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https://www.readbyqxmd.com/read/29352324/efficient-genome-wide-genotyping-strategies-and-data-integration-in-crop-plants
#1
REVIEW
Davoud Torkamaneh, Brian Boyle, François Belzile
Next-generation sequencing (NGS) has revolutionized plant and animal research by providing powerful genotyping methods. This review describes and discusses the advantages, challenges and, most importantly, solutions to facilitate data processing, the handling of missing data, and cross-platform data integration. Next-generation sequencing technologies provide powerful and flexible genotyping methods to plant breeders and researchers. These methods offer a wide range of applications from genome-wide analysis to routine screening with a high level of accuracy and reproducibility...
January 19, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29329426/a-practical-guide-to-estimating-the-heritability-of-pathogen-traits
#2
Venelin Mitov, Tanja Stadler
Pathogen traits, such as the virulence of an infection, can vary significantly between patients. A major challenge is to measure the extent to which genetic differences between infecting strains explain the observed variation of the trait. This is quantified by the trait's broad-sense heritability, H2. A recent discrepancy between estimates of the heritability of HIV-virulence has opened a debate on the estimators' accuracy. Here, we show that the discrepancy originates from model limitations and important lifecycle differences between sexually reproducing organisms and transmittable pathogens...
January 9, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29322918/a-linear-programming-computational-framework-integrates-phosphor-proteomics-and-prior-knowledge-to-predict-drug-efficacy
#3
Zhiwei Ji, Bing Wang, Ke Yan, Ligang Dong, Guanmin Meng, Lei Shi
BACKGROUND: In recent years, the integration of 'omics' technologies, high performance computation, and mathematical modeling of biological processes marks that the systems biology has started to fundamentally impact the way of approaching drug discovery. The LINCS public data warehouse provides detailed information about cell responses with various genetic and environmental stressors. It can be greatly helpful in developing new drugs and therapeutics, as well as improving the situations of lacking effective drugs, drug resistance and relapse in cancer therapies, etc...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29321234/plasma-neurofilament-light-chain-concentration-in-the-inherited-peripheral-neuropathies
#4
Åsa Sandelius, Henrik Zetterberg, Kaj Blennow, Rocco Adiutori, Andrea Malaspina, Matilde Laura, Mary M Reilly, Alexander M Rossor
OBJECTIVE: To perform a cross-sectional study to determine whether plasma neurofilament light chain (NfL) concentration is elevated in patients with Charcot-Marie-Tooth disease (CMT) and if it correlates with disease severity. METHODS: Blood samples were collected from 75 patients with CMT and 67 age-matched healthy controls over a 1-year period. Disease severity was measured using the Rasch modified CMT Examination and neuropathy scores. Plasma NfL concentration was measured using an in-house-developed Simoa assay...
January 10, 2018: Neurology
https://www.readbyqxmd.com/read/29320965/alterations-of-the-gut-microbiota-in-hashimoto-s-thyroiditis-patients
#5
Fuya Zhao, Jing Feng, Jun Li, Lei Zhao, Yang Liu, Huinan Chen, Ye Jin, Biqiang Zhu, Yunwei Wei
BACKGROUND: Hashimoto's thyroiditis (HT) is an organ-specific autoimmune disease in which both genetic predisposition and environmental factors serve as disease triggers. Many studies have indicated that alterations in the gut microbiota are important environmental factors in the development of inflammatory and autoimmune diseases. We systematically performed a comparative analysis of the gut microbiota in HT patients and healthy controls. METHODS: We first conducted a cross-sectional study of 28 HT patients and 16 matched healthy controls...
January 10, 2018: Thyroid: Official Journal of the American Thyroid Association
https://www.readbyqxmd.com/read/29312619/systematic-assessment-of-cervical-cancer-initiation-and-progression-uncovers-genetic-panels-for-deep-learning-based-early-diagnosis-and-proposes-novel-diagnostic-and-prognostic-biomarkers
#6
Nguyen Phuoc Long, Kyung Hee Jung, Sang Jun Yoon, Nguyen Hoang Anh, Tran Diem Nghi, Yun Pyo Kang, Hong Hua Yan, Jung Eun Min, Soon-Sun Hong, Sung Won Kwon
Although many outstanding achievements in the management of cervical cancer (CxCa) have obtained, it still imposes a major burden which has prompted scientists to discover and validate new CxCa biomarkers to improve the diagnostic and prognostic assessment of CxCa. In this study, eight different gene expression data sets containing 202 cancer, 115 cervical intraepithelial neoplasia (CIN), and 105 normal samples were utilized for an integrative systems biology assessment in a multi-stage carcinogenesis manner...
