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Genetic algorithms in medicine

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https://www.readbyqxmd.com/read/28198728/personalized-medicine-in-interstitial-lung-diseases
#1
Paolo Spagnolo, Justin M Oldham, Mark G Jones, Joyce S Lee
PURPOSE OF REVIEW: A number of recent studies have explored the possibility to apply personalized medicine to interstitial lung diseases (ILDs), particularly idiopathic pulmonary fibrosis (IPF), the most common and deadly of the idiopathic interstitial pneumonias. In our review, we summarize and discuss the most recent literature on personalized medicine in IPF as well as hypersensitivity pneumonitis and sarcoidosis, with emphasis on patient subgroups for which a personalized approach to disease prognostication and management may become a reality in the near future...
February 13, 2017: Current Opinion in Pulmonary Medicine
https://www.readbyqxmd.com/read/28198666/design-connecting-gene-expression-with-therapeutics-for-drug-repurposing-and-development
#2
Bernard Kok Bang Lee, Kai Hung Tiong, Jit Kang Chang, Chee Sun Liew, Zainal Ariff Abdul Rahman, Aik Choon Tan, Tsung Fei Khang, Sok Ching Cheong
BACKGROUND: The drug discovery and development pipeline is a long and arduous process that inevitably hampers rapid drug development. Therefore, strategies to improve the efficiency of drug development are urgently needed to enable effective drugs to enter the clinic. Precision medicine has demonstrated that genetic features of cancer cells can be used for predicting drug response, and emerging evidence suggest that gene-drug connections could be predicted more accurately by exploring the cumulative effects of many genes simultaneously...
January 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28197794/therapeutic-options-in-refractory-diabetic-macular-oedema
#3
Sanket U Shah, Raj K Maturi
Diabetic macular oedema (DMO) results from alterations of several biochemical pathways in diabetic eyes. Centre-involving DMO is an important cause of visual loss in diabetes. Anti-vascular endothelial growth factor agents are now the mainstay of centre-involving DMO treatment. Oedema that does not achieve optimal response to these agents occurs in a sizeable proportion of eyes and is called refractory or persistent DMO. Management of refractory DMO is challenging. In this paper, the pathophysiology of DMO, and the definitions used in various studies are summarised...
February 15, 2017: Drugs
https://www.readbyqxmd.com/read/28133611/diagnostic-method-of-diabetes-based-on-support-vector-machine-and-tongue-images
#4
Jianfeng Zhang, Jiatuo Xu, Xiaojuan Hu, Qingguang Chen, Liping Tu, Jingbin Huang, Ji Cui
Objective. The purpose of this research is to develop a diagnostic method of diabetes based on standardized tongue image using support vector machine (SVM). Methods. Tongue images of 296 diabetic subjects and 531 nondiabetic subjects were collected by the TDA-1 digital tongue instrument. Tongue body and tongue coating were separated by the division-merging method and chrominance-threshold method. With extracted color and texture features of the tongue image as input variables, the diagnostic model of diabetes with SVM was trained...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28121178/classification-of-sphingosine-kinase-inhibitors-using-counter-propagation-artificial-neural-networks-a-systematic-route-for-designing-selective-sphk-inhibitors
#5
M S Neiband, A Mani-Varnosfaderani, A Benvidi
Accurate and robust classification models for describing and predicting the activity of 330 chemicals that are sphingosine kinase 1 (SphK1) and/or sphingosine kinase 2 (SphK2) inhibitors were derived. The classification models developed in this work assist in finding selective subspaces in chemical space occupied by particular groups of SphK inhibitors. A combination of a genetic algorithm (GA) and a counter propagation artificial neural network (CPANN) was utilized to select the most efficient subsets of the molecular descriptors...
