 00:00:00
abstract：:Intestinal epithelial cells continuously migrate and mature along crypt-villus axis (CVA), while the changes in energy metabolism during maturation are unclear in neonates. The present study was conducted to test the hypothesis that the energy metabolism in intestinal epithelial cells would be changed during maturatio...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep31917
更新日期：2016-08-25 00:00:00
abstract：:We have successfully grown centimeter-sized layered [Formula: see text] single crystals under high oxygen pressures of 120-150 bar by the floating zone technique. This enabled us to perform neutron scattering experiments where we observe close to quarter-integer magnetic peaks below [Formula: see text] that are accomp...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-74884-2
更新日期：2020-10-22 00:00:00