December 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29305701/qtl-seq-for-rapid-identification-of-candidate-genes-for-flowering-time-in-broccoli%C3%A2-%C3%A3-%C3%A2-cabbage
#7
Jinshuai Shu, Yumei Liu, Lili Zhang, Zhansheng Li, Zhiyuan Fang, Limei Yang, Mu Zhuang, Yangyong Zhang, Honghao Lv
A major QTL controlling early flowering in broccoli × cabbage was identified by marker analysis and next-generation sequencing, corresponding to GRF6 gene conditioning flowering time in Arabidopsis. Flowering is an important agronomic trait for hybrid production in broccoli and cabbage, but the genetic mechanism underlying this process is unknown. In this study, segregation analysis with BC1P1, BC1P2, F2, and F2:3 populations derived from a cross between two inbred lines "195" (late-flowering) and "93219" (early flowering) suggested that flowering time is a quantitative trait...
January 5, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29276722/validating-candidate-congenital-heart-disease-genes-in-drosophila
#8
Jun-Yi Zhu, Yulong Fu, Adam Richman, Zhe Han
Genomic sequencing efforts can implicate large numbers of genes and de novo mutations as potential disease risk factors. A high throughput in vivo model system to validate candidate gene association with pathology is therefore useful. We present such a system employing Drosophila to validate candidate congenital heart disease (CHD) genes. The protocols exploit comprehensive libraries of UAS-GeneX-RNAi fly strains that when crossed into a 4×Hand-Gal4 genetic background afford highly efficient cardiac-specific knockdown of endogenous fly orthologs of human genes...
June 20, 2017: Bio-protocol
https://www.readbyqxmd.com/read/29274071/genome-wide-association-analysis-of-lead-accumulation-in-maize
#9
Xiongwei Zhao, Yajuan Liu, Wenmei Wu, Yuhua Li, Longxin Luo, Yuzhou Lan, Yanhua Cao, Zhiming Zhang, Shibin Gao, Guangsheng Yuan, Li Liu, Yaou Shen, Guangtang Pan, Haijian Lin
Large phenotypic variations in the lead (Pb) concentration were observed in grains and leaves of maize plants. A further understanding of inheritance of Pb accumulation may facilitate improvement of low-Pb-accumulating cultivars in maize. A genome-wide association study was conducted in a population of 269 maize accessions with 43,737 single-nucleotide polymorphisms (SNPs). The Pb concentrations in leaves and kernels of 269 accessions were collected in pot-culture and field experiments in years of 2015 and 2016...
December 22, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29273097/current-state-of-research-and-summary-of-preceding%C3%A2-summits
#10
EDITORIAL
David A Norris
During its 25th anniversary year, the National Alopecia Areata Foundation (NAAF) undertook a project to completely re-evaluate their research program and to help focus and direct future directions of alopecia areata (AA) research to better meet the goals of individuals with and the scientists working to discover mechanisms of disease and better treatments for AA. This project was embodied in five research summits in 2008, 2009, 2010, 2012, and 2014 as part of the NAAF's main strategic initiative, the Alopecia Areata Treatment Development Program, to accelerate progress toward a viable treatment...
January 2018: Journal of Investigative Dermatology. Symposium Proceedings
https://www.readbyqxmd.com/read/29249345/analysis-and-multiclass-classification-of-pathological-knee-joints-using-vibroarthrographic-signals
#11
Krzysztof Kręcisz, Dawid Bączkowicz
BACKGROUND AND OBJECTIVE: Vibroarthrography (VAG) is a method developed for sensitive and objective assessment of articular function. Although the VAG method is still in development, it shows high accuracy, sensitivity and specificity when comparing results obtained from controls and the non-specific, knee-related disorder group. However, the multiclass classification remains practically unknown. Therefore the aim of this study was to extend the VAG method classification to 5 classes, according to different disorders of the patellofemoral joint...
