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Computable phenotype

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https://www.readbyqxmd.com/read/28436883/a-bipartite-network-and-resource-transfer-based-approach-to-infer-lncrna-environmental-factor-associations
#1
Jie Zhou, Yuan-Yuan Shi
Phenotypes and diseases are often determined by the complex interactions between genetic factors and environmental factors (EFs). However, compared with protein-coding genes and microRNAs, there is a paucity of computational methods for understanding the associations between long non-coding RNAs (lncRNAs) and EFs. In this study, we focused on the associations between lncRNA and EFs. By using the common miRNA partners of any pair of lncRNA and EF, based on the competing endogenous RNA (ceRNA) hypothesis and the technique of resources transfer within the experimentally-supported lncRNA-miRNA and miRNA-EF association bipartite networks, we propose an algorithm for predicting new lncRNA-EF associations...
April 18, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28436541/pdx1-mody-and-dorsal-pancreatic-agenesis-new-phenotype-of-a-rare-disease
#2
L A Caetano, L S Santana, A D Costa-Riquetto, A M Lerario, M Nery, G F Nogueira, C D Ortega, M S Rocha, Aal Jorge, M G Teles
Maturity-Onset Diabetes of the Young (MODY) type 4 or PDX1-MODY is a rare form of monogenic diabetes caused by heterozygous variants in PDX1. Pancreatic developmental anomalies related to PDX1 are reported only in neonatal diabetes cases. Here, we describe dorsal pancreatic agenesis in two patients with PDX1-MODY. The proband presented with diabetes since 14 years of age and maintained regular glycemic control with low doses of basal insulin and detectable C-peptide levels after 30 years with diabetes. A diagnosis of MODY was suspected...
April 24, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28436422/rational-design-of-non-resistant-targeted-cancer-therapies
#3
Francisco Martínez-Jiménez, John P Overington, Bissan Al-Lazikani, Marc A Marti-Renom
Drug resistance is one of the major problems in targeted cancer therapy. A major cause of resistance is changes in the amino acids that form the drug-target binding site. Despite of the numerous efforts made to individually understand and overcome these mutations, there is a lack of comprehensive analysis of the mutational landscape that can prospectively estimate drug-resistance mutations. Here we describe and computationally validate a framework that combines the cancer-specific likelihood with the resistance impact to enable the detection of single point mutations with the highest chance to be responsible of resistance to a particular targeted cancer therapy...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28434615/searching-for-cross-diagnostic-convergence-neural-mechanisms-governing-excitation-and-inhibition-balance-in-schizophrenia-and-autism-spectrum-disorders
#4
REVIEW
Jennifer H Foss-Feig, Brendan D Adkinson, Jie Lisa Ji, Genevieve Yang, Vinod H Srihari, James C McPartland, John H Krystal, John D Murray, Alan Anticevic
Recent theoretical accounts have proposed excitation and inhibition (E/I) imbalance as a possible mechanistic, network-level hypothesis underlying neural and behavioral dysfunction across neurodevelopmental disorders, particularly autism spectrum disorder (ASD) and schizophrenia (SCZ). These two disorders share some overlap in their clinical presentation as well as convergence in their underlying genes and neurobiology. However, there are also clear points of dissociation in terms of phenotypes and putatively affected neural circuitry...
May 15, 2017: Biological Psychiatry
https://www.readbyqxmd.com/read/28434585/translating-dynamic-defense-patterns-from-rodents-to-people
#5
REVIEW
D Caroline Blanchard
Specific defensive behaviors of rodents are shaped by features of the eliciting threat stimuli and situation. Threat scenarios confirmed these relationships in people, with results substantially replicated in 4 additional scenario studies. Subsequent human studies involve computer games measuring fear as flight from threat stimuli and anxiety as alternation between two threats. Stabilometric studies have shown reduction in sway (freezing) to inescapable (e.g. with gun pointed at subject) threatening photographs; but enhanced lateral sway (flight attempts) to escapable threats; (gun pointed away from subject)...