January 25, 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/28117080/genomic-and-clinical-profiling-of-a-national-nephrotic-syndrome-cohort-advocates-a-precision-medicine-approach-to-disease-management
#6
Agnieszka Bierzynska, Hugh J McCarthy, Katrina Soderquest, Ethan S Sen, Elizabeth Colby, Wen Y Ding, Marwa M Nabhan, Larissa Kerecuk, Shivram Hegde, David Hughes, Stephen Marks, Sally Feather, Caroline Jones, Nicholas J A Webb, Milos Ognjanovic, Martin Christian, Rodney D Gilbert, Manish D Sinha, Graham M Lord, Michael Simpson, Ania B Koziell, Gavin I Welsh, Moin A Saleem
Steroid Resistant Nephrotic Syndrome (SRNS) in children and young adults has differing etiologies with monogenic disease accounting for 2.9-30% in selected series. Using whole exome sequencing we sought to stratify a national population of children with SRNS into monogenic and non-monogenic forms, and further define those groups by detailed phenotypic analysis. Pediatric patients with SRNS were identified via a national United Kingdom Renal Registry. Whole exome sequencing was performed on 187 patients, of which 12% have a positive family history with a focus on the 53 genes currently known to be associated with nephrotic syndrome...
January 20, 2017: Kidney International
https://www.readbyqxmd.com/read/28104618/hysa-a-hybrid-structural-variant-assembly-approach-using-next-generation-and-single-molecule-sequencing-technologies
#7
Xian Fan, Mark Chaisson, Luay Nakhleh, Ken Chen
Achieving complete, accurate and cost-effective assembly of human genomes is of great importance for realizing the promise of precision medicine. The abundance of repeats and genetic variations in human genomes and the limitations of existing sequencing technologies call for the development of novel assembly methods that can leverage the complementary strengths of multiple technologies. We propose a hybrid structural variant assembly (HySA) approach that integrates sequencing reads from next-generation sequencing and single-molecule sequencing technologies to accurately assemble and detect structural variations in human genomes...
January 19, 2017: Genome Research
https://www.readbyqxmd.com/read/28056037/accurate-promoter-and-enhancer-identification-in-127-encode-and-roadmap-epigenomics-cell-types-and-tissues-by-genostan
#8
Benedikt Zacher, Margaux Michel, Björn Schwalb, Patrick Cramer, Achim Tresch, Julien Gagneur
Accurate maps of promoters and enhancers are required for understanding transcriptional regulation. Promoters and enhancers are usually mapped by integration of chromatin assays charting histone modifications, DNA accessibility, and transcription factor binding. However, current algorithms are limited by unrealistic data distribution assumptions. Here we propose GenoSTAN (Genomic STate ANnotation), a hidden Markov model overcoming these limitations. We map promoters and enhancers for 127 cell types and tissues from the ENCODE and Roadmap Epigenomics projects, today's largest compendium of chromatin assays...
2017: PloS One
https://www.readbyqxmd.com/read/28031973/life-as-an-early-career-researcher-interview-with-heloisa-helena-milioli
#9
Heloisa Helena Milioli
Heloisa Helena Milioli speaks to Francesca Lake, Managing Editor: Heloisa received a BSc degree in Biological Sciences (2008) from the Universidade Federal de Santa Catarina (Brazil) and obtained a MSc degree in Genetics (2011) from Universidade Federal do Paraná (Brazil). In 2011 and 2012, she worked as a lecturer and tutor in the Department of Cell Biology, Embryology and Genetics (Universidade Federal de Santa Catarina). She moved to Australia in 2012 to obtain her PhD in Biological Sciences, with emphasis on Bioinformatics, from The University of Newcastle...