February 2018: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/29241659/a-novel-method-for-predicting-kidney-stone-type-using-ensemble-learning
#12
Yassaman Kazemi, Seyed Abolghasem Mirroshandel
The high morbidity rate associated with kidney stone disease, which is a silent killer, is one of the main concerns in healthcare systems all over the world. Advanced data mining techniques such as classification can help in the early prediction of this disease and reduce its incidence and associated costs. The objective of the present study is to derive a model for the early detection of the type of kidney stone and the most influential parameters with the aim of providing a decision-support system. Information was collected from 936 patients with nephrolithiasis at the kidney center of the Razi Hospital in Rasht from 2012 through 2016...
December 11, 2017: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/29225351/metabolome-wide-association-studies-for-agronomic-traits-of-rice
#13
Julong Wei, Aiguo Wang, Ruidong Li, Han Qu, Zhenyu Jia
Identification of trait-associated metabolites will advance the knowledge and understanding of the biosynthetic and catabolic pathways that are relevant to the complex traits of interest. In the past, the association between metabolites (treated as quantitative traits) and genetic variants (e.g., SNPs) has been extensively studied using metabolomic quantitative trait locus (mQTL) mapping. Nevertheless, the research on the association between metabolites with agronomic traits has been inadequate. In practice, the regular approaches for QTL mapping analysis may be adopted for metabolites-phenotypes association analysis due to the similarity in data structure of these two types of researches...
December 11, 2017: Heredity
https://www.readbyqxmd.com/read/29224171/genetic-mapping-and-validation-of-the-loci-controlling-7s-%C3%AE-and-11s-a-type-storage-protein-subunits-in-soybean-glycine-max-l-merr
#14
Jeffrey D Boehm, Vi Nguyen, Rebecca M Tashiro, Dale Anderson, Chun Shi, Xiaoguang Wu, Lorna Woodrow, Kangfu Yu, Yuhai Cui, Zenglu Li
Four soybean storage protein subunit QTLs were mapped using bulked segregant analysis and an F2 population, which were validated with an F5 RIL population. The storage protein globulins β-conglycinin (7S subunit) and glycinin (11S subunits) can affect the quantity and quality of proteins found in soybean seeds and account for more than 70% of the total soybean protein. Manipulating the storage protein subunits to enhance soymeal nutrition and for desirable tofu manufacturing characteristics are two end-use quality goals in soybean breeding programs...
December 9, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29220522/meta-analysis-of-genome-wide-association-studies-identifies-8-novel-loci-involved-in-shape-variation-of-human-head-hair
#15
Fan Liu, Yan Chen, Gu Zhu, Pirro G Hysi, Sijie Wu, Kaustubh Adhikari, Krystal Breslin, Ewelina Pospiech, Merel A Hamer, Fuduan Peng, Charanya Muralidharan, Victor Acuna-Alonzo, Samuel Canizales-Quinteros, Gabriel Bedoya, Carla Gallo, Giovanni Poletti, Francisco Rothhammer, Maria Catira Bortolini, Rolando Gonzalez-Jose, Changqing Zeng, Shuhua Xu, Li Jin, André G Uitterlinden, M Arfan Ikram, Cornelia M van Duijn, Tamar Nijsten, Susan Walsh, Wojciech Branicki, Sijia Wang, Andrés Ruiz-Linares, Timothy D Spector, Nicholas G Martin, Sarah E Medland, Manfred Kayser
Shape variation of human head hair shows striking variation within and between human populations, while its genetic basis is far from being understood. We performed a series of genome-wide association studies (GWASs) and replication studies in a total of 28,964 subjects from 9 cohorts from multiple geographic origins. A meta-analysis of three European GWASs identified 8 novel loci (1p36.23 ERRFI1/SLC45A1, 1p36.22 PEX14, 1p36.13 PADI3, 2p13.3 TGFA, 11p14.1 LGR4, 12q13.13 HOXC13, 17q21.2 KRTAP, and 20q13.33 PTK6), and confirmed 4 previously known ones (1q21...