May 2017: Neuroscience and Biobehavioral Reviews
https://www.readbyqxmd.com/read/28430005/issues-in-current-microrna-target-identification-methods
#6
Hervé Seitz
microRNAs are currently believed to control a large diversity of physiological processes, through the collective repression of thousands of target genes. Both experimental and computational analyses indeed suggest that each microRNA regulates tens or hundreds of genes. But some observations suggest that the phenotypic consequences of many published miRNA/mRNA interactions are dubious. For example, the reported amplitude of miRNA-guided repression is very small, while biological processes tend to be robust to small changes in gene expression...
April 21, 2017: RNA Biology
https://www.readbyqxmd.com/read/28429188/18f-fluorodeoxyglucose-uptake-on-positron-emission-tomography-computed-tomography-is-associated-with-metastasis-and-epithelial-mesenchymal-transition-in-hepatocellular-carcinoma
#7
Misu Lee, Jeong Yong Jeon, Micheal L Neugent, Jung-Whan Kim, Mijin Yun
Hepatocellular carcinoma (HCC) is the fifth leading cause of cancer mortality worldwide. Several studies have investigated the relationship between (18)F-fluorodeoxyglucose ((18)F-FDG) uptake on positron emission tomography and the prognosis of patients with HCC, although the relationship between (18)F-FDG uptake and expression of EMT-related proteins in these patients remains unclear. We retrospectively enrolled 116 patients with HCC treated by curative surgical resection and who underwent (18)F-FDG positron emission tomography/computed tomography (PET/CT) for preoperative staging...
April 20, 2017: Clinical & Experimental Metastasis
https://www.readbyqxmd.com/read/28428742/a-set-based-mixed-effect-model-for-gene-environment-interaction-and-its-application-to-neuroimaging-phenotypes
#8
Changqing Wang, Jianping Sun, Bryan Guillaume, Tian Ge, Derrek P Hibar, Celia M T Greenwood, Anqi Qiu
Imaging genetics is an emerging field for the investigation of neuro-mechanisms linked to genetic variation. Although imaging genetics has recently shown great promise in understanding biological mechanisms for brain development and psychiatric disorders, studying the link between genetic variants and neuroimaging phenotypes remains statistically challenging due to the high-dimensionality of both genetic and neuroimaging data. This becomes even more challenging when studying gene-environment interaction (G×E) on neuroimaging phenotypes...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28427911/safety-parameter-considerations-of-anodal-transcranial-directcurrentstimulation-in-rats
#9
Mark P Jackson, Dennis Truong, Milene L Brownlow, Jessica A Wagner, R Andy McKinley, Marom Bikson, Ryan Jankord
A commonly referenced transcranial Direct Current Stimulation (tDCS) safety threshold derives from tDCS lesion studies in the rat and relies on electrode current density (and related electrode charge density) to support clinical guidelines. Concerns about the role of polarity (e.g. anodal tDCS), sub-lesion threshold injury (e.g. neuroinflammatory processes), and role of electrode montage across rodent and human studies support further investigation into animal models of tDCS safety. Thirty-two anesthetized rats received anodal tDCS between 0-5 mA for 60 minutes through one of three epicranial electrode montages...
April 17, 2017: Brain, Behavior, and Immunity
https://www.readbyqxmd.com/read/28427321/in-silico-assessment-of-biomedical-products-the-conundrum-of-rare-but-not-so-rare-events-in-two-case-studies
#10
Marco Viceconti, Claudio Cobelli, Tarek Haddad, Adam Himes, Boris Kovatchev, Mark Palmer
In silico clinical trials, defined as "The use of individualized computer simulation in the development or regulatory evaluation of a medicinal product, medical device, or medical intervention," have been proposed as a possible strategy to reduce the regulatory costs of innovation and the time to market for biomedical products. We review some of the the literature on this topic, focusing in particular on those applications where the current practice is recognized as inadequate, as for example, the detection of unexpected severe adverse events too rare to be detected in a clinical trial, but still likely enough to be of concern...