June 2016: Future Science OA
https://www.readbyqxmd.com/read/27897013/harnessing-big-data-for-precision-medicine-infrastructures-and-applications
#10
Kun-Hsing Yu, Steven N Hart, Rachel Goldfeder, Qiangfeng Cliff Zhang, Stephen C J Parker, Michael Snyder
Precision medicine is a health management approach that accounts for individual differences in genetic backgrounds and environmental exposures. With the recent advancements in high-throughput omics profiling technologies, collections of large study cohorts, and the developments of data mining algorithms, big data in biomedicine is expected to provide novel insights into health and disease states, which can be translated into personalized disease prevention and treatment plans. However, petabytes of biomedical data generated by multiple measurement modalities poses a significant challenge for data analysis, integration, storage, and result interpretation...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896995/muse-a-multi-locus-sampling-based-epistasis-algorithm-for-quantitative-genetic-trait-prediction
#11
Dan He, Laxmi Parida
Quantitative genetic trait prediction based on high-density genotyping arrays plays an important role for plant and animal breeding, as well as genetic epidemiology such as complex diseases. The prediction can be very helpful to develop breeding strategies and is crucial to translate the findings in genetics to precision medicine. Epistasis, the phenomena where the SNPs interact with each other, has been studied extensively in Genome Wide Association Studies (GWAS) but received relatively less attention for quantitative genetic trait prediction...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27860446/a-genetic-algorithm-based-framework-for-wavelength-selection-on-sample-categorization
#12
Michel J Anzanello, Gabrielli Yamashita, Marcelo Marcelo, Flavio F Fogliatto, Rafael S Ortiz, Kristiane Mariotti, Marco F Ferrão
In forensic and pharmaceutical scenarios, the application of chemometrics and optimization techniques have unveiled common and peculiar features of seized medicine and drug samples, helping investigative forces towards tracking illegal operations. This paper proposes a novel framework aimed at identifying relevant subsets of attenuated total reflectance Fourier transform infrared (ATR-FTIR) wavelengths for classifying samples into two classes, e.g. authentic or forged categories in case of medicines, or salt or base form in cocaine analysis...
November 18, 2016: Drug Testing and Analysis
https://www.readbyqxmd.com/read/27798253/oxytocin-receptor-gene-variations-predict-neural-and-behavioral-response-to-oxytocin-in-autism
#13
Takamitsu Watanabe, Takeshi Otowa, Osamu Abe, Hitoshi Kuwabara, Yuta Aoki, Tatsunobu Natsubori, Hidemasa Takao, Chihiro Kakiuchi, Kenji Kondo, Masashi Ikeda, Nakao Iwata, Kiyoto Kasai, Tsukasa Sasaki, Hidenori Yamasue
Oxytocin appears beneficial for autism spectrum disorder (ASD), and more than 20 single-nucleotide polymorphisms (SNPs) in oxytocin receptor (OXTR) are relevant to ASD. However, neither biological functions of OXTR SNPs in ASD nor critical OXTR SNPs that determine oxytocin's effects on ASD remains known. Here, using a machine-learning algorithm that was designed to evaluate collective effects of multiple SNPs and automatically identify most informative SNPs, we examined relationships between 27 representative OXTR SNPs and six types of behavioral/neural response to oxytocin in ASD individuals...
October 19, 2016: Social Cognitive and Affective Neuroscience
https://www.readbyqxmd.com/read/27792843/integrative-genetic-risk-prediction-using-non-parametric-empirical-bayes-classification
#14
Sihai Dave Zhao
Genetic risk prediction is an important component of individualized medicine, but prediction accuracies remain low for many complex diseases. A fundamental limitation is the sample sizes of the studies on which the prediction algorithms are trained. One way to increase the effective sample size is to integrate information from previously existing studies. However, it can be difficult to find existing data that examine the target disease of interest, especially if that disease is rare or poorly studied. Furthermore, individual-level genotype data from these auxiliary studies are typically difficult to obtain...
October 28, 2016: Biometrics
https://www.readbyqxmd.com/read/27730209/combinatorial-microfluidic-droplet-engineering-for-biomimetic-material-synthesis
#15
Lukmaan A Bawazer, Ciara S McNally, Christopher J Empson, William J Marchant, Tim P Comyn, Xize Niu, Soongwon Cho, Michael J McPherson, Bernard P Binks, Andrew deMello, Fiona C Meldrum
Although droplet-based systems are used in a wide range of technologies, opportunities for systematically customizing their interface chemistries remain relatively unexplored. This article describes a new microfluidic strategy for rapidly tailoring emulsion droplet compositions and properties. The approach uses a simple platform for screening arrays of droplet-based microfluidic devices and couples this with combinatorial selection of the droplet compositions. Through the application of genetic algorithms over multiple screening rounds, droplets with target properties can be rapidly generated...