December 6, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/29218911/convergent-downstream-candidate-mechanisms-of-independent-intergenic-polymorphisms-between-co-classified-diseases-implicate-epistasis-among-noncoding-elements
#16
Jiali Han, Jianrong Li, Ikbel Achour, Lorenzo Pesce, Ian Foster, Haiquan Li, Yves A Lussier
Eighty percent of DNA outside protein coding regions was shown biochemically functional by the ENCODE project, enabling studies of their interactions. Studies have since explored how convergent downstream mechanisms arise from independent genetic risks of one complex disease. However, the cross-talk and epistasis between intergenic risks associated with distinct complex diseases have not been comprehensively characterized. Our recent integrative genomic analysis unveiled downstream biological effectors of disease-specific polymorphisms buried in intergenic regions, and we then validated their genetic synergy and antagonism in distinct GWAS...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29216209/preliminary-study-of-tumor-heterogeneity-in-imaging-predicts-two-year-survival-in-pancreatic-cancer-patients
#17
Jayasree Chakraborty, Liana Langdon-Embry, Kristen M Cunanan, Joanna G Escalon, Peter J Allen, Maeve A Lowery, Eileen M O'Reilly, Mithat Gönen, Richard G Do, Amber L Simpson
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers in the United States with a five-year survival rate of 7.2% for all stages. Although surgical resection is the only curative treatment, currently we are unable to differentiate between resectable patients with occult metastatic disease from those with potentially curable disease. Identification of patients with poor prognosis via early classification would help in initial management including the use of neoadjuvant chemotherapy or radiation, or in the choice of postoperative adjuvant therapy...
2017: PloS One
https://www.readbyqxmd.com/read/29212543/gene-gravity-like-algorithm-for-disease-gene-prediction-based-on-phenotype-specific-network
#18
Limei Lin, Tinghong Yang, Ling Fang, Jian Yang, Fan Yang, Jing Zhao
BACKGROUND: Polygenic diseases are usually caused by the dysfunction of multiple genes. Unravelling such disease genes is crucial to fully understand the genetic landscape of diseases on molecular level. With the advent of 'omic' data era, network-based methods have prominently boosted disease gene discovery. However, how to make better use of different types of data for the prediction of disease genes remains a challenge. RESULTS: In this study, we improved the performance of disease gene prediction by integrating the similarity of disease phenotype, biological function and network topology...
December 6, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29212472/autism-risk-classification-using-placental-chorionic-surface-vascular-network-features
#19
Jen-Mei Chang, Hui Zeng, Ruxu Han, Ya-Mei Chang, Ruchit Shah, Carolyn M Salafia, Craig Newschaffer, Richard K Miller, Philip Katzman, Jack Moye, Margaret Fallin, Cheryl K Walker, Lisa Croen
BACKGROUND: Autism Spectrum Disorder (ASD) is one of the fastest-growing developmental disorders in the United States. It was hypothesized that variations in the placental chorionic surface vascular network (PCSVN) structure may reflect both the overall effects of genetic and environmentally regulated variations in branching morphogenesis within the conceptus and the fetus' vital organs. This paper provides sound evidences to support the study of ASD risks with PCSVN through a combination of feature-selection and classification algorithms...
December 6, 2017: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/29204795/inferring-gene-regulatory-networks-based-on-a-hybrid-parallel-genetic-algorithm-and-the-threshold-restriction-method
#20
Ming Zheng, Shugong Zhang, You Zhou, Guixia Liu
Inferring gene regulatory networks (GRNs) is a challenging computational task in system biology. Many inference algorithms have been proposed along with related modifications to various problems. Every algorithm has its own advantages and drawbacks. In particular, the efficiency of each algorithm is not as good as people expect. A novel inference algorithm is proposed in this paper that can be divided into two parts. In the first part, the pre-computational part, two tasks must be accomplished: singular value decomposition for solution space determination and the threshold restriction method for redundant edge deletion...
December 4, 2017: Interdisciplinary Sciences, Computational Life Sciences
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