May 2017: Proceedings of the Institution of Mechanical Engineers. Part H, Journal of Engineering in Medicine
https://www.readbyqxmd.com/read/28424303/distribution-of-genotype-network-sizes-in-sequence-to-structure-genotype-phenotype-maps
#11
Susanna Manrubia, José A Cuesta
An essential quantity to ensure evolvability of populations is the navigability of the genotype space. Navigability, understood as the ease with which alternative phenotypes are reached, relies on the existence of sufficiently large and mutually attainable genotype networks. The size of genotype networks (e.g. the number of RNA sequences folding into a particular secondary structure or the number of DNA sequences coding for the same protein structure) is astronomically large in all functional molecules investigated: an exhaustive experimental or computational study of all RNA folds or all protein structures becomes impossible even for moderately long sequences...
April 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28421868/rknnmda-ranking-based-knn-for-mirna-disease-association-prediction
#12
Xing Chen, Qiao-Feng Wu, Gui-Ying Yan
Cumulative verified experimental studies have demonstrated that microRNAs (miRNAs) could be closely related with the development and progression of human complex diseases. Based on the assumption that functional similar miRNAs may have a strong correlation with phenotypically similar diseases and vice versa, researchers developed various effective computational models which combine heterogeneous biological datasets including disease similarity network, miRNA similarity network, and known disease-miRNA association network to identify potential relationships between miRNAs and diseases in biomedical research...
April 19, 2017: RNA Biology
https://www.readbyqxmd.com/read/28421705/cover-image-volume-173a-number-5-may-2017
#13
Toshiki Takenouchi, Tomu Kuchikata, Hiroshi Yoshihashi, Mineko Fujiwara, Tomoko Uehara, Sahoko Miyama, Shiro Yamada, Kenjiro Kosaki
The cover image, by Toshiki Takenouchi et al., is based on the Clinical Report Diagnostic use of computational retrotransposon detection: Successful definition of pathogenetic mechanism in a ciliopathy phenotype, DOI: 10.1002/ajmg.a.38167.
May 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28420690/identification-of-protein-features-encoded-by-alternative-exons-using-exon-ontology
#14
Léon-Charles Tranchevent, Fabien Aubé, Louis Dulaurier, Clara Benoit-Pilven, Amandine Rey, Arnaud Poret, Emilie Chautard, Hussein Mortada, François-Olivier Desmet, Fatima Zahra Chakrama, Maira Alejandra Moreno-Garcia, Evelyne Goillot, Stéphane Janczarski, Franck Mortreux, Cyril F Bourgeois, Didier Auboeuf
Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution of alternative splicing variation in physiological- or pathological-associated cellular phenotypes. Toward this end, we developed a computational approach, named Exon Ontology, based on terms corresponding to well-characterized protein features organized in an ontology tree. Exon Ontology is conceptually similar to Gene Ontology-based approaches but focuses on exon-encoded protein features instead of gene level functional annotations...
April 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28420677/tcup-typing-and-characterization-of-bacteria-using-bottom-up-tandem-mass-spectrometry-proteomics
#15
Fredrik Boulund, Roger Karlsson, Lucia Gonzales-Siles, Anna Johnning, Nahid Karami, Omar Al-Bayati, Christina Ahren, Edward R B Moore, Erik Kristiansson
Methods for rapid and reliable microbial identification are essential in modern healthcare. The ability to detect and correctly identify pathogenic species and their resistance phenotype is necessary for accurate diagnosis and efficient treatment of infectious diseases. Bottom-up tandem mass spectrometry (MS) proteomics enables rapid characterization of large parts of the expressed genes of microorganisms. However, the generated data is highly fragmented, making down-stream analyses complex. Here we present TCUP, a new computational method for typing and characterizing bacteria using proteomics data from bottom-up tandem MS...
April 18, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28420620/identification-of-lrp5-mutations-in-families-with-familial-exudative-vitreoretinopathy
#16
Liu Yuqing, Zhu Xiong, Li Shujin, Yang Yeming, Yang Mu, Zhao Peiquan, Zhu Xianjun
Familial exudative vitreoretinopathy (FEVR) is a hereditary eye disease characterized by defects in the development of periphery retinal vessels. However, the clinical phenotypes of FEVR vary widely from asymptomatic to complete blindness. We analyzed patients from three Chinese families and one sporadic patient with FEVR to investigate the clinical features and disease-causing mutations. Ocular phenotypes included increased ramification of the peripheral retinal vessels, a peripheral avascular zone, inferotemporal dragging of the optic disc and macula, and retinal folds...