October 2016: Science Advances
https://www.readbyqxmd.com/read/27718149/the-topology-prediction-of-membrane-proteins-a-web-based-tutorial
#16
Cagin Kandemir-Cavas, Levent Cavas, Hakan Alyuruk
There is a great need for development of educational materials on the transfer of current bioinformatics knowledge to undergraduate students in bioscience departments. In this study, it is aimed to prepare an example in silico laboratory tutorial on the topology prediction of membrane proteins by bioinformatics tools. This laboratory tutorial is prepared for biochemistry lessons at bioscience departments (biology, chemistry, biochemistry, molecular biology and genetics, and faculty of medicine). The tutorial is intended for students who have not taken a bioinformatics course yet or already have taken a course as an introduction to bioinformatics...
October 7, 2016: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27649726/optimization-of-the-production-of-extracellular-polysaccharide-from-the-shiitake-medicinal-mushroom-lentinus-edodes-agaricomycetes-using-mutation-and-a-genetic-algorithm-coupled-artificial-neural-network-ga-ann
#17
Adeyemi Ojutalayo Adeeyo, Agbaje Lateef, Evariste Bosco Gueguim-Kana
Exopolysaccharide (EPS) production by a strain of Lentinus edodes was studied via the effects of treatments with ultraviolet (UV) irradiation and acridine orange. Furthermore, optimization of EPS production was studied using a genetic algorithm coupled with an artificial neural network in submerged fermentation. Exposure to irradiation and acridine orange resulted in improved EPS production (2.783 and 5.548 g/L, respectively) when compared with the wild strain (1.044 g/L), whereas optimization led to improved productivity (23...
2016: International Journal of Medicinal Mushrooms
https://www.readbyqxmd.com/read/27595102/a-computational-method-for-optimizing-experimental-environments-for-phellinus-igniarius-via-genetic-algorithm-and-bp-neural-network
#18
Zhongwei Li, Beibei Sun, Yuezhen Xin, Xun Wang, Hu Zhu
Flavones, the secondary metabolites of Phellinus igniarius fungus, have the properties of antioxidation and anticancer. Because of the great medicinal value, there are large demands on flavones for medical use and research. Flavones abstracted from natural Phellinus can not meet the medical and research need, since Phellinus in the natural environment is very rare and is hard to be cultivated artificially. The production of flavones is mainly related to the fermentation culture of Phellinus, which made the optimization of culture conditions an important problem...
2016: BioMed Research International
https://www.readbyqxmd.com/read/27586041/xmrf-an-r-package-to-fit-markov-networks-to-high-throughput-genetics-data
#19
Ying-Wooi Wan, Genevera I Allen, Yulia Baker, Eunho Yang, Pradeep Ravikumar, Matthew Anderson, Zhandong Liu
BACKGROUND: Technological advances in medicine have led to a rapid proliferation of high-throughput "omics" data. Tools to mine this data and discover disrupted disease networks are needed as they hold the key to understanding complicated interactions between genes, mutations and aberrations, and epi-genetic markers. RESULTS: We developed an R software package, XMRF, that can be used to fit Markov Networks to various types of high-throughput genomics data. Encoding the models and estimation techniques of the recently proposed exponential family Markov Random Fields (Yang et al...
2016: BMC Systems Biology
https://www.readbyqxmd.com/read/27509654/-frequency-and-medical-social-aspects-premature-birth
#20
REVIEW
M Sandeva, E Uchikova
Premature birth (PB) remains an unresolved problem, despite progress in prenatal medicine and the introduction of new methods and techniques of prolonged respiratory resuscitation in recent decades. Premature birth is the cause of 70% of neonatal mortality and 50% of long-term neurological complications in newborns, many of whom debilitating. Notwithstanding the significant progress prenatal care in the last twenty years in developed countries is a trend towards a gradual and continuous increase in premature births...
2016: Akusherstvo i Ginekologii︠a︡
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