March 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28420343/on-the-association-analysis-of-cnv-data-a-fast-and-robust-family-based-association-method
#17
Meiling Liu, Sanghoon Moon, Longfei Wang, Sulgi Kim, Yeon-Jung Kim, Mi Yeong Hwang, Young Jin Kim, Robert C Elston, Bong-Jo Kim, Sungho Won
BACKGROUND: Copy number variation (CNV) is known to play an important role in the genetics of complex diseases and several methods have been proposed to detect association of CNV with phenotypes of interest. Statistical methods for CNV association analysis can be categorized into two different strategies. First, the copy number is estimated by maximum likelihood and association of the expected copy number with the phenotype is tested. Second, the observed probe intensity measurements can be directly used to detect association of CNV with the phenotypes of interest...
April 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28418928/erk-signalling-modulates-epigenome-to-drive-epithelial-to-mesenchymal-transition
#18
Mohit Navandar, Angela Garding, Sanjeeb Kumar Sahu, Abhijeet Pataskar, Sandra Schick, Vijay K Tiwari
The series of events that allow the conversion from adherent epithelial cells into migratory cells is collectively known as epithelial-mesenchymal transition (EMT). EMT is employed during embryonic development such as for gastrulation and neural crest migration and is misused in diseases, such as cancer metastasis. ERK signalling is known to be essential for EMT, however its influence on the epigenetic and transcriptional programme underlying EMT is poorly understood. Here, using a comprehensive genome-wide analysis of H3K27ac mark and gene expression in mammary epithelial cells undergoing EMT, we found that ERK signalling is essential for the epigenetic reprogramming underlying hallmark gene expression and phenotypic changes of EMT...
March 23, 2017: Oncotarget
https://www.readbyqxmd.com/read/28418693/validating-the-predicted-effect-of-astemizole-and-ketoconazole-using-a-drosophila-model-of-parkinson-s-disease
#19
Katarzyna Styczyńska-Soczka, Luigi Zechini, Lysimachos Zografos
Parkinson's disease is a growing threat to an ever-ageing population. Despite progress in our understanding of the molecular and cellular mechanisms underlying the disease, all therapeutics currently available only act to improve symptoms and do not stop the disease process. It is therefore imperative that more effective drug discovery methods and approaches are developed, validated, and used for the discovery of disease-modifying treatments for Parkinson's. Drug repurposing has been recognized as being equally as promising as de novo drug discovery in the field of neurodegeneration and Parkinson's disease specifically...
April 2017: Assay and Drug Development Technologies
https://www.readbyqxmd.com/read/28418069/genetic-control-of-plasticity-of-oil-yield-for-combined-abiotic-stresses-using-a-joint-approach-of-crop-modeling-and-genome-wide-association
#20
Brigitte Mangin, Pierre Casadebaig, Eléna Cadic, Nicolas Blanchet, Marie-Claude Boniface, Sébastien Carrère, Jérôme Gouzy, Ludovic Legrand, Baptiste Mayjonade, Nicolas Pouilly, Thierry André, Marie Coque, Joël Piquemal, Marion Laporte, Patrick Vincourt, Stéphane Muños, Nicolas B Langlade
Understanding the genetic basis of phenotypic plasticity is crucial for predicting and managing climate change effects on wild plants and crops. Here, we combined crop modeling and quantitative genetics to study the genetic control of oil yield plasticity for multiple abiotic stresses in sunflower. First we developed stress indicators to characterize 14 environments for three abiotic stresses (cold, drought and nitrogen) using the SUNFLO crop model and phenotypic variations of three commercial varieties. The computed plant stress indicators better explain yield variation than descriptors at the climatic or crop levels...
April 18, 2017: Plant, Cell & Environment